diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index cffd62b9e09..43d0180780a 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -20,8 +20,14 @@ If this is a new visual feature please add a before/after screenshot or gif
 here with e.g. [GifGrabber](http://www.gifgrabber.com/).
 
 # Notify reviewers
-If your pull request involves changes to an existing file, one or more of the
-people that edited before you might be good candidates to review it. Please use
-`git blame <filename>` to determine that and notify them here. Otherwise notify
-everybody in the core team:
-@cBioPortal/core-developers
+Read our [Pull request merging
+policy](../CONTRIBUTING.md#pull-request-merging-policy). If you are part of the
+cBioPortal organization, notify the approprate team (remove inappropriate):
+
+@cBioPortal/frontend
+@cBioPortal/backend
+@cBioPortal/devops
+
+If you are not part of the cBioPortal organization look at who worked on the
+file before you. Please use `git blame <filename>` to determine that
+and notify them here:
diff --git a/.gitignore b/.gitignore
index 4d19924dfed..ff84bb544be 100644
--- a/.gitignore
+++ b/.gitignore
@@ -77,3 +77,5 @@ nbactions.xml
 */.project
 dependency-reduced-pom.xml
 /core/nbactions-private.xml
+.profile.d/
+Procfile
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index b7c7a7c5ef0..f6655e21280 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -86,6 +86,67 @@ Once you downloaded the images you do the following for each screenshot:
 - If the change in the screenshot is **desired**, add the screenshot to the
   repo, commit it and push it to your PR's branch.
 
+## Pull Request Merging Policy
+Pull Requests (PRs) are reviewed by the
+[backend](https://github.com/orgs/cBioPortal/teams/backend),
+[frontend](https://github.com/orgs/cBioPortal/teams/frontend) and
+[devops](https://github.com/orgs/cBioPortal/teams/devops) teams of cBioPortal.
+For each PR the submitter should propose what team(s) is/are appropriate to
+review it. This is the current merging policy:
+
+- A documentation change needs one **Approve**
+- A simple bugfix to rc or hotfix requires one **Approve**
+- A new feature requires two **Approve**. One from someone at MSKCC and one from
+  another institution.
+
+If these requirements are met, any person with merge rights can merge to rc or
+hotfix.
+
+## Pull Request Reviewers Guide
+Here we describe the guidelines for the reviewer. Always follow the checks in
+general, then follow the other checks that apply:
+
+### General
+- Double check all the things in the **Checks** section of the Pull Request.
+  Remind the submitter if any of them are not fulfilled
+- Are the test cases spanning a decent amount of scenarios? It is the
+  submitters as well as the reviewers responsibility to not let any errors
+  sneak into the portal.
+
+Bug fixes:
+
+- Should the bug that causes the issue be added as a test case?
+
+New features:
+
+- If this is a new feature make sure the proposed changes are in line with the
+  current planning of cBioPortal e.g. is the right API used, is this in line
+  with current refactoring efforts.
+
+### Backend
+New features:
+
+- Is the new persistence stack used?
+
+### Frontend
+New features:
+
+- What APIs are used to get the data? Is the REST API used?
+- Should this be a separate library in a separate repo or should it be part of cBioPortal?
+- Are dependencies properly listed? Ideally in a package.json
+- How is the package included in cBioPortal?
+
+### Devops
+New features:
+
+- Does the configuration style follow the config guidelines? That is compile
+  (Maven) config goes in the appriopriate `pom.xml` (root, `scripts/`, `portal/`, `core/`).
+  Runtime (Spring) goes in `portal.properties`. Default values should be in `GlobalProperties.java`.
+- Non-stable configuration should be done through war overlays.
+- Is the configuration tested as part of Travis CI? It's not a necessity but be
+  aware that untested configuration will be tough to maintain.
+- Is there documentation on the proposed changes?
+
 ## Additional Resources
 
 * [cBioPortal Issue Tracker](https://github.com/cBioPortal/cbioportal/issues)
diff --git a/business/pom.xml b/business/pom.xml
index f4386f9b128..b724c35f2f0 100644
--- a/business/pom.xml
+++ b/business/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>master</artifactId>
     <groupId>org.mskcc.cbio</groupId>
-    <version>1.2.4</version>
+    <version>1.2.5</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
   <artifactId>business</artifactId>
diff --git a/core/pom.xml b/core/pom.xml
index b5fa7daaf68..29a59b66e4a 100644
--- a/core/pom.xml
+++ b/core/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>master</artifactId>
     <groupId>org.mskcc.cbio</groupId>
-    <version>1.2.4</version>
+    <version>1.2.5</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
   <artifactId>core</artifactId>
diff --git a/core/src/main/java/org/mskcc/cbio/portal/model/ExtendedMutation.java b/core/src/main/java/org/mskcc/cbio/portal/model/ExtendedMutation.java
index a48ea665403..b63a026e43a 100644
--- a/core/src/main/java/org/mskcc/cbio/portal/model/ExtendedMutation.java
+++ b/core/src/main/java/org/mskcc/cbio/portal/model/ExtendedMutation.java
@@ -255,6 +255,14 @@ public String getOncotatorUniprotName() {
             return oncotatorUniprotName;
         }
 
+        /**
+         * Set the UniprotKB name (formerly known as ID) of the protein record.
+         *
+         * @param oncotatorUniprotName the UniprotKB name
+         * @deprecated set the accession with
+         *             {@link #setOncotatorUniprotAccession(String)} instead
+         */
+        @Deprecated
         public void setOncotatorUniprotName(String oncotatorUniprotName) {
             this.oncotatorUniprotName = oncotatorUniprotName;
         }
@@ -835,6 +843,14 @@ public String getOncotatorUniprotName()
         return event.getOncotatorUniprotName();
     }
 
+    /**
+     * Set the UniprotKB name (formerly known as ID) of the protein record.
+     *
+     * @param oncotatorUniprotName the UniprotKB name
+     * @deprecated set the accession with
+     *             {@link #setOncotatorUniprotAccession(String)} instead
+     */
+    @Deprecated
     public void setOncotatorUniprotName(String oncotatorUniprotName)
     {
         event.setOncotatorUniprotName(oncotatorUniprotName);
diff --git a/core/src/main/java/org/mskcc/cbio/portal/model/GeneticProfile.java b/core/src/main/java/org/mskcc/cbio/portal/model/GeneticProfile.java
index c091e60fffd..83eca3ff0cc 100644
--- a/core/src/main/java/org/mskcc/cbio/portal/model/GeneticProfile.java
+++ b/core/src/main/java/org/mskcc/cbio/portal/model/GeneticProfile.java
@@ -32,6 +32,8 @@
 
 package org.mskcc.cbio.portal.model;
 
+import java.util.Properties;
+
 import org.apache.commons.lang.builder.ToStringBuilder;
 
 /**
@@ -47,6 +49,7 @@ public class GeneticProfile {
     private String profileDescription;
     private String targetLine;
     private boolean showProfileInAnalysisTab;
+    private Properties otherMetadataFields;
 
     public GeneticProfile() {
       super();
@@ -54,7 +57,7 @@ public GeneticProfile() {
 
    public GeneticProfile(String stableId, int cancerStudyId, GeneticAlterationType geneticAlterationType,
 						 String datatype, String profileName, String profileDescription, boolean showProfileInAnalysisTab) {
-      super();
+      this();
       this.stableId = stableId;
       this.cancerStudyId = cancerStudyId;
       this.geneticAlterationType = geneticAlterationType;
@@ -64,6 +67,26 @@ public GeneticProfile(String stableId, int cancerStudyId, GeneticAlterationType
       this.showProfileInAnalysisTab = showProfileInAnalysisTab;
    }
 
+
+   /**
+    * Constructs a new genetic profile object with the same attributes as the one given as an argument.
+    *
+    * @param template  the object to copy
+    */
+   public GeneticProfile(GeneticProfile template) {
+       this(
+               template.getStableId(),
+               template.getCancerStudyId(),
+               template.getGeneticAlterationType(),
+               template.getDatatype(),
+               template.getProfileName(),
+               template.getProfileDescription(),
+               template.showProfileInAnalysisTab());
+       this.setGeneticProfileId(template.geneticProfileId);
+       this.setTargetLine(template.getTargetLine());
+       this.setOtherMetadataFields(template.getAllOtherMetadataFields());
+   }
+
    public int getGeneticProfileId() {
         return geneticProfileId;
     }
@@ -135,10 +158,42 @@ public boolean showProfileInAnalysisTab() {
     public void setShowProfileInAnalysisTab(boolean showProfileInAnalysisTab) {
         this.showProfileInAnalysisTab = showProfileInAnalysisTab;
     }
-    
+
+    /**
+     * Stores metadata fields only recognized in particular data file types.
+     *
+     * @param fields  a properties instance holding the keys and values
+     */
+    public void setOtherMetadataFields(Properties fields) {
+        this.otherMetadataFields = fields;
+    }
+
+    /**
+     * Returns all file-specific metadata fields as a Properties object.
+     *
+     * @return  a properties instance holding the keys and values or null
+     */
+    public Properties getAllOtherMetadataFields() {
+        return this.otherMetadataFields;
+    }
+
+    /**
+     * Retrieves metadata fields specific to certain data file types.
+     *
+     * @param fieldname  the name of the field to retrieve
+     * @return  the value of the field or null
+     */
+    public String getOtherMetaDataField(String fieldname) {
+        if (otherMetadataFields == null) {
+            return null;
+        } else {
+            return otherMetadataFields.getProperty(fieldname);
+        }
+    }
+
     @Override
     public String toString() {
        return ToStringBuilder.reflectionToString(this);
     }
-    
+
 }
\ No newline at end of file
diff --git a/core/src/main/java/org/mskcc/cbio/portal/scripts/FetchPfamGraphicsData.java b/core/src/main/java/org/mskcc/cbio/portal/scripts/FetchPfamGraphicsData.java
index dc4ddd158ec..5df5349322a 100644
--- a/core/src/main/java/org/mskcc/cbio/portal/scripts/FetchPfamGraphicsData.java
+++ b/core/src/main/java/org/mskcc/cbio/portal/scripts/FetchPfamGraphicsData.java
@@ -48,7 +48,7 @@
  */
 public class FetchPfamGraphicsData
 {
-	public static final String URL_PREFIX = "http://pfam.sanger.ac.uk/protein/";
+	public static final String URL_PREFIX = "http://pfam.xfam.org/protein/";
 	public static final String URL_SUFFIX = "/graphic";
 
 	/**
diff --git a/core/src/main/java/org/mskcc/cbio/portal/scripts/ImportCaisesClinicalXML.java b/core/src/main/java/org/mskcc/cbio/portal/scripts/ImportCaisesClinicalXML.java
index 4a83ca336ce..dc6dbab6a6f 100644
--- a/core/src/main/java/org/mskcc/cbio/portal/scripts/ImportCaisesClinicalXML.java
+++ b/core/src/main/java/org/mskcc/cbio/portal/scripts/ImportCaisesClinicalXML.java
@@ -35,79 +35,105 @@
 import java.io.File;
 import org.mskcc.cbio.portal.dao.*;
 import org.mskcc.cbio.portal.model.*;
-import org.mskcc.cbio.portal.util.SpringUtil;
 
 import org.dom4j.*;
 import org.dom4j.io.SAXReader;
 import joptsimple.*;
 
 import java.util.*;
-import java.io.FileInputStream;
-
 /**
  *
  * @author jgao
  */
-public final class ImportCaisesClinicalXML {
+public class ImportCaisesClinicalXML extends ConsoleRunnable {
+    
+    private File xmlFile;
+    private int cancerStudyId;
     
-    private ImportCaisesClinicalXML() {}
+    public ImportCaisesClinicalXML(String[] args) {
+        super(args);
+    }
+    
+        /**
+     * Runs the command as a script and exits with an appropriate exit code.
+     *
+     * @param args  the arguments given on the command line
+     */
+    public static void main(String[] args) {
+        ConsoleRunnable runner = new ImportCaisesClinicalXML(args);
+        runner.runInConsole();
+    }
     
-    public static void main(String[] args) throws Exception {
+    public void run() {
 //        args = new String[] {"--data","/Users/jgao/projects/cbio-portal-data/studies/prad/su2c/data_clinical_caises.xml",
 //            "--meta","/Users/jgao/projects/cbio-portal-data/studies/prad/su2c/meta_clinical_caises.txt",
 //            "--loadMode", "bulkLoad"};
-        if (args.length < 4) {
-            System.out.println("command line usage:  importCaisesXml --data <data_clinical_caises.xml> --meta <meta_clinical_caises.txt>");
-            return;
-        }
-        
-       OptionParser parser = new OptionParser();
-       parser.accepts("noprogress");
-       OptionSpec<String> data = parser.accepts( "data",
-               "caises data file" ).withRequiredArg().describedAs( "data_clinical_caises.xml" ).ofType( String.class );
-       OptionSpec<String> meta = parser.accepts( "meta",
-               "meta (description) file" ).withRequiredArg().describedAs( "meta_clinical_caises.txt" ).ofType( String.class );
-       parser.acceptsAll(Arrays.asList("dbmsAction", "loadMode"));
-       OptionSet options = null;
-      try {
-         options = parser.parse( args );
-         //exitJVM = !options.has(returnFromMain);
-      } catch (OptionException e) {
-          e.printStackTrace();
-      }
-       
-       String dataFile = null;
-       if( options.has( data ) ){
-          dataFile = options.valueOf( data );
-       }else{
-           throw new Exception( "'data' argument required.");
-       }
+        try {
+            String progName = "ImportCaisesClinicalXML";
+            String description = "Import clinical Caises XML files";
 
-       String descriptorFile = null;
-       if( options.has( meta ) ){
-          descriptorFile = options.valueOf( meta );
-       }else{
-           throw new Exception( "'meta' argument required.");
-       }
-        
-        Properties properties = new TrimmedProperties();
-        properties.load(new FileInputStream(descriptorFile));
-		SpringUtil.initDataSource();
-      
-        CancerStudy cancerStudy = DaoCancerStudy.getCancerStudyByStableId(properties.getProperty("cancer_study_identifier"));
-        if (cancerStudy == null) {
-            throw new Exception("Unknown cancer study: " + properties.getProperty("cancer_study_identifier"));
+           OptionParser parser = new OptionParser();
+           parser.accepts("noprogress");
+           OptionSpec<String> data = parser.accepts( "data",
+                   "caises data file" ).withRequiredArg().describedAs( "data_clinical_caises.xml" ).ofType( String.class );  
+           OptionSpec<String> study = parser.accepts("study",
+                   "cancer study identifier").withRequiredArg().describedAs("study").ofType(String.class);
+           parser.acceptsAll(Arrays.asList("dbmsAction", "loadMode"));
+           OptionSet options = null;
+          try {
+             options = parser.parse( args );
+             //exitJVM = !options.has(returnFromMain);
+          } catch (OptionException e) {
+              throw new UsageException(
+                            progName, description, parser,
+                            e.getMessage());
+          }
+
+           String dataFile = null;
+           if( options.has( data ) ){
+              dataFile = options.valueOf( data );
+           } else{
+                throw new UsageException(
+                            progName, description, parser,
+                           "'data' argument required");
+           }       
+           
+            String cancerStudyIdentifier = null;
+           if( options.has( study ) ){
+              cancerStudyIdentifier = options.valueOf( study );
+           } else{
+                throw new UsageException(
+                            progName, description, parser,
+                           "'study' argument required");
+           }
+
+            CancerStudy cancerStudy = DaoCancerStudy.getCancerStudyByStableId(cancerStudyIdentifier);
+            if (cancerStudy == null) {
+                throw new RuntimeException("Unknown cancer study: " + cancerStudyIdentifier);
+            }
+
+            this.cancerStudyId = cancerStudy.getInternalId();
+            DaoClinicalEvent.deleteByCancerStudyId(cancerStudyId);
+            this.xmlFile = new File(dataFile);
+            
+            importData();
+            
+            System.out.println("Done!");                                
+        }
+        catch (RuntimeException e) {
+            throw e;
+        } catch (Exception e) {
+            throw new RuntimeException(e);
         }
         
-        int cancerStudyId = cancerStudy.getInternalId();
-        DaoClinicalEvent.deleteByCancerStudyId(cancerStudyId);
-        
-        importData(new File(dataFile), cancerStudy.getInternalId());
-
-        System.out.println("Done!");
     }
     
-    static void importData(File xmlFile, int cancerStudyId) throws Exception {
+    public void setFile(File xmlFile, CancerStudy cancerStudy) {
+        this.xmlFile = xmlFile;
+        this.cancerStudyId = cancerStudy.getInternalId();
+    }
+    
+    public void importData() throws Exception {
         MySQLbulkLoader.bulkLoadOn();
         
         // add unknow attriutes -- this 
diff --git a/core/src/main/java/org/mskcc/cbio/portal/scripts/ImportExtendedMutationData.java b/core/src/main/java/org/mskcc/cbio/portal/scripts/ImportExtendedMutationData.java
index b0ff8654bb4..d826fbb6f0e 100644
--- a/core/src/main/java/org/mskcc/cbio/portal/scripts/ImportExtendedMutationData.java
+++ b/core/src/main/java/org/mskcc/cbio/portal/scripts/ImportExtendedMutationData.java
@@ -60,6 +60,7 @@ public class ImportExtendedMutationData{
 
 	private File mutationFile;
 	private int geneticProfileId;
+	private boolean swissprotIsAccession;
 	private MutationFilter myMutationFilter;
 	private int entriesSkipped = 0;
 	private int samplesSkipped = 0;
@@ -73,11 +74,23 @@ public class ImportExtendedMutationData{
 	public ImportExtendedMutationData(File mutationFile, int geneticProfileId) {
 		this.mutationFile = mutationFile;
 		this.geneticProfileId = geneticProfileId;
+		this.swissprotIsAccession = false;
 
 		// create default MutationFilter
 		myMutationFilter = new MutationFilter( );
 	}
 
+    /**
+     * Turns parsing the SWISSPROT column as an accession on or off again.
+     *
+     * If off, the column will be parsed as the name (formerly ID).
+     *
+     * @param swissprotIsAccession  whether to parse the column as an accession
+     */
+    public void setSwissprotIsAccession(boolean swissprotIsAccession) {
+        this.swissprotIsAccession = swissprotIsAccession;
+    }
+
 	public void importData() throws IOException, DaoException {
 		MySQLbulkLoader.bulkLoadOn();
 
@@ -212,7 +225,6 @@ public void importData() throws IOException, DaoException {
 					aaChange,
 					codonChange,
 					refseqMrnaId,
-					uniprotName,
 					uniprotAccession;
 
 				int proteinPosStart,
@@ -244,8 +256,12 @@ public void importData() throws IOException, DaoException {
 				aaChange = record.getAminoAcidChange();
 				codonChange = record.getCodons();
 				refseqMrnaId = record.getRefSeq();
-				uniprotName = record.getSwissprot();
-				uniprotAccession = DaoUniProtIdMapping.mapFromUniprotIdToAccession(record.getSwissprot());
+                if (this.swissprotIsAccession) {
+                    uniprotAccession = record.getSwissprot();
+                } else {
+                    String uniprotName = record.getSwissprot();
+                    uniprotAccession = DaoUniProtIdMapping.mapFromUniprotIdToAccession(uniprotName);
+                }
 				proteinPosStart = ExtendedMutationUtil.getProteinPosStart(
 						record.getProteinPosition(), proteinChange);
 				proteinPosEnd = ExtendedMutationUtil.getProteinPosEnd(
@@ -369,7 +385,6 @@ public void importData() throws IOException, DaoException {
 					// TODO rename the oncotator column names (remove "oncotator")
 					mutation.setOncotatorCodonChange(codonChange);
 					mutation.setOncotatorRefseqMrnaId(refseqMrnaId);
-					mutation.setOncotatorUniprotName(uniprotName);
 					mutation.setOncotatorUniprotAccession(uniprotAccession);
 					mutation.setOncotatorProteinPosStart(proteinPosStart);
 					mutation.setOncotatorProteinPosEnd(proteinPosEnd);
diff --git a/core/src/main/java/org/mskcc/cbio/portal/scripts/ImportProfileData.java b/core/src/main/java/org/mskcc/cbio/portal/scripts/ImportProfileData.java
index fae85ea922d..9a2e8357855 100644
--- a/core/src/main/java/org/mskcc/cbio/portal/scripts/ImportProfileData.java
+++ b/core/src/main/java/org/mskcc/cbio/portal/scripts/ImportProfileData.java
@@ -78,6 +78,16 @@ public void run() {
 	   
 	            ImportExtendedMutationData importer = new ImportExtendedMutationData( dataFile,
 	                  geneticProfile.getGeneticProfileId());
+	            String swissprotIdType = geneticProfile.getOtherMetaDataField("swissprot_identifier");
+	            if (swissprotIdType != null && swissprotIdType.equals("accession")) {
+	                importer.setSwissprotIsAccession(true);
+	            } else if (
+	                    swissprotIdType != null &&
+	                    swissprotIdType != "name") {
+	                throw new RuntimeException(
+	                        "Unrecognized swissprot_identifier " +
+	                        "specification, must be 'name' or 'accession'.");
+	            }
 	            importer.importData();
 	        }
 		    else if (geneticProfile.getGeneticAlterationType().equals(GeneticAlterationType.FUSION)) {
diff --git a/core/src/main/java/org/mskcc/cbio/portal/scripts/NormalizeExpressionLevels.java b/core/src/main/java/org/mskcc/cbio/portal/scripts/NormalizeExpressionLevels.java
index 79d05fa3991..0ff5649d3b8 100644
--- a/core/src/main/java/org/mskcc/cbio/portal/scripts/NormalizeExpressionLevels.java
+++ b/core/src/main/java/org/mskcc/cbio/portal/scripts/NormalizeExpressionLevels.java
@@ -260,7 +260,7 @@ private static void computeZScoreXP(String file){
                       // Double.NaN indicates an invalid expression value
                       if(zscores[k] != Double.NaN){
                          // limit precision
-                         outputLine.add( String.format( "%.4f", zscores[k] ) );
+                         outputLine.add( String.format( Locale.US, "%.4f", zscores[k] ) ); 
                       }else{
                          outputLine.add( NOT_AVAILABLE );
                       }
diff --git a/core/src/main/java/org/mskcc/cbio/portal/util/GeneticProfileReader.java b/core/src/main/java/org/mskcc/cbio/portal/util/GeneticProfileReader.java
index ad5259be8d1..8fed3c6ab2b 100644
--- a/core/src/main/java/org/mskcc/cbio/portal/util/GeneticProfileReader.java
+++ b/core/src/main/java/org/mskcc/cbio/portal/util/GeneticProfileReader.java
@@ -84,7 +84,12 @@ public static GeneticProfile loadGeneticProfile(File file) throws IOException, D
              // For mutation data only we can have multiple files with the same genetic_profile.
              // There is a constraint in the mutation database table to prevent duplicated data
              // If this constraint is hit (mistakenly importing the same maf twice) MySqlBulkLoader will throw an exception
-             return existingGeneticProfile;
+
+             // make an object combining the pre-existing profile with the file-specific properties of the current file
+             GeneticProfile gp = new GeneticProfile(existingGeneticProfile);
+             gp.setTargetLine(geneticProfile.getTargetLine());
+             gp.setOtherMetadataFields(geneticProfile.getAllOtherMetadataFields());
+             return gp;
          }
       }
       // add new profile
@@ -178,6 +183,7 @@ public static GeneticProfile loadGeneticProfileFromMeta(File file) throws IOExce
 	  geneticProfile.setDatatype(datatype);
       geneticProfile.setShowProfileInAnalysisTab(showProfileInAnalysisTab);
       geneticProfile.setTargetLine(properties.getProperty("target_line"));
+      geneticProfile.setOtherMetadataFields(properties);
       return geneticProfile;
    }
 }
diff --git a/core/src/main/scripts/importer/cbioportal_common.py b/core/src/main/scripts/importer/cbioportal_common.py
index 1fa8d88ea76..e145ee31c02 100644
--- a/core/src/main/scripts/importer/cbioportal_common.py
+++ b/core/src/main/scripts/importer/cbioportal_common.py
@@ -124,7 +124,8 @@ class MetaFileTypes(object):
         'profile_name': True,
         'profile_description': True,
         'data_filename': True,
-        'normal_samples_list': False
+        'normal_samples_list': False,
+        'swissprot_identifier': False
     },
     MetaFileTypes.EXPRESSION: {
         'cancer_study_identifier': True,
@@ -640,6 +641,16 @@ def parse_metadata_file(filename,
                 extra={'filename_': filename,
                        'cause': metaDictionary['reference_genome_id']})
             meta_file_type = None
+    if meta_file_type == MetaFileTypes.MUTATION:
+        if ('swissprot_identifier' in metaDictionary and
+                metaDictionary['swissprot_identifier'] not in ('name',
+                                                               'accession')):
+            logger.error(
+                "Invalid swissprot_identifier specification, must be either "
+                "'name' or 'accession'",
+                extra={'filename_': filename,
+                       'cause': metaDictionary['swissprot_identifier']})
+            meta_file_type = None
 
     logger.info('Validation of meta file complete', extra={'filename_': filename})
     return metaDictionary, meta_file_type
diff --git a/core/src/main/scripts/importer/validateData.py b/core/src/main/scripts/importer/validateData.py
index f10aea6d020..205167a7ae8 100755
--- a/core/src/main/scripts/importer/validateData.py
+++ b/core/src/main/scripts/importer/validateData.py
@@ -1,9 +1,32 @@
 #!/usr/bin/env python2.7
 
-# ------------------------------------------------------------------------------
-# Data validation script - validates files before import into portal.
-# ------------------------------------------------------------------------------
-
+#
+# Copyright (c) 2016 The Hyve B.V.
+# This code is licensed under the GNU Affero General Public License (AGPL),
+# version 3, or (at your option) any later version.
+#
+
+#
+# This file is part of cBioPortal.
+#
+# cBioPortal is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+
+"""Data validation script - validate files before import into portal.
+
+Run with the command line option --help for usage information.
+"""
 
 # imports
 import sys
@@ -291,7 +314,12 @@ def _validate_file(self):
 
         self.logger.debug('Starting validation of file')
 
-        with open(self.filename, 'rU') as data_file:
+        try:
+            opened_file = open(self.filename, 'rU')
+        except IOError:
+            self.logger.error('File could not be opened')
+            return
+        with opened_file as data_file:
 
             # parse any block of start-of-file comment lines and the tsv header
             top_comments = []
@@ -967,6 +995,12 @@ def checkHeader(self, cols):
                 'that the Uniprot canonical isoform is used when drawing Pfam '
                 'domains in the mutations view',
                 extra={'line_number': self.line_number})
+        elif not 'swissprot_identifier' in self.meta_dict:
+            self.logger.warning(
+                "A SWISSPROT column was found in a file without an "
+                "associated 'swissprot_identifier' metadatum, assuming "
+                "'swissprot_identifier: name'.",
+                extra={'column_number': self.cols.index('SWISSPROT') + 1})
 
         # one of these columns should be present:
         if not ('HGVSp_Short' in self.cols or 'Amino_Acid_Change' in self.cols):
@@ -1189,18 +1223,38 @@ def checkNotBlank(self, value):
         if value is None or value.strip() == '':
             return False
         return True
-    
+
     def checkSwissProt(self, value):
-        """Test whether SWISSPROT string is blank and give warning if blank."""
+        """Validate the name or accession in the SWISSPROT column."""
         if value is None or value.strip() == '':
             self.logger.warning(
                 'Missing value in SWISSPROT column; this column is '
                 'recommended to make sure that the Uniprot canonical isoform '
                 'is used when drawing Pfam domains in the mutations view',
                 extra={'line_number': self.line_number,
-                       'cause':'blank value in SWISSPROT column'})
-            
-        # it is just a warning, so we can return True always:
+                       'cause':'<blank>'})
+            # no value to test, return without error
+            return True
+        if self.meta_dict.get('swissprot_identifier', 'name') == 'accession':
+            if not re.match(
+                    # regex from http://www.uniprot.org/help/accession_numbers
+                    r'^([OPQ][0-9][A-Z0-9]{3}[0-9]|'
+                    r'[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2})$',
+                     value):
+                # return this as an error
+                self.extra = 'SWISSPROT value is not a UniprotKB accession'
+                self.extra_exists = True
+                return False
+        else:
+            # format described on http://www.uniprot.org/help/entry_name
+            if not re.match(
+                        r'^[A-Z0-9]{2,5}_[A-Z0-9]{2,5}$',
+                        value):
+                # return this as an error
+                self.extra = 'SWISSPROT value is not a UniprotKB/Swiss-Prot name'
+                self.extra_exists = True
+                return False
+        # if no reasons to return with a message were found, return valid
         return True
 
 
@@ -2344,28 +2398,28 @@ def process_metadata_files(directory, portal_instance, logger):
 
 
 def processCaseListDirectory(caseListDir, cancerStudyId, logger,
-                             stableid_files=None):
-    """Validate the case lists in a directory and log findings.
+                             prev_stableid_files=None):
+    """Validate the case lists in a directory and return an id/file mapping.
 
     Args:
         caseListDir (str): path to the case list directory.
         cancerStudyId (str): cancer_study_identifier expected in the files.
         logger: logging.Logger instance through which to send output.
-        stableid_files (Optional): dict mapping the stable ids of any case
+        prev_stableid_files (Optional): dict mapping the stable IDs of any case
             lists already defined to the files they were defined in.
+
+    Returns:
+        Dict[str, str]: dict mapping the stable IDs of all valid defined case
+            lists to the files they were defined in, including the
+            prev_stableid_files argument
     """
 
     logger.debug('Validating case lists')
 
-    # start with an empty dictionary if none was given
-    # (using mutable objects as default arguments directly is confusing)
-    if stableid_files == None:
-        stableid_files = {}
-
-    # TODO: include ids based on the defined profiles here
-    required_id_suffixes = ('all', )
-    required_stable_ids = [cancerStudyId + '_' + suffix for suffix in
-                           required_id_suffixes]
+    stableid_files = {}
+    # include the previously defined stable IDs
+    if prev_stableid_files is not None:
+        stableid_files.update(prev_stableid_files)
 
     case_list_fns = [os.path.join(caseListDir, fn) for
                      fn in os.listdir(caseListDir) if
@@ -2411,21 +2465,30 @@ def processCaseListDirectory(caseListDir, cancerStudyId, logger,
                     'White space in sample id is not supported',
                     extra={'filename_': case,
                            'cause': value})
-                
 
-    for required_id in required_stable_ids:
-        if required_id not in stableid_files:
-            if required_id == cancerStudyId + '_all':
-                suggestion = ("Consider adding 'add_global_case_list: true' "
-                              "to the study metadata file")
-            else:
-                suggestion = "Please define it in the 'case_lists' folder"
-            logger.error("No  case list found for stable_id '%s'. %s",
-                         required_id,
-                         suggestion)
+    logger.info('Validation of case list folder complete')
+
+    return stableid_files
 
-    logger.info('Validation of case lists complete')
 
+def validate_defined_caselists(cancer_study_id, case_list_ids, file_types, logger):
+
+    """Validate the set of case lists defined in a study.
+
+    Args:
+        cancer_study_id (str): the study ID to be expected in the stable IDs
+        case_list_ids (Iterable[str]): stable ids of defined case lists
+        file_types (Dict[str, str]): listing of the MetaFileTypes with high-
+            dimensional data in this study--these may imply certain case lists
+        logger: logging.Logger instance to log output to
+    """
+
+    if cancer_study_id + '_all' not in case_list_ids:
+        logger.error(
+                "No case list found for stable_id '%s', consider adding "
+                    "'add_global_case_list: true' to the study metadata file",
+                cancer_study_id + '_all')
+    # TODO: check for required suffixes based on the defined profiles
 
 def request_from_portal_api(server_url, api_name, logger):
     """Send a request to the portal API and return the decoded JSON object."""
@@ -2736,13 +2799,20 @@ def validate_study(study_dir, portal_instance, logger):
                 continue
             validator.validate()
 
-    # finally validate case lists if present
+    # finally validate the case list directory if present
     case_list_dirname = os.path.join(study_dir, 'case_lists')
     if not os.path.isdir(case_list_dirname):
         logger.info("No directory named 'case_lists' found, so assuming no custom case lists.")
     else:
-        processCaseListDirectory(case_list_dirname, study_id, logger,
-                                 stableid_files=defined_case_list_fns)
+        # add case lists IDs defined in the directory to any previous ones
+        defined_case_list_fns = processCaseListDirectory(
+                case_list_dirname, study_id, logger,
+                prev_stableid_files=defined_case_list_fns)
+
+    validate_defined_caselists(
+        study_id, defined_case_list_fns.keys(),
+        file_types=validators_by_meta_type.keys(),
+        logger=logger)
 
     logger.info('Validation complete')
 
diff --git a/core/src/test/java/org/mskcc/cbio/portal/scripts/TestImportCaisesClinicalXML.java b/core/src/test/java/org/mskcc/cbio/portal/scripts/TestImportCaisesClinicalXML.java
index 93692e19871..a5c12ce538f 100644
--- a/core/src/test/java/org/mskcc/cbio/portal/scripts/TestImportCaisesClinicalXML.java
+++ b/core/src/test/java/org/mskcc/cbio/portal/scripts/TestImportCaisesClinicalXML.java
@@ -61,33 +61,27 @@
 public class TestImportCaisesClinicalXML {
     
     @Before
-    public void setUp() {
-        try {
-            
-            TypeOfCancer typeOfCancer = new TypeOfCancer();
-            typeOfCancer.setTypeOfCancerId("prad");
-            typeOfCancer.setName("prad");
-            typeOfCancer.setShortName("prad");
-            DaoTypeOfCancer.addTypeOfCancer(typeOfCancer);
-            
-            CancerStudy cancerStudy = new CancerStudy("prad","prad","prad","prad",true);
-            DaoCancerStudy.addCancerStudy(cancerStudy);
-            
-            int studyId = DaoCancerStudy.getCancerStudyByStableId("prad").getInternalId();
+    public void setUp() throws Exception {
+        TypeOfCancer typeOfCancer = new TypeOfCancer();
+        typeOfCancer.setTypeOfCancerId("prad");
+        typeOfCancer.setName("prad");
+        typeOfCancer.setShortName("prad");
+        DaoTypeOfCancer.addTypeOfCancer(typeOfCancer);
 
-            DaoPatient.addPatient(new Patient(cancerStudy, "97115001"));
-            DaoPatient.addPatient(new Patient(cancerStudy, "97115002"));
-            DaoPatient.addPatient(new Patient(cancerStudy, "97115003"));
+        CancerStudy cancerStudy = new CancerStudy("prad","prad","prad","prad",true);
+        DaoCancerStudy.addCancerStudy(cancerStudy);
+        
+        int studyId = DaoCancerStudy.getCancerStudyByStableId("prad").getInternalId();
 
-            int patient1 = DaoPatient.getPatientByCancerStudyAndPatientId(studyId, "97115001").getInternalId();
-            int patient2 = DaoPatient.getPatientByCancerStudyAndPatientId(studyId, "97115002").getInternalId();
+        DaoPatient.addPatient(new Patient(cancerStudy, "97115001"));
+        DaoPatient.addPatient(new Patient(cancerStudy, "97115002"));
+        DaoPatient.addPatient(new Patient(cancerStudy, "97115003"));
 
-            DaoSample.addSample(new Sample("SC_9022-Tumor", patient1, "prad"));
-            DaoSample.addSample(new Sample("SC_9023-Tumor", patient2, "prad"));
-             
-        } catch (Exception e) {
-            e.printStackTrace();
-        }
+        int patient1 = DaoPatient.getPatientByCancerStudyAndPatientId(studyId, "97115001").getInternalId();
+        int patient2 = DaoPatient.getPatientByCancerStudyAndPatientId(studyId, "97115002").getInternalId();
+
+        DaoSample.addSample(new Sample("SC_9022-Tumor", patient1, "prad"));
+        DaoSample.addSample(new Sample("SC_9023-Tumor", patient2, "prad"));
     }
     
     // TODO add test methods here.
@@ -96,7 +90,10 @@ public void setUp() {
      @Test
      public void test() throws Exception {
         File xmlFile = new File("target/test-classes/data_clinical_caises.xml");
-        ImportCaisesClinicalXML.importData(xmlFile, 1);
+        CancerStudy cancerStudy = DaoCancerStudy.getCancerStudyByStableId("prad");
+        ImportCaisesClinicalXML importCaisesClinicalXML = new ImportCaisesClinicalXML(null);
+        importCaisesClinicalXML.setFile(xmlFile, cancerStudy);
+        importCaisesClinicalXML.importData();
      }
      
 //     @Test
@@ -110,4 +107,4 @@ public void test() throws Exception {
 //            "--meta","/Users/jgao/projects/cbio-portal-data/studies/prad/su2c/meta_clinical_caises.txt",
 //            "--loadMode", "bulkLoad"});
 //     }
-}
\ No newline at end of file
+}
diff --git a/core/src/test/java/org/mskcc/cbio/portal/scripts/TestImportExtendedMutationData.java b/core/src/test/java/org/mskcc/cbio/portal/scripts/TestImportExtendedMutationData.java
index 91b6f461f96..74f519ba1b6 100644
--- a/core/src/test/java/org/mskcc/cbio/portal/scripts/TestImportExtendedMutationData.java
+++ b/core/src/test/java/org/mskcc/cbio/portal/scripts/TestImportExtendedMutationData.java
@@ -33,10 +33,7 @@
 package org.mskcc.cbio.portal.scripts;
 
 import org.junit.Before;
-import org.junit.Ignore;
 import org.junit.Test;
-import org.junit.Rule;
-import org.junit.rules.ExpectedException;
 import org.junit.runner.RunWith;
 import org.mskcc.cbio.portal.dao.*;
 import org.mskcc.cbio.portal.model.*;
@@ -47,7 +44,6 @@
 import org.springframework.transaction.annotation.Transactional;
 
 import static org.junit.Assert.*;
-import static org.junit.matchers.JUnitMatchers.containsString;
 
 import java.io.*;
 import java.util.ArrayList;
@@ -82,33 +78,15 @@ public void setUp() throws DaoException {
         ProgressMonitor.setConsoleMode(false);
 
         loadGenes();
-	}
-	
-	@Rule
-	public ExpectedException exception = ExpectedException.none();
-
-	
-	@Test
-	public void testException() {
-        MySQLbulkLoader.bulkLoadOn();
-        
-		// TBD: change this to use getResourceAsStream()
-        File file = new File("target/test-classes/data_mutations_extended.txt");
-        
-        //TODO - find new exception, germline option was removed some time ago already....
-        //exception.expect(IllegalArgumentException.class);
-        //exception.expectMessage(containsString("Gene list 'no_such_germline_whitelistfile' not found"));
+    }
 
-        new ImportExtendedMutationData(file, geneticProfileId);
-	}
-	
 	@Test
     public void testImportExtendedMutationDataExtended() throws IOException, DaoException {
 		
         MySQLbulkLoader.bulkLoadOn();
         
 		// TBD: change this to use getResourceAsStream()
-        File file = new File("target/test-classes/data_mutations_extended.txt");
+        File file = new File("src/test/resources/data_mutations_extended.txt");
         ImportExtendedMutationData parser = new ImportExtendedMutationData(file, geneticProfileId);
         parser.importData();
         MySQLbulkLoader.flushAll();
@@ -121,8 +99,82 @@ public void testImportExtendedMutationDataExtended() throws IOException, DaoExce
         // accept everything else
         validateMutationAminoAcid(geneticProfileId, sampleId, 51806, "P113L");   // valid Unknown
         validateMutationAminoAcid(geneticProfileId, sampleId, 89, "S116R"); // Unknown  Somatic
-	}
-	
+    }
+
+    /**
+     * Tests import of data files with names in the SWISSPROT column.
+     *
+     * @throws IOException  if something goes wrong reading from the data file
+     * @throws DaoException  if something goes wrong talking to the database
+     */
+    @Test
+    public void testImportExtendedMutationDataSwissprotName() throws IOException, DaoException {
+        loadStudyContext1();
+        MySQLbulkLoader.bulkLoadOn();
+
+        File file = new File("src/test/resources/data_mutations_swissprotname.maf");
+        ImportExtendedMutationData parser = new ImportExtendedMutationData(file, geneticProfileId);
+        parser.importData();
+        MySQLbulkLoader.flushAll();
+
+        checkSwissprotLoaded();
+        // unknown accessions are only loaded if the column lists accessions
+        int sampleId = DaoSample.getSampleByCancerStudyAndSampleId(studyId, "TCGA-A2-A0CR-01").getInternalId();
+        ExtendedMutation m = DaoMutation.getMutations(
+                geneticProfileId, sampleId, 64581).get(0);
+        assertNull(m.getOncotatorUniprotAccession());
+    }
+
+    /**
+     * Tests import of data files with accessions in the SWISSPROT column.
+     *
+     * @throws IOException  if something goes wrong reading from the data file
+     * @throws DaoException  if something goes wrong talking to the database
+     */
+    @Test
+    public void testImportExtendedMutationDataSwissprotAccession() throws IOException, DaoException {
+        loadStudyContext1();
+        MySQLbulkLoader.bulkLoadOn();
+
+        File file = new File("src/test/resources/data_mutations_swissprotaccession.maf");
+        ImportExtendedMutationData parser = new ImportExtendedMutationData(file, geneticProfileId);
+        parser.setSwissprotIsAccession(true);
+        parser.importData();
+        MySQLbulkLoader.flushAll();
+
+        checkSwissprotLoaded();
+        // unknown accessions are only loaded if the column lists accessions
+        int sampleId = DaoSample.getSampleByCancerStudyAndSampleId(studyId, "TCGA-A2-A0CR-01").getInternalId();
+        ExtendedMutation m = DaoMutation.getMutations(
+                geneticProfileId, sampleId, 64581).get(0);
+        assertEquals("Z9ZZZ9ZZZ9", m.getOncotatorUniprotAccession());
+    }
+
+    /**
+     * Performs common assertions for the tests about the SWISSPROT column.
+     *
+     * @throws DaoException  on errors reading from the database
+     */
+    private void checkSwissprotLoaded() throws DaoException {
+
+        int sampleId;
+        ExtendedMutation m;
+
+        sampleId = DaoSample.getSampleByCancerStudyAndSampleId(studyId, "TCGA-A2-A0CR-01").getInternalId();
+        validateMutationAminoAcid(geneticProfileId, sampleId, 64581, "K145Q");
+
+        sampleId = DaoSample.getSampleByCancerStudyAndSampleId(studyId, "TCGA-A2-A0T5-01").getInternalId();
+        validateMutationAminoAcid(geneticProfileId, sampleId, 3339, "X4137?");
+        m = DaoMutation.getMutations(
+                geneticProfileId, sampleId, 3339).get(0);
+        assertEquals("P98160", m.getOncotatorUniprotAccession());
+        validateMutationAminoAcid(geneticProfileId, sampleId, 54407, "T32P");
+        m = DaoMutation.getMutations(
+                geneticProfileId, sampleId, 54407).get(0);
+        assertEquals("Q96QD8", m.getOncotatorUniprotAccession());
+
+    }
+
 	/**
 	 * Check that import of oncotated data works
 	 * @throws IOException
@@ -130,7 +182,7 @@ public void testImportExtendedMutationDataExtended() throws IOException, DaoExce
 	 */
 	@Test
     public void testImportExtendedMutationDataOncotated() throws IOException, DaoException {
-        File file = new File("target/test-classes/data_mutations_oncotated.txt");
+        File file = new File("src/test/resources/data_mutations_oncotated.txt");
         ImportExtendedMutationData parser = new ImportExtendedMutationData(file, geneticProfileId);
         parser.importData();
         MySQLbulkLoader.flushAll();
@@ -149,14 +201,6 @@ public void testImportExtendedMutationDataOncotated() throws IOException, DaoExc
 //		             mutationList.get(15).getOncotatorCosmicOverlapping());
 }
 
-    // reject somatic mutations that aren't valid somatic, or on one of the somatic whitelists
-    private void acceptEverythingElse() throws DaoException {
-        int sampleId = DaoSample.getSampleByCancerStudyAndSampleId(studyId, "TCGA-AA-3664-01").getInternalId();
-
-        assertEquals(1, DaoMutation.getMutations(geneticProfileId, sampleId, 51806).size());   // valid Unknown
-        assertEquals(1, DaoMutation.getMutations(geneticProfileId, sampleId, 89).size()); // Unknown  Somatic
-    }
-
     private void checkBasicFilteringRules() throws DaoException {
         rejectSilentLOHIntronWildtype();
         acceptValidSomaticMutations();
@@ -223,6 +267,30 @@ private void loadGenes() throws DaoException {
         daoGene.addGene(new CanonicalGene(6667L, "SP1"));
         daoGene.addGene(new CanonicalGene(2842L, "GPR19"));
 
+        boolean origBulkLoad = MySQLbulkLoader.isBulkLoad();
+        try {
+            MySQLbulkLoader.bulkLoadOn();
+            DaoUniProtIdMapping.addUniProtIdMapping("Q08043", "ACTN3_HUMAN", 89);
+            DaoUniProtIdMapping.addUniProtIdMapping("Q9H694", "BICC1_HUMAN", 80114);
+            DaoUniProtIdMapping.addUniProtIdMapping("Q9NZT1", "CALL5_HUMAN", 51806);
+            DaoUniProtIdMapping.addUniProtIdMapping("Q9BXN2", "CLC7A_HUMAN", 64581);
+            DaoUniProtIdMapping.addUniProtIdMapping("Q15760", "GPR19_HUMAN", 2842);
+            DaoUniProtIdMapping.addUniProtIdMapping("P98160", "PGBM_HUMAN", 3339);
+            DaoUniProtIdMapping.addUniProtIdMapping("Q96P20", "NALP3_HUMAN", 114548);
+            DaoUniProtIdMapping.addUniProtIdMapping("Q8NH19", "O10AG_HUMAN", 282770);
+            DaoUniProtIdMapping.addUniProtIdMapping("Q7Z3Z2", "RD3_HUMAN", 343035);
+            DaoUniProtIdMapping.addUniProtIdMapping("Q96QD8", "S38A2_HUMAN", 54407);
+            DaoUniProtIdMapping.addUniProtIdMapping("P17405", "ASM_HUMAN", 6609);
+            DaoUniProtIdMapping.addUniProtIdMapping("P08047", "SP1_HUMAN", 6667);
+            DaoUniProtIdMapping.addUniProtIdMapping("Q6ZVD7", "STOX1_HUMAN", 219736);
+            DaoUniProtIdMapping.addUniProtIdMapping("Q9NYW0", "T2R10_HUMAN", 50839);
+            DaoUniProtIdMapping.addUniProtIdMapping("Q9P0N5", "TM216_HUMAN", 51259);
+        } finally {
+            if (!origBulkLoad) {
+                MySQLbulkLoader.bulkLoadOff();
+            }
+        }
+
 	    // additional genes for "data_mutations_oncotated.txt"
 	    daoGene.addGene(new CanonicalGene(55138L, "FAM90A1"));
 	    daoGene.addGene(new CanonicalGene(10628L, "TXNIP"));
@@ -248,4 +316,30 @@ private void loadGenes() throws DaoException {
             
             MySQLbulkLoader.flushAll();
     }
+
+    /**
+     * Loads the study context (defined samples) for specific test data files.
+     *
+     * @throws DaoException  if failing to write to the database
+     */
+    private void loadStudyContext1() throws DaoException {
+        CancerStudy study = DaoCancerStudy.getCancerStudyByInternalId(studyId);
+        int pId;
+        pId = DaoPatient.addPatient(new Patient(study, "TCGA-A2-A04T"));
+        DaoSample.addSample(new Sample("TCGA-A2-A04T-01", pId, "brca"));
+        pId = DaoPatient.addPatient(new Patient(study, "TCGA-A2-A0CR"));
+        DaoSample.addSample(new Sample("TCGA-A2-A0CR-01", pId, "brca"));
+        pId = DaoPatient.addPatient(new Patient(study, "TCGA-A2-A0CW"));
+        DaoSample.addSample(new Sample("TCGA-A2-A0CW-01", pId, "brca"));
+        pId = DaoPatient.addPatient(new Patient(study, "TCGA-A2-A0D3"));
+        DaoSample.addSample(new Sample("TCGA-A2-A0D3-01", pId, "brca"));
+        pId = DaoPatient.addPatient(new Patient(study, "TCGA-A2-A0SY"));
+        DaoSample.addSample(new Sample("TCGA-A2-A0SY-01", pId, "brca"));
+        pId = DaoPatient.addPatient(new Patient(study, "TCGA-A2-A0T5"));
+        DaoSample.addSample(new Sample("TCGA-A2-A0T5-01", pId, "brca"));
+        pId = DaoPatient.addPatient(new Patient(study, "TCGA-A2-A25D"));
+        DaoSample.addSample(new Sample("TCGA-A2-A25D-01", pId, "brca"));
+        pId = DaoPatient.addPatient(new Patient(study, "TCGA-A2-A4RW"));
+        DaoSample.addSample(new Sample("TCGA-A2-A4RW-01", pId, "brca"));
+    }
 }
diff --git a/core/src/test/java/org/mskcc/cbio/portal/scripts/TestImportProfileData.java b/core/src/test/java/org/mskcc/cbio/portal/scripts/TestImportProfileData.java
index aea280d4339..17cd435be95 100644
--- a/core/src/test/java/org/mskcc/cbio/portal/scripts/TestImportProfileData.java
+++ b/core/src/test/java/org/mskcc/cbio/portal/scripts/TestImportProfileData.java
@@ -24,6 +24,7 @@
 package org.mskcc.cbio.portal.scripts;
 
 import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNull;
 
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -77,7 +78,7 @@ public void setUp() throws DaoException {
 	public ExpectedException exception = ExpectedException.none();
 
 	@Test
-	public void testImportMutationsFile() throws Exception {
+	public void testImportMutationFiles() throws Exception {
         String[] args = {
                 "--data","src/test/resources/data_mutations_extended.txt",
                 "--meta","src/test/resources/meta_mutations_extended.txt",
@@ -89,10 +90,25 @@ public void testImportMutationsFile() throws Exception {
         //dataset study id (e.g. studyStableId + "_breast_mutations"):
         String studyStableId = "study_tcga_pub";
 		studyId = DaoCancerStudy.getCancerStudyByStableId(studyStableId).getInternalId();
+        // the sample is added on the fly when encountered in the mutation data file
 		int sampleId = DaoSample.getSampleByCancerStudyAndSampleId(studyId, "TCGA-AA-3664-01").getInternalId();
 
         geneticProfileId = DaoGeneticProfile.getGeneticProfileByStableId(studyStableId + "_breast_mutations").getGeneticProfileId();
-        validateMutationAminoAcid (geneticProfileId, sampleId, 54407, "T433A");  
+        validateMutationAminoAcid (geneticProfileId, sampleId, 54407, "T433A");
+
+        // data for this sample should not exist before loading the next data file
+        assertNull(DaoSample.getSampleByCancerStudyAndSampleId(studyId, "TCGA-AA-3665-01"));
+        // load a second mutation data file
+        String[] secondArgs = {
+                "--data","src/test/resources/data_mutations_extended_continued.txt",
+                "--meta","src/test/resources/meta_mutations_extended.txt",
+                "--loadMode", "bulkLoad"
+        };
+        ImportProfileData secondRunner = new ImportProfileData(secondArgs);
+        secondRunner.run();
+        // again, the sample is added on the fly
+        int secondSampleId = DaoSample.getSampleByCancerStudyAndSampleId(studyId, "TCGA-AA-3665-01").getInternalId();
+        validateMutationAminoAcid (geneticProfileId, secondSampleId, 2842, "L113P");
     }
 
 	@Test
diff --git a/core/src/test/resources/data_mutations_extended_continued.txt b/core/src/test/resources/data_mutations_extended_continued.txt
new file mode 100644
index 00000000000..d62e1dfbe14
--- /dev/null
+++ b/core/src/test/resources/data_mutations_extended_continued.txt
@@ -0,0 +1,3 @@
+Hugo_Symbol	Entrez_Gene_Id	Center	Tumor_Sample_Barcode	Verification_Status	Validation_Status	Mutation_Status	Sequencer	Chromosome	Start_position	End_position	Variant_Classification	HGVSp_Short	MA:FImpact	MA:link.MSA	MA:link.PDB
+GPR19	2842	broad.mit.edu	TCGA-AA-3665-01	Unknown	valid	Germline	Illumina GAIIx	chr12	12706312	12706312	Nonsense_Mutation	L113P	high	mutationassessor.org/?cm=msa&ty=f&p=GPR19_HUMAN&rb=82&re=330&var=L113P	mutationassessor.org/pdb.php?prot=GPR19_HUMAN&from=82&to=330&var=L113P
+SP1	6667	broad.mit.edu	TCGA-AA-3665-01	Unknown	valid	Somatic	Illumina GAIIx	chr12	52063536	52063536	Missense_Mutation	A513V	low	mutationassessor.org/?cm=msa&ty=f&p=SP1_HUMAN&rb=401&re=600&var=A513V	
diff --git a/core/src/test/resources/data_mutations_swissprotaccession.maf b/core/src/test/resources/data_mutations_swissprotaccession.maf
new file mode 100644
index 00000000000..0c28f8c85d1
--- /dev/null
+++ b/core/src/test/resources/data_mutations_swissprotaccession.maf
@@ -0,0 +1,12 @@
+Hugo_Symbol	Tumor_Sample_Barcode	Variant_Classification	HGVSp_Short	SWISSPROT
+BICC1	TCGA-A2-A04T-01	Missense_Mutation	p.L405S	Q9H694
+CLEC7A	TCGA-A2-A0CR-01	Missense_Mutation	p.K145Q	Z9ZZZ9ZZZ9
+HSPG2	TCGA-A2-A0CW-01	Missense_Mutation	p.D468N	P98160
+NLRP3	TCGA-A2-A0D3-01	Nonsense_Mutation	p.R699*	Q96P20
+SMPD1	TCGA-A2-A0SY-01	Silent	p.P63P	P17405
+HSPG2	TCGA-A2-A0T5-01	Splice_Site	p.X4137?	P98160
+HSPG2	TCGA-A2-A0T5-01	Silent        p.=     P98160
+HSPG2	TCGA-A2-A0T5-01	Intron	p.(=)	P98160
+SLC38A2	TCGA-A2-A0T5-01	Missense_Mutation	p.T32P	Q96QD8
+SLC38A2	TCGA-A2-A25D-01	Silent	p.V485V	Q96QD8
+TMEM216	TCGA-A2-A4RW-01	Missense_Mutation	p.R115C	Q9P0N5
diff --git a/core/src/test/resources/data_mutations_swissprotname.maf b/core/src/test/resources/data_mutations_swissprotname.maf
new file mode 100644
index 00000000000..0a5a3518e6d
--- /dev/null
+++ b/core/src/test/resources/data_mutations_swissprotname.maf
@@ -0,0 +1,12 @@
+Hugo_Symbol	Tumor_Sample_Barcode	Variant_Classification	HGVSp_Short	SWISSPROT
+BICC1	TCGA-A2-A04T-01	Missense_Mutation	p.L405S	BICC1_HUMAN
+CLEC7A	TCGA-A2-A0CR-01	Missense_Mutation	p.K145Q	HBB_YEAST
+HSPG2	TCGA-A2-A0CW-01	Missense_Mutation	p.D468N	PGBM_HUMAN
+NLRP3	TCGA-A2-A0D3-01	Nonsense_Mutation	p.R699*	NALP3_HUMAN
+SMPD1	TCGA-A2-A0SY-01	Silent	p.P63P	ASM_HUMAN
+HSPG2	TCGA-A2-A0T5-01	Splice_Site	p.X4137?	PGBM_HUMAN
+HSPG2	TCGA-A2-A0T5-01	Silent	p.=	PGBM_HUMAN
+HSPG2	TCGA-A2-A0T5-01	Intron	p.(=)	PGBM_HUMAN
+SLC38A2	TCGA-A2-A0T5-01	Missense_Mutation	p.T32P	S38A2_HUMAN
+SLC38A2	TCGA-A2-A25D-01	Silent	p.V485V	S38A2_HUMAN
+TMEM216	TCGA-A2-A4RW-01	Missense_Mutation	p.R115C	TM216_HUMAN
diff --git a/core/src/test/resources/meta_mutations_extended.txt b/core/src/test/resources/meta_mutations_extended.txt
index d1bc7856a22..5aa1eed1048 100644
--- a/core/src/test/resources/meta_mutations_extended.txt
+++ b/core/src/test/resources/meta_mutations_extended.txt
@@ -1,6 +1,7 @@
 cancer_study_identifier: study_tcga_pub
 cancer_type_id: breast
 genetic_alteration_type: MUTATION_EXTENDED
+datatype: MAF
 stable_id: breast_mutations
 show_profile_in_analysis_tab: true
 profile_description: Mutation data from whole exome sequencing.
diff --git a/core/src/test/scripts/system_tests_validate_data.py b/core/src/test/scripts/system_tests_validate_data.py
index 8c806b07e18..418b83cc77b 100755
--- a/core/src/test/scripts/system_tests_validate_data.py
+++ b/core/src/test/scripts/system_tests_validate_data.py
@@ -239,7 +239,7 @@ def test_files_with_quotes(self):
         # should fail because of errors with quotes
         self.assertEquals(1, exit_status)
         self.assertFileGenerated(out_file_name,
-                                 'test_data/study_quotes/result_report.html')        
+                                 'test_data/study_quotes/result_report.html')
 
 
 if __name__ == '__main__':
diff --git a/core/src/test/scripts/test_data/mutations/data_mutations_invalid_norm_samples.maf b/core/src/test/scripts/test_data/mutations/data_mutations_invalid_norm_samples.maf
index d12f5f2afa2..f5e0c30b686 100644
--- a/core/src/test/scripts/test_data/mutations/data_mutations_invalid_norm_samples.maf
+++ b/core/src/test/scripts/test_data/mutations/data_mutations_invalid_norm_samples.maf
@@ -1,8 +1,8 @@
 Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_Position	End_Position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_File	Sequencer	ONCOTATOR_COSMIC_OVERLAPPING	ONCOTATOR_DBSNP_RS	ONCOTATOR_DBSNP_VAL_STATUS	ONCOTATOR_VARIANT_CLASSIFICATION	HGVSp_Short	SWISSPROT	ONCOTATOR_REFSEQ_MRNA_ID	ONCOTATOR_REFSEQ_PROT_ID	ONCOTATOR_UNIPROT_ENTRY_NAME	ONCOTATOR_UNIPROT_ACCESSION	ONCOTATOR_CODON_CHANGE	ONCOTATOR_TRANSCRIPT_CHANGE	ONCOTATOR_EXON_AFFECTED	ONCOTATOR_PROTEIN_POS_START	ONCOTATOR_PROTEIN_POS_END	ONCOTATOR_VARIANT_CLASSIFICATION_BEST_EFFECT	ONCOTATOR_PROTEIN_CHANGE_BEST_EFFECT	ONCOTATOR_GENE_SYMBOL_BEST_EFFECT	ONCOTATOR_REFSEQ_MRNA_ID_BEST_EFFECT	ONCOTATOR_REFSEQ_PROT_ID_BEST_EFFECT	ONCOTATOR_UNIPROT_ENTRY_NAME_BEST_EFFECT	ONCOTATOR_UNIPROT_ACCESSION_BEST_EFFECT	ONCOTATOR_CODON_CHANGE_BEST_EFFECT	ONCOTATOR_TRANSCRIPT_CHANGE_BEST_EFFECT	ONCOTATOR_EXON_AFFECTED_BEST_EFFECT	ONCOTATOR_PROTEIN_POS_START_BEST_EFFECT	ONCOTATOR_PROTEIN_POS_END_BEST_EFFECT	MA:FImpact	MA:FIS	MA:protein.change	MA:link.MSA	MA:link.PDB	MA:link.var	chromosome_name_WU	start_WU	stop_WU	reference_WU	variant_WU	type_WU	gene_name_WU	transcript_name_WU	transcript_species_WU	transcript_source_WU	transcript_version_WU	strand_WU	transcript_status_WU	trv_type_WU	Protein_position	amino_acid_change_WU	ucsc_cons_WU	domain_WU	all_domains_WU	deletion_substructures_WU	annotation_errors_WU
-A1CF	29974	genome.wustl.edu	37	10	52573692	52573692	+	Missense_Mutation	SNP	G	G	T	novel	unknown	TCGA-B6-A0RS-01	TCGA-B6-A0RS-10	G	G	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Missense_Mutation	p.D424E	A1CF	NM_138932	NP_620310	A1CF_HUMAN	Q9NQ94	c.(1270-1272)GAC>GAA	c.1272C>A	10	424	424	Missense_Mutation	p.D432E	A1CF	NM_138933	NP_620311	A1CF_HUMAN	Q9NQ94	c.(1294-1296)GAC>GAA	c.1296C>A	12	432	432	neutral	0.345	D424E	getma.org/?cm=msa&ty=f&p=A1CF_HUMAN&rb=298&re=497&var=D424E	NA	getma.org/?cm=var&var=hg19,10,52573692,G,T&fts=all	10	52573692	52573692	G	T	SNP	A1CF	NM_138932	human	genbank	57_37b	-1	reviewed	missense	c.1272	p.D424E	0.768	NULL	superfamily_RNA-binding domain RBD,HMMSmart_SM00360,HMMPfam_RRM_1,superfamily_dsRNA-binding domain-like	-	no_errors
-A1CF	29974	genome.wustl.edu	37	10	52595854	52595854	+	Missense_Mutation	SNP	G	G	A	novel	unknown	TCGA-BH-A0HP-01	TCGA-BH-A0HP-10	G	G	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Missense_Mutation	p.A195V	A1CF	NM_138932	NP_620310	A1CF_HUMAN	Q9NQ94	c.(583-585)GCG>GTG	c.584C>T	6	195	195	Missense_Mutation	p.A203V	A1CF	NM_138933	NP_620311	A1CF_HUMAN	Q9NQ94	c.(607-609)GCG>GTG	c.608C>T	8	203	203	medium	2.955	A195V	getma.org/?cm=msa&ty=f&p=A1CF_HUMAN&rb=138&re=203&var=A195V	getma.org/pdb.php?prot=A1CF_HUMAN&from=138&to=203&var=A195V	getma.org/?cm=var&var=hg19,10,52595854,G,A&fts=all	10	52595854	52595854	G	A	SNP	A1CF	NM_138932	human	genbank	57_37b	-1	reviewed	missense	c.584	p.A195V	1.000	superfamily_RNA-binding domain RBD,HMMSmart_SM00360,HMMPfam_RRM_1	superfamily_RNA-binding domain RBD,HMMSmart_SM00360,HMMPfam_RRM_1,superfamily_dsRNA-binding domain-like	-	no_errors
-A1CF	29974	genome.wustl.edu	37	10	52595937	52595937	+	Silent	SNP	G	G	A	novel	unknown	TCGA-BH-A18P-01	TCGA-BH-A18P-11	G	G	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Silent	p.I167I	A1CF	NM_138932	NP_620310	A1CF_HUMAN	Q9NQ94	c.(499-501)ATC>ATT	c.501C>T	6	167	167	Silent	p.I175I	A1CF	NM_138933	NP_620311	A1CF_HUMAN	Q9NQ94	c.(523-525)ATC>ATT	c.525C>T	8	175	175	NA	NA	NA	NA	NA	NA	10	52595937	52595937	G	A	SNP	A1CF	NM_138932	human	genbank	57_37b	-1	reviewed	silent	c.501	p.I167	0.615	superfamily_RNA-binding domain RBD,HMMSmart_SM00360,HMMPfam_RRM_1	superfamily_RNA-binding domain RBD,HMMSmart_SM00360,HMMPfam_RRM_1,superfamily_dsRNA-binding domain-like	-	no_errors
-A2M	2	genome.wustl.edu	37	12	9230409	9230409	+	Missense_Mutation	SNP	T	T	C	novel	unknown	TCGA-BH-A18H-01	TCGA-BH-A18H-10	T	T	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Missense_Mutation	p.Y1055C	A2M	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(3163-3165)TAC>TGC	c.3164A>G	26	1055	1055	Missense_Mutation	p.Y1055C	A2M	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(3163-3165)TAC>TGC	c.3164A>G	26	1055	1055	high	3.73	Y1055C	getma.org/?cm=msa&ty=f&p=A2MG_HUMAN&rb=1010&re=1266&var=Y1055C	getma.org/pdb.php?prot=A2MG_HUMAN&from=1010&to=1266&var=Y1055C	getma.org/?cm=var&var=hg19,12,9230409,T,C&fts=all	12	9230409	9230409	T	C	SNP	A2M	NM_000014	human	genbank	57_37b	-1	reviewed	missense	c.3164	p.Y1055C	0.143	superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_A2M_comp	PatternScan_TONB_DEPENDENT_REC_1,HMMPfam_A2M_N,HMMPfam_A2M_N_2,HMMPfam_A2M,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN,HMMPfam_A2M_comp,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_recep	-	no_errors
-A2M	2	genome.wustl.edu	37	12	9242995	9242995	+	Silent	SNP	G	G	A	novel	unknown	TCGA-C8-A138-01	TCGA-C8-A138-10	G	G	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Silent	p.N851N	A2M	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(2551-2553)AAC>AAT	c.2553C>T	20	851	851	Silent	p.N851N	A2M	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(2551-2553)AAC>AAT	c.2553C>T	20	851	851	NA	NA	NA	NA	NA	NA	12	9242995	9242995	G	A	SNP	A2M	NM_000014	human	genbank	57_37b	-1	reviewed	silent	c.2553	p.N851	0.003	NULL	PatternScan_TONB_DEPENDENT_REC_1,HMMPfam_A2M_N,HMMPfam_A2M_N_2,HMMPfam_A2M,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN,HMMPfam_A2M_comp,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_recep	-	no_errors
-A2M	2	genome.wustl.edu	37	12	9246090	9246090	+	Silent	SNP	C	C	T	novel	unknown	TCGA-A2-A0EY-01	TCGA-A2-A0EY-10	C	C	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Silent	p.E737E	A2M	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(2209-2211)GAG>GAA	c.2211G>A	18	737	737	Silent	p.E737E	A2M	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(2209-2211)GAG>GAA	c.2211G>A	18	737	737	NA	NA	NA	NA	NA	NA	12	9246090	9246090	C	T	SNP	A2M	NM_000014	human	genbank	57_37b	-1	reviewed	silent	c.2211	p.E737	1.000	NULL	PatternScan_TONB_DEPENDENT_REC_1,HMMPfam_A2M_N,HMMPfam_A2M_N_2,HMMPfam_A2M,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN,HMMPfam_A2M_comp,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_recep	-	no_errors
-A2M	2	genome.wustl.edu	37	12	9251298	9251298	+	Nonsense_Mutation	SNP	G	G	A	novel	unknown	TCGA-A8-A08G-01	TCGA-A8-A08G-10	G	G	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Nonsense_Mutation	p.R586*	A2M	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(1756-1758)CGA>TGA	c.1756C>T	15	586	586	Nonsense_Mutation	p.R586*	A2M	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(1756-1758)CGA>TGA	c.1756C>T	15	586	586	NA	0.0	R586*	NA	NA	getma.org/?cm=var&var=hg19,12,9251298,G,A&fts=all	12	9251298	9251298	G	A	SNP	A2M	NM_000014	human	genbank	57_37b	-1	reviewed	nonsense	c.1756	p.R586*	0.003	HMMPfam_A2M_N_2	PatternScan_TONB_DEPENDENT_REC_1,HMMPfam_A2M_N,HMMPfam_A2M_N_2,HMMPfam_A2M,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN,HMMPfam_A2M_comp,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_recep	-	no_errors
+A1CF	29974	genome.wustl.edu	37	10	52573692	52573692	+	Missense_Mutation	SNP	G	G	T	novel	unknown	TCGA-B6-A0RS-01	TCGA-B6-A0RS-10	G	G	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Missense_Mutation	p.D424E	Q9NQ94	NM_138932	NP_620310	A1CF_HUMAN	Q9NQ94	c.(1270-1272)GAC>GAA	c.1272C>A	10	424	424	Missense_Mutation	p.D432E	A1CF	NM_138933	NP_620311	A1CF_HUMAN	Q9NQ94	c.(1294-1296)GAC>GAA	c.1296C>A	12	432	432	neutral	0.345	D424E	getma.org/?cm=msa&ty=f&p=A1CF_HUMAN&rb=298&re=497&var=D424E	NA	getma.org/?cm=var&var=hg19,10,52573692,G,T&fts=all	10	52573692	52573692	G	T	SNP	A1CF	NM_138932	human	genbank	57_37b	-1	reviewed	missense	c.1272	p.D424E	0.768	NULL	superfamily_RNA-binding domain RBD,HMMSmart_SM00360,HMMPfam_RRM_1,superfamily_dsRNA-binding domain-like	-	no_errors
+A1CF	29974	genome.wustl.edu	37	10	52595854	52595854	+	Missense_Mutation	SNP	G	G	A	novel	unknown	TCGA-BH-A0HP-01	TCGA-BH-A0HP-10	G	G	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Missense_Mutation	p.A195V	Q9NQ94	NM_138932	NP_620310	A1CF_HUMAN	Q9NQ94	c.(583-585)GCG>GTG	c.584C>T	6	195	195	Missense_Mutation	p.A203V	A1CF	NM_138933	NP_620311	A1CF_HUMAN	Q9NQ94	c.(607-609)GCG>GTG	c.608C>T	8	203	203	medium	2.955	A195V	getma.org/?cm=msa&ty=f&p=A1CF_HUMAN&rb=138&re=203&var=A195V	getma.org/pdb.php?prot=A1CF_HUMAN&from=138&to=203&var=A195V	getma.org/?cm=var&var=hg19,10,52595854,G,A&fts=all	10	52595854	52595854	G	A	SNP	A1CF	NM_138932	human	genbank	57_37b	-1	reviewed	missense	c.584	p.A195V	1.000	superfamily_RNA-binding domain RBD,HMMSmart_SM00360,HMMPfam_RRM_1	superfamily_RNA-binding domain RBD,HMMSmart_SM00360,HMMPfam_RRM_1,superfamily_dsRNA-binding domain-like	-	no_errors
+A1CF	29974	genome.wustl.edu	37	10	52595937	52595937	+	Silent	SNP	G	G	A	novel	unknown	TCGA-BH-A18P-01	TCGA-BH-A18P-11	G	G	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Silent	p.I167I	Q9NQ94	NM_138932	NP_620310	A1CF_HUMAN	Q9NQ94	c.(499-501)ATC>ATT	c.501C>T	6	167	167	Silent	p.I175I	A1CF	NM_138933	NP_620311	A1CF_HUMAN	Q9NQ94	c.(523-525)ATC>ATT	c.525C>T	8	175	175	NA	NA	NA	NA	NA	NA	10	52595937	52595937	G	A	SNP	A1CF	NM_138932	human	genbank	57_37b	-1	reviewed	silent	c.501	p.I167	0.615	superfamily_RNA-binding domain RBD,HMMSmart_SM00360,HMMPfam_RRM_1	superfamily_RNA-binding domain RBD,HMMSmart_SM00360,HMMPfam_RRM_1,superfamily_dsRNA-binding domain-like	-	no_errors
+A2M	2	genome.wustl.edu	37	12	9230409	9230409	+	Missense_Mutation	SNP	T	T	C	novel	unknown	TCGA-BH-A18H-01	TCGA-BH-A18H-10	T	T	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Missense_Mutation	p.Y1055C	P01023	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(3163-3165)TAC>TGC	c.3164A>G	26	1055	1055	Missense_Mutation	p.Y1055C	A2M	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(3163-3165)TAC>TGC	c.3164A>G	26	1055	1055	high	3.73	Y1055C	getma.org/?cm=msa&ty=f&p=A2MG_HUMAN&rb=1010&re=1266&var=Y1055C	getma.org/pdb.php?prot=A2MG_HUMAN&from=1010&to=1266&var=Y1055C	getma.org/?cm=var&var=hg19,12,9230409,T,C&fts=all	12	9230409	9230409	T	C	SNP	A2M	NM_000014	human	genbank	57_37b	-1	reviewed	missense	c.3164	p.Y1055C	0.143	superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_A2M_comp	PatternScan_TONB_DEPENDENT_REC_1,HMMPfam_A2M_N,HMMPfam_A2M_N_2,HMMPfam_A2M,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN,HMMPfam_A2M_comp,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_recep	-	no_errors
+A2M	2	genome.wustl.edu	37	12	9242995	9242995	+	Silent	SNP	G	G	A	novel	unknown	TCGA-C8-A138-01	TCGA-C8-A138-10	G	G	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Silent	p.N851N	P01023	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(2551-2553)AAC>AAT	c.2553C>T	20	851	851	Silent	p.N851N	A2M	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(2551-2553)AAC>AAT	c.2553C>T	20	851	851	NA	NA	NA	NA	NA	NA	12	9242995	9242995	G	A	SNP	A2M	NM_000014	human	genbank	57_37b	-1	reviewed	silent	c.2553	p.N851	0.003	NULL	PatternScan_TONB_DEPENDENT_REC_1,HMMPfam_A2M_N,HMMPfam_A2M_N_2,HMMPfam_A2M,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN,HMMPfam_A2M_comp,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_recep	-	no_errors
+A2M	2	genome.wustl.edu	37	12	9246090	9246090	+	Silent	SNP	C	C	T	novel	unknown	TCGA-A2-A0EY-01	TCGA-A2-A0EY-10	C	C	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Silent	p.E737E	P01023	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(2209-2211)GAG>GAA	c.2211G>A	18	737	737	Silent	p.E737E	A2M	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(2209-2211)GAG>GAA	c.2211G>A	18	737	737	NA	NA	NA	NA	NA	NA	12	9246090	9246090	C	T	SNP	A2M	NM_000014	human	genbank	57_37b	-1	reviewed	silent	c.2211	p.E737	1.000	NULL	PatternScan_TONB_DEPENDENT_REC_1,HMMPfam_A2M_N,HMMPfam_A2M_N_2,HMMPfam_A2M,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN,HMMPfam_A2M_comp,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_recep	-	no_errors
+A2M	2	genome.wustl.edu	37	12	9251298	9251298	+	Nonsense_Mutation	SNP	G	G	A	novel	unknown	TCGA-A8-A08G-01	TCGA-A8-A08G-10	G	G	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Nonsense_Mutation	p.R586*	P01023	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(1756-1758)CGA>TGA	c.1756C>T	15	586	586	Nonsense_Mutation	p.R586*	A2M	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(1756-1758)CGA>TGA	c.1756C>T	15	586	586	NA	0.0	R586*	NA	NA	getma.org/?cm=var&var=hg19,12,9251298,G,A&fts=all	12	9251298	9251298	G	A	SNP	A2M	NM_000014	human	genbank	57_37b	-1	reviewed	nonsense	c.1756	p.R586*	0.003	HMMPfam_A2M_N_2	PatternScan_TONB_DEPENDENT_REC_1,HMMPfam_A2M_N,HMMPfam_A2M_N_2,HMMPfam_A2M,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN,HMMPfam_A2M_comp,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_recep	-	no_errors
diff --git a/core/src/test/scripts/test_data/mutations/data_mutations_invalid_swissprot.maf b/core/src/test/scripts/test_data/mutations/data_mutations_invalid_swissprot.maf
new file mode 100644
index 00000000000..aff874f34f7
--- /dev/null
+++ b/core/src/test/scripts/test_data/mutations/data_mutations_invalid_swissprot.maf
@@ -0,0 +1,8 @@
+Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_Position	End_Position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_File	Sequencer	ONCOTATOR_COSMIC_OVERLAPPING	ONCOTATOR_DBSNP_RS	ONCOTATOR_DBSNP_VAL_STATUS	ONCOTATOR_VARIANT_CLASSIFICATION	HGVSp_Short	SWISSPROT	ONCOTATOR_REFSEQ_MRNA_ID	ONCOTATOR_REFSEQ_PROT_ID	ONCOTATOR_UNIPROT_ENTRY_NAME	ONCOTATOR_UNIPROT_ACCESSION	ONCOTATOR_CODON_CHANGE	ONCOTATOR_TRANSCRIPT_CHANGE	ONCOTATOR_EXON_AFFECTED	ONCOTATOR_PROTEIN_POS_START	ONCOTATOR_PROTEIN_POS_END	ONCOTATOR_VARIANT_CLASSIFICATION_BEST_EFFECT	ONCOTATOR_PROTEIN_CHANGE_BEST_EFFECT	ONCOTATOR_GENE_SYMBOL_BEST_EFFECT	ONCOTATOR_REFSEQ_MRNA_ID_BEST_EFFECT	ONCOTATOR_REFSEQ_PROT_ID_BEST_EFFECT	ONCOTATOR_UNIPROT_ENTRY_NAME_BEST_EFFECT	ONCOTATOR_UNIPROT_ACCESSION_BEST_EFFECT	ONCOTATOR_CODON_CHANGE_BEST_EFFECT	ONCOTATOR_TRANSCRIPT_CHANGE_BEST_EFFECT	ONCOTATOR_EXON_AFFECTED_BEST_EFFECT	ONCOTATOR_PROTEIN_POS_START_BEST_EFFECT	ONCOTATOR_PROTEIN_POS_END_BEST_EFFECT	MA:FImpact	MA:FIS	MA:protein.change	MA:link.MSA	MA:link.PDB	MA:link.var	chromosome_name_WU	start_WU	stop_WU	reference_WU	variant_WU	type_WU	gene_name_WU	transcript_name_WU	transcript_species_WU	transcript_source_WU	transcript_version_WU	strand_WU	transcript_status_WU	trv_type_WU	Protein_position	amino_acid_change_WU	ucsc_cons_WU	domain_WU	all_domains_WU	deletion_substructures_WU	annotation_errors_WU
+A1CF	29974	genome.wustl.edu	37	10	52573692	52573692	+	Missense_Mutation	SNP	G	G	T	novel	unknown	TCGA-B6-A0RS-01	TCGA-B6-A0RS-10	G	G	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Missense_Mutation	p.D424E	P99999	NM_138932	NP_620310	A1CF_HUMAN	Q9NQ94	c.(1270-1272)GAC>GAA	c.1272C>A	10	424	424	Missense_Mutation	p.D432E	A1CF	NM_138933	NP_620311	A1CF_HUMAN	Q9NQ94	c.(1294-1296)GAC>GAA	c.1296C>A	12	432	432	neutral	0.345	D424E	getma.org/?cm=msa&ty=f&p=A1CF_HUMAN&rb=298&re=497&var=D424E	NA	getma.org/?cm=var&var=hg19,10,52573692,G,T&fts=all	10	52573692	52573692	G	T	SNP	A1CF	NM_138932	human	genbank	57_37b	-1	reviewed	missense	c.1272	p.D424E	0.768	NULL	superfamily_RNA-binding domain RBD,HMMSmart_SM00360,HMMPfam_RRM_1,superfamily_dsRNA-binding domain-like	-	no_errors
+A1CF	29974	genome.wustl.edu	37	10	52595854	52595854	+	Missense_Mutation	SNP	G	G	A	novel	unknown	TCGA-BH-A0HP-01	TCGA-BH-A0HP-10	G	G	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Missense_Mutation	p.A195V	A1CF_HUMAN	NM_138932	NP_620310	A1CF_HUMAN	Q9NQ94	c.(583-585)GCG>GTG	c.584C>T	6	195	195	Missense_Mutation	p.A203V	A1CF	NM_138933	NP_620311	A1CF_HUMAN	Q9NQ94	c.(607-609)GCG>GTG	c.608C>T	8	203	203	medium	2.955	A195V	getma.org/?cm=msa&ty=f&p=A1CF_HUMAN&rb=138&re=203&var=A195V	getma.org/pdb.php?prot=A1CF_HUMAN&from=138&to=203&var=A195V	getma.org/?cm=var&var=hg19,10,52595854,G,A&fts=all	10	52595854	52595854	G	A	SNP	A1CF	NM_138932	human	genbank	57_37b	-1	reviewed	missense	c.584	p.A195V	1.000	superfamily_RNA-binding domain RBD,HMMSmart_SM00360,HMMPfam_RRM_1	superfamily_RNA-binding domain RBD,HMMSmart_SM00360,HMMPfam_RRM_1,superfamily_dsRNA-binding domain-like	-	no_errors
+A1CF	29974	genome.wustl.edu	37	10	52595937	52595937	+	Silent	SNP	G	G	A	novel	unknown	TCGA-BH-A18P-01	TCGA-BH-A18P-11	G	G	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Silent	p.I167I	P99999	NM_138932	NP_620310	A1CF_HUMAN	Q9NQ94	c.(499-501)ATC>ATT	c.501C>T	6	167	167	Silent	p.I175I	A1CF	NM_138933	NP_620311	A1CF_HUMAN	Q9NQ94	c.(523-525)ATC>ATT	c.525C>T	8	175	175	NA	NA	NA	NA	NA	NA	10	52595937	52595937	G	A	SNP	A1CF	NM_138932	human	genbank	57_37b	-1	reviewed	silent	c.501	p.I167	0.615	superfamily_RNA-binding domain RBD,HMMSmart_SM00360,HMMPfam_RRM_1	superfamily_RNA-binding domain RBD,HMMSmart_SM00360,HMMPfam_RRM_1,superfamily_dsRNA-binding domain-like	-	no_errors
+A2M	2	genome.wustl.edu	37	12	9230409	9230409	+	Missense_Mutation	SNP	T	T	C	novel	unknown	TCGA-BH-A18H-01	TCGA-BH-A18H-10	T	T	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Missense_Mutation	p.Y1055C	P99999,Z9ZZZ9ZZZ9	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(3163-3165)TAC>TGC	c.3164A>G	26	1055	1055	Missense_Mutation	p.Y1055C	A2M	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(3163-3165)TAC>TGC	c.3164A>G	26	1055	1055	high	3.73	Y1055C	getma.org/?cm=msa&ty=f&p=A2MG_HUMAN&rb=1010&re=1266&var=Y1055C	getma.org/pdb.php?prot=A2MG_HUMAN&from=1010&to=1266&var=Y1055C	getma.org/?cm=var&var=hg19,12,9230409,T,C&fts=all	12	9230409	9230409	T	C	SNP	A2M	NM_000014	human	genbank	57_37b	-1	reviewed	missense	c.3164	p.Y1055C	0.143	superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_A2M_comp	PatternScan_TONB_DEPENDENT_REC_1,HMMPfam_A2M_N,HMMPfam_A2M_N_2,HMMPfam_A2M,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN,HMMPfam_A2M_comp,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_recep	-	no_errors
+A2M	2	genome.wustl.edu	37	12	9242995	9242995	+	Silent	SNP	G	G	A	novel	unknown	TCGA-C8-A138-01	TCGA-C8-A138-10	G	G	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Silent	p.N851N	P99999	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(2551-2553)AAC>AAT	c.2553C>T	20	851	851	Silent	p.N851N	A2M	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(2551-2553)AAC>AAT	c.2553C>T	20	851	851	NA	NA	NA	NA	NA	NA	12	9242995	9242995	G	A	SNP	A2M	NM_000014	human	genbank	57_37b	-1	reviewed	silent	c.2553	p.N851	0.003	NULL	PatternScan_TONB_DEPENDENT_REC_1,HMMPfam_A2M_N,HMMPfam_A2M_N_2,HMMPfam_A2M,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN,HMMPfam_A2M_comp,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_recep	-	no_errors
+A2M	2	genome.wustl.edu	37	12	9246090	9246090	+	Silent	SNP	C	C	T	novel	unknown	TCGA-A2-A0EY-01	TCGA-A2-A0EY-10	C	C	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Silent	p.E737E	P99999	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(2209-2211)GAG>GAA	c.2211G>A	18	737	737	Silent	p.E737E	A2M	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(2209-2211)GAG>GAA	c.2211G>A	18	737	737	NA	NA	NA	NA	NA	NA	12	9246090	9246090	C	T	SNP	A2M	NM_000014	human	genbank	57_37b	-1	reviewed	silent	c.2211	p.E737	1.000	NULL	PatternScan_TONB_DEPENDENT_REC_1,HMMPfam_A2M_N,HMMPfam_A2M_N_2,HMMPfam_A2M,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN,HMMPfam_A2M_comp,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_recep	-	no_errors
+A2M	2	genome.wustl.edu	37	12	9251298	9251298	+	Nonsense_Mutation	SNP	G	G	A	novel	unknown	TCGA-A8-A08G-01	TCGA-A8-A08G-10	G	G	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Nonsense_Mutation	p.R586*	Z9ZZZ9ZZZ9	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(1756-1758)CGA>TGA	c.1756C>T	15	586	586	Nonsense_Mutation	p.R586*	A2M	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(1756-1758)CGA>TGA	c.1756C>T	15	586	586	NA	0.0	R586*	NA	NA	getma.org/?cm=var&var=hg19,12,9251298,G,A&fts=all	12	9251298	9251298	G	A	SNP	A2M	NM_000014	human	genbank	57_37b	-1	reviewed	nonsense	c.1756	p.R586*	0.003	HMMPfam_A2M_N_2	PatternScan_TONB_DEPENDENT_REC_1,HMMPfam_A2M_N,HMMPfam_A2M_N_2,HMMPfam_A2M,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN,HMMPfam_A2M_comp,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_recep	-	no_errors
diff --git a/core/src/test/scripts/test_data/mutations/data_mutations_name_swissprot.maf b/core/src/test/scripts/test_data/mutations/data_mutations_name_swissprot.maf
new file mode 100644
index 00000000000..f9dad84fe97
--- /dev/null
+++ b/core/src/test/scripts/test_data/mutations/data_mutations_name_swissprot.maf
@@ -0,0 +1,8 @@
+Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_Position	End_Position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_File	Sequencer	ONCOTATOR_COSMIC_OVERLAPPING	ONCOTATOR_DBSNP_RS	ONCOTATOR_DBSNP_VAL_STATUS	ONCOTATOR_VARIANT_CLASSIFICATION	HGVSp_Short	SWISSPROT	ONCOTATOR_REFSEQ_MRNA_ID	ONCOTATOR_REFSEQ_PROT_ID	ONCOTATOR_UNIPROT_ENTRY_NAME	ONCOTATOR_UNIPROT_ACCESSION	ONCOTATOR_CODON_CHANGE	ONCOTATOR_TRANSCRIPT_CHANGE	ONCOTATOR_EXON_AFFECTED	ONCOTATOR_PROTEIN_POS_START	ONCOTATOR_PROTEIN_POS_END	ONCOTATOR_VARIANT_CLASSIFICATION_BEST_EFFECT	ONCOTATOR_PROTEIN_CHANGE_BEST_EFFECT	ONCOTATOR_GENE_SYMBOL_BEST_EFFECT	ONCOTATOR_REFSEQ_MRNA_ID_BEST_EFFECT	ONCOTATOR_REFSEQ_PROT_ID_BEST_EFFECT	ONCOTATOR_UNIPROT_ENTRY_NAME_BEST_EFFECT	ONCOTATOR_UNIPROT_ACCESSION_BEST_EFFECT	ONCOTATOR_CODON_CHANGE_BEST_EFFECT	ONCOTATOR_TRANSCRIPT_CHANGE_BEST_EFFECT	ONCOTATOR_EXON_AFFECTED_BEST_EFFECT	ONCOTATOR_PROTEIN_POS_START_BEST_EFFECT	ONCOTATOR_PROTEIN_POS_END_BEST_EFFECT	MA:FImpact	MA:FIS	MA:protein.change	MA:link.MSA	MA:link.PDB	MA:link.var	chromosome_name_WU	start_WU	stop_WU	reference_WU	variant_WU	type_WU	gene_name_WU	transcript_name_WU	transcript_species_WU	transcript_source_WU	transcript_version_WU	strand_WU	transcript_status_WU	trv_type_WU	Protein_position	amino_acid_change_WU	ucsc_cons_WU	domain_WU	all_domains_WU	deletion_substructures_WU	annotation_errors_WU
+A1CF	29974	genome.wustl.edu	37	10	52573692	52573692	+	Missense_Mutation	SNP	G	G	T	novel	unknown	TCGA-B6-A0RS-01	TCGA-B6-A0RS-10	G	G	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Missense_Mutation	p.D424E	A1CF_HUMAN	NM_138932	NP_620310	A1CF_HUMAN	Q9NQ94	c.(1270-1272)GAC>GAA	c.1272C>A	10	424	424	Missense_Mutation	p.D432E	A1CF	NM_138933	NP_620311	A1CF_HUMAN	Q9NQ94	c.(1294-1296)GAC>GAA	c.1296C>A	12	432	432	neutral	0.345	D424E	getma.org/?cm=msa&ty=f&p=A1CF_HUMAN&rb=298&re=497&var=D424E	NA	getma.org/?cm=var&var=hg19,10,52573692,G,T&fts=all	10	52573692	52573692	G	T	SNP	A1CF	NM_138932	human	genbank	57_37b	-1	reviewed	missense	c.1272	p.D424E	0.768	NULL	superfamily_RNA-binding domain RBD,HMMSmart_SM00360,HMMPfam_RRM_1,superfamily_dsRNA-binding domain-like	-	no_errors
+A1CF	29974	genome.wustl.edu	37	10	52595854	52595854	+	Missense_Mutation	SNP	G	G	A	novel	unknown	TCGA-BH-A0HP-01	TCGA-BH-A0HP-10	G	G	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Missense_Mutation	p.A195V	Q9NQ94	NM_138932	NP_620310	A1CF_HUMAN	Q9NQ94	c.(583-585)GCG>GTG	c.584C>T	6	195	195	Missense_Mutation	p.A203V	A1CF	NM_138933	NP_620311	A1CF_HUMAN	Q9NQ94	c.(607-609)GCG>GTG	c.608C>T	8	203	203	medium	2.955	A195V	getma.org/?cm=msa&ty=f&p=A1CF_HUMAN&rb=138&re=203&var=A195V	getma.org/pdb.php?prot=A1CF_HUMAN&from=138&to=203&var=A195V	getma.org/?cm=var&var=hg19,10,52595854,G,A&fts=all	10	52595854	52595854	G	A	SNP	A1CF	NM_138932	human	genbank	57_37b	-1	reviewed	missense	c.584	p.A195V	1.000	superfamily_RNA-binding domain RBD,HMMSmart_SM00360,HMMPfam_RRM_1	superfamily_RNA-binding domain RBD,HMMSmart_SM00360,HMMPfam_RRM_1,superfamily_dsRNA-binding domain-like	-	no_errors
+A1CF	29974	genome.wustl.edu	37	10	52595937	52595937	+	Silent	SNP	G	G	A	novel	unknown	TCGA-BH-A18P-01	TCGA-BH-A18P-11	G	G	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Silent	p.I167I	A1CF_HUMAN	NM_138932	NP_620310	A1CF_HUMAN	Q9NQ94	c.(499-501)ATC>ATT	c.501C>T	6	167	167	Silent	p.I175I	A1CF	NM_138933	NP_620311	A1CF_HUMAN	Q9NQ94	c.(523-525)ATC>ATT	c.525C>T	8	175	175	NA	NA	NA	NA	NA	NA	10	52595937	52595937	G	A	SNP	A1CF	NM_138932	human	genbank	57_37b	-1	reviewed	silent	c.501	p.I167	0.615	superfamily_RNA-binding domain RBD,HMMSmart_SM00360,HMMPfam_RRM_1	superfamily_RNA-binding domain RBD,HMMSmart_SM00360,HMMPfam_RRM_1,superfamily_dsRNA-binding domain-like	-	no_errors
+A2M	2	genome.wustl.edu	37	12	9230409	9230409	+	Missense_Mutation	SNP	T	T	C	novel	unknown	TCGA-BH-A18H-01	TCGA-BH-A18H-10	T	T	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Missense_Mutation	p.Y1055C	A1CF_HUMAN,HBB_YEAST	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(3163-3165)TAC>TGC	c.3164A>G	26	1055	1055	Missense_Mutation	p.Y1055C	A2M	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(3163-3165)TAC>TGC	c.3164A>G	26	1055	1055	high	3.73	Y1055C	getma.org/?cm=msa&ty=f&p=A2MG_HUMAN&rb=1010&re=1266&var=Y1055C	getma.org/pdb.php?prot=A2MG_HUMAN&from=1010&to=1266&var=Y1055C	getma.org/?cm=var&var=hg19,12,9230409,T,C&fts=all	12	9230409	9230409	T	C	SNP	A2M	NM_000014	human	genbank	57_37b	-1	reviewed	missense	c.3164	p.Y1055C	0.143	superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_A2M_comp	PatternScan_TONB_DEPENDENT_REC_1,HMMPfam_A2M_N,HMMPfam_A2M_N_2,HMMPfam_A2M,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN,HMMPfam_A2M_comp,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_recep	-	no_errors
+A2M	2	genome.wustl.edu	37	12	9242995	9242995	+	Silent	SNP	G	G	A	novel	unknown	TCGA-C8-A138-01	TCGA-C8-A138-10	G	G	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Silent	p.N851N	A2MG_HUMAN	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(2551-2553)AAC>AAT	c.2553C>T	20	851	851	Silent	p.N851N	A2M	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(2551-2553)AAC>AAT	c.2553C>T	20	851	851	NA	NA	NA	NA	NA	NA	12	9242995	9242995	G	A	SNP	A2M	NM_000014	human	genbank	57_37b	-1	reviewed	silent	c.2553	p.N851	0.003	NULL	PatternScan_TONB_DEPENDENT_REC_1,HMMPfam_A2M_N,HMMPfam_A2M_N_2,HMMPfam_A2M,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN,HMMPfam_A2M_comp,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_recep	-	no_errors
+A2M	2	genome.wustl.edu	37	12	9246090	9246090	+	Silent	SNP	C	C	T	novel	unknown	TCGA-A2-A0EY-01	TCGA-A2-A0EY-10	C	C	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Silent	p.E737E	A2MG_HUMAN	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(2209-2211)GAG>GAA	c.2211G>A	18	737	737	Silent	p.E737E	A2M	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(2209-2211)GAG>GAA	c.2211G>A	18	737	737	NA	NA	NA	NA	NA	NA	12	9246090	9246090	C	T	SNP	A2M	NM_000014	human	genbank	57_37b	-1	reviewed	silent	c.2211	p.E737	1.000	NULL	PatternScan_TONB_DEPENDENT_REC_1,HMMPfam_A2M_N,HMMPfam_A2M_N_2,HMMPfam_A2M,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN,HMMPfam_A2M_comp,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_recep	-	no_errors
+A2M	2	genome.wustl.edu	37	12	9251298	9251298	+	Nonsense_Mutation	SNP	G	G	A	novel	unknown	TCGA-A8-A08G-01	TCGA-A8-A08G-10	G	G	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Nonsense_Mutation	p.R586*	HBB_YEAST	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(1756-1758)CGA>TGA	c.1756C>T	15	586	586	Nonsense_Mutation	p.R586*	A2M	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(1756-1758)CGA>TGA	c.1756C>T	15	586	586	NA	0.0	R586*	NA	NA	getma.org/?cm=var&var=hg19,12,9251298,G,A&fts=all	12	9251298	9251298	G	A	SNP	A2M	NM_000014	human	genbank	57_37b	-1	reviewed	nonsense	c.1756	p.R586*	0.003	HMMPfam_A2M_N_2	PatternScan_TONB_DEPENDENT_REC_1,HMMPfam_A2M_N,HMMPfam_A2M_N_2,HMMPfam_A2M,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN,HMMPfam_A2M_comp,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_recep	-	no_errors
diff --git a/core/src/test/scripts/test_data/mutations/data_mutations_wrong_aa_change.maf b/core/src/test/scripts/test_data/mutations/data_mutations_wrong_aa_change.maf
index 755d9353b3e..7118c04caef 100644
--- a/core/src/test/scripts/test_data/mutations/data_mutations_wrong_aa_change.maf
+++ b/core/src/test/scripts/test_data/mutations/data_mutations_wrong_aa_change.maf
@@ -1,8 +1,8 @@
 Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_Position	End_Position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_File	Sequencer	ONCOTATOR_COSMIC_OVERLAPPING	ONCOTATOR_DBSNP_RS	ONCOTATOR_DBSNP_VAL_STATUS	ONCOTATOR_VARIANT_CLASSIFICATION	Amino_Acid_Change	SWISSPROT	ONCOTATOR_REFSEQ_MRNA_ID	ONCOTATOR_REFSEQ_PROT_ID	ONCOTATOR_UNIPROT_ENTRY_NAME	ONCOTATOR_UNIPROT_ACCESSION	ONCOTATOR_CODON_CHANGE	ONCOTATOR_TRANSCRIPT_CHANGE	ONCOTATOR_EXON_AFFECTED	ONCOTATOR_PROTEIN_POS_START	ONCOTATOR_PROTEIN_POS_END	ONCOTATOR_VARIANT_CLASSIFICATION_BEST_EFFECT	ONCOTATOR_PROTEIN_CHANGE_BEST_EFFECT	ONCOTATOR_GENE_SYMBOL_BEST_EFFECT	ONCOTATOR_REFSEQ_MRNA_ID_BEST_EFFECT	ONCOTATOR_REFSEQ_PROT_ID_BEST_EFFECT	ONCOTATOR_UNIPROT_ENTRY_NAME_BEST_EFFECT	ONCOTATOR_UNIPROT_ACCESSION_BEST_EFFECT	ONCOTATOR_CODON_CHANGE_BEST_EFFECT	ONCOTATOR_TRANSCRIPT_CHANGE_BEST_EFFECT	ONCOTATOR_EXON_AFFECTED_BEST_EFFECT	ONCOTATOR_PROTEIN_POS_START_BEST_EFFECT	ONCOTATOR_PROTEIN_POS_END_BEST_EFFECT	MA:FImpact	MA:FIS	MA:protein.change	MA:link.MSA	MA:link.PDB	MA:link.var	chromosome_name_WU	start_WU	stop_WU	reference_WU	variant_WU	type_WU	gene_name_WU	transcript_name_WU	transcript_species_WU	transcript_source_WU	transcript_version_WU	strand_WU	transcript_status_WU	trv_type_WU	Protein_position	amino_acid_change_WU	ucsc_cons_WU	domain_WU	all_domains_WU	deletion_substructures_WU	annotation_errors_WU
-A1CF	29974	genome.wustl.edu	37	10	52573692	52573692	+	Missense_Mutation	SNP	G	G	T	novel	unknown	TCGA-B6-A0RS-01	TCGA-B6-A0RS-10	G	G	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Missense_Mutation		A1CF	NM_138932	NP_620310	A1CF_HUMAN	Q9NQ94	c.(1270-1272)GAC>GAA	c.1272C>A	10	424	424	Missense_Mutation	p.D432E	A1CF	NM_138933	NP_620311	A1CF_HUMAN	Q9NQ94	c.(1294-1296)GAC>GAA	c.1296C>A	12	432	432	neutral	0.345	D424E	getma.org/?cm=msa&ty=f&p=A1CF_HUMAN&rb=298&re=497&var=D424E	NA	getma.org/?cm=var&var=hg19,10,52573692,G,T&fts=all	10	52573692	52573692	G	T	SNP	A1CF	NM_138932	human	genbank	57_37b	-1	reviewed	missense	c.1272		0.768	NULL	superfamily_RNA-binding domain RBD,HMMSmart_SM00360,HMMPfam_RRM_1,superfamily_dsRNA-binding domain-like	-	no_errors
-A1CF	29974	genome.wustl.edu	37	10	52595854	52595854	+	Missense_Mutation	SNP	G	G	A	novel	unknown	TCGA-BH-A0HP-01	TCGA-BH-A0HP-10	G	G	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Missense_Mutation	p.A195V p.I167I	A1CF	NM_138932	NP_620310	A1CF_HUMAN	Q9NQ94	c.(583-585)GCG>GTG	c.584C>T	6	195	195	Missense_Mutation	p.A203V	A1CF	NM_138933	NP_620311	A1CF_HUMAN	Q9NQ94	c.(607-609)GCG>GTG	c.608C>T	8	203	203	medium	2.955	A195V	getma.org/?cm=msa&ty=f&p=A1CF_HUMAN&rb=138&re=203&var=A195V	getma.org/pdb.php?prot=A1CF_HUMAN&from=138&to=203&var=A195V	getma.org/?cm=var&var=hg19,10,52595854,G,A&fts=all	10	52595854	52595854	G	A	SNP	A1CF	NM_138932	human	genbank	57_37b	-1	reviewed	missense	c.584	p.A195V	1.000	superfamily_RNA-binding domain RBD,HMMSmart_SM00360,HMMPfam_RRM_1	superfamily_RNA-binding domain RBD,HMMSmart_SM00360,HMMPfam_RRM_1,superfamily_dsRNA-binding domain-like	-	no_errors
-A1CF	29974	genome.wustl.edu	37	10	52595937	52595937	+	Silent	SNP	G	G	A	novel	unknown	TCGA-BH-A18P-01	TCGA-BH-A18P-11	G	G	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Silent	p.I167=	A1CF	NM_138932	NP_620310	A1CF_HUMAN	Q9NQ94	c.(499-501)ATC>ATT	c.501C>T	6	167	167	Silent	p.I175I	A1CF	NM_138933	NP_620311	A1CF_HUMAN	Q9NQ94	c.(523-525)ATC>ATT	c.525C>T	8	175	175	NA	NA	NA	NA	NA	NA	10	52595937	52595937	G	A	SNP	A1CF	NM_138932	human	genbank	57_37b	-1	reviewed	silent	c.501	p.I167	0.615	superfamily_RNA-binding domain RBD,HMMSmart_SM00360,HMMPfam_RRM_1	superfamily_RNA-binding domain RBD,HMMSmart_SM00360,HMMPfam_RRM_1,superfamily_dsRNA-binding domain-like	-	no_errors
-A2M	2	genome.wustl.edu	37	12	9230409	9230409	+	Missense_Mutation	SNP	T	T	C	novel	unknown	TCGA-BH-A18H-01	TCGA-BH-A18H-10	T	T	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Missense_Mutation	p.N851,Y1055delinsCC	A2M	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(3163-3165)TAC>TGC	c.3164A>G	26	1055	1055	Missense_Mutation	p.Y1055C	A2M	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(3163-3165)TAC>TGC	c.3164A>G	26	1055	1055	high	3.73	Y1055C	getma.org/?cm=msa&ty=f&p=A2MG_HUMAN&rb=1010&re=1266&var=Y1055C	getma.org/pdb.php?prot=A2MG_HUMAN&from=1010&to=1266&var=Y1055C	getma.org/?cm=var&var=hg19,12,9230409,T,C&fts=all	12	9230409	9230409	T	C	SNP	A2M	NM_000014	human	genbank	57_37b	-1	reviewed	missense	c.3164	p.Y1055C	0.143	superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_A2M_comp	PatternScan_TONB_DEPENDENT_REC_1,HMMPfam_A2M_N,HMMPfam_A2M_N_2,HMMPfam_A2M,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN,HMMPfam_A2M_comp,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_recep	-	no_errors
-A2M	2	genome.wustl.edu	37	12	9242995	9242995	+	Missense_Mutation	SNP	G	G	A	novel	unknown	TCGA-C8-A138-01	TCGA-C8-A138-10	G	G	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Missense_Mutation	p.[N851N];[Y1055C]	A2M	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(2551-2553)AAC>AAT	c.2553C>T	20	851	851	Missense_Mutation	p.N851N	A2M	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(2551-2553)AAC>AAT	c.2553C>T	20	851	851	NA	NA	NA	NA	NA	NA	12	9242995	9242995	G	A	SNP	A2M	NM_000014	human	genbank	57_37b	-1	reviewed	missense	c.2553	p.N851	0.003	NULL	PatternScan_TONB_DEPENDENT_REC_1,HMMPfam_A2M_N,HMMPfam_A2M_N_2,HMMPfam_A2M,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN,HMMPfam_A2M_comp,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_recep	-	no_errors
-A2M	2	genome.wustl.edu	37	12	9246090	9246090	+	Silent	SNP	C	C	T	novel	unknown	TCGA-A2-A0EY-01	TCGA-A2-A0EY-10	C	C	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Silent	p.E737E	A2M	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(2209-2211)GAG>GAA	c.2211G>A	18	737	737	Silent	p.E737E	A2M	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(2209-2211)GAG>GAA	c.2211G>A	18	737	737	NA	NA	NA	NA	NA	NA	12	9246090	9246090	C	T	SNP	A2M	NM_000014	human	genbank	57_37b	-1	reviewed	silent	c.2211	p.E737	1.000	NULL	PatternScan_TONB_DEPENDENT_REC_1,HMMPfam_A2M_N,HMMPfam_A2M_N_2,HMMPfam_A2M,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN,HMMPfam_A2M_comp,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_recep	-	no_errors
-A2M	2	genome.wustl.edu	37	12	9251298	9251298	+	Nonsense_Mutation	SNP	G	G	A	novel	unknown	TCGA-A8-A08G-01	TCGA-A8-A08G-10	G	G	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Nonsense_Mutation	NULL	A2M	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(1756-1758)CGA>TGA	c.1756C>T	15	586	586	Nonsense_Mutation	p.R586*	A2M	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(1756-1758)CGA>TGA	c.1756C>T	15	586	586	NA	0.0	R586*	NA	NA	getma.org/?cm=var&var=hg19,12,9251298,G,A&fts=all	12	9251298	9251298	G	A	SNP	A2M	NM_000014	human	genbank	57_37b	-1	reviewed	nonsense	c.1756	p.R586*	0.003	HMMPfam_A2M_N_2	PatternScan_TONB_DEPENDENT_REC_1,HMMPfam_A2M_N,HMMPfam_A2M_N_2,HMMPfam_A2M,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN,HMMPfam_A2M_comp,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_recep	-	no_errors
+A1CF	29974	genome.wustl.edu	37	10	52573692	52573692	+	Missense_Mutation	SNP	G	G	T	novel	unknown	TCGA-B6-A0RS-01	TCGA-B6-A0RS-10	G	G	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Missense_Mutation		Q9NQ94	NM_138932	NP_620310	A1CF_HUMAN	Q9NQ94	c.(1270-1272)GAC>GAA	c.1272C>A	10	424	424	Missense_Mutation	p.D432E	A1CF	NM_138933	NP_620311	A1CF_HUMAN	Q9NQ94	c.(1294-1296)GAC>GAA	c.1296C>A	12	432	432	neutral	0.345	D424E	getma.org/?cm=msa&ty=f&p=A1CF_HUMAN&rb=298&re=497&var=D424E	NA	getma.org/?cm=var&var=hg19,10,52573692,G,T&fts=all	10	52573692	52573692	G	T	SNP	A1CF	NM_138932	human	genbank	57_37b	-1	reviewed	missense	c.1272		0.768	NULL	superfamily_RNA-binding domain RBD,HMMSmart_SM00360,HMMPfam_RRM_1,superfamily_dsRNA-binding domain-like	-	no_errors
+A1CF	29974	genome.wustl.edu	37	10	52595854	52595854	+	Missense_Mutation	SNP	G	G	A	novel	unknown	TCGA-BH-A0HP-01	TCGA-BH-A0HP-10	G	G	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Missense_Mutation	p.A195V p.I167I	Q9NQ94	NM_138932	NP_620310	A1CF_HUMAN	Q9NQ94	c.(583-585)GCG>GTG	c.584C>T	6	195	195	Missense_Mutation	p.A203V	A1CF	NM_138933	NP_620311	A1CF_HUMAN	Q9NQ94	c.(607-609)GCG>GTG	c.608C>T	8	203	203	medium	2.955	A195V	getma.org/?cm=msa&ty=f&p=A1CF_HUMAN&rb=138&re=203&var=A195V	getma.org/pdb.php?prot=A1CF_HUMAN&from=138&to=203&var=A195V	getma.org/?cm=var&var=hg19,10,52595854,G,A&fts=all	10	52595854	52595854	G	A	SNP	A1CF	NM_138932	human	genbank	57_37b	-1	reviewed	missense	c.584	p.A195V	1.000	superfamily_RNA-binding domain RBD,HMMSmart_SM00360,HMMPfam_RRM_1	superfamily_RNA-binding domain RBD,HMMSmart_SM00360,HMMPfam_RRM_1,superfamily_dsRNA-binding domain-like	-	no_errors
+A1CF	29974	genome.wustl.edu	37	10	52595937	52595937	+	Silent	SNP	G	G	A	novel	unknown	TCGA-BH-A18P-01	TCGA-BH-A18P-11	G	G	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Silent	p.I167=	Q9NQ94	NM_138932	NP_620310	A1CF_HUMAN	Q9NQ94	c.(499-501)ATC>ATT	c.501C>T	6	167	167	Silent	p.I175I	A1CF	NM_138933	NP_620311	A1CF_HUMAN	Q9NQ94	c.(523-525)ATC>ATT	c.525C>T	8	175	175	NA	NA	NA	NA	NA	NA	10	52595937	52595937	G	A	SNP	A1CF	NM_138932	human	genbank	57_37b	-1	reviewed	silent	c.501	p.I167	0.615	superfamily_RNA-binding domain RBD,HMMSmart_SM00360,HMMPfam_RRM_1	superfamily_RNA-binding domain RBD,HMMSmart_SM00360,HMMPfam_RRM_1,superfamily_dsRNA-binding domain-like	-	no_errors
+A2M	2	genome.wustl.edu	37	12	9230409	9230409	+	Missense_Mutation	SNP	T	T	C	novel	unknown	TCGA-BH-A18H-01	TCGA-BH-A18H-10	T	T	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Missense_Mutation	p.N851,Y1055delinsCC	P01023	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(3163-3165)TAC>TGC	c.3164A>G	26	1055	1055	Missense_Mutation	p.Y1055C	A2M	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(3163-3165)TAC>TGC	c.3164A>G	26	1055	1055	high	3.73	Y1055C	getma.org/?cm=msa&ty=f&p=A2MG_HUMAN&rb=1010&re=1266&var=Y1055C	getma.org/pdb.php?prot=A2MG_HUMAN&from=1010&to=1266&var=Y1055C	getma.org/?cm=var&var=hg19,12,9230409,T,C&fts=all	12	9230409	9230409	T	C	SNP	A2M	NM_000014	human	genbank	57_37b	-1	reviewed	missense	c.3164	p.Y1055C	0.143	superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_A2M_comp	PatternScan_TONB_DEPENDENT_REC_1,HMMPfam_A2M_N,HMMPfam_A2M_N_2,HMMPfam_A2M,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN,HMMPfam_A2M_comp,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_recep	-	no_errors
+A2M	2	genome.wustl.edu	37	12	9242995	9242995	+	Missense_Mutation	SNP	G	G	A	novel	unknown	TCGA-C8-A138-01	TCGA-C8-A138-10	G	G	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Missense_Mutation	p.[N851N];[Y1055C]	P01023	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(2551-2553)AAC>AAT	c.2553C>T	20	851	851	Missense_Mutation	p.N851N	A2M	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(2551-2553)AAC>AAT	c.2553C>T	20	851	851	NA	NA	NA	NA	NA	NA	12	9242995	9242995	G	A	SNP	A2M	NM_000014	human	genbank	57_37b	-1	reviewed	missense	c.2553	p.N851	0.003	NULL	PatternScan_TONB_DEPENDENT_REC_1,HMMPfam_A2M_N,HMMPfam_A2M_N_2,HMMPfam_A2M,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN,HMMPfam_A2M_comp,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_recep	-	no_errors
+A2M	2	genome.wustl.edu	37	12	9246090	9246090	+	Silent	SNP	C	C	T	novel	unknown	TCGA-A2-A0EY-01	TCGA-A2-A0EY-10	C	C	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Silent	p.E737E	P01023	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(2209-2211)GAG>GAA	c.2211G>A	18	737	737	Silent	p.E737E	A2M	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(2209-2211)GAG>GAA	c.2211G>A	18	737	737	NA	NA	NA	NA	NA	NA	12	9246090	9246090	C	T	SNP	A2M	NM_000014	human	genbank	57_37b	-1	reviewed	silent	c.2211	p.E737	1.000	NULL	PatternScan_TONB_DEPENDENT_REC_1,HMMPfam_A2M_N,HMMPfam_A2M_N_2,HMMPfam_A2M,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN,HMMPfam_A2M_comp,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_recep	-	no_errors
+A2M	2	genome.wustl.edu	37	12	9251298	9251298	+	Nonsense_Mutation	SNP	G	G	A	novel	unknown	TCGA-A8-A08G-01	TCGA-A8-A08G-10	G	G	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Nonsense_Mutation	NULL	P01023	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(1756-1758)CGA>TGA	c.1756C>T	15	586	586	Nonsense_Mutation	p.R586*	A2M	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(1756-1758)CGA>TGA	c.1756C>T	15	586	586	NA	0.0	R586*	NA	NA	getma.org/?cm=var&var=hg19,12,9251298,G,A&fts=all	12	9251298	9251298	G	A	SNP	A2M	NM_000014	human	genbank	57_37b	-1	reviewed	nonsense	c.1756	p.R586*	0.003	HMMPfam_A2M_N_2	PatternScan_TONB_DEPENDENT_REC_1,HMMPfam_A2M_N,HMMPfam_A2M_N_2,HMMPfam_A2M,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN,HMMPfam_A2M_comp,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_recep	-	no_errors
diff --git a/core/src/test/scripts/test_data/mutations/meta_mutations_invalid_swissprot_idspec.txt b/core/src/test/scripts/test_data/mutations/meta_mutations_invalid_swissprot_idspec.txt
new file mode 100644
index 00000000000..fe4ec15ce93
--- /dev/null
+++ b/core/src/test/scripts/test_data/mutations/meta_mutations_invalid_swissprot_idspec.txt
@@ -0,0 +1,9 @@
+cancer_study_identifier: spam
+genetic_alteration_type: MUTATION_EXTENDED
+datatype: MAF
+stable_id: mutations
+show_profile_in_analysis_tab: true
+profile_description: Mutation data from whole exome sequencing.
+profile_name: Mutations
+data_filename: spam.maf
+swissprot_identifier: namelessly
diff --git a/core/src/test/scripts/test_data/study_cancertype_two_files/meta_study.txt b/core/src/test/scripts/test_data/study_cancertype_two_files/meta_study.txt
index a9f15f74da7..89f18fc3683 100644
--- a/core/src/test/scripts/test_data/study_cancertype_two_files/meta_study.txt
+++ b/core/src/test/scripts/test_data/study_cancertype_two_files/meta_study.txt
@@ -3,3 +3,4 @@ type_of_cancer: luad
 name: Spam (spam)
 description: Baked beans
 short_name: Spam
+add_global_case_list: true
diff --git a/core/src/test/scripts/test_data/study_es_0/meta_mutations_extended.txt b/core/src/test/scripts/test_data/study_es_0/meta_mutations_extended.txt
index be1b8b72dba..813510be072 100644
--- a/core/src/test/scripts/test_data/study_es_0/meta_mutations_extended.txt
+++ b/core/src/test/scripts/test_data/study_es_0/meta_mutations_extended.txt
@@ -6,3 +6,4 @@ show_profile_in_analysis_tab: true
 profile_description: Mutation data from whole exome sequencing.
 profile_name: Mutations
 data_filename: brca_tcga_pub.maf
+swissprot_identifier: name
diff --git a/core/src/test/scripts/test_data/study_es_0/result_report.html b/core/src/test/scripts/test_data/study_es_0/result_report.html
index 78a1bc2760d..e2464d0e8d1 100644
--- a/core/src/test/scripts/test_data/study_es_0/result_report.html
+++ b/core/src/test/scripts/test_data/study_es_0/result_report.html
@@ -170,7 +170,7 @@ <h4 class="panel-title">General</h4>
                 <td><span class="glyphicon glyphicon-ok" aria-hidden="true"></span><span class="sr-only">Info</span></td>
                 <td>&ndash;</td>
                 <td>&ndash;</td>
-                <td>Validation of case lists complete</td>
+                <td>Validation of case list folder complete</td>
                 <td>&ndash;</td>
               </tr>
               <tr class="success">
diff --git a/core/src/test/scripts/test_data/study_maf_test/brca_tcga_pub.maf b/core/src/test/scripts/test_data/study_maf_test/brca_tcga_pub.maf
index b9cf1fede57..9bf69c8ca71 100644
--- a/core/src/test/scripts/test_data/study_maf_test/brca_tcga_pub.maf
+++ b/core/src/test/scripts/test_data/study_maf_test/brca_tcga_pub.maf
@@ -1,16 +1,16 @@
 Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_Position	End_Position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_File	Sequencer	ONCOTATOR_COSMIC_OVERLAPPING	ONCOTATOR_DBSNP_RS	ONCOTATOR_DBSNP_VAL_STATUS	ONCOTATOR_VARIANT_CLASSIFICATION	HGVSp_Short	SWISSPROT	ONCOTATOR_REFSEQ_MRNA_ID	ONCOTATOR_REFSEQ_PROT_ID	ONCOTATOR_UNIPROT_ENTRY_NAME	ONCOTATOR_UNIPROT_ACCESSION	ONCOTATOR_CODON_CHANGE	ONCOTATOR_TRANSCRIPT_CHANGE	ONCOTATOR_EXON_AFFECTED	ONCOTATOR_PROTEIN_POS_START	ONCOTATOR_PROTEIN_POS_END	ONCOTATOR_VARIANT_CLASSIFICATION_BEST_EFFECT	ONCOTATOR_PROTEIN_CHANGE_BEST_EFFECT	ONCOTATOR_GENE_SYMBOL_BEST_EFFECT	ONCOTATOR_REFSEQ_MRNA_ID_BEST_EFFECT	ONCOTATOR_REFSEQ_PROT_ID_BEST_EFFECT	ONCOTATOR_UNIPROT_ENTRY_NAME_BEST_EFFECT	ONCOTATOR_UNIPROT_ACCESSION_BEST_EFFECT	ONCOTATOR_CODON_CHANGE_BEST_EFFECT	ONCOTATOR_TRANSCRIPT_CHANGE_BEST_EFFECT	ONCOTATOR_EXON_AFFECTED_BEST_EFFECT	ONCOTATOR_PROTEIN_POS_START_BEST_EFFECT	ONCOTATOR_PROTEIN_POS_END_BEST_EFFECT	MA:FImpact	MA:FIS	MA:protein.change	MA:link.MSA	MA:link.PDB	MA:link.var	chromosome_name_WU	Protein_position	stop_WU	reference_WU	variant_WU	type_WU	gene_name_WU	transcript_name_WU	transcript_species_WU	transcript_source_WU	transcript_version_WU	strand_WU	transcript_status_WU	trv_type_WU	c_position_WU	amino_acid_change_WU	ucsc_cons_WU	domain_WU	all_domains_WU	deletion_substructures_WU	annotation_errors_WU
-A1CF	29974	genome.wustl.edu	37	10	52573692	52573692	+	Missense_Mutation	SNP	G	G	T	novel	unknown	TCGA-B6-A0RS-01	TCGA-B6-A0RS-10	G	G	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Missense_Mutation	p.D424E	A1CF	NM_138932	NP_620310	A1CF_HUMAN	Q9NQ94	c.(1270-1272)GAC>GAA	c.1272C>A	10	424	424	Missense_Mutation	p.D432E	A1CF	NM_138933	NP_620311	A1CF_HUMAN	Q9NQ94	c.(1294-1296)GAC>GAA	c.1296C>A	12	432	432	neutral	0.345	D424E	getma.org/?cm=msa&ty=f&p=A1CF_HUMAN&rb=298&re=497&var=D424E	NA	getma.org/?cm=var&var=hg19,10,52573692,G,T&fts=all	10	52573692	52573692	G	T	SNP	A1CF	NM_138932	human	genbank	57_37b	-1	reviewed	missense	c.1272	p.D424E	0.768	NULL	superfamily_RNA-binding domain RBD,HMMSmart_SM00360,HMMPfam_RRM_1,superfamily_dsRNA-binding domain-like	-	no_errors
-A1CF	29974	genome.wustl.edu	37	10	52595854	52595854	+	Missense_Mutation	SNP	G	G	A	novel	unknown	TCGA-BH-A0HP-01	TCGA-BH-A0HP-10	G	G	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Missense_Mutation	p.A195V	A1CF	NM_138932	NP_620310	A1CF_HUMAN	Q9NQ94	c.(583-585)GCG>GTG	c.584C>T	6	195	195	Missense_Mutation	p.A203V	A1CF	NM_138933	NP_620311	A1CF_HUMAN	Q9NQ94	c.(607-609)GCG>GTG	c.608C>T	8	203	203	medium	2.955	A195V	getma.org/?cm=msa&ty=f&p=A1CF_HUMAN&rb=138&re=203&var=A195V	getma.org/pdb.php?prot=A1CF_HUMAN&from=138&to=203&var=A195V	getma.org/?cm=var&var=hg19,10,52595854,G,A&fts=all	10	52595854	52595854	G	A	SNP	A1CF	NM_138932	human	genbank	57_37b	-1	reviewed	missense	c.584	p.A195V	1.000	superfamily_RNA-binding domain RBD,HMMSmart_SM00360,HMMPfam_RRM_1	superfamily_RNA-binding domain RBD,HMMSmart_SM00360,HMMPfam_RRM_1,superfamily_dsRNA-binding domain-like	-	no_errors
-A1CF	29974	genome.wustl.edu	37	10	52595937	52595937	+	Silent	SNP	G	G	A	novel	unknown	TCGA-BH-A18P-01	TCGA-BH-A18P-11	G	G	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Silent	p.I167I	A1CF	NM_138932	NP_620310	A1CF_HUMAN	Q9NQ94	c.(499-501)ATC>ATT	c.501C>T	6	167	167	Silent	p.I175I	A1CF	NM_138933	NP_620311	A1CF_HUMAN	Q9NQ94	c.(523-525)ATC>ATT	c.525C>T	8	175	175	NA	NA	NA	NA	NA	NA	10	52595937	52595937	G	A	SNP	A1CF	NM_138932	human	genbank	57_37b	-1	reviewed	silent	c.501	p.I167	0.615	superfamily_RNA-binding domain RBD,HMMSmart_SM00360,HMMPfam_RRM_1	superfamily_RNA-binding domain RBD,HMMSmart_SM00360,HMMPfam_RRM_1,superfamily_dsRNA-binding domain-like	-	no_errors
-A2M	2	genome.wustl.edu	37	12	9230409	9230409	+	Missense_Mutation	SNP	T	T	C	novel	unknown	TCGA-BH-A18H-01	TCGA-BH-A18H-10	T	T	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Missense_Mutation	p.Y1055C	A2M	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(3163-3165)TAC>TGC	c.3164A>G	26	1055	1055	Missense_Mutation	p.Y1055C	A2M	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(3163-3165)TAC>TGC	c.3164A>G	26	1055	1055	high	3.73	Y1055C	getma.org/?cm=msa&ty=f&p=A2MG_HUMAN&rb=1010&re=1266&var=Y1055C	getma.org/pdb.php?prot=A2MG_HUMAN&from=1010&to=1266&var=Y1055C	getma.org/?cm=var&var=hg19,12,9230409,T,C&fts=all	12	9230409	9230409	T	C	SNP	A2M	NM_000014	human	genbank	57_37b	-1	reviewed	missense	c.3164	p.Y1055C	0.143	superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_A2M_comp	PatternScan_TONB_DEPENDENT_REC_1,HMMPfam_A2M_N,HMMPfam_A2M_N_2,HMMPfam_A2M,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN,HMMPfam_A2M_comp,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_recep	-	no_errors
-A2M	2	genome.wustl.edu	37	12	9242995	9242995	+	Silent	SNP	G	G	A	novel	unknown	TCGA-C8-A138-01	TCGA-C8-A138-10	G	G	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Silent	p.N851N	A2M	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(2551-2553)AAC>AAT	c.2553C>T	20	851	851	Silent	p.N851N	A2M	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(2551-2553)AAC>AAT	c.2553C>T	20	851	851	NA	NA	NA	NA	NA	NA	12	9242995	9242995	G	A	SNP	A2M	NM_000014	human	genbank	57_37b	-1	reviewed	silent	c.2553	p.N851	0.003	NULL	PatternScan_TONB_DEPENDENT_REC_1,HMMPfam_A2M_N,HMMPfam_A2M_N_2,HMMPfam_A2M,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN,HMMPfam_A2M_comp,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_recep	-	no_errors
-A2M	2	genome.wustl.edu	37	12	9246090	9246090	+	Silent	SNP	C	C	T	novel	unknown	TCGA-A2-A0EY-01	TCGA-A2-A0EY-10	C	C	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Silent	p.E737E	A2M	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(2209-2211)GAG>GAA	c.2211G>A	18	737	737	Silent	p.E737E	A2M	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(2209-2211)GAG>GAA	c.2211G>A	18	737	737	NA	NA	NA	NA	NA	NA	12	9246090	9246090	C	T	SNP	A2M	NM_000014	human	genbank	57_37b	-1	reviewed	silent	c.2211	p.E737	1.000	NULL	PatternScan_TONB_DEPENDENT_REC_1,HMMPfam_A2M_N,HMMPfam_A2M_N_2,HMMPfam_A2M,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN,HMMPfam_A2M_comp,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_recep	-	no_errors
-A2M	2	genome.wustl.edu	37	12	9251298	9251298	+	Nonsense_Mutation	SNP	G	G	A	novel	unknown	TCGA-A8-A08G-01	TCGA-A8-A08G-10	G	G	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Nonsense_Mutation	p.R586*	A2M	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(1756-1758)CGA>TGA	c.1756C>T	15	586	586	Nonsense_Mutation	p.R586*	A2M	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(1756-1758)CGA>TGA	c.1756C>T	15	586	586	NA	0.0	R586*	NA	NA	getma.org/?cm=var&var=hg19,12,9251298,G,A&fts=all	12	9251298	9251298	G	A	SNP	A2M	NM_000014	human	genbank	57_37b	-1	reviewed	nonsense	c.1756	p.R586*	0.003	HMMPfam_A2M_N_2	PatternScan_TONB_DEPENDENT_REC_1,HMMPfam_A2M_N,HMMPfam_A2M_N_2,HMMPfam_A2M,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN,HMMPfam_A2M_comp,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_recep	-	no_errors
-A2M	2	genome.wustl.edu	37	12	9256962	9256962	+	Missense_Mutation	SNP	G	G	T	novel	unknown	TCGA-B6-A0IQ-01	TCGA-B6-A0IQ-10	G	G	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Missense_Mutation	p.P380Q	A2M	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(1138-1140)CCA>CAA	c.1139C>A	11	380	380	Missense_Mutation	p.P380Q	A2M	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(1138-1140)CCA>CAA	c.1139C>A	11	380	380	medium	2.625	P380Q	getma.org/?cm=msa&ty=f&p=A2MG_HUMAN&rb=222&re=421&var=P380Q	getma.org/pdb.php?prot=A2MG_HUMAN&from=222&to=421&var=P380Q	getma.org/?cm=var&var=hg19,12,9256962,G,T&fts=all	12	9256962	9256962	G	T	SNP	A2M	NM_000014	human	genbank	57_37b	-1	reviewed	missense	c.1139	p.P380Q	0.957	NULL	PatternScan_TONB_DEPENDENT_REC_1,HMMPfam_A2M_N,HMMPfam_A2M_N_2,HMMPfam_A2M,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN,HMMPfam_A2M_comp,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_recep	-	no_errors
-A2ML1	144568	genome.wustl.edu	37	12	8975820	8975820	+	Silent	SNP	C	C	A	novel	unknown	TCGA-C8-A12Y-01	TCGA-C8-A12Y-10	C	C	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Silent	p.S35S	A2ML1	NM_144670	NP_653271	A2ML1_HUMAN	A8K2U0	c.(103-105)TCC>TCA	c.105C>A	2	35	35	Silent	p.S35S	A2ML1	NM_144670	NP_653271	A2ML1_HUMAN	A8K2U0	c.(103-105)TCC>TCA	c.105C>A	2	35	35	NA	NA	NA	NA	NA	NA	12	8975820	8975820	C	A	SNP	A2ML1	NM_144670	human	genbank	57_37b	+1	validated	silent	c.105	p.S35	0.801	HMMPfam_A2M_N	HMMPfam_A2M_N,HMMPfam_A2M_N_2,HMMPfam_A2M,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN,HMMPfam_A2M_comp,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_recep	-	no_errors
-A2ML1	144568	genome.wustl.edu	37	12	8994108	8994108	+	Missense_Mutation	SNP	G	G	C	novel	unknown	TCGA-A1-A0SO-01	TCGA-A1-A0SO-10	G	G	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Missense_Mutation	p.W408C	A2ML1	NM_144670	NP_653271	A2ML1_HUMAN	A8K2U0	c.(1222-1224)TGG>TGC	c.1224G>C	11	408	408	Missense_Mutation	p.W408C	A2ML1	NM_144670	NP_653271	A2ML1_HUMAN	A8K2U0	c.(1222-1224)TGG>TGC	c.1224G>C	11	408	408	medium	2.005	W408C	getma.org/?cm=msa&ty=f&p=A2ML1_HUMAN&rb=239&re=438&var=W408C	getma.org/pdb.php?prot=A2ML1_HUMAN&from=239&to=438&var=W408C	getma.org/?cm=var&var=hg19,12,8994108,G,C&fts=all	12	8994108	8994108	G	C	SNP	A2ML1	NM_144670	human	genbank	57_37b	+1	validated	missense	c.1224	p.W408C	0.995	NULL	HMMPfam_A2M_N,HMMPfam_A2M_N_2,HMMPfam_A2M,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN,HMMPfam_A2M_comp,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_recep	-	no_errors
-A2ML1	144568	genome.wustl.edu	37	12	8995779	8995779	+	Missense_Mutation	SNP	G	G	A	novel	unknown	TCGA-A8-A08P-01	TCGA-A8-A08P-10	G	G	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Missense_Mutation	p.R433H	A2ML1	NM_144670	NP_653271	A2ML1_HUMAN	A8K2U0	c.(1297-1299)CGT>CAT	c.1298G>A	12	433	433	Missense_Mutation	p.R433H	A2ML1	NM_144670	NP_653271	A2ML1_HUMAN	A8K2U0	c.(1297-1299)CGT>CAT	c.1298G>A	12	433	433	neutral	0.255	R433H	getma.org/?cm=msa&ty=f&p=A2ML1_HUMAN&rb=239&re=438&var=R433H	getma.org/pdb.php?prot=A2ML1_HUMAN&from=239&to=438&var=R433H	getma.org/?cm=var&var=hg19,12,8995779,G,A&fts=all	12	8995779	8995779	G	A	SNP	A2ML1	NM_144670	human	genbank	57_37b	+1	validated	missense	c.1298	p.R433H	0.108	NULL	HMMPfam_A2M_N,HMMPfam_A2M_N_2,HMMPfam_A2M,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN,HMMPfam_A2M_comp,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_recep	-	no_errors
-A2ML1	144568	genome.wustl.edu	37	12	8995942	8995942	+	Silent	SNP	C	C	T	novel	unknown	TCGA-C8-A12T-01	TCGA-C8-A12T-10	C	C	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Silent	p.I487I	A2ML1	NM_144670	NP_653271	A2ML1_HUMAN	A8K2U0	c.(1459-1461)ATC>ATT	c.1461C>T	12	487	487	Silent	p.I487I	A2ML1	NM_144670	NP_653271	A2ML1_HUMAN	A8K2U0	c.(1459-1461)ATC>ATT	c.1461C>T	12	487	487	NA	NA	NA	NA	NA	NA	12	8995942	8995942	C	T	SNP	A2ML1	NM_144670	human	genbank	57_37b	+1	validated	silent	c.1461	p.I487	0.040	HMMPfam_A2M_N_2	HMMPfam_A2M_N,HMMPfam_A2M_N_2,HMMPfam_A2M,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN,HMMPfam_A2M_comp,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_recep	-	no_errors
-A2ML1	144568	genome.wustl.edu	37	12	8998791	8998791	+	Silent	SNP	C	C	T	novel	unknown	TCGA-BH-A0AV-01	TCGA-BH-A0AV-10	C	C	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Silent	p.F552F	A2ML1	NM_144670	NP_653271	A2ML1_HUMAN	A8K2U0	c.(1654-1656)TTC>TTT	c.1656C>T	14	552	552	Silent	p.F552F	A2ML1	NM_144670	NP_653271	A2ML1_HUMAN	A8K2U0	c.(1654-1656)TTC>TTT	c.1656C>T	14	552	552	NA	NA	NA	NA	NA	NA	12	8998791	8998791	C	T	SNP	A2ML1	NM_144670	human	genbank	57_37b	+1	validated	silent	c.1656	p.F552	0.669	HMMPfam_A2M_N_2	HMMPfam_A2M_N,HMMPfam_A2M_N_2,HMMPfam_A2M,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN,HMMPfam_A2M_comp,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_recep	-	no_errors
-A2ML1	144568	genome.wustl.edu	37	12	9000231	9000231	+	Silent	SNP	G	G	A	novel	unknown	TCGA-AN-A0FT-01	TCGA-AN-A0FT-10	G	G	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Silent	p.A590A	A2ML1	NM_144670	NP_653271	A2ML1_HUMAN	A8K2U0	c.(1768-1770)GCG>GCA	c.1770G>A	15	590	590	Silent	p.A590A	A2ML1	NM_144670	NP_653271	A2ML1_HUMAN	A8K2U0	c.(1768-1770)GCG>GCA	c.1770G>A	15	590	590	NA	NA	NA	NA	NA	NA	12	9000231	9000231	G	A	SNP	A2ML1	NM_144670	human	genbank	57_37b	+1	validated	silent	c.1770	p.A590	0.000	HMMPfam_A2M_N_2	HMMPfam_A2M_N,HMMPfam_A2M_N_2,HMMPfam_A2M,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN,HMMPfam_A2M_comp,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_recep	-	no_errors
-A2ML1	144568	genome.wustl.edu	37	12	9001389	9001389	+	Missense_Mutation	SNP	C	C	G	novel	unknown	TCGA-BH-A0HP-01	TCGA-BH-A0HP-10	C	C	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Missense_Mutation	p.S636C	A2ML1	NM_144670	NP_653271	A2ML1_HUMAN	A8K2U0	c.(1906-1908)TCT>TGT	c.1907C>G	16	636	636	Missense_Mutation	p.S636C	A2ML1	NM_144670	NP_653271	A2ML1_HUMAN	A8K2U0	c.(1906-1908)TCT>TGT	c.1907C>G	16	636	636	neutral	-0.22	S636C	getma.org/?cm=msa&ty=f&p=A2ML1_HUMAN&rb=602&re=735&var=S636C	getma.org/pdb.php?prot=A2ML1_HUMAN&from=602&to=735&var=S636C	getma.org/?cm=var&var=hg19,12,9001389,C,G&fts=all	12	9001389	9001389	C	G	SNP	A2ML1	NM_144670	human	genbank	57_37b	+1	validated	missense	c.1907	p.S636C	0.165	NULL	HMMPfam_A2M_N,HMMPfam_A2M_N_2,HMMPfam_A2M,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN,HMMPfam_A2M_comp,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_recep	-	no_errors
+A1CF	29974	genome.wustl.edu	37	10	52573692	52573692	+	Missense_Mutation	SNP	G	G	T	novel	unknown	TCGA-B6-A0RS-01	TCGA-B6-A0RS-10	G	G	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Missense_Mutation	p.D424E	Q9NQ94	NM_138932	NP_620310	A1CF_HUMAN	Q9NQ94	c.(1270-1272)GAC>GAA	c.1272C>A	10	424	424	Missense_Mutation	p.D432E	A1CF	NM_138933	NP_620311	A1CF_HUMAN	Q9NQ94	c.(1294-1296)GAC>GAA	c.1296C>A	12	432	432	neutral	0.345	D424E	getma.org/?cm=msa&ty=f&p=A1CF_HUMAN&rb=298&re=497&var=D424E	NA	getma.org/?cm=var&var=hg19,10,52573692,G,T&fts=all	10	52573692	52573692	G	T	SNP	A1CF	NM_138932	human	genbank	57_37b	-1	reviewed	missense	c.1272	p.D424E	0.768	NULL	superfamily_RNA-binding domain RBD,HMMSmart_SM00360,HMMPfam_RRM_1,superfamily_dsRNA-binding domain-like	-	no_errors
+A1CF	29974	genome.wustl.edu	37	10	52595854	52595854	+	Missense_Mutation	SNP	G	G	A	novel	unknown	TCGA-BH-A0HP-01	TCGA-BH-A0HP-10	G	G	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Missense_Mutation	p.A195V	Q9NQ94	NM_138932	NP_620310	A1CF_HUMAN	Q9NQ94	c.(583-585)GCG>GTG	c.584C>T	6	195	195	Missense_Mutation	p.A203V	A1CF	NM_138933	NP_620311	A1CF_HUMAN	Q9NQ94	c.(607-609)GCG>GTG	c.608C>T	8	203	203	medium	2.955	A195V	getma.org/?cm=msa&ty=f&p=A1CF_HUMAN&rb=138&re=203&var=A195V	getma.org/pdb.php?prot=A1CF_HUMAN&from=138&to=203&var=A195V	getma.org/?cm=var&var=hg19,10,52595854,G,A&fts=all	10	52595854	52595854	G	A	SNP	A1CF	NM_138932	human	genbank	57_37b	-1	reviewed	missense	c.584	p.A195V	1.000	superfamily_RNA-binding domain RBD,HMMSmart_SM00360,HMMPfam_RRM_1	superfamily_RNA-binding domain RBD,HMMSmart_SM00360,HMMPfam_RRM_1,superfamily_dsRNA-binding domain-like	-	no_errors
+A1CF	29974	genome.wustl.edu	37	10	52595937	52595937	+	Silent	SNP	G	G	A	novel	unknown	TCGA-BH-A18P-01	TCGA-BH-A18P-11	G	G	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Silent	p.I167I	Q9NQ94	NM_138932	NP_620310	A1CF_HUMAN	Q9NQ94	c.(499-501)ATC>ATT	c.501C>T	6	167	167	Silent	p.I175I	A1CF	NM_138933	NP_620311	A1CF_HUMAN	Q9NQ94	c.(523-525)ATC>ATT	c.525C>T	8	175	175	NA	NA	NA	NA	NA	NA	10	52595937	52595937	G	A	SNP	A1CF	NM_138932	human	genbank	57_37b	-1	reviewed	silent	c.501	p.I167	0.615	superfamily_RNA-binding domain RBD,HMMSmart_SM00360,HMMPfam_RRM_1	superfamily_RNA-binding domain RBD,HMMSmart_SM00360,HMMPfam_RRM_1,superfamily_dsRNA-binding domain-like	-	no_errors
+A2M	2	genome.wustl.edu	37	12	9230409	9230409	+	Missense_Mutation	SNP	T	T	C	novel	unknown	TCGA-BH-A18H-01	TCGA-BH-A18H-10	T	T	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Missense_Mutation	p.Y1055C	P01023	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(3163-3165)TAC>TGC	c.3164A>G	26	1055	1055	Missense_Mutation	p.Y1055C	A2M	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(3163-3165)TAC>TGC	c.3164A>G	26	1055	1055	high	3.73	Y1055C	getma.org/?cm=msa&ty=f&p=A2MG_HUMAN&rb=1010&re=1266&var=Y1055C	getma.org/pdb.php?prot=A2MG_HUMAN&from=1010&to=1266&var=Y1055C	getma.org/?cm=var&var=hg19,12,9230409,T,C&fts=all	12	9230409	9230409	T	C	SNP	A2M	NM_000014	human	genbank	57_37b	-1	reviewed	missense	c.3164	p.Y1055C	0.143	superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_A2M_comp	PatternScan_TONB_DEPENDENT_REC_1,HMMPfam_A2M_N,HMMPfam_A2M_N_2,HMMPfam_A2M,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN,HMMPfam_A2M_comp,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_recep	-	no_errors
+A2M	2	genome.wustl.edu	37	12	9242995	9242995	+	Silent	SNP	G	G	A	novel	unknown	TCGA-C8-A138-01	TCGA-C8-A138-10	G	G	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Silent	p.N851N	P01023	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(2551-2553)AAC>AAT	c.2553C>T	20	851	851	Silent	p.N851N	A2M	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(2551-2553)AAC>AAT	c.2553C>T	20	851	851	NA	NA	NA	NA	NA	NA	12	9242995	9242995	G	A	SNP	A2M	NM_000014	human	genbank	57_37b	-1	reviewed	silent	c.2553	p.N851	0.003	NULL	PatternScan_TONB_DEPENDENT_REC_1,HMMPfam_A2M_N,HMMPfam_A2M_N_2,HMMPfam_A2M,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN,HMMPfam_A2M_comp,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_recep	-	no_errors
+A2M	2	genome.wustl.edu	37	12	9246090	9246090	+	Silent	SNP	C	C	T	novel	unknown	TCGA-A2-A0EY-01	TCGA-A2-A0EY-10	C	C	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Silent	p.E737E	P01023	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(2209-2211)GAG>GAA	c.2211G>A	18	737	737	Silent	p.E737E	A2M	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(2209-2211)GAG>GAA	c.2211G>A	18	737	737	NA	NA	NA	NA	NA	NA	12	9246090	9246090	C	T	SNP	A2M	NM_000014	human	genbank	57_37b	-1	reviewed	silent	c.2211	p.E737	1.000	NULL	PatternScan_TONB_DEPENDENT_REC_1,HMMPfam_A2M_N,HMMPfam_A2M_N_2,HMMPfam_A2M,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN,HMMPfam_A2M_comp,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_recep	-	no_errors
+A2M	2	genome.wustl.edu	37	12	9251298	9251298	+	Nonsense_Mutation	SNP	G	G	A	novel	unknown	TCGA-A8-A08G-01	TCGA-A8-A08G-10	G	G	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Nonsense_Mutation	p.R586*	P01023	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(1756-1758)CGA>TGA	c.1756C>T	15	586	586	Nonsense_Mutation	p.R586*	A2M	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(1756-1758)CGA>TGA	c.1756C>T	15	586	586	NA	0.0	R586*	NA	NA	getma.org/?cm=var&var=hg19,12,9251298,G,A&fts=all	12	9251298	9251298	G	A	SNP	A2M	NM_000014	human	genbank	57_37b	-1	reviewed	nonsense	c.1756	p.R586*	0.003	HMMPfam_A2M_N_2	PatternScan_TONB_DEPENDENT_REC_1,HMMPfam_A2M_N,HMMPfam_A2M_N_2,HMMPfam_A2M,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN,HMMPfam_A2M_comp,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_recep	-	no_errors
+A2M	2	genome.wustl.edu	37	12	9256962	9256962	+	Missense_Mutation	SNP	G	G	T	novel	unknown	TCGA-B6-A0IQ-01	TCGA-B6-A0IQ-10	G	G	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Missense_Mutation	p.P380Q	P01023	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(1138-1140)CCA>CAA	c.1139C>A	11	380	380	Missense_Mutation	p.P380Q	A2M	NM_000014	NP_000005	A2MG_HUMAN	P01023	c.(1138-1140)CCA>CAA	c.1139C>A	11	380	380	medium	2.625	P380Q	getma.org/?cm=msa&ty=f&p=A2MG_HUMAN&rb=222&re=421&var=P380Q	getma.org/pdb.php?prot=A2MG_HUMAN&from=222&to=421&var=P380Q	getma.org/?cm=var&var=hg19,12,9256962,G,T&fts=all	12	9256962	9256962	G	T	SNP	A2M	NM_000014	human	genbank	57_37b	-1	reviewed	missense	c.1139	p.P380Q	0.957	NULL	PatternScan_TONB_DEPENDENT_REC_1,HMMPfam_A2M_N,HMMPfam_A2M_N_2,HMMPfam_A2M,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN,HMMPfam_A2M_comp,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_recep	-	no_errors
+A2ML1	144568	genome.wustl.edu	37	12	8975820	8975820	+	Silent	SNP	C	C	A	novel	unknown	TCGA-C8-A12Y-01	TCGA-C8-A12Y-10	C	C	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Silent	p.S35S	A8K2U0	NM_144670	NP_653271	A2ML1_HUMAN	A8K2U0	c.(103-105)TCC>TCA	c.105C>A	2	35	35	Silent	p.S35S	A2ML1	NM_144670	NP_653271	A2ML1_HUMAN	A8K2U0	c.(103-105)TCC>TCA	c.105C>A	2	35	35	NA	NA	NA	NA	NA	NA	12	8975820	8975820	C	A	SNP	A2ML1	NM_144670	human	genbank	57_37b	+1	validated	silent	c.105	p.S35	0.801	HMMPfam_A2M_N	HMMPfam_A2M_N,HMMPfam_A2M_N_2,HMMPfam_A2M,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN,HMMPfam_A2M_comp,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_recep	-	no_errors
+A2ML1	144568	genome.wustl.edu	37	12	8994108	8994108	+	Missense_Mutation	SNP	G	G	C	novel	unknown	TCGA-A1-A0SO-01	TCGA-A1-A0SO-10	G	G	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Missense_Mutation	p.W408C	A8K2U0	NM_144670	NP_653271	A2ML1_HUMAN	A8K2U0	c.(1222-1224)TGG>TGC	c.1224G>C	11	408	408	Missense_Mutation	p.W408C	A2ML1	NM_144670	NP_653271	A2ML1_HUMAN	A8K2U0	c.(1222-1224)TGG>TGC	c.1224G>C	11	408	408	medium	2.005	W408C	getma.org/?cm=msa&ty=f&p=A2ML1_HUMAN&rb=239&re=438&var=W408C	getma.org/pdb.php?prot=A2ML1_HUMAN&from=239&to=438&var=W408C	getma.org/?cm=var&var=hg19,12,8994108,G,C&fts=all	12	8994108	8994108	G	C	SNP	A2ML1	NM_144670	human	genbank	57_37b	+1	validated	missense	c.1224	p.W408C	0.995	NULL	HMMPfam_A2M_N,HMMPfam_A2M_N_2,HMMPfam_A2M,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN,HMMPfam_A2M_comp,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_recep	-	no_errors
+A2ML1	144568	genome.wustl.edu	37	12	8995779	8995779	+	Missense_Mutation	SNP	G	G	A	novel	unknown	TCGA-A8-A08P-01	TCGA-A8-A08P-10	G	G	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Missense_Mutation	p.R433H	A8K2U0	NM_144670	NP_653271	A2ML1_HUMAN	A8K2U0	c.(1297-1299)CGT>CAT	c.1298G>A	12	433	433	Missense_Mutation	p.R433H	A2ML1	NM_144670	NP_653271	A2ML1_HUMAN	A8K2U0	c.(1297-1299)CGT>CAT	c.1298G>A	12	433	433	neutral	0.255	R433H	getma.org/?cm=msa&ty=f&p=A2ML1_HUMAN&rb=239&re=438&var=R433H	getma.org/pdb.php?prot=A2ML1_HUMAN&from=239&to=438&var=R433H	getma.org/?cm=var&var=hg19,12,8995779,G,A&fts=all	12	8995779	8995779	G	A	SNP	A2ML1	NM_144670	human	genbank	57_37b	+1	validated	missense	c.1298	p.R433H	0.108	NULL	HMMPfam_A2M_N,HMMPfam_A2M_N_2,HMMPfam_A2M,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN,HMMPfam_A2M_comp,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_recep	-	no_errors
+A2ML1	144568	genome.wustl.edu	37	12	8995942	8995942	+	Silent	SNP	C	C	T	novel	unknown	TCGA-C8-A12T-01	TCGA-C8-A12T-10	C	C	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Silent	p.I487I	A8K2U0	NM_144670	NP_653271	A2ML1_HUMAN	A8K2U0	c.(1459-1461)ATC>ATT	c.1461C>T	12	487	487	Silent	p.I487I	A2ML1	NM_144670	NP_653271	A2ML1_HUMAN	A8K2U0	c.(1459-1461)ATC>ATT	c.1461C>T	12	487	487	NA	NA	NA	NA	NA	NA	12	8995942	8995942	C	T	SNP	A2ML1	NM_144670	human	genbank	57_37b	+1	validated	silent	c.1461	p.I487	0.040	HMMPfam_A2M_N_2	HMMPfam_A2M_N,HMMPfam_A2M_N_2,HMMPfam_A2M,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN,HMMPfam_A2M_comp,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_recep	-	no_errors
+A2ML1	144568	genome.wustl.edu	37	12	8998791	8998791	+	Silent	SNP	C	C	T	novel	unknown	TCGA-BH-A0AV-01	TCGA-BH-A0AV-10	C	C	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Silent	p.F552F	A8K2U0	NM_144670	NP_653271	A2ML1_HUMAN	A8K2U0	c.(1654-1656)TTC>TTT	c.1656C>T	14	552	552	Silent	p.F552F	A2ML1	NM_144670	NP_653271	A2ML1_HUMAN	A8K2U0	c.(1654-1656)TTC>TTT	c.1656C>T	14	552	552	NA	NA	NA	NA	NA	NA	12	8998791	8998791	C	T	SNP	A2ML1	NM_144670	human	genbank	57_37b	+1	validated	silent	c.1656	p.F552	0.669	HMMPfam_A2M_N_2	HMMPfam_A2M_N,HMMPfam_A2M_N_2,HMMPfam_A2M,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN,HMMPfam_A2M_comp,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_recep	-	no_errors
+A2ML1	144568	genome.wustl.edu	37	12	9000231	9000231	+	Silent	SNP	G	G	A	novel	unknown	TCGA-AN-A0FT-01	TCGA-AN-A0FT-10	G	G	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Silent	p.A590A	A8K2U0	NM_144670	NP_653271	A2ML1_HUMAN	A8K2U0	c.(1768-1770)GCG>GCA	c.1770G>A	15	590	590	Silent	p.A590A	A2ML1	NM_144670	NP_653271	A2ML1_HUMAN	A8K2U0	c.(1768-1770)GCG>GCA	c.1770G>A	15	590	590	NA	NA	NA	NA	NA	NA	12	9000231	9000231	G	A	SNP	A2ML1	NM_144670	human	genbank	57_37b	+1	validated	silent	c.1770	p.A590	0.000	HMMPfam_A2M_N_2	HMMPfam_A2M_N,HMMPfam_A2M_N_2,HMMPfam_A2M,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN,HMMPfam_A2M_comp,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_recep	-	no_errors
+A2ML1	144568	genome.wustl.edu	37	12	9001389	9001389	+	Missense_Mutation	SNP	C	C	G	novel	unknown	TCGA-BH-A0HP-01	TCGA-BH-A0HP-10	C	C	NA	NA	NA	NA	Unknown	Untested	Somatic	Phase_IV	Capture	NA	1	dbGAP	Illumina GAIIx	NA	NA	NA	Missense_Mutation	p.S636C	A8K2U0	NM_144670	NP_653271	A2ML1_HUMAN	A8K2U0	c.(1906-1908)TCT>TGT	c.1907C>G	16	636	636	Missense_Mutation	p.S636C	A2ML1	NM_144670	NP_653271	A2ML1_HUMAN	A8K2U0	c.(1906-1908)TCT>TGT	c.1907C>G	16	636	636	neutral	-0.22	S636C	getma.org/?cm=msa&ty=f&p=A2ML1_HUMAN&rb=602&re=735&var=S636C	getma.org/pdb.php?prot=A2ML1_HUMAN&from=602&to=735&var=S636C	getma.org/?cm=var&var=hg19,12,9001389,C,G&fts=all	12	9001389	9001389	C	G	SNP	A2ML1	NM_144670	human	genbank	57_37b	+1	validated	missense	c.1907	p.S636C	0.165	NULL	HMMPfam_A2M_N,HMMPfam_A2M_N_2,HMMPfam_A2M,superfamily_Terpenoid cyclases/Protein prenyltransferases,HMMPfam_Thiol-ester_cl,PatternScan_ALPHA_2_MACROGLOBULIN,HMMPfam_A2M_comp,superfamily_Alpha-macroglobulin receptor domain,HMMPfam_A2M_recep	-	no_errors
diff --git a/core/src/test/scripts/test_data/study_maf_test/meta_mutations_extended.txt b/core/src/test/scripts/test_data/study_maf_test/meta_mutations_extended.txt
index fa760e233dd..bb41d75e38f 100644
--- a/core/src/test/scripts/test_data/study_maf_test/meta_mutations_extended.txt
+++ b/core/src/test/scripts/test_data/study_maf_test/meta_mutations_extended.txt
@@ -7,3 +7,4 @@ profile_description: Mutation data from whole exome sequencing.
 profile_name: Mutations
 data_filename: brca_tcga_pub.maf
 normal_samples_list: TCGA-B6-A0RS-10,TCGA-BH-A0HP-10,TCGA-BH-A18P-11,TCGA-BH-A18H-10,TCGA-C8-A138-10,TCGA-BH-A0HP-10
+swissprot_identifier: accession
diff --git a/core/src/test/scripts/test_data/study_maf_test/result_report.html b/core/src/test/scripts/test_data/study_maf_test/result_report.html
index c52e4061056..0ba0bdb1a5e 100644
--- a/core/src/test/scripts/test_data/study_maf_test/result_report.html
+++ b/core/src/test/scripts/test_data/study_maf_test/result_report.html
@@ -159,18 +159,18 @@ <h4 class="panel-title">General</h4>
                 <td>Validating case lists</td>
                 <td>&ndash;</td>
               </tr>
-              <tr class="danger">
-                <td><span class="glyphicon glyphicon-remove" aria-hidden="true"></span><span class="sr-only">Error</span></td>
+              <tr class="success">
+                <td><span class="glyphicon glyphicon-ok" aria-hidden="true"></span><span class="sr-only">Info</span></td>
                 <td>&ndash;</td>
                 <td>&ndash;</td>
-                <td>No  case list found for stable_id &#39;brca_tcga_pub_all&#39;. Consider adding &#39;add_global_case_list: true&#39; to the study metadata file</td>
+                <td>Validation of case list folder complete</td>
                 <td>&ndash;</td>
               </tr>
-              <tr class="success">
-                <td><span class="glyphicon glyphicon-ok" aria-hidden="true"></span><span class="sr-only">Info</span></td>
+              <tr class="danger">
+                <td><span class="glyphicon glyphicon-remove" aria-hidden="true"></span><span class="sr-only">Error</span></td>
                 <td>&ndash;</td>
                 <td>&ndash;</td>
-                <td>Validation of case lists complete</td>
+                <td>No case list found for stable_id &#39;brca_tcga_pub_all&#39;, consider adding &#39;add_global_case_list: true&#39; to the study metadata file</td>
                 <td>&ndash;</td>
               </tr>
               <tr class="success">
diff --git a/core/src/test/scripts/test_data/study_missing_caselists/data_samples.txt b/core/src/test/scripts/test_data/study_missing_caselists/data_samples.txt
new file mode 100644
index 00000000000..50f22028c97
--- /dev/null
+++ b/core/src/test/scripts/test_data/study_missing_caselists/data_samples.txt
@@ -0,0 +1,13 @@
+#Patient Identifier	Sample Identifier	Subtype	Cancer Type	Cancer Type Detailed
+#Identifier to uniquely specify a patient.	A unique sample identifier.	Subtype description.	Disease type.	Cancer Type Detailed.
+#STRING	STRING	STRING	STRING	STRING
+#1	1	1	1	1
+PATIENT_ID	SAMPLE_ID	SUBTYPE	CANCER_TYPE	CANCER_TYPE_DETAILED
+TEST-PAT1	TEST-PAT1-SAMPLE1	Luminal A	Cancer_type20	Cancer_type20_Sub16
+TEST-PAT1	TEST-PAT1-SAMPLE2	Luminal B	Cancer_type27	Cancer_type27_Sub16
+TEST-PAT1	TEST-PAT1-SAMPLE3	basal-like	Cancer_type8	Cancer_type8_Sub13
+TEST-PAT1	TEST-PAT1-SAMPLE4	basal-like	Cancer_type17	Cancer_type17_Sub10
+TEST-PAT1	TEST-PAT1-SAMPLE5	Her2 enriched	Cancer_type27	Cancer_type27_Sub18
+TEST-PAT1	TEST-PAT1-SAMPLE6	Luminal A	Cancer_type7	Cancer_type7_Sub13
+TEST-PAT2	TEST-PAT2-SAMPLE1	Luminal A	Cancer_type23	Cancer_type23_Sub3
+TEST-PAT2	TEST-PAT2-SAMPLE2	basal-like	Cancer_type7	Cancer_type7_Sub5
diff --git a/core/src/test/scripts/test_data/study_missing_caselists/meta_samples.txt b/core/src/test/scripts/test_data/study_missing_caselists/meta_samples.txt
new file mode 100644
index 00000000000..3dba005bab9
--- /dev/null
+++ b/core/src/test/scripts/test_data/study_missing_caselists/meta_samples.txt
@@ -0,0 +1,4 @@
+cancer_study_identifier: spam
+genetic_alteration_type: CLINICAL
+datatype: SAMPLE_ATTRIBUTES
+data_filename: data_samples.txt
diff --git a/core/src/test/scripts/test_data/study_missing_caselists/meta_study.txt b/core/src/test/scripts/test_data/study_missing_caselists/meta_study.txt
new file mode 100644
index 00000000000..9ccec17d188
--- /dev/null
+++ b/core/src/test/scripts/test_data/study_missing_caselists/meta_study.txt
@@ -0,0 +1,5 @@
+cancer_study_identifier: spam
+type_of_cancer: brca
+name: Spam (spam)
+description: Baked beans
+short_name: Spam
diff --git a/core/src/test/scripts/test_data/study_quotes/meta_mutations_extended.txt b/core/src/test/scripts/test_data/study_quotes/meta_mutations_extended.txt
index be1b8b72dba..813510be072 100644
--- a/core/src/test/scripts/test_data/study_quotes/meta_mutations_extended.txt
+++ b/core/src/test/scripts/test_data/study_quotes/meta_mutations_extended.txt
@@ -6,3 +6,4 @@ show_profile_in_analysis_tab: true
 profile_description: Mutation data from whole exome sequencing.
 profile_name: Mutations
 data_filename: brca_tcga_pub.maf
+swissprot_identifier: name
diff --git a/core/src/test/scripts/test_data/study_quotes/result_report.html b/core/src/test/scripts/test_data/study_quotes/result_report.html
index 98e8bb25d9d..4da015163ed 100644
--- a/core/src/test/scripts/test_data/study_quotes/result_report.html
+++ b/core/src/test/scripts/test_data/study_quotes/result_report.html
@@ -163,7 +163,7 @@ <h4 class="panel-title">General</h4>
                 <td><span class="glyphicon glyphicon-ok" aria-hidden="true"></span><span class="sr-only">Info</span></td>
                 <td>&ndash;</td>
                 <td>&ndash;</td>
-                <td>Validation of case lists complete</td>
+                <td>Validation of case list folder complete</td>
                 <td>&ndash;</td>
               </tr>
               <tr class="success">
diff --git a/core/src/test/scripts/unit_tests_validate_data.py b/core/src/test/scripts/unit_tests_validate_data.py
index 9e12d38e9e8..d5355df79e6 100755
--- a/core/src/test/scripts/unit_tests_validate_data.py
+++ b/core/src/test/scripts/unit_tests_validate_data.py
@@ -686,11 +686,12 @@ def test_normal_samples_list_in_maf(self):
                                     {'normal_samples_list':
                                         'TCGA-BH-A18H-10,'
                                         'TCGA-B6-A0RS-10,'
-                                        ''  # TCGA-BH-A0HP-10
+                                        ''   # TCGA-BH-A0HP-10
                                         'TCGA-BH-A18P-11, '
                                         'TCGA-C8-A138-10'
                                         'TCGA-A2-A0EY-10,'
-                                        ''})  # TCGA-A8-A08G-10
+                                        '',  # TCGA-A8-A08G-10
+                                     'swissprot_identifier': 'accession'})
         # we expect 2 errors about invalid normal samples
         self.assertEqual(len(record_list), 2)
         # check if both messages come from printDataInvalidStatement:
@@ -727,14 +728,94 @@ def test_warning_for_missing_SWISSPROT(self):
         # WARNING: data_mutations_missing_swissprot.maf: line 1: SWISSPROT column is recommended if you want to make sure that a specific isoform is used for the PFAM domains drawing in the mutations view.; wrong value: 'SWISSPROT column not found'
         self.assertEqual(len(record_list), 1)
         # check if both messages come from printDataInvalidStatement:
-        self.assertIn("swissprot", record_list[0].getMessage().lower())
+        self.assertIn("swissprot column is recommended",
+                      record_list[0].getMessage().lower())
+
+    def test_unknown_or_invalid_swissprot(self):
+        """Test errors for invalid and unknown accessions under SWISSPROT."""
+        self.logger.setLevel(logging.WARNING)
+        record_list = self.validate(
+                'mutations/data_mutations_invalid_swissprot.maf',
+                validateData.MutationsExtendedValidator,
+                extra_meta_fields={
+                    'swissprot_identifier': 'accession'})
+        self.assertEqual(len(record_list), 2)
+        record_iterator = iter(record_list)
+        # used a name instead of an accession
+        record = record_iterator.next()
+        self.assertEqual(record.levelno, logging.ERROR)
+        self.assertEqual(record.line_number, 3)
+        self.assertEqual(record.cause, 'A1CF_HUMAN')
+        self.assertNotIn('portal', record.getMessage().lower())
+        # neither a name nor an accession
+        record = record_iterator.next()
+        self.assertEqual(record.levelno, logging.ERROR)
+        self.assertEqual(record.line_number, 5)
+        self.assertEqual(record.cause, 'P99999,Z9ZZZ9ZZZ9')
+        self.assertNotIn('portal', record.getMessage().lower())
+
+    def test_name_as_swissprot_identifier(self):
+        """Test if the SWISSPROT column is parsed as a name if meta says so."""
+        self.logger.setLevel(logging.WARNING)
+        record_list = self.validate(
+                'mutations/data_mutations_name_swissprot.maf',
+                validateData.MutationsExtendedValidator,
+                extra_meta_fields={'swissprot_identifier': 'name'})
+        # the same errors as in test_implicit_name_as_swissprot_identifier()
+        self.assert_swissprotname_validated(record_list)
+
+    def test_implicit_name_as_swissprot_identifier(self):
+        """Test if the SWISSPROT column is parsed as a name if unspecified."""
+        self.logger.setLevel(logging.WARNING)
+        record_list = self.validate(
+                'mutations/data_mutations_name_swissprot.maf',
+                validateData.MutationsExtendedValidator)
+        # warning about the implicit Swiss-Prot identifier type
+        record = record_list[0]
+        self.assertEqual(record.levelno, logging.WARNING)
+        self.assertIn('swissprot_identifier', record.getMessage())
+        # the same errors as in test_name_as_swissprot_identifier()
+        self.assert_swissprotname_validated(record_list[1:])
+
+    def assert_swissprotname_validated(self, record_list):
+        """Assert names are validated in data_mutations_name_swissprot.maf."""
+        self.assertEqual(len(record_list), 2)
+        record_iterator = iter(record_list)
+        # used an accession instead of a name
+        record = record_iterator.next()
+        self.assertEqual(record.levelno, logging.ERROR)
+        self.assertEqual(record.line_number, 3)
+        self.assertEqual(record.cause, 'Q9NQ94')
+        self.assertNotIn('portal', record.getMessage().lower())
+        # neither a name nor an accession
+        record = record_iterator.next()
+        self.assertEqual(record.levelno, logging.ERROR)
+        self.assertEqual(record.line_number, 5)
+        self.assertEqual(record.cause, 'A1CF_HUMAN,HBB_YEAST')
+        self.assertNotIn('portal', record.getMessage().lower())
+
+    def test_invalid_swissprot_identifier_type(self):
+        """Test if the validator rejects files with nonsensical id types."""
+        self.logger.setLevel(logging.ERROR)
+        mvals, mtype = validateData.cbioportal_common.parse_metadata_file(
+                'test_data/mutations/meta_mutations_invalid_swissprot_idspec.txt',
+                self.logger,
+                study_id='spam')
+        record_list = self.get_log_records()
+        self.assertEqual(len(record_list), 1)
+        record = record_list.pop()
+        self.assertEqual(record.levelno, logging.ERROR)
+        self.assertEqual(record.cause, 'namelessly')
+        self.assertIsNone(mtype, 'metadata file was not rejected as invalid')
 
     def test_isValidAminoAcidChange(self):
         """Test if proper warnings are given for wrong/blank AA change vals."""
         # set level according to this test case:
         self.logger.setLevel(logging.WARNING)
-        record_list = self.validate('mutations/data_mutations_wrong_aa_change.maf',
-                                    validateData.MutationsExtendedValidator)
+        record_list = self.validate(
+                'mutations/data_mutations_wrong_aa_change.maf',
+                validateData.MutationsExtendedValidator,
+                extra_meta_fields={'swissprot_identifier': 'accession'})
         self.assertEqual(len(record_list), 5)
         record_iterator = iter(record_list)
         # empty field (and no HGVSp_Short column)
@@ -774,7 +855,9 @@ def test_silent_mutation_skipped(self):
         # set level according to this test case:
         self.logger.setLevel(logging.INFO)
         record_list = self.validate('mutations/data_mutations_some_silent.maf',
-                                    validateData.MutationsExtendedValidator)
+                                    validateData.MutationsExtendedValidator,
+                                    extra_meta_fields={
+                                            'swissprot_identifier': 'name'})
         # we expect 5 infos: 3 about silent mutations, 2 general info messages:
         self.assertEqual(len(record_list), 5)
         # First 3 INFO messages should be something like: "Validation of line skipped due to cBioPortal's filtering. Filtered types:"
@@ -795,7 +878,9 @@ def test_alternative_notation_for_intergenic_mutation(self):
         # set level according to this test case:
         self.logger.setLevel(logging.WARNING)
         record_list = self.validate('mutations/data_mutations_silent_alternative.maf',
-                                    validateData.MutationsExtendedValidator)
+                                    validateData.MutationsExtendedValidator,
+                                    extra_meta_fields={
+                                            'swissprot_identifier': 'name'})
         # we expect 1 ERROR and 2 WARNINGs :
         self.assertEqual(len(record_list), 3)
         
@@ -1096,6 +1181,21 @@ def test_duplicated_stable_id(self):
         self.assertTrue(record.cause.startswith('brca_tcga_pub_all'),
                         "Error is not about the id 'brca_tcga_pub_all'")
 
+    def test_missing_caselists(self):
+        """Test if errors are issued if certain case lists are not defined."""
+        self.logger.setLevel(logging.ERROR)
+        validateData.validate_study(
+                'test_data/study_missing_caselists',
+                PORTAL_INSTANCE,
+                self.logger)
+        record_list = self.get_log_records()
+        self.assertEqual(len(record_list), 1)
+        # <study ID>_all
+        record = record_list.pop()
+        self.assertEqual(record.levelno, logging.ERROR)
+        self.assertIn('spam_all', record.getMessage())
+        self.assertIn('add_global_case_list', record.getMessage())
+
 
 class StableIdValidationTestCase(LogBufferTestCase):
 
@@ -1129,5 +1229,19 @@ def test_unnecessary_and_wrong_stable_id(self):
         self.assertEqual(warning.cause, 'stable_id')
 
 
+class DataFileIOTestCase(PostClinicalDataFileTestCase):
+    """Test if the right behavior occurs if study files cannot be read."""
+
+    def test_missing_datafile(self):
+        """Test the error if files referenced from meta files do not exist."""
+        self.logger.setLevel(logging.ERROR)
+        record_list = self.validate('filename-that-does-not-exist.txt',
+                                    validateData.ContinuousValuesValidator)
+        self.assertEqual(len(record_list), 1)
+        record = record_list.pop()
+        self.assertEqual(record.levelno, logging.ERROR)
+        self.assertIn('file', record.getMessage().lower())
+
+
 if __name__ == '__main__':
     unittest.main(buffer=True)
diff --git a/docs/File-Formats.md b/docs/File-Formats.md
index 33596124a6e..c0e670383c3 100644
--- a/docs/File-Formats.md
+++ b/docs/File-Formats.md
@@ -34,7 +34,7 @@ This file contains metadata about the cancer study. The file contains the follow
 3. **name**: The name of the cancer study, e.g., "Breast Cancer (Jones Lab 2013)".
 4. **description**: A description of the cancer study, e.g., "Comprehensive profiling of 103 breast cancer samples. Generated by the Jones Lab 2013". This description may contain one or more URLs to relevant information.
 5. **citation (optional)**: A relevant citation, e.g., "TCGA, Nature 2012".
-6. **pmid (optional)**: A relevant pubmed id.
+6. **pmid (optional)**: A relevant pubmed id. If used, the field citation has to be filled, too.
 7. **short_name**:  A short name used for display used on various web pages within the cBioPortal, e.g., "BRCA (Jones)".
 8. **groups (optional)**: When using an authenticating cBioPortal, lists the user-groups that are allowed access to this study. Multiple groups are separated with a semicolon ";". The study will be invisible to users not in _at least one_ of the listed groups, as if it wasn't loaded at all. e.g., "PUBLIC;GDAC;SU2C-PI3K". see [User-Authorization](User-Authorization.md) for more information on groups
 9. **add_global_case_list (optional)**: set to 'true' if you would like the "All samples" case list to be generated automatically for you. See also [Case lists](#case-lists).
@@ -484,7 +484,8 @@ The mutation metadata file should contain the following fields:
 5. **show_profile_in_analysis_tab**: true
 6. **profile_name**: A name for the mutation data, e.g., "Mutations".
 7. **profile_description**: A description of the mutation data, e.g., "Mutation data from whole exome sequencing.".
-8. **data_filename**: &lt;your datafile&gt;
+8. **data_filename**: &lt;your data file&gt;
+9. **swissprot_identifier (optional)**: either `accession` or `name`, indicating the type of identifier in the `SWISSPROT` column
 
 An example metadata file would be:
 
@@ -516,7 +517,7 @@ Note: next to Hugo_Symbol, it is recommended to have the Entrez gene ID:
 The following extra annotation columns are also important for making sure mutation specific UI functionality works well in the portal:
 
 * **Protein_position**: (annotation column) Required to initialize the 3D viewer in [mutations view](http://www.cbioportal.org/index.do?cancer_study_list=brca_tcga_pub&cancer_study_id=brca_tcga_pub&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=brca_tcga_pub_mutations&genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION=brca_tcga_pub_gistic&genetic_profile_ids_PROFILE_MRNA_EXPRESSION=brca_tcga_pub_mrna_median_Zscores&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&data_priority=0&case_set_id=brca_tcga_pub_complete&case_ids=&patient_case_select=sample&gene_set_choice=prostate-cancer%3A-ar-signaling-%2810-genes%29&gene_list=TP53&clinical_param_selection=null&tab_index=tab_visualize&Action=Submit#mutation_details)
-* **SWISSPROT**: (annotation column) swissprot code, e.g. O11H1_HUMAN. Is not absolutely required, but not having it may result in inconsistent PDB structure matching in [mutations view](http://www.cbioportal.org/index.do?cancer_study_list=brca_tcga_pub&cancer_study_id=brca_tcga_pub&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=brca_tcga_pub_mutations&genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION=brca_tcga_pub_gistic&genetic_profile_ids_PROFILE_MRNA_EXPRESSION=brca_tcga_pub_mrna_median_Zscores&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&data_priority=0&case_set_id=brca_tcga_pub_complete&case_ids=&patient_case_select=sample&gene_set_choice=prostate-cancer%3A-ar-signaling-%2810-genes%29&gene_list=TP53&clinical_param_selection=null&tab_index=tab_visualize&Action=Submit#mutation_details). :warning: After running vcf2maf (or VEP) the SWISSPROT column contains the uniprot accession and **NOT** the entry name (e.g. for TP53 the column will contain P04637 and not P53_HUMAN). cBioPortal currently only supports the entry name. Work is presently being done to allow cBioPortal to import the accessions, but until that work is finished you will have to convert the accessions to entry names yourself. 
+* **SWISSPROT**: (annotation column) UniProtKB/SWISS-PROT name (formerly called ID) or accession code depending on the value of the `swissprot_identifier` metadatum, e.g. O11H1_HUMAN or Q8NG94. Is not absolutely required, but not having it may result in inconsistent PDB structure matching in [mutations view](http://www.cbioportal.org/index.do?cancer_study_list=brca_tcga_pub&cancer_study_id=brca_tcga_pub&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=brca_tcga_pub_mutations&genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION=brca_tcga_pub_gistic&genetic_profile_ids_PROFILE_MRNA_EXPRESSION=brca_tcga_pub_mrna_median_Zscores&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&data_priority=0&case_set_id=brca_tcga_pub_complete&case_ids=&patient_case_select=sample&gene_set_choice=prostate-cancer%3A-ar-signaling-%2810-genes%29&gene_list=TP53&clinical_param_selection=null&tab_index=tab_visualize&Action=Submit#mutation_details).
 
 ##### Extending the MAF format
 :warning: **Attention**: for the list of ***required*** and ***recommended*** fields, check the subsection above :arrow_up:. The section below :arrow_down: only describes some of the *extra* fields you can have in your mutations file.
@@ -720,7 +721,7 @@ When **not** using the *add_global_case_list* attribute in [Study metadata](#can
 The case list file should contain the following fields:
 
 1. **cancer_study_identifier**: same value as specified in [study meta file](#cancer-study)
-2. **stable_id**: typically the cancer_study_identifier with an relevant suffix, e.g., "_custom". There are some naming rules to follow if you want the case list to be selected automatically in the query UI base on the selected sample profiles. See subsection below.
+2. **stable_id**: it must contain the cancer_study_identifier followed by an underscore. Typically, after this a relevant suffix, e.g., "_custom", is added. There are some naming rules to follow if you want the case list to be selected automatically in the query UI base on the selected sample profiles. See subsection below.
 3. **case_list_name**: A name for the patient list, e.g., "All Tumors".
 4. **case_list_description**: A description of the patient list, e.g., "All tumor samples (825 samples).".
 5. **case_list_ids**: A tab-delimited list of sample ids from the dataset.
diff --git a/docs/Updating-pfam_graphics-table.md b/docs/Updating-pfam_graphics-table.md
new file mode 100644
index 00000000000..b89e93bd33a
--- /dev/null
+++ b/docs/Updating-pfam_graphics-table.md
@@ -0,0 +1,18 @@
+# Updating pfam_graphics table
+
+Updating the pfam_graphics table is easy using the scripts provided in cBioPortal. There is no need to download any file previously.
+
+1- Empty the table `pfam_graphics` (the scripts raise an error if one of the domains that we want to add is already in the table). 
+```sql
+TRUNCATE TABLE pfam_graphics;
+```
+
+2- Run the script `FetchPfamGraphics.java` with the file path of the output file and its name as an argument. This function first searches for all the proteins from mouse that have been reviewed in UniProtKB, then tries to retrieve their Pfam domains, and finally saves the information in a file. This script can also be run in the command line by going into  `<your_cbioportal_folder>/core/src/main/scripts/` and typing:
+```
+fetchPfamGraphicsData.sh <output_pfam_mapping_file>
+```
+
+3- Run the script `ImportPfamGraphics.java`, which uses the output of the previous script as an input to write all the information retrieved to the database. This script can also be run in the command line by typing:
+```
+importPfamGraphics.pl <pfam_mapping_file>
+```
\ No newline at end of file
diff --git a/docs/portal.properties-Reference.md b/docs/portal.properties-Reference.md
index 96db601ebf8..4fab42e212c 100644
--- a/docs/portal.properties-Reference.md
+++ b/docs/portal.properties-Reference.md
@@ -45,7 +45,15 @@ google_analytics_profile_id
 
 # Password Authentication
 
-The portal supports password authentication via Google+.  To active password authentication, then the following properties are required:
+The portal supports password authentication via Google+. Before you start you need to setup a google account that will own the authentication API. Follow https://developers.google.com/identity/sign-in/web/devconsole-project to get clientID and secret. Fill it in portal.properties:
+```
+googleplus.consumer.key=195047654890-499gl89hj65j8d2eorqe0jvjnfaxcln0.apps.googleusercontent.com 
+googleplus.consumer.secret=2jCfg4SPWdGfXF44WC588dK
+```
+(note: these are just examples, you need to get your own) You will also need to go to "Google+ API" and click Enable button. In case of problems make sure to enable DEBUG logging for org.springframework.social and org.springframework.security.web.authentication.
+
+
+To active password authentication, then the following properties are required:
 ```
 app.name=
 authenticate=googleplus
diff --git a/pom.xml b/pom.xml
index 97742048ee1..b7a145b88ab 100644
--- a/pom.xml
+++ b/pom.xml
@@ -6,7 +6,7 @@
   <artifactId>master</artifactId>
   <packaging>pom</packaging>
   <name>Portal Master</name>
-  <version>1.2.4</version>
+  <version>1.2.5</version>
   <description>master maven module</description>
 
   <scm>
diff --git a/portal/pom.xml b/portal/pom.xml
index 550f1b45e02..ef43fc1b192 100644
--- a/portal/pom.xml
+++ b/portal/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>master</artifactId>
     <groupId>org.mskcc.cbio</groupId>
-    <version>1.2.4</version>
+    <version>1.2.5</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
   <artifactId>cbioportal</artifactId>
diff --git a/portal/src/main/webapp/WEB-INF/jsp/mutation_details.jsp b/portal/src/main/webapp/WEB-INF/jsp/mutation_details.jsp
index ed1497cff97..530f87ac509 100644
--- a/portal/src/main/webapp/WEB-INF/jsp/mutation_details.jsp
+++ b/portal/src/main/webapp/WEB-INF/jsp/mutation_details.jsp
@@ -97,8 +97,8 @@
             },
             view: {
                 vis3d: {
-	                //for https, use a proxy since rcsb.org is not serving https and browsers will complain about the mixed https/http content
-                    pdbUri: (document.location.protocol != "https:"? "http://files.rcsb.org/view/" : "api/proxy/jsmol/")
+	                // use https for all portal instances
+                    pdbUri: "https://files.rcsb.org/view/"
                 },       
                 mutationTable: {
                     columnRender: {
diff --git a/portal/src/main/webapp/WEB-INF/jsp/patient_view/clinical_timeline.jsp b/portal/src/main/webapp/WEB-INF/jsp/patient_view/clinical_timeline.jsp
index 180829df094..2b1614a9e18 100644
--- a/portal/src/main/webapp/WEB-INF/jsp/patient_view/clinical_timeline.jsp
+++ b/portal/src/main/webapp/WEB-INF/jsp/patient_view/clinical_timeline.jsp
@@ -134,10 +134,11 @@
                         if (specRefNum) {
                             if (specRefNum.length > 1) {
                                 console.warn("More than 1 specimen reference number found in tooltip table");
-                            }
-                            sortOrder = caseIds.indexOf(specRefNum[0][1]);
-                            if (sortOrder === -1) {
-                                sortOrder = Infinity;
+                            } else if (specRefNum.length === 1) {
+                                sortOrder = caseIds.indexOf(specRefNum[0][1]);
+                                if (sortOrder === -1) {
+                                    sortOrder = Infinity;
+                                }
                             }
                         }
                         return sortOrder;
diff --git a/portal/src/main/webapp/WEB-INF/jsp/patient_view/cna.jsp b/portal/src/main/webapp/WEB-INF/jsp/patient_view/cna.jsp
index 5367207d10c..198b2dbc4dd 100644
--- a/portal/src/main/webapp/WEB-INF/jsp/patient_view/cna.jsp
+++ b/portal/src/main/webapp/WEB-INF/jsp/patient_view/cna.jsp
@@ -35,39 +35,14 @@
 
 <script type="text/javascript">
     var cnaTableIndices = cbio.util.arrayToAssociatedArrayIndices(["id","case_ids","gene","alteration", "annotation","cytoband","mrna","altrate","drug"]);
+    var cnaOncokbInstance;
     function buildCnaDataTable(cnas, cnaEventIds, table_id, sDom, iDisplayLength, sEmptyInfo) {
         var data = [];
-        var oncokbInstance;
-
-        if(OncoKB.getAccess()) {
-            var oncokbInstanceManager = new OncoKB.addInstanceManager();
-            oncokbInstance = oncokbInstanceManager.addInstance('patient-cna');
-            if(oncokbGeneStatus) {
-                oncokbInstance.setGeneStatus(oncokbGeneStatus);
-            }
-            oncokbInstance.setTumorType(OncoKB.utils.getTumorTypeFromClinicalDataMap(clinicalDataMap));
-        }
 
         for (var i=0, nEvents=cnaEventIds.length; i<nEvents; i++) {
-            if(oncokbInstance) {
-                var _id = cnaEventIds[i];
-                var alter = '';
-                switch(cnas.getValue(_id, "alter")) {
-                    case 2:
-                        alter = 'amplification';
-                        break;
-                    case -2:
-                        alter = 'deletion';
-                        break;
-                    default:
-                        alter = null;
-                }
-                oncokbInstance.addVariant(_id, cnas.getValue(_id, "entrez"), cnas.getValue(_id, "gene"), alter,
-                    (_.isObject(patientInfo) ? (patientInfo.CANCER_TYPE_DETAILED || patientInfo.CANCER_TYPE) : '') || cancerType,
-                    alter);
-            }
             data.push([cnaEventIds[i]]);
         }
+        
         var oTable = $('#'+table_id).dataTable( {
                 "sDom": sDom, // selectable columns
                 "bJQueryUI": true,
@@ -325,10 +300,10 @@
                     plotCnaAltRate("."+table_id+"-cna-cohort",cnas);
                     addNoteTooltip("."+table_id+"-tip");
                     addDrugsTooltip("."+table_id+"-drug-tip", 'top right', 'bottom center');
-                    if(oncokbInstance){
-                        oncokbInstance.addEvents(this, 'gene');
-                        oncokbInstance.addEvents(this, 'alteration');
-                        oncokbInstance.addEvents(this, 'column');
+                    if(cnaOncokbInstance){
+                        cnaOncokbInstance.addEvents(this, 'gene');
+                        cnaOncokbInstance.addEvents(this, 'alteration');
+                        cnaOncokbInstance.addEvents(this, 'column');
                     }
                 },
                 "bPaginate": true,
@@ -343,25 +318,7 @@
                 "iDisplayLength": iDisplayLength,
                 "aLengthMenu": [[5,10, 25, 50, 100, -1], [5, 10, 25, 50, 100, "All"]]
         } );
-
-        if(oncokbInstance) {
-            oncokbInstance.getIndicator().then(function () {
-                var tableData = oTable.fnGetData();
-                var oncokbEvidence = [];
-                _.each(tableData, function(ele, i) {
-                    oncokbEvidence.push(oncokbInstance.getVariant(ele[0]));
-                });
-                cnas.addData('oncokb', oncokbEvidence)
-                if (tableData.length > 0)
-                {
-                    _.each(tableData, function(ele, i) {
-                        oTable.fnUpdate(null, i, cnaTableIndices["annotation"], false, false);
-                    });
-
-                    oTable.fnUpdate(null, 0, cnaTableIndices['annotation']);
-                }
-            });
-        }
+        
         oTable.css("width","100%");
         addNoteTooltip("#"+table_id+" th.cna-header");
         return oTable;
@@ -519,6 +476,38 @@
                 $('.all-cna-table-name').addClass("datatable-name");
                 $('#cna_wrapper_table').show();
                 $('#cna_wait').remove();
+                
+                // Get OncoKB info
+                cnaOncokbInstance = initOncoKB('patient-cna', genomicEventObs.cnas.getEventIds(false), genomicEventObs.cnas, 'cna', function(instance) {
+                    var cnaSummaryTable = $('#cna_summary_table').dataTable();
+                    var cnaTable = $('#cna_table').dataTable();
+
+                    var cnaSummaryTableData = cnaSummaryTable.fnGetData();
+                    var cnaTableData = cnaTable.fnGetData();
+                    
+                    var oncokbEvidence = [];
+                    _.each(cnaTableData, function(ele, i) {
+                        oncokbEvidence.push(cnaOncokbInstance.getVariant(ele[0]));
+                    });
+
+                    genomicEventObs.cnas.addData('oncokb', oncokbEvidence);
+                    
+                    if (cnaTableData.length > 0){
+                        _.each(cnaTableData, function(ele, i) {
+                            cnaTable.fnUpdate(null, i, cnaTableIndices["annotation"], false, false);
+                        });
+
+                        cnaTable.fnUpdate(null, 0, cnaTableIndices['annotation']);
+                    }
+
+                    if (cnaSummaryTableData.length > 0){
+                        _.each(cnaSummaryTableData, function(ele, i) {
+                            cnaSummaryTable.fnUpdate(null, i, cnaTableIndices["annotation"], false, false);
+                        });
+
+                        cnaSummaryTable.fnUpdate(null, 0, cnaTableIndices['annotation']);
+                    }
+                });
             }
             ,"json"
         );
diff --git a/portal/src/main/webapp/WEB-INF/jsp/patient_view/mutations.jsp b/portal/src/main/webapp/WEB-INF/jsp/patient_view/mutations.jsp
index 59f9f4ada8f..828cc488a51 100644
--- a/portal/src/main/webapp/WEB-INF/jsp/patient_view/mutations.jsp
+++ b/portal/src/main/webapp/WEB-INF/jsp/patient_view/mutations.jsp
@@ -108,29 +108,12 @@
             });
         });
     };
+    var mutationOncokbInstance;
 
     function buildMutationsDataTable(mutations,mutEventIds, table_id, sDom, iDisplayLength, sEmptyInfo, compact) {
         var data = [];
-        var oncokbInstance;
-        if(OncoKB.getAccess()) {
-            var oncokbInstanceManager = new OncoKB.addInstanceManager();
-            oncokbInstance = oncokbInstanceManager.addInstance('patient-mutation');
-            if(oncokbGeneStatus) {
-                oncokbInstance.setGeneStatus(oncokbGeneStatus);
-            }
-            oncokbInstance.setTumorType(OncoKB.utils.getTumorTypeFromClinicalDataMap(clinicalDataMap));
-        }
         for (var i=0, nEvents=mutEventIds.length; i<nEvents; i++) {
             var _id = mutEventIds[i];
-            if(oncokbInstance) {
-                oncokbInstance.addVariant(_id, mutations.getValue(_id, "entrez"), mutations.getValue(_id, "gene"), 
-                    mutations.getValue(_id, "aa"), 
-                    (_.isObject(patientInfo) ? (patientInfo.CANCER_TYPE_DETAILED || patientInfo.CANCER_TYPE) : '') || cancerType, 
-                    mutations.getValue(_id, "type") ? mutations.getValue(_id, "type") : 'any', 
-                    findCosmic(mutations.getValue(_id, "cosmic"), mutations.getValue(_id, "aa")), 
-                    mutations.getValue(_id, "is-hotspot"), mutations.getValue(_id, 'protein-start'), 
-                    mutations.getValue(_id, 'protein-end'));
-            }
             data.push([mutEventIds[i]]);
         }
 
@@ -257,7 +240,8 @@
                                 var datum = {
                                     mutation: {
                                         myCancerGenome: [],
-                                        isHotspot: false
+                                        isHotspot: false,
+                                        get: function(a) { return this[a];}
                                     },
                                     oncokb:{}
                                 };
@@ -928,10 +912,10 @@
                     addCosmicTooltip(table_id);
                     listenToBamIgvClick(".igv-link");
                     //drawPanCanThumbnails(this);
-                    if(oncokbInstance){
-                        oncokbInstance.addEvents(this, 'gene');
-                        oncokbInstance.addEvents(this, 'alteration');
-                        oncokbInstance.addEvents(this, 'column');
+                    if(mutationOncokbInstance){
+                        mutationOncokbInstance.addEvents(this, 'gene');
+                        mutationOncokbInstance.addEvents(this, 'alteration');
+                        mutationOncokbInstance.addEvents(this, 'column');
                     }
                 },
                 "bPaginate": true,
@@ -947,25 +931,6 @@
                 "aLengthMenu": [[5,10, 25, 50, 100, -1], [5, 10, 25, 50, 100, "All"]]
         } );
 
-        if(oncokbInstance) {
-            oncokbInstance.getIndicator().then(function () {
-                var tableData = oTable.fnGetData();
-                var oncokbEvidence = [];
-                _.each(tableData, function(ele, i) {
-                    oncokbEvidence.push(oncokbInstance.getVariant(ele[0]));
-                });
-                mutations.addData('oncokb', oncokbEvidence)
-                if (tableData.length > 0)
-                {
-                    _.each(tableData, function(ele, i) {
-                        oTable.fnUpdate(null, i, mutTableIndices["annotation"], false, false);
-                    });
-
-                    oTable.fnUpdate(null, 0, mutTableIndices['annotation']);
-                }
-            });
-        }
-
         oTable.css("width","100%");
         addNoteTooltip("#"+table_id+" th.mut-header");
 
@@ -1254,7 +1219,37 @@
                                 _.extend(munge(byProteinPosResponse, "protein_start_with_hugo"), munge(byKeywordResponse, "keyword"), munge(byHugoResponse, "hugo")));
                         genomicEventObs.fire("pancan-mutation-frequency-built");
                     });
+                    
+                    // Get OncoKB info
+                    mutationOncokbInstance = initOncoKB('patient-mutation', genomicEventObs.mutations.getEventIds(false), genomicEventObs.mutations, 'mutation', function() {
+                        var mutationSummaryTable = $('#mutation_summary_table').dataTable();
+                        var mutationTable = $('#mutation_table').dataTable();
+
+                        var mutationSummaryTableData = mutationSummaryTable.fnGetData();
+                        var mutationTableData = mutationTable.fnGetData();
+
+                        var oncokbEvidence = [];
+                        _.each(mutationTableData, function(ele, i) {
+                            oncokbEvidence.push(mutationOncokbInstance.getVariant(ele[0]));
+                        });
+                        genomicEventObs.mutations.addData('oncokb', oncokbEvidence);
+
+                        if (mutationTableData.length > 0){
+                            _.each(mutationTableData, function(ele, i) {
+                                mutationTable.fnUpdate(null, i, mutTableIndices["annotation"], false, false);
+                            });
+
+                            mutationTable.fnUpdate(null, 0, mutTableIndices['annotation']);
+                        }
 
+                        if (mutationSummaryTableData.length > 0){
+                            _.each(mutationSummaryTableData, function(ele, i) {
+                                mutationSummaryTable.fnUpdate(null, i, mutTableIndices["annotation"], false, false);
+                            });
+
+                            mutationSummaryTable.fnUpdate(null, 0, mutTableIndices['annotation']);
+                        }
+                    });
                 }
                 ,"json"
         );
diff --git a/portal/src/main/webapp/WEB-INF/jsp/patient_view/patient_view.jsp b/portal/src/main/webapp/WEB-INF/jsp/patient_view/patient_view.jsp
index c3dabc48bcb..ddc23ffa05a 100644
--- a/portal/src/main/webapp/WEB-INF/jsp/patient_view/patient_view.jsp
+++ b/portal/src/main/webapp/WEB-INF/jsp/patient_view/patient_view.jsp
@@ -481,6 +481,62 @@ function fixCytoscapeWebRedraw() {
     });
 }
 
+
+function initOncoKB(instanceId, ids, mapData, type, indicatorCallback) {
+    var instance;
+    
+    if(OncoKB.getAccess() && _.isArray(ids)) {
+        var eventIdsLength = ids.length;
+
+        var oncokbInstanceManager = new OncoKB.addInstanceManager();
+        instance = oncokbInstanceManager.addInstance(instanceId);
+        if(oncokbGeneStatus) {
+            instance.setGeneStatus(oncokbGeneStatus);
+        }
+        instance.setTumorType(OncoKB.utils.getTumorTypeFromClinicalDataMap(clinicalDataMap));
+
+
+        for (var i=0, nEvents= eventIdsLength; i<nEvents; i++) {
+            var _id = ids[i];
+            if(instance) {
+                if(type === 'mutation') {
+                    instance.addVariant(_id, mapData.getValue(_id, "entrez"), mapData.getValue(_id, "gene"),
+                        mapData.getValue(_id, "aa"),
+                        (_.isObject(patientInfo) ? (patientInfo.CANCER_TYPE_DETAILED || patientInfo.CANCER_TYPE) : '') || cancerType,
+                        mapData.getValue(_id, "type") ? mapData.getValue(_id, "type") : 'any',
+                        findCosmic(mapData.getValue(_id, "cosmic"), mapData.getValue(_id, "aa")),
+                        mapData.getValue(_id, "is-hotspot"), mapData.getValue(_id, 'protein-start'),
+                        mapData.getValue(_id, 'protein-end'));
+                }else if(type === 'cna') {
+                    var alter = '';
+                    switch(mapData.getValue(_id, "alter")) {
+                        case 2:
+                            alter = 'amplification';
+                            break;
+                        case -2:
+                            alter = 'deletion';
+                            break;
+                        default:
+                            alter = null;
+                    }
+                    instance.addVariant(_id, mapData.getValue(_id, "entrez"), mapData.getValue(_id, "gene"), alter,
+                        (_.isObject(patientInfo) ? (patientInfo.CANCER_TYPE_DETAILED || patientInfo.CANCER_TYPE) : '') || cancerType,
+                        alter);
+                }
+            }
+        }
+
+        if(instance) {
+            instance.getIndicator().then(function () {
+                if(_.isFunction(indicatorCallback)) {
+                    indicatorCallback(instance);
+                }
+            });
+        }
+    }
+    return instance;
+}
+
 function switchToTab(toTab) {
     $('.patient-section').hide();
     $('.patient-section#'+toTab).show();
diff --git a/portal/src/main/webapp/WEB-INF/jsp/step1_json.jsp b/portal/src/main/webapp/WEB-INF/jsp/step1_json.jsp
index 08a8eac8b29..2e48aa27479 100644
--- a/portal/src/main/webapp/WEB-INF/jsp/step1_json.jsp
+++ b/portal/src/main/webapp/WEB-INF/jsp/step1_json.jsp
@@ -31,7 +31,7 @@
 --%>
 
 <%@ taglib prefix="c" uri="http://java.sun.com/jsp/jstl/core" %>
-<%@ taglib prefix="fn" uri="http://java.sun.com/jsp/jstl/functions" %>
+<%@taglib prefix="s" uri="http://www.springframework.org/tags" %>
 
 <%
     String step1ErrorMsg = (String) request.getAttribute(QueryBuilder.STEP1_ERROR_MSG);
@@ -48,16 +48,10 @@
                   <span class="sr-only">Toggle Dropdown</span>
                 </button>
                 <%-- loop over the configured query suggestions --%>
-               <ul class="dropdown-menu dropdown-menu-right" role="menu" title="Select from dropdown">
-                    <li role="presentation"><a role="menuitem" tabindex="-1"  href='javascript:void(0)' onclick='$("#jstree_search_input").val("tcga");$("#jstree_search_input").trigger("input");' >tcga</a></li>
-                    <li role="presentation"><a role="menuitem" tabindex="-1"  href='javascript:void(0)' onclick='$("#jstree_search_input").val("tcga -provisional");$("#jstree_search_input").trigger("input");' >tcga -provisional</a></li>
-                    <li role="presentation"><a role="menuitem" tabindex="-1"  href='javascript:void(0)' onclick='$("#jstree_search_input").val("tcga -moratorium");$("#jstree_search_input").trigger("input");' >tcga -moratorium</a></li>
-                    <li role="presentation"><a role="menuitem" tabindex="-1"  href='javascript:void(0)' onclick='$("#jstree_search_input").val("tcga OR icgc");$("#jstree_search_input").trigger("input");'>tcga OR icgc</a></li>
-                    <li role="presentation"><a role="menuitem" tabindex="-1"  href='javascript:void(0)' onclick='$("#jstree_search_input").val("-\"cell line\"");$("#jstree_search_input").trigger("input");'>-"cell line"</a></li>
-                    <li role="presentation"><a role="menuitem" tabindex="-1"  href='javascript:void(0)' onclick='$("#jstree_search_input").val("prostate mskcc");$("#jstree_search_input").trigger("input");'>prostate mskcc</a></li>
-                    <li role="presentation"><a role="menuitem" tabindex="-1"  href='javascript:void(0)' onclick='$("#jstree_search_input").val("esophageal OR stomach");$("#jstree_search_input").trigger("input");'>esophageal OR stomach</a></li>
-                    <li role="presentation"><a role="menuitem" tabindex="-1"  href='javascript:void(0)' onclick='$("#jstree_search_input").val("serous");$("#jstree_search_input").trigger("input");'>serous</a></li>
-                    <li role="presentation"><a role="menuitem" tabindex="-1"  href='javascript:void(0)' onclick='$("#jstree_search_input").val("breast");$("#jstree_search_input").trigger("input");'>breast</a></li>
+                <ul class="dropdown-menu dropdown-menu-right" role="menu" title="Select from dropdown"><c:forEach var="query" items="${exampleStudyQueries}">
+                    <%-- escape \ to \\ and " to \" inside the JS string --%>
+                    <c:set var="escapedJsString"><s:escapeBody javaScriptEscape="true"><c:out value="${query}" escapeXml="false" /></s:escapeBody></c:set>
+                    <li role="presentation"><a role="menuitem" tabindex="-1" href='javascript:void(0)' onclick='$("#jstree_search_input").val("${escapedJsString}");$("#jstree_search_input").trigger("input");'><c:out value="${query}" /></a></li></c:forEach>
                 </ul>
             </div>
         </div>
diff --git a/portal/src/main/webapp/js/src/crosscancer.js b/portal/src/main/webapp/js/src/crosscancer.js
index 3a66559c095..9363f8ba1ec 100644
--- a/portal/src/main/webapp/js/src/crosscancer.js
+++ b/portal/src/main/webapp/js/src/crosscancer.js
@@ -1242,8 +1242,8 @@
 		                        },
 		                        view: {
                                     vis3d: {
-                                    	//for https, use a proxy since rcsb.org is not serving https and browsers will complain about the mixed https/http content
-                                        pdbUri: (document.location.protocol != "https:"? "http://files.rcsb.org/view/" : "api/proxy/jsmol/")
+                                    	// use https for all portal instances
+                                        pdbUri: "https://files.rcsb.org/view/"
                                     },
                                     mutationDiagram: {
 				                        showStats: true
diff --git a/portal/src/main/webapp/js/src/download-util.js b/portal/src/main/webapp/js/src/download-util.js
index b5b52beb6cc..125a9c98c44 100644
--- a/portal/src/main/webapp/js/src/download-util.js
+++ b/portal/src/main/webapp/js/src/download-util.js
@@ -222,6 +222,11 @@ cbio.download = (function() {
 				"<svg", "<svg xmlns='http://www.w3.org/2000/svg' version='1.1'");
 		}
 
+        // work around for Adobe Illustrator bug
+        if(svg.indexOf("sans-serif") !== -1) {
+            svg = svg.replace(/sans-serif/g, "verdana");    
+        }
+        
 		return svg;
 	}
 
diff --git a/portal/src/main/webapp/js/src/enrichments/MiniOnco.js b/portal/src/main/webapp/js/src/enrichments/MiniOnco.js
index ce7f663bc89..65bf136b81b 100644
--- a/portal/src/main/webapp/js/src/enrichments/MiniOnco.js
+++ b/portal/src/main/webapp/js/src/enrichments/MiniOnco.js
@@ -130,7 +130,7 @@ function MiniOnco(plotDiv, miniOncoDiv, originalData){
     function buildMiniOnco(bardata){
         // if there is no mini-onco yet, append the div and create the histogram
         if (!stackedHistogram) {
-            $("#" + plotDiv).append("<div id='" + miniOncoDiv + "'/>");
+            $("#" + plotDiv).append("<div id='" + miniOncoDiv + "' style='margin-left: -20px;'/>");
             stackedHistogram = new stacked_histogram("#" + miniOncoDiv);
             stackedHistogram.createStackedHistogram(bardata);
             stackedHistogram.addTextToLane("None selected", "Select gene in table or volcano plot");
diff --git a/portal/src/main/webapp/js/src/enrichments/plots.js b/portal/src/main/webapp/js/src/enrichments/plots.js
index 1906bc3f28e..4d2d2db1ff0 100644
--- a/portal/src/main/webapp/js/src/enrichments/plots.js
+++ b/portal/src/main/webapp/js/src/enrichments/plots.js
@@ -49,97 +49,97 @@ var enrichmentsTabPlots = (function() {
     var dotsArr = [], xAxisTextSet = ["Altered", "Unaltered"];
 
     var elem = {
-            svg : "",
-            xScale : "",
-            yScale : "",
-            xAxis : "",
-            yAxis : "",
-            dotsGroup : ""   //Group of single Dots
-        }, settings = {
-            canvas_width: 720,
-            canvas_height: 600,
-            dots_fill_color: "#58ACFA",
-            dots_stroke_color: "#0174DF"
-        };
+        svg : "",
+        xScale : "",
+        yScale : "",
+        xAxis : "",
+        yAxis : "",
+        dotsGroup : ""   //Group of single Dots
+    }, settings = {
+        canvas_width: 350,
+        canvas_height: 350,
+        dots_fill_color: "#58ACFA",
+        dots_stroke_color: "#0174DF"
+    };
 
     function data_process(result) {
 
-	window.QuerySession.getGenomicEventData().then(function(data) {
-		var order = {};
-		var sample_ids = window.QuerySession.getSampleIds();
-		for (var i=0; i<sample_ids.length; i++) {
-			order[sample_ids[i]] = i;
-		}
-		var oncoprintData = _.sortBy(data, function(d) { return order[d.sample];});
-		dotsArr = [];
-		dotsArr.length = 0;
-		window.QuerySession.getAlteredSamples().then(function(altered_sample_ids) {
-			$.each(Object.keys(result[gene]), function(index, _sampleId) {
-			    var _obj = result[gene][_sampleId];
-			    var _datum = {};
-			    _datum.alteration = "";
-			    if (!isNaN(_obj[profile_id])) {
-				if ($.inArray(_sampleId, altered_sample_ids) !== -1) { //sample is altered
-				    _datum.x_val = 0;
-				} else { //sample is unaltered
-				    _datum.x_val = 1;
-				}
-
-				//if rna seq data, apply log 10
-				if (profile_id.indexOf("rna_seq") !== -1 && _datum.y_val !== 0) _datum.y_val = Math.log(parseFloat(_obj[profile_id]) + 1.0) / Math.log(2);
-				else _datum.y_val = parseFloat(_obj[profile_id]);
-
-				_datum.case_id = _sampleId;
-				if ($.inArray(_sampleId, altered_sample_ids) !== -1) { //sample is altered
-
-					//iterate over items (alteration info for each gene in each sample):
-				    $.each(oncoprintData, function(inner_key, inner_obj) {
-				    	//if sample is the current sample, then analyze alterations:
-					    if (_sampleId === inner_obj.sample) {
-					    	var _str = "";
-							if (inner_obj.hasOwnProperty("mutation")) {
-							    _str += " MUT;";
-							}
-							if (inner_obj.hasOwnProperty("cna")) {
-							    if (inner_obj.cna === "AMPLIFIED") {
-								_str += " AMP;";
-							    } else if (inner_obj.cna === "GAINED") {
-								_str += " GAIN;";
-							    } else if (inner_obj.cna === "HEMIZYGOUSLYDELETED") {
-								_str += " HETLOSS;";
-							    } else if (inner_obj.cna === "HOMODELETED") {
-								_str += " HOMDEL;";
-							    }
-							}
-							if (inner_obj.hasOwnProperty("mrna")) {
-							    if (inner_obj.mrna === "UPREGULATED") {
-								_str += " UP;";
-							    } else if (inner_obj.mrna === "DOWNREGULATED") {
-								_str += " DOWN;";
-							    }
-							}
-							if (inner_obj.hasOwnProperty("rppa")) {
-							    if (inner_obj.rppa === "UPREGULATED") {
-								_str += " RPPA-UP;";
-							    } else if (inner_obj.rppa === "DOWNREGULATED") {
-								_str += " RPPA-DOWN;";
-							    }
-							}
-							if (_str !== "") {
-							    _str = inner_obj.gene + ":" + _str;
-							    //record all alterations found for this sample:
-							    _datum.alteration += _str;
-							}
-					    }
-				    });
-				}
-				dotsArr.push(_datum);
-			    }
-			});
-
-			generate_plots();
-		});
-	});
+        window.QuerySession.getGenomicEventData().then(function(data) {
+            var order = {};
+            var sample_ids = window.QuerySession.getSampleIds();
+            for (var i=0; i<sample_ids.length; i++) {
+                order[sample_ids[i]] = i;
+            }
+            var oncoprintData = _.sortBy(data, function(d) { return order[d.sample];});
+            dotsArr = [];
+            dotsArr.length = 0;
+            window.QuerySession.getAlteredSamples().then(function(altered_sample_ids) {
+                $.each(Object.keys(result[gene]), function(index, _sampleId) {
+                    var _obj = result[gene][_sampleId];
+                    var _datum = {};
+                    _datum.alteration = "";
+                    if (!isNaN(_obj[profile_id])) {
+                        if ($.inArray(_sampleId, altered_sample_ids) !== -1) { //sample is altered
+                            _datum.x_val = 0;
+                        } else { //sample is unaltered
+                            _datum.x_val = 1;
+                        }
+
+                        //if rna seq data, apply log 10
+                        if (profile_id.indexOf("rna_seq") !== -1 && _datum.y_val !== 0) _datum.y_val = Math.log(parseFloat(_obj[profile_id]) + 1.0) / Math.log(2);
+                        else _datum.y_val = parseFloat(_obj[profile_id]);
+
+                        _datum.case_id = _sampleId;
+                        if ($.inArray(_sampleId, altered_sample_ids) !== -1) { //sample is altered
+
+                            //iterate over items (alteration info for each gene in each sample):
+                            $.each(oncoprintData, function(inner_key, inner_obj) {
+                                //if sample is the current sample, then analyze alterations:
+                                if (_sampleId === inner_obj.sample) {
+                                    var _str = "";
+                                    if (inner_obj.hasOwnProperty("mutation")) {
+                                        _str += " MUT;";
+                                    }
+                                    if (inner_obj.hasOwnProperty("cna")) {
+                                        if (inner_obj.cna === "AMPLIFIED") {
+                                            _str += " AMP;";
+                                        } else if (inner_obj.cna === "GAINED") {
+                                            _str += " GAIN;";
+                                        } else if (inner_obj.cna === "HEMIZYGOUSLYDELETED") {
+                                            _str += " HETLOSS;";
+                                        } else if (inner_obj.cna === "HOMODELETED") {
+                                            _str += " HOMDEL;";
+                                        }
+                                    }
+                                    if (inner_obj.hasOwnProperty("mrna")) {
+                                        if (inner_obj.mrna === "UPREGULATED") {
+                                            _str += " UP;";
+                                        } else if (inner_obj.mrna === "DOWNREGULATED") {
+                                            _str += " DOWN;";
+                                        }
+                                    }
+                                    if (inner_obj.hasOwnProperty("rppa")) {
+                                        if (inner_obj.rppa === "UPREGULATED") {
+                                            _str += " RPPA-UP;";
+                                        } else if (inner_obj.rppa === "DOWNREGULATED") {
+                                            _str += " RPPA-DOWN;";
+                                        }
+                                    }
+                                    if (_str !== "") {
+                                        _str = inner_obj.gene + ":" + _str;
+                                        //record all alterations found for this sample:
+                                        _datum.alteration += _str;
+                                    }
+                                }
+                            });
+                        }
+                        dotsArr.push(_datum);
+                    }
+                });
+
+                generate_plots();
+            });
+        });
 
     };
 
@@ -191,7 +191,7 @@ var enrichmentsTabPlots = (function() {
         //init axis scales
         elem.xScale = d3.scale.linear() //x axis scale
             .domain([-0.7, 1.7])
-            .range([100, 600]);
+            .range([80, 280]);
         var _yValArr = []; //y axis scale
         $.each(dotsArr, function(index, val){
             _yValArr.push(val.y_val);
@@ -199,7 +199,7 @@ var enrichmentsTabPlots = (function() {
         var _results = enrichmentsTabUtil.analyse_data(_yValArr);
         elem.yScale = d3.scale.linear()
             .domain([_results.min, _results.max])
-            .range([520, 20]);
+            .range([220, 20]);
         elem.xAxis = d3.svg.axis()
             .scale(elem.xScale)
             .orient("bottom");
@@ -213,7 +213,7 @@ var enrichmentsTabPlots = (function() {
             .style("fill", "none")
             .style("stroke", "grey")
             .style("shape-rendering", "crispEdges")
-            .attr("transform", "translate(0, 520)")
+            .attr("transform", "translate(0, 220)")
             .attr("class", "rppa-plots-x-axis-class")
             .call(elem.xAxis.ticks(xAxisTextSet.length))
             .selectAll("text")
@@ -236,7 +236,7 @@ var enrichmentsTabPlots = (function() {
             .style("fill", "none")
             .style("stroke", "grey")
             .style("shape-rendering", "crispEdges")
-            .attr("transform", "translate(100, 0)")
+            .attr("transform", "translate(80, 0)")
             .attr("class", "rppa-plots-y-axis-class")
             .call(elem.yAxis)
             .selectAll("text")
@@ -250,23 +250,23 @@ var enrichmentsTabPlots = (function() {
             .style("fill", "none")
             .style("stroke", "grey")
             .style("shape-rendering", "crispEdges")
-            .attr("transform", "translate(600, 0)")
+            .attr("transform", "translate(280, 0)")
             .call(elem.yAxis.orient("left").ticks(0));
 
         //Append Axis Titles
         var axisTitleGroup = elem.svg.append("svg:g");
         axisTitleGroup.append("text")
             .attr("class", "rppa-plots-x-axis-title")
-            .attr("x", 350)
-            .attr("y", 580)
+            .attr("x", 180)
+            .attr("y", 270)
             .style("text-anchor", "middle")
             .style("font-size", "13px")
             .text("Query: " + window.QuerySession.getQueryGenes().join(" ") + " (p-Value: " + p_value + ")");
         axisTitleGroup.append("text")
             .attr("class", "rppa-plots-y-axis-title")
             .attr("transform", "rotate(-90)")
-            .attr("x", -270)
-            .attr("y", 45)
+            .attr("x", -140)
+            .attr("y", 25)
             .style("text-anchor", "middle")
             .style("font-size", "13px")
             .text(gene + ", " + profile_name);
@@ -300,8 +300,8 @@ var enrichmentsTabPlots = (function() {
             } else if (tmp_y_arr.length === 1) {
                 mean = elem.yScale(tmp_y_arr[0]);
                 boxPlotsElem.append("line")
-                    .attr("x1", midLine - 30)
-                    .attr("x2", midLine + 30)
+                    .attr("x1", midLine - 10)
+                    .attr("x2", midLine + 10)
                     .attr("y1", mean)
                     .attr("y2", mean)
                     .attr("stroke-width", 1)
@@ -347,30 +347,30 @@ var enrichmentsTabPlots = (function() {
                     bottom = scaled_y_arr[index_bottom];
                 }
                 boxPlotsElem.append("rect")
-                    .attr("x", midLine - 60)
+                    .attr("x", midLine - 30)
                     .attr("y", quan2)
-                    .attr("width", 120)
+                    .attr("width", 60)
                     .attr("height", IQR)
                     .attr("fill", "none")
                     .attr("stroke-width", 1)
                     .attr("stroke", "#BDBDBD");
                 boxPlotsElem.append("line")
-                    .attr("x1", midLine - 60)
-                    .attr("x2", midLine + 60)
+                    .attr("x1", midLine - 30)
+                    .attr("x2", midLine + 30)
                     .attr("y1", mean)
                     .attr("y2", mean)
                     .attr("stroke-width", 3)
                     .attr("stroke", "#BDBDBD");
                 boxPlotsElem.append("line")
-                    .attr("x1", midLine - 40)
-                    .attr("x2", midLine + 40)
+                    .attr("x1", midLine - 15)
+                    .attr("x2", midLine + 15)
                     .attr("y1", top)
                     .attr("y2", top)
                     .attr("stroke-width", 1)
                     .attr("stroke", "#BDBDBD");
                 boxPlotsElem.append("line")
-                    .attr("x1", midLine - 40)
-                    .attr("x2", midLine + 40)
+                    .attr("x1", midLine - 15)
+                    .attr("x2", midLine + 15)
                     .attr("y1", bottom)
                     .attr("y2", bottom)
                     .attr("stroke", "#BDBDBD")
@@ -395,14 +395,14 @@ var enrichmentsTabPlots = (function() {
         //draw dots
         elem.dotsGroup = elem.svg.append("svg:g");
         elem.dotsGroup.selectAll("path").remove();
-        var ramRatio = 80;  //Noise
+        var ramRatio = 40;  //Noise
         elem.dotsGroup.selectAll("path")
             .data(dotsArr)
             .enter()
             .append("svg:path")
             .attr("transform", function(d){
                 return "translate(" + (elem.xScale(d.x_val) + (Math.random() * ramRatio - ramRatio/2)) +
-                       ", " + elem.yScale(d.y_val) + ")";
+                    ", " + elem.yScale(d.y_val) + ")";
             })
             .attr("d", d3.svg.symbol()
                 .size(20)
@@ -429,11 +429,11 @@ var enrichmentsTabPlots = (function() {
                 }
                 content = content + "</font>";
                 //make qtip for an element on first mouseenter:
-            	cbio.util.addTargetedQTip($(this), { content: {text: content} });
+                cbio.util.addTargetedQTip($(this), { content: {text: content} });
             }
         );
 
-		//Add nice resize effect when item is hovered:
+        //Add nice resize effect when item is hovered:
         var mouseOn = function() {
             var dot = d3.select(this);
             dot.transition()
@@ -453,7 +453,7 @@ var enrichmentsTabPlots = (function() {
         };
         elem.dotsGroup.selectAll("path").on("mouseover", mouseOn);
         elem.dotsGroup.selectAll("path").on("mouseout", mouseOff);
-        
+
     };
 
 
@@ -480,4 +480,4 @@ var enrichmentsTabPlots = (function() {
         }
     };
 
-}());
+}());
\ No newline at end of file
diff --git a/portal/src/main/webapp/js/src/enrichments/view.js b/portal/src/main/webapp/js/src/enrichments/view.js
index 6e9c5f76605..f0f03a2eaa7 100644
--- a/portal/src/main/webapp/js/src/enrichments/view.js
+++ b/portal/src/main/webapp/js/src/enrichments/view.js
@@ -28,19 +28,20 @@
  *
  * You should have received a copy of the GNU Affero General Public License
  * along with this program.  If not, see <http://www.gnu.org/licenses/>.
-*/
+ */
 
 /**
  * Enrichment Analysis Tab data table.
  * @param plot_div: optional parameter, i.e. the div where to add a volcano plot representation of the data.
-                    If set, a volcano plot is rendered next to the data table.
+ If set, a volcano plot is rendered next to the data table.
  */
-var enrichmentsTabTable = function(plot_div, minionco_div, loading_div) {
+var enrichmentsTabTable = function(plot_div, minionco_div, loading_div, profile_plot_div) {
 
-	var self = this;
-	self.plot_div = plot_div;
-	self.minionco_div = minionco_div;
+    var self = this;
+    self.plot_div = plot_div;
+    self.minionco_div = minionco_div;
     self.loading_div = loading_div;
+    self.profile_plot_div = profile_plot_div;
 
     var div_id, table_id, data, titles; //titles is formatted string of column names with html markdown in
     var col_index, enrichmentsTableInstance, profile_type, profile_id, table_title, data_type;
@@ -78,7 +79,7 @@ var enrichmentsTabTable = function(plot_div, minionco_div, loading_div) {
         };
         jQuery.fn.dataTableExt.oSort['enrichments-q-value-desc'] = function(a,b) {
 
-             if (profile_type === enrichmentsTabSettings.profile_type.mrna) {
+            if (profile_type === enrichmentsTabSettings.profile_type.mrna) {
                 if (a.indexOf("up1") !== -1) a = a.replace("<img src=\"images/up1.png\"/>",  "");
                 if (a.indexOf("down1") !== -1) a = a.replace("<img src=\"images/down1.png\"/>",  "");
                 if (b.indexOf("up1") !== -1) b = b.replace("<img src=\"images/up1.png\"/>",  "");
@@ -186,14 +187,10 @@ var enrichmentsTabTable = function(plot_div, minionco_div, loading_div) {
                     "mDataProp": function (data, type, val) {
                         // for display, add the tags; for other purposes (e.g. filtering), use the data
                         if ( type === 'display' ) {
-                            // if the table supports the mini-onco, add classes for selecting a gene and highlighting
-                            if(self.supportsMiniOnco()){
-                                return "<div class='geneCheckboxDiv'>" +
-                                    "<input type='checkbox' class='" +table_id + enrichmentsTabSettings.postfix.datatable_gene_checkbox_class + "' value='"+ data[col_index.gene] + "'>" +
-                                    "<span class='selectHighlight_"+table_id+" selectHighlight'>" + data[col_index.gene] + "</span>" +
-                                    "</div>";
-                            }
-                            return "<input type='checkbox' class='" +table_id + enrichmentsTabSettings.postfix.datatable_gene_checkbox_class + "' value='"+ data[col_index.gene] + "'>" + data[col_index.gene];
+                            return "<div class='geneCheckboxDiv'>" +
+                                "<input type='checkbox' class='" +table_id + enrichmentsTabSettings.postfix.datatable_gene_checkbox_class + "' value='"+ data[col_index.gene] + "'>" +
+                                "<span class='selectHighlight_"+table_id+" selectHighlight'>" + data[col_index.gene] + "</span>" +
+                                "</div>";
                         }
                         return data[col_index.gene];
                     }
@@ -226,16 +223,7 @@ var enrichmentsTabTable = function(plot_div, minionco_div, loading_div) {
                     "sType": 'enrichments-pct-unaltered',
                     "bSearchable": false,
                     "aTargets": [col_index.unaltered_pct]
-                },
-                {
-                    "bSearchable": false,
-                    "bSortable": false,
-                    "mRender": function () {
-                        return "<img class='" + table_id + "_enrichments_details_img' src='images/details_open.png'>";
-                    },
-                    "aTargets": [ col_index.plot ]
                 }
-
             ],
             "fnRowCallback": function(nRow, aData) {
                 $('td:eq(' + col_index.gene + ')', nRow).css("font-weight", "bold");
@@ -253,7 +241,7 @@ var enrichmentsTabTable = function(plot_div, minionco_div, loading_div) {
                     } else if (aData[col_index.log_ratio] < 0 || aData[col_index.log_ratio] === "<-10") {
                         $('td:eq(' + col_index.log_ratio + ')', nRow).css("color", "#B40404");
                     }
-                    //bold siginicant pvalue and qvalue
+                    //bold significant pvalue and qvalue
                     if (aData[col_index.p_val] === "<0.001" ||
                         aData[col_index.p_val] < enrichmentsTabSettings.settings.p_val_threshold) { //significate p value
                         $('td:eq(' + col_index.p_val + ')', nRow).css("font-weight", "bold");
@@ -276,7 +264,7 @@ var enrichmentsTabTable = function(plot_div, minionco_div, loading_div) {
                     if (_q_val === "<0.001" || _q_val < enrichmentsTabSettings.settings.p_val_threshold) {
                         $('td:eq(' + col_index.q_val + ')', nRow).css("font-weight", "bold");
                     }
-                    
+
                     // Check whether we encounter a negative value. 
                     // If we do, assume data is already in log-space. This is a workaround for the data not
                     // having a descriptive data_type
@@ -286,14 +274,9 @@ var enrichmentsTabTable = function(plot_div, minionco_div, loading_div) {
                 }
             },
             "fnDrawCallback": function() {
-                event_listener_details_btn();
                 activateUpdateQueryBtns(table_id + enrichmentsTabSettings.postfix.datatable_update_query_button);
                 activeDownloadBtn();
-
-                // If the table supports the mini-onco, add gene-click functionality
-                if(self.supportsMiniOnco()){
-                    addGeneClick();
-                }
+                addGeneClick();
             },
             "bDeferRender": true,
             "iDisplayLength": 14
@@ -307,7 +290,11 @@ var enrichmentsTabTable = function(plot_div, minionco_div, loading_div) {
     function addGeneClick(){
         $('.selectHighlight_'+table_id).on('click', function() {
             var current_gene = $(this).text();
-            self.miniOnco.render(current_gene);
+            if (profile_type === enrichmentsTabSettings.profile_type.mrna || profile_type === enrichmentsTabSettings.profile_type.protein_exp) {
+                enrichmentsTabPlots.init(self.profile_plot_div, current_gene, profile_type, profile_id, table_title, "");
+            } else {
+                self.miniOnco.render(current_gene);
+            }
         });
     }
 
@@ -366,7 +353,7 @@ var enrichmentsTabTable = function(plot_div, minionco_div, loading_div) {
     }
 
     /**
-     * check whether the datatype is LOG-VALUE, LOG2-VALUE or whether LOG space is assumed because 
+     * check whether the datatype is LOG-VALUE, LOG2-VALUE or whether LOG space is assumed because
      * a negative value was found to prevent logging it again
      * assumeLogSpace is a backwards compatibility for MSK
      * @returns {boolean}
@@ -394,6 +381,7 @@ var enrichmentsTabTable = function(plot_div, minionco_div, loading_div) {
     function attachFilters() {
 
         if (profile_type === enrichmentsTabSettings.profile_type.copy_num || profile_type === enrichmentsTabSettings.profile_type.mutations) {
+
             $("#" + div_id).find("." + table_id + "_filter").append(
                 "<input type='checkbox' class='" + table_id + "-checkbox' checked id='" + table_id + "-checkbox-mutex'><span style='font-size:10px;'>Mutual exclusivity</span></option> &nbsp;&nbsp;" +
                 "<input type='checkbox' class='" + table_id + "-checkbox' checked id='" + table_id + "-checkbox-co-oc'><span style='font-size:10px;'>Co-occurrence</span></option> &nbsp;&nbsp;" +
@@ -465,7 +453,6 @@ var enrichmentsTabTable = function(plot_div, minionco_div, loading_div) {
                     }
                     self.volcanoPlot.selectItems(remainingGenes);
                 }
-
             });
         }
 
@@ -509,8 +496,8 @@ var enrichmentsTabTable = function(plot_div, minionco_div, loading_div) {
         });
         $("#" + table_id + enrichmentsTabSettings._title_ids.direction).qtip({
             content: { text:'Log odds ratio > 0&nbsp;&nbsp;&nbsp;: Enriched in altered group<br>' +
-                            'Log odds ratio <= 0&nbsp;: Enriched in unaltered group<br>' +
-                            'p-Value < 0.05&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;: Significant association'},
+            'Log odds ratio <= 0&nbsp;: Enriched in unaltered group<br>' +
+            'p-Value < 0.05&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;: Significant association'},
             style: { classes: 'ui-tooltip-light ui-tooltip-rounded ui-tooltip-shadow ui-tooltip-lightyellow qtip-ui-wide'},
             show: {event: "mouseover"},
             hide: {fixed:true, delay: 100, event: "mouseout"},
@@ -569,13 +556,13 @@ var enrichmentsTabTable = function(plot_div, minionco_div, loading_div) {
         $("#" + btn_id).click(function() {
 
             if (window.QuerySession.getCaseSetId() !== "-1") {
-            	var _start_pos_gene_list = document.URL.indexOf("gene_list=") + "gene_list=".length;
-				var _end_pos_gene_list = document.URL.indexOf("&", _start_pos_gene_list);
-				var pre_gene_list = document.URL.substring(0, _start_pos_gene_list);
-				var post_gene_list = document.URL.substring(_end_pos_gene_list);
-				var new_gene_list = encodeURIComponent(window.QuerySession.getOQLQuery() + "\n" + selected_genes.join("\n"));
-				var _new_url = pre_gene_list + new_gene_list + post_gene_list;
-				window.location.replace(_new_url);
+                var _start_pos_gene_list = document.URL.indexOf("gene_list=") + "gene_list=".length;
+                var _end_pos_gene_list = document.URL.indexOf("&", _start_pos_gene_list);
+                var pre_gene_list = document.URL.substring(0, _start_pos_gene_list);
+                var post_gene_list = document.URL.substring(_end_pos_gene_list);
+                var new_gene_list = encodeURIComponent(window.QuerySession.getOQLQuery() + "\n" + selected_genes.join("\n"));
+                var _new_url = pre_gene_list + new_gene_list + post_gene_list;
+                window.location.replace(_new_url);
             } else {
                 var _original_url = document.URL.substring(0, document.URL.indexOf("index.do") + ("index.do").length);
 
@@ -600,23 +587,6 @@ var enrichmentsTabTable = function(plot_div, minionco_div, loading_div) {
         });
     }
 
-    function event_listener_details_btn() {
-        $("." + table_id + "_enrichments_details_img").click( function () {
-            var nTr = this.parentNode.parentNode;
-            if (this.src.indexOf('details_close') !== -1) {
-                this.src = "images/details_open.png";
-                enrichmentsTableInstance.fnClose(nTr);
-            } else {
-                var aData = enrichmentsTableInstance.fnGetData(nTr);
-                var _gene_name = aData[0];
-                var _plots_div_id = table_id + "_" + _gene_name + "_plots";
-                this.src = "images/details_close.png";
-                enrichmentsTableInstance.fnOpen(nTr, "<div id=" + _plots_div_id + "><img style='padding:200px;' src='images/ajax-loader.gif' alt='loading' /></div>", "rppa-details");
-                enrichmentsTabPlots.init(_plots_div_id, _gene_name, profile_type, profile_id, table_title, aData[col_index.p_val]);
-            }
-        });
-    }
-
     function activeDownloadBtn() {
         $("#" + table_id + "_download_btn").click(function() {
             cbio.download.clientSideDownload([get_tab_delimited_data()], "enrichments-analysis-result.txt");
@@ -692,7 +662,6 @@ var enrichmentsTabTable = function(plot_div, minionco_div, loading_div) {
             _title_str += "<th colspan='2'>Standard deviation of mRNA expression &nbsp;<img class='help-img-icon' src='" + enrichmentsTabSettings.settings.help_icon_img_src + "' id='" + table_id + enrichmentsTabSettings._title_ids.stdev_alt + "'></th>";
             _title_str += "<th rowspan='2' width='" + enrichmentsTabSettings.col_width.p_val + "'>p-Value &nbsp;<img class='help-img-icon' src='" + enrichmentsTabSettings.settings.help_icon_img_src + "' id='" + table_id + enrichmentsTabSettings._title_ids.p_val_t_test + "'></th>";
             _title_str += "<th rowspan='2' width='" + enrichmentsTabSettings.col_width.q_val + "'>q-Value &nbsp;<img class='help-img-icon' src='" + enrichmentsTabSettings.settings.help_icon_img_src + "' id='" + table_id + enrichmentsTabSettings._title_ids.q_val + "'></th>";
-            _title_str += "<th rowspan='2' width='" + enrichmentsTabSettings.col_width.plot + "'>Plot</th>";
             _title_str += "</tr><tr>";
             _title_str += "<th width='100'>in altered group</th>";
             _title_str += "<th width='100'>in unaltered group</th>";
@@ -705,7 +674,6 @@ var enrichmentsTabTable = function(plot_div, minionco_div, loading_div) {
             _title_str += "<th colspan='2'>Standard deviation of protein expression &nbsp;<img class='help-img-icon' src='" + enrichmentsTabSettings.settings.help_icon_img_src + "' id='" + table_id + enrichmentsTabSettings._title_ids.stdev_alt + "'></th>";
             _title_str += "<th rowspan='2' width='" + enrichmentsTabSettings.col_width.p_val + "'>p-Value &nbsp;<img class='help-img-icon' src='" + enrichmentsTabSettings.settings.help_icon_img_src + "' id='" + table_id + enrichmentsTabSettings._title_ids.p_val_t_test + "'></th>";
             _title_str += "<th rowspan='2' width='" + enrichmentsTabSettings.col_width.q_val + "'>q-Value &nbsp;<img class='help-img-icon' src='" + enrichmentsTabSettings.settings.help_icon_img_src + "' id='" + table_id + enrichmentsTabSettings._title_ids.q_val + "'></th>";
-            _title_str += "<th rowspan='2' width='" + enrichmentsTabSettings.col_width.plot + "'>Plot</th>";
             _title_str += "</tr><tr>";
             _title_str += "<th width='100'>in altered group</th>";
             _title_str += "<th width='100'>in unaltered group</th>";
@@ -717,15 +685,15 @@ var enrichmentsTabTable = function(plot_div, minionco_div, loading_div) {
     }
 
     return {
-    	/**
-    	 * Init function to bind data to table and optionally to the plot and render it.
-    	 *
-    	 * @param originalData : the original (json) data as received from enrichmentsTabData.get() function
-    	 * @param _converted_data : the originalData converted to array format, compatible with the table render function
-    	 */
+        /**
+         * Init function to bind data to table and optionally to the plot and render it.
+         *
+         * @param originalData : the original (json) data as received from enrichmentsTabData.get() function
+         * @param _converted_data : the originalData converted to array format, compatible with the table render function
+         */
         init: function(originalData, _converted_data, _div_id, _table_div, _table_id, _table_title, _profile_type, _profile_id, _last_profile, _data_type) {
 
-        	self.originalData = originalData;
+            self.originalData = originalData;
             if (Object.keys(_converted_data).length !== 0 &&
                 Object.keys(_converted_data)[0] !== enrichmentsTabSettings.texts.null_result &&
                 Object.keys(_converted_data)[0] !== "") {
@@ -754,11 +722,11 @@ var enrichmentsTabTable = function(plot_div, minionco_div, loading_div) {
 
                 $("#" + _table_div).empty();
                 $("#" + _table_div).append("<span style='font-weight:bold;'>" + _table_title +
-                      "</span>&nbsp;&nbsp;&nbsp;&nbsp;<button type='button' id='" + table_id +
-                      enrichmentsTabSettings.postfix.datatable_update_query_button + "'>Add checked genes to query" +
-                      "</button>" +
-                      "<img class='help-img-icon' src='" + enrichmentsTabSettings.settings.help_icon_img_src + "' id='" + table_id + enrichmentsTabSettings._title_ids.gene + "'>" +
-                      "<span id='" + table_id + enrichmentsTabSettings.postfix.update_query_gene_list + "'></span>");
+                    "</span>&nbsp;&nbsp;&nbsp;&nbsp;<button type='button' id='" + table_id +
+                    enrichmentsTabSettings.postfix.datatable_update_query_button + "'>Add checked genes to query" +
+                    "</button>" +
+                    "<img class='help-img-icon' src='" + enrichmentsTabSettings.settings.help_icon_img_src + "' id='" + table_id + enrichmentsTabSettings._title_ids.gene + "'>" +
+                    "<span id='" + table_id + enrichmentsTabSettings.postfix.update_query_gene_list + "'></span>");
                 document.getElementById(table_id + enrichmentsTabSettings.postfix.datatable_update_query_button).disabled = true;
 
                 $("#" + _table_div).append("<table id='" + table_id + "' cellpadding='0' cellspacing='0' border='0' class='" + table_id + "_datatable_class'></table>");
@@ -767,11 +735,6 @@ var enrichmentsTabTable = function(plot_div, minionco_div, loading_div) {
                 attachFilters();
                 addHeaderQtips();
 
-                //initially hiding all the mrna data tables
-                if (_profile_type === enrichmentsTabSettings.profile_type.mrna) {
-                    $("#" + _table_div).hide();
-                }
-
             } else {
                 if (_profile_type === enrichmentsTabSettings.profile_type.mrna) {
                     $("#" + _table_div).empty();
@@ -784,7 +747,7 @@ var enrichmentsTabTable = function(plot_div, minionco_div, loading_div) {
                     }
                 }
             }
-			//if plot_div is set, add a volcano plot:
+            //if plot_div is set, add a volcano plot:
             if (self.plot_div != null) {
                 if (_profile_type === enrichmentsTabSettings.profile_type.mutations || _profile_type === enrichmentsTabSettings.profile_type.copy_num) {
                     // create mini onco and render it
@@ -793,10 +756,12 @@ var enrichmentsTabTable = function(plot_div, minionco_div, loading_div) {
                 }
 
                 // create volcanoplot and render it
-            	self.volcanoPlot = new VolcanoPlot();
+                self.volcanoPlot = new VolcanoPlot();
                 self.volcanoPlot.render(self);
             }
 
+
+
         }
     };
 }; //close enrichmentsTabTable
@@ -838,37 +803,48 @@ var orSubTabView = function() {
                     $.each(_profile_list, function(_index, _profile_obj) {
                         var usableId = _profile_obj.STABLE_ID.replace(/\./g, "_");
                         if (_profile_obj.STABLE_ID !== selected_profile_id) {
-                            $("#" + usableId + enrichmentsTabSettings.postfix.datatable_div).hide();
-                            $("#" + usableId + enrichmentsTabSettings.postfix.plot_div).hide();
+                            $("#" + usableId + "_container_table").hide();
                         } else {
-                            $("#" + usableId + enrichmentsTabSettings.postfix.datatable_div).show();
-                            $("#" + usableId + enrichmentsTabSettings.postfix.plot_div).show();
+                            $("#" + usableId + "_container_table").show();
                         }
                     });
                 });
                 //adding loading image for table
-                $("#" + _div_id).append("<div id='" + _div_id + "_table_loading_img'><img style='padding:20px;' src='images/ajax-loader.gif' alt='loading' /></div>")
+                $("#" + _div_id).append("<div id='" + _div_id + "_table_loading_img'><img style='padding:20px;' src='images/ajax-loader.gif' alt='loading' /></div>");
             }
 
             $.each(_profile_list, function(_index, _profile_obj) {
-                var element = $("." + _profile_obj.STABLE_ID.replace(/\./g, "_") + enrichmentsTabSettings.postfix.datatable_class); //avoid duplicated initiation
-                if (element.length === 0) {
+
+                var element = $("." + _profile_obj.STABLE_ID.replace(/\./g, "_") + enrichmentsTabSettings.postfix.datatable_class);
+                if (element.length === 0) { //avoid duplicated initiation
                     var _table_div = _profile_obj.STABLE_ID.replace(/\./g, "_") + enrichmentsTabSettings.postfix.datatable_div;
                     var _table_id = _profile_obj.STABLE_ID.replace(/\./g, "_") + enrichmentsTabSettings.postfix.datatable_id;
                     var _plot_div = _profile_obj.STABLE_ID.replace(/\./g, "_") + enrichmentsTabSettings.postfix.plot_div;
+                    var _profile_plot_div = _profile_obj.STABLE_ID.replace(/\./g, "_") + enrichmentsTabSettings.postfix.profile_plot_div;
                     var loading_div = _table_div + "_loading_img";
-                    //for the mini-onco diagram
-                    var minionco_div = "minionco" + _plot_div;
-
-                    var html = "<div id='"+_profile_obj.STABLE_ID.replace(/\./g, "_")+"_container' style='float: left; position: relative'>"+
-                        "<div id='" + _plot_div + "' style='width: 30%; display:block; margin-left: 0; margin-right: auto; margin-top: 10px; float: left'></div>"+
-                        "<div id='" + _table_div + "' style='width: 65%; display:table; margin-left: auto; margin-right: 0; '></div>"+
+                    var minionco_div = "minionco" + _plot_div; //for the mini-onco diagram
+
+                    var html = "<div id='" + _profile_obj.STABLE_ID.replace(/\./g, "_") + "_container' style='float: left; position: relative; width: 100%;'>"+
+                        "<table width='100%' id='" + _profile_obj.STABLE_ID.replace(/\./g, "_") + "_container_table'><tr>" +
+                        "<td width='40%'>" +
+                        "<div id='" + _plot_div + "' style='position: absolute; top: 5px; float: left;'></div>" +
+                        "<div id='" + _profile_plot_div + "' style='position: relative; top:200px; float: left;'></div>" +
+                        "</td>" +
+                        "<td width='60%'>" +
+                        "<div id='" + _table_div + "' style='float:right;'></div>" +
+                        "</td>" +
+                        "</tr></table>" +
                         "<div id='" + loading_div + "' class='loaderIcon'><img src='images/ajax-loader.gif' alt='loading' /></div>"+
                         "</div>";
                     $("#" + _div_id).append(html);
                     //adding this to contain floated plot (see "float: left"  above):
                     $("#" + _div_id).css("overflow", "hidden");
 
+                    // default message for profile plots
+                    if (_profile_type === enrichmentsTabSettings.profile_type.mrna || _profile_type === enrichmentsTabSettings.profile_type.protein_exp) {
+                        $("#" + _profile_plot_div).append("<span style='margin-left: 55px; color: darkgray;'><b>Click on a gene in table to render plots here. </b></span>");
+                    }
+
                     //if this is the last profile
                     var last_profile = false;
                     if (_index + 1 === _profile_list.length) { //if it's last table, the instance would also in charge of clear the loading img and put an error msg
@@ -881,18 +857,18 @@ var orSubTabView = function() {
                     var param = new orAjaxParam(enrichmentsTab.getAlteredCaseList(), enrichmentsTab.getUnalteredCaseList(), _profile_obj.STABLE_ID, _gene_set);
                     var or_data = new enrichmentsTabData();
                     or_data.init(param, _table_id);
-                    var or_table = new enrichmentsTabTable(_plot_div, minionco_div, loading_div);
+                    var or_table = new enrichmentsTabTable(_plot_div, minionco_div, loading_div, _profile_plot_div);
                     if (_profile_obj.STABLE_ID.indexOf("rna_seq") !== -1) {
                         or_data.get(or_table.init, _div_id, _table_div, _table_id, _profile_obj.NAME + enrichmentsTabSettings.postfix.title_log, _profile_type, _profile_obj.STABLE_ID.replace(/\./g, "_"), last_profile,_profile_obj.DATATYPE);
                     } else {
                         or_data.get(or_table.init, _div_id, _table_div, _table_id, _profile_obj.NAME, _profile_type, _profile_obj.STABLE_ID.replace(/\./g, "_"), last_profile, _profile_obj.DATATYPE);
                     }
 
-                    //hide mrna tables initially
+                    $("#" + loading_div).empty();
+
+                    // hide mrna tables initially
                     if (_profile_type === enrichmentsTabSettings.profile_type.mrna) {
-                        $("#" + _profile_obj.STABLE_ID.replace(/\./g, "_") + enrichmentsTabSettings.postfix.datatable_div).hide();
-                        // also hide the volcanoplot
-                        $("#" + _profile_obj.STABLE_ID.replace(/\./g, "_") + enrichmentsTabSettings.postfix.plot_div).hide();
+                        $("#" + _profile_obj.STABLE_ID.replace(/\./g, "_") + "_container_table").hide();
                     }
                 }
 
@@ -907,9 +883,7 @@ var orSubTabView = function() {
                     if (!$( "#" + _target_table_div).is(":empty")) {
                         clearInterval(tmp);
                         $("#" + _div_id + "_table_loading_img").empty();
-                        $("#" + _target_table_div).show();
-                        // also show the corresponding volcanoplot
-                        $("#"+selectedVal+enrichmentsTabSettings.postfix.plot_div).show();
+                        $("#" + selectedVal + "_container_table").show();
                     }
                 }
             }
@@ -926,4 +900,3 @@ var orSubTabView = function() {
 
 
 
-
diff --git a/portal/src/main/webapp/js/src/enrichments/volcano_plot_view.js b/portal/src/main/webapp/js/src/enrichments/volcano_plot_view.js
index 1af099a68de..8c5ddc2a3bf 100644
--- a/portal/src/main/webapp/js/src/enrichments/volcano_plot_view.js
+++ b/portal/src/main/webapp/js/src/enrichments/volcano_plot_view.js
@@ -146,8 +146,8 @@ function VolcanoPlot() {
         var xLabel = self.orTable.assumedLogSpace()?'mean alt. group - mean unalt. group':'log Ratio';
         
         var axisOptions = {
-            width: 360,
-            height: 400,
+            width: 330,
+            height: 330,
             xaxis:{
                 title: xLabel
             },
diff --git a/portal/src/main/webapp/js/src/oncokb/OncoKBConnector.js b/portal/src/main/webapp/js/src/oncokb/OncoKBConnector.js
index 5e881fb1786..0180f0ec92a 100644
--- a/portal/src/main/webapp/js/src/oncokb/OncoKBConnector.js
+++ b/portal/src/main/webapp/js/src/oncokb/OncoKBConnector.js
@@ -392,31 +392,55 @@ var OncoKB = (function(_, $) {
                 }
             }
             if (category === 'mycancergenome') {
-                if (!x.mutation || !x.mutation.myCancerGenome || x.mutation.myCancerGenome.length === 0) {
-                    if (!y.mutation || !y.mutation.myCancerGenome || y.mutation.myCancerGenome.length === 0) {
+                if (!hasMyCancerGenomeInfo(x.mutation)) {
+                    if (!hasMyCancerGenomeInfo(y.mutation)) {
                         return 0;
                     }
                     return yWeight;
                 }
-                if (!y.mutation || !y.mutation.myCancerGenome || y.mutation.myCancerGenome.length === 0) {
+                if (!hasMyCancerGenomeInfo(y.mutation)) {
                     return xWeight;
                 }
                 return 0;
             }
             if (category === 'hotspot') {
-                if (!x.mutation || !x.mutation.hasOwnProperty('isHotspot') || !x.mutation.isHotspot) {
-                    if (!y.mutation || !y.mutation.hasOwnProperty('isHotspot') || !y.mutation.isHotspot) {
+                if (!isHotspot(x.mutation)) {
+                    if (!isHotspot(y.mutation)) {
                         return 0;
                     }
                     return yWeight;
                 }
-                if (!y.mutation || !y.mutation.hasOwnProperty('isHotspot') || !y.mutation.isHotspot) {
+                if (!isHotspot(y.mutation)) {
                     return xWeight;
                 }
                 return 0;
             }
         }
 
+        function hasMyCancerGenomeInfo(mutation) {
+            try {
+                if(mutation.get("myCancerGenome").length > 0) {
+                    return true;
+                }else {
+                    return false;
+                }
+            }catch (e){
+                return false;
+            }
+        }
+
+        function isHotspot(mutation) {
+            try {
+                if(mutation.get("isHotspot")) {
+                    return true;
+                }else {
+                    return false;
+                }
+            }catch (e){
+                return false;
+            }
+        }
+        
         function processEvidence(evidences) {
             var result = {}; //id based.
             if (evidences && evidences.length > 0) {
@@ -859,6 +883,9 @@ OncoKB.Instance.prototype = {
             contentType: 'application/json',
             data: JSON.stringify(oncokbServiceData)
         }).done(function(d1) {
+            if(_.isString(d1)) {
+                d1 = $.parseJSON(d1);
+            }
             if (d1 && d1.length > 0) {
                 d1.forEach(function(record) {
                     var id = record.query.id;
@@ -943,6 +970,9 @@ OncoKB.Instance.prototype = {
                 data: JSON.stringify(oncokbServiceData)
             })
                 .done(function(d1) {
+                    if(_.isString(d1)) {
+                        d1 = $.parseJSON(d1);
+                    }
                     var result = OncoKB.utils.processEvidence(d1);
                     _.each(result, function(item, index) {
                         self.variants[index].evidence.gene = item.gene;
@@ -1003,6 +1033,9 @@ OncoKB.Instance.prototype = {
                 data: JSON.stringify(oncokbSummaryData)
             })
                 .done(function(d) {
+                    if(_.isString(d)) {
+                        d = $.parseJSON(d);
+                    }
                     var data = _.isArray(d) && _.isObject(d[0]) ? d[0] : null;
                     if (data && data.summary) {
                         if (data.id) {
@@ -1041,6 +1074,7 @@ OncoKB.Instance.prototype = {
             if (typeof  type === 'undefined' || type === 'gene') {
                 $(target).find('.oncokb_gene').each(function() {
                     var oncokbId = $(this).attr('oncokbId');
+                    if(_.isObject(self.variants[oncokbId])) {
                     var gene = self.variants[oncokbId].evidence.gene;
                     var hasGene = self.variants[oncokbId].hasGene;
                     var _tip = '';
@@ -1089,6 +1123,7 @@ OncoKB.Instance.prototype = {
                             });
                         });
                     }
+                    }
                 });
             }
 
diff --git a/portal/src/main/webapp/js/src/oncoprint/webgl/oncoprint-bundle.js b/portal/src/main/webapp/js/src/oncoprint/webgl/oncoprint-bundle.js
index d00e414d45a..41e92bb70ef 100644
--- a/portal/src/main/webapp/js/src/oncoprint/webgl/oncoprint-bundle.js
+++ b/portal/src/main/webapp/js/src/oncoprint/webgl/oncoprint-bundle.js
@@ -3655,24 +3655,21 @@ var OncoprintWebGLCellView = (function () {
 
 	(function initializeOverlayEvents(self) {
 	    var dragging = false;
-	    var drag_time_minimum = 100;
 	    var drag_diff_minimum = 10;
-	    var drag_is_valid = false;
-	    var drag_is_valid_timeout = null;
 	    var drag_start_x;
 	    var drag_end_x;
 	    var prev_overlapping_cell = null;
 	    
+	    var dragIsValid = function(drag_start_x, drag_end_x) {
+		return Math.abs(drag_start_x - drag_end_x) >= drag_diff_minimum;
+	    };
 	    var executeDrag = function() {
 		if (!dragging) {
 		    return;
 		}
 		dragging = false;
-		clearTimeout(drag_is_valid_timeout);
-		if (!drag_is_valid) {
-		    return;
-		}
-		if (Math.abs(drag_start_x - drag_end_x) < drag_diff_minimum) {
+		
+		if (!dragIsValid(drag_start_x, drag_end_x)) {
 		    return;
 		}
 		var left = Math.min(drag_start_x, drag_end_x);
@@ -3719,16 +3716,13 @@ var OncoprintWebGLCellView = (function () {
 		    drag_end_x = mouseX;
 		    var left = Math.min(mouseX, drag_start_x);
 		    var right = Math.max(mouseX, drag_start_x);
-		    overlayFillRect(self, left, 0, right-left, model.getCellViewHeight(), 'rgba(0,0,0,0.3)');
+		    var drag_rect_fill = dragIsValid(drag_start_x, drag_end_x) ? 'rgba(0,0,0,0.3)' : 'rgba(0,0,0,0.2)';
+		    overlayFillRect(self, left, 0, right-left, model.getCellViewHeight(), drag_rect_fill);
 		}
 	    });
 	    
 	    self.$overlay_canvas.on("mousedown", function(evt) {
 		dragging = true;
-		drag_is_valid = false;
-		drag_is_valid_timeout = setTimeout(function() {
-		    drag_is_valid = true;
-		}, drag_time_minimum);
 		drag_start_x = evt.pageX - self.$overlay_canvas.offset().left;
 		drag_end_x = drag_start_x;
 		
diff --git a/portal/src/main/webapp/js/src/oncoprint/webgl/oncoprinttrackoptionsview.js b/portal/src/main/webapp/js/src/oncoprint/webgl/oncoprinttrackoptionsview.js
index 60266473565..3f9b6f2630f 100644
--- a/portal/src/main/webapp/js/src/oncoprint/webgl/oncoprinttrackoptionsview.js
+++ b/portal/src/main/webapp/js/src/oncoprint/webgl/oncoprinttrackoptionsview.js
@@ -98,7 +98,7 @@ var OncoprintTrackOptionsView = (function() {
 	var $div,$img,$dropdown;
 	//if (model.isTrackRemovable(track_id) || model.isTrackSortDirectionChangeable(track_id)) {
 	    $div = $('<div>').appendTo(view.$div).css({'position': 'absolute', 'left': '0px', 'top': model.getTrackTops(track_id) + 'px'});
-	    $img = $('<img/>').appendTo($div).attr({'src': 'images/menudots.svg', 'width': view.img_size, 'height': view.img_size}).css({'float': 'left', 'cursor': 'pointer', 'border': '1px solid rgba(125,125,125,0)'});
+	    $img = $('<img/>').appendTo($div).attr({'src': 'images/menudots.svg', 'width': view.img_size, 'height': view.img_size, 'alt': 'Track options'}).css({'float': 'left', 'cursor': 'pointer', 'border': '1px solid rgba(125,125,125,0)'});
 	    $dropdown = $('<ul>').appendTo($div).css({'width': 120, 'display': 'none', 'list-style-type': 'none', 'padding-left': '6', 'padding-right': '6', 'float': 'right', 'background-color': 'rgb(255,255,255)'});
 	    view.track_options_$elts[track_id] = {'$div': $div, '$img': $img, '$dropdown': $dropdown};
 	    
diff --git a/portal/src/main/webapp/js/src/oncoprint/webgl/oncoprintwebglcellview.js b/portal/src/main/webapp/js/src/oncoprint/webgl/oncoprintwebglcellview.js
index 0a96d52a0b8..92419e62755 100644
--- a/portal/src/main/webapp/js/src/oncoprint/webgl/oncoprintwebglcellview.js
+++ b/portal/src/main/webapp/js/src/oncoprint/webgl/oncoprintwebglcellview.js
@@ -126,24 +126,21 @@ var OncoprintWebGLCellView = (function () {
 
 	(function initializeOverlayEvents(self) {
 	    var dragging = false;
-	    var drag_time_minimum = 100;
 	    var drag_diff_minimum = 10;
-	    var drag_is_valid = false;
-	    var drag_is_valid_timeout = null;
 	    var drag_start_x;
 	    var drag_end_x;
 	    var prev_overlapping_cell = null;
 	    
+	    var dragIsValid = function(drag_start_x, drag_end_x) {
+		return Math.abs(drag_start_x - drag_end_x) >= drag_diff_minimum;
+	    };
 	    var executeDrag = function() {
 		if (!dragging) {
 		    return;
 		}
 		dragging = false;
-		clearTimeout(drag_is_valid_timeout);
-		if (!drag_is_valid) {
-		    return;
-		}
-		if (Math.abs(drag_start_x - drag_end_x) < drag_diff_minimum) {
+		
+		if (!dragIsValid(drag_start_x, drag_end_x)) {
 		    return;
 		}
 		var left = Math.min(drag_start_x, drag_end_x);
@@ -190,16 +187,13 @@ var OncoprintWebGLCellView = (function () {
 		    drag_end_x = mouseX;
 		    var left = Math.min(mouseX, drag_start_x);
 		    var right = Math.max(mouseX, drag_start_x);
-		    overlayFillRect(self, left, 0, right-left, model.getCellViewHeight(), 'rgba(0,0,0,0.3)');
+		    var drag_rect_fill = dragIsValid(drag_start_x, drag_end_x) ? 'rgba(0,0,0,0.3)' : 'rgba(0,0,0,0.2)';
+		    overlayFillRect(self, left, 0, right-left, model.getCellViewHeight(), drag_rect_fill);
 		}
 	    });
 	    
 	    self.$overlay_canvas.on("mousedown", function(evt) {
 		dragging = true;
-		drag_is_valid = false;
-		drag_is_valid_timeout = setTimeout(function() {
-		    drag_is_valid = true;
-		}, drag_time_minimum);
 		drag_start_x = evt.pageX - self.$overlay_canvas.offset().left;
 		drag_end_x = drag_start_x;
 		
diff --git a/portal/src/main/webapp/mutation_mapper.jsp b/portal/src/main/webapp/mutation_mapper.jsp
index 44fdb8ac67f..b8ea1d2b51b 100644
--- a/portal/src/main/webapp/mutation_mapper.jsp
+++ b/portal/src/main/webapp/mutation_mapper.jsp
@@ -209,8 +209,8 @@ $(document).ready(function() {
 			view: {
 				mutationTable: tableOpts,
                 vis3d: {
-                	//for https, use a proxy since rcsb.org is not serving https and browsers will complain about the mixed https/http content
-                    pdbUri: (document.location.protocol != "https:"? "http://files.rcsb.org/view/" : "api/proxy/jsmol/")
+                	// // use https for all portal instances
+                    pdbUri: "https://files.rcsb.org/view/"
                 }
 			}
 		};
diff --git a/test/end-to-end/screenshots/chrome/patient_view_lgg_ucsf_2014_case_id_P04.png b/test/end-to-end/screenshots/chrome/patient_view_lgg_ucsf_2014_case_id_P04.png
index 86c78665b14..2d8c94c2916 100644
Binary files a/test/end-to-end/screenshots/chrome/patient_view_lgg_ucsf_2014_case_id_P04.png and b/test/end-to-end/screenshots/chrome/patient_view_lgg_ucsf_2014_case_id_P04.png differ
diff --git a/test/end-to-end/screenshots/chrome/study_view_lgg_ucsf_2014.png b/test/end-to-end/screenshots/chrome/study_view_lgg_ucsf_2014.png
index bc9bb53365f..4f6883acbbe 100644
Binary files a/test/end-to-end/screenshots/chrome/study_view_lgg_ucsf_2014.png and b/test/end-to-end/screenshots/chrome/study_view_lgg_ucsf_2014.png differ
diff --git a/test/end-to-end/screenshots/firefox/patient_view_lgg_ucsf_2014_case_id_P04.png b/test/end-to-end/screenshots/firefox/patient_view_lgg_ucsf_2014_case_id_P04.png
index 9f7ae9da931..08e50e73eeb 100644
Binary files a/test/end-to-end/screenshots/firefox/patient_view_lgg_ucsf_2014_case_id_P04.png and b/test/end-to-end/screenshots/firefox/patient_view_lgg_ucsf_2014_case_id_P04.png differ
diff --git a/web/pom.xml b/web/pom.xml
index 021aedca4ea..28b255c88f7 100644
--- a/web/pom.xml
+++ b/web/pom.xml
@@ -4,7 +4,7 @@
   <parent>
     <artifactId>master</artifactId>
     <groupId>org.mskcc.cbio</groupId>
-    <version>1.2.4</version>
+    <version>1.2.5</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
   <artifactId>web</artifactId>
diff --git a/web/src/main/java/org/mskcc/cbio/portal/web/api/ApiController.java b/web/src/main/java/org/mskcc/cbio/portal/web/api/ApiController.java
index b52a849b805..39d2bdff6ba 100644
--- a/web/src/main/java/org/mskcc/cbio/portal/web/api/ApiController.java
+++ b/web/src/main/java/org/mskcc/cbio/portal/web/api/ApiController.java
@@ -69,7 +69,10 @@ public class ApiController {
             notes = "")
     @Transactional
     @RequestMapping(value = "/mutation_count", method = {RequestMethod.GET, RequestMethod.POST})
-    public @ResponseBody List<Map<String, String>> getMutationsCounts(HttpServletRequest request, @RequestParam(required = true) String type, @RequestParam(required = true) Boolean per_study, @RequestParam(required = false) List<String> studyId, @RequestParam(required = true) List<String> gene, @RequestParam(required = false) List<Integer> start, @RequestParam(required = false) List<Integer> end, @RequestParam(required = false) List<String> echo) {
+    public @ResponseBody List<Map<String, String>> getMutationsCounts(
+        HttpServletRequest request,
+        @ApiParam(required = true, value = "\"count\" or \"frequency\"")
+        @RequestParam(required = true) String type, @RequestParam(required = true) Boolean per_study, @RequestParam(required = false) List<String> studyId, @RequestParam(required = true) List<String> gene, @RequestParam(required = false) List<Integer> start, @RequestParam(required = false) List<Integer> end, @RequestParam(required = false) List<String> echo) {
         Enumeration<String> parameterNames = request.getParameterNames();
         String[] fixedInput = {"type", "per_study", "gene", "start", "end", "echo"};
         Map<String,String[]> customizedAttrs = new HashMap<String,String[]>();