diff --git a/docs/docs/loading-data/through-data-config.md b/docs/docs/loading-data/through-data-config.md index fbbe6a18..142fe9fa 100644 --- a/docs/docs/loading-data/through-data-config.md +++ b/docs/docs/loading-data/through-data-config.md @@ -72,3 +72,143 @@ A multi-sample example: } ] ``` + +# Genome Interpretation Panel + +The data for the genome interpretation panel can be recorded as additional features of the configuration file. +![Screenshot 2025-01-15 at 10 46 28 AM](https://github.com/user-attachments/assets/02d15e04-0986-4e8e-8da8-2a07eb1119a4) +For each sample, there is an optional field: `clinicalInfo`, which will display the clinical info if present. +The `clinicalInfo` has the following fields: +`summary`, `variants`, `signatures` + +The `summary` field is a list of elements with two fields: `label` and `value`. Label can be any string, and will be displayed next to `value` which can also be any string. + +The `variants` field is a list of variants, each with the following fields: +| Property | Type | Note | +|---|---|---| +| `gene` | `string` | Required. Gene name | +| `chr` | `string` | Required. Chromosome with the variant, including the chr prefix| +| `position` | `int` | Required. Chromosomal coordinate of the mutation| +| `type` | `string` | Optional. Type of variant, eg. bi-allelic, germline, deletion | +| `cDNA` | `string` | Optional. cDNA coordinate of the mutation, eg. c.524G>A | +| `protein change` | `string` | Optional. protein consequence of the mutation, eg. p.Arg175His | +| `VAF` | `float` | Optional. Variant allele fraction of a mutation in the sample, eg. 0.45 | +| `mutation` | `string` | Optional. Reference and alternative allele in genomic DNA, eg. G>T | + +Example of a configuration with the information necessary for the genome interpretation panel +```js +[ + { + id: "SRR7890905_Hartwig", + cancer: "breast", + assembly: "hg38", + vcf: "https://somatic-browser-test.s3.amazonaws.com/SNV_test_tumor_normal_with_panel.vcf.gz", + vcfIndex: "https://somatic-browser-test.s3.amazonaws.com/SNV_test_tumor_normal_with_panel.vcf.gz.tbi", + vcf2: "https://somatic-browser-test.s3.amazonaws.com/INDEL_test_tumor_normal_with_panel.vcf.gz", + vcf2Index: "https://somatic-browser-test.s3.amazonaws.com/INDEL_test_tumor_normal_with_panel.vcf.gz.tbi", + sv: "https://somatic-browser-test.s3.amazonaws.com/SRR7890905/SRR7890905.gripss.filtered.bedpe", + cnv: "https://somatic-browser-test.s3.amazonaws.com/SRR7890905/SRR7890905.purple.cnv.somatic.reformatted.tsv", + bam: "https://somatic-browser-test.s3.amazonaws.com/SRR7890905_GAPFI2USVS21.bam", + bai: "https://somatic-browser-test.s3.amazonaws.com/SRR7890905_GAPFI2USVS21.bam.bai", + note: "CNV profile - Purple. SVs - Gridss. Mutations and indels - Sentieon", + clinicalInfo: { + summary: [ + { + label: "grade", + value: "2" + }, + { + label: "age", + value: "32" + }, + { + label: "AIMS Subtype", + value: "Basal" + }, + { + label: "Treatment", + value: "None" + }, + { + label: "Lymph node status", + value: "Negative" + } + ], + variants: [ + { + gene: "TP53", + type: "biallelic", + cDNA: "c.524G>A", + protein change: "p.Arg175His", + VAF: "0.97", + chr: "chr17", + position: "7677976", + mutation: "C>T" + }, + { + gene: "BRCA2", + cDNA: "c.4777G>T", + protein change: "p.Glu1593Ter", + VAF: "0.45", + chr: "chr13", + position: "32357888", + mutation: "G>T" + }, + { + gene: "PTEN", + type: "deletion", + chr: "chr10", + position: "87917777" + }, + { + gene: "CDKN2A", + type: "deletion", + chr: "chr9", + position: "21981538" + }, + { + gene: "MET", + type: "amplification", + chr: "chr7", + position: "116735286" + } + ], + signatures: [ + { + type: "point_mutations", + count: "5100", + label: "HRD-attributed point mutations", + hrDetect: true + }, + { + type: "indels", + count: "500", + label: "HRD-attributed small deletions with micro-homology", + hrDetect: true + }, + { + type: "svs_duplications", + count: "120", + label: "HRD-attributed small tandem duplications", + hrDetect: true + }, + { + type: "svs_deletions", + count: "50", + label: "HRD-attributed small deletions", + hrDetect: true + }, + { + type: "point_mutations", + count: "1000", + label: "APOBEC-attributed small substitutions", + hrDetect: false + } + ] + } + } +] +``` + + +