From d070c1df55d9dce33d7ae7608ddb96b0a871d5d2 Mon Sep 17 00:00:00 2001 From: Oliver Stolpe Date: Fri, 2 Aug 2024 15:54:03 +0200 Subject: [PATCH] feat: display hemizgote counts for x chromosome (#236) (#237) --- .../annonars/fixture.variantInfo.chrX.json | 2356 +++++++++++++++++ .../SeqvarFreqsCard/AutosomalFreqs.spec.ts | 37 + .../SeqvarFreqsCard/AutosomalFreqs.vue | 23 +- .../SeqvarFreqsCard/SeqvarFreqsCard.spec.ts | 30 + .../SeqvarFreqsCard/SeqvarFreqsCard.vue | 11 +- src/components/SeqvarFreqsCard/lib.spec.ts | 220 +- src/components/SeqvarFreqsCard/lib.ts | 48 + 7 files changed, 2722 insertions(+), 3 deletions(-) create mode 100644 src/api/annonars/fixture.variantInfo.chrX.json diff --git a/src/api/annonars/fixture.variantInfo.chrX.json b/src/api/annonars/fixture.variantInfo.chrX.json new file mode 100644 index 0000000..01cd68f --- /dev/null +++ b/src/api/annonars/fixture.variantInfo.chrX.json @@ -0,0 +1,2356 @@ +{ + "server_version": "0.40.0", + "query": { + "genome_release": "grch37", + "chromosome": "X", + "pos": 100871273, + "reference": "C", + "alternative": "G" + }, + "result": { + "cadd": { + "Chrom": "X", + "Pos": 100871273, + "Ref": "C", + "Alt": "G", + "Type": "SNV", + "Length": 0, + "AnnoType": "CodingTranscript", + "Consequence": "NON_SYNONYMOUS", + "ConsScore": 7, + "ConsDetail": "missense", + "GC": 0.457, + "CpG": 0.027, + "motifECount": null, + "motifEName": null, + "motifEHIPos": null, + "motifEScoreChng": null, + "oAA": "W", + "nAA": "S", + "GeneID": "ENSG00000198960", + "FeatureID": "ENST00000539247", + "GeneName": "ARMCX6", + "CCDS": "CCDS14488.1", + "Intron": null, + "Exon": "4/4", + "cDNApos": 771, + "relcDNApos": 0.4, + "CDSpos": 338, + "relCDSpos": 0.374, + "protPos": 113, + "relProtPos": 0.377, + "Domain": "ndomain", + "Dst2Splice": null, + "Dst2SplType": null, + "minDistTSS": 1628, + "minDistTSE": 70, + "SIFTcat": "tolerated", + "SIFTval": 0.1, + "PolyPhenCat": "possibly_damaging", + "PolyPhenVal": 0.782, + "priPhCons": 0.788, + 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"population": "nfe_swe", "counts": {} }, + { + "population": "oth", + "counts": { "overall": { "an": 758 }, "xx": { "an": 546 }, "xy": { "an": 212 } } + }, + { "population": "sas", "counts": {} } + ], + "bySex": { + "overall": { "ac": 2, "an": 18706, "af": 0.00010691799980122596 }, + "xx": { "ac": 2, "an": 12578, "af": 0.00015900800644885749 }, + "xy": { "an": 6128 } + }, + "raw": { "ac": 2, "an": 19603, "af": 0.00010202499834122136 }, + "popmax": "nfe", + "afPopmax": 0.00024937698617577553, + "acPopmax": 2, + "anPopmax": 8020, + "nhomaltPopmax": 0 + } + ], + "nonpar": true, + "variantInfo": { "variantType": "multi-snv", "alleleType": "snv", "nAltAlleles": 2 }, + "qualityInfo": { + "fs": 0.0, + "inbreedingCoeff": 0.05860000103712082, + "mq": 60.0, + "mqRankSum": 0.10700000077486038, + "qd": 14.359999656677246, + "readPosRankSum": 0.8420000076293945, + "baseQRankSum": -1.812999963760376, + "clippingRankSum": -0.38600000739097595, + "sor": 0.6809999942779541, + "dp": 466950, + "vqslod": 15.170000076293945, + "vqsrCulprit": "MQ", + "pabMax": 0.3367840051651001 + }, + "ageInfo": { + "ageHistHomNSmaller": 0, + "ageHistHomNLarger": 0, + "ageHistHetNSmaller": 0, + "ageHistHetNLarger": 0 + } + }, + "helixmtdb": null, + "ucsc_conservation": [ + { + "records": [ + { + "chrom": "X", + "start": 100871272, + "stop": 100871272, + "hgncId": "HGNC:26094", + "enstId": "ENST00000361910", + "exonNum": 1, + "exonCount": 1, + "alignment": "W-WWWWWWWWWWWWWWWWWWWWWWWWWWW-WWWWWWWWWWWWWWWWWWQWWWSCWWWW------------------------------------------" + }, + { + "chrom": "X", + "start": 100871272, + "stop": 100871272, + "hgncId": "HGNC:26094", + "enstId": "ENST00000539247", + "exonNum": 1, + "exonCount": 1, + "alignment": "W-WWWWWWWWWWWWWWWWWWWWWWWWWWW-WWWWWWWWWWWWWWWWWWQWWWSCWWWW------------------------------------------" + } + ] + } + ], + "clinvar": { + "records": [ + { + "accession": { "accession": "VCV003129706", "version": 1 }, + "rcvs": [ + { + "accession": { "accession": "RCV004418051", "version": 1 }, + "title": "NM_019007.4(ARMCX6):c.338G>C (p.Trp113Ser) AND not specified", + "classifications": { + "germlineClassification": { + "reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", + "description": { + "value": "Uncertain significance", + "dateLastEvaluated": "2024-03-11T00:00:00+00:00", + "submissionCount": 1 + } + } + } + } + ], + "name": "NM_019007.4(ARMCX6):c.338G>C (p.Trp113Ser)", + "variationType": "VARIATION_TYPE_SNV", + "classifications": { + "germlineClassification": { + "reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", + "description": "Uncertain significance", + "dateLastEvaluated": "2024-03-11T00:00:00+00:00", + "dateCreated": "2024-05-01T00:00:00+00:00", + "mostRecentSubmission": "2024-05-01T00:00:00+00:00", + "numberOfSubmitters": 1, + "numberOfSubmissions": 1 + } + }, + "sequenceLocation": { + "assembly": "GRCh37", + "chr": "CHROMOSOME_X", + "accession": "NC_000023.10", + "start": 100871273, + "stop": 100871273, + "displayStart": 100871273, + "displayStop": 100871273, + "variantLength": 1, + "positionVcf": 100871273, + "referenceAlleleVcf": "C", + "alternateAlleleVcf": "G" + }, + "hgncIds": ["HGNC:26094"] + } + ] + } + } +} diff --git a/src/components/SeqvarFreqsCard/AutosomalFreqs.spec.ts b/src/components/SeqvarFreqsCard/AutosomalFreqs.spec.ts index 05216cb..98823a4 100644 --- a/src/components/SeqvarFreqsCard/AutosomalFreqs.spec.ts +++ b/src/components/SeqvarFreqsCard/AutosomalFreqs.spec.ts @@ -16,6 +16,14 @@ const seqvarInfoResponseBrca1 = SeqvarInfoResponse.fromJson( ) ) ) +const seqvarInfoResponseChrX = SeqvarInfoResponse.fromJson( + JSON.parse( + fs.readFileSync( + path.resolve(__dirname, '../../api/annonars/fixture.variantInfo.chrX.json'), + 'utf-8' + ) + ) +) // Sequence Variant in BRCA1 const seqvarBrca1: Seqvar = { @@ -27,6 +35,16 @@ const seqvarBrca1: Seqvar = { userRepr: 'grch37-17-41215920-G-T' } +// Sequence Variant in X in PAR region +const seqvarChrX: Seqvar = { + genomeBuild: 'grch37', + chrom: 'X', + pos: 100871273, + del: 'C', + ins: 'G', + userRepr: 'grch37-X-100871273-C-G' +} + describe.concurrent('AutosomalFreqs.vue', async () => { it('renders the info', async () => { // arrange: @@ -68,4 +86,23 @@ describe.concurrent('AutosomalFreqs.vue', async () => { expect(wrapper.text()).toContain('gnomAD Genomes') expect(wrapper.text()).toContain('No allele frequency information available in local database.') }) + + it('renders hemizygote counts in X', async () => { + // arrange: + const { wrapper } = await setupMountedComponents( + { component: AutosomalFreqs }, + { + props: { + seqvar: seqvarChrX, + varAnnos: seqvarInfoResponseChrX.result, + dataset: 'gnomadExomes' + } + } + ) + + // act: nothing, only test rendering + + // assert: + expect(wrapper.text()).toContain('Hemizygote') + }) }) diff --git a/src/components/SeqvarFreqsCard/AutosomalFreqs.vue b/src/components/SeqvarFreqsCard/AutosomalFreqs.vue index cc2e254..528540a 100644 --- a/src/components/SeqvarFreqsCard/AutosomalFreqs.vue +++ b/src/components/SeqvarFreqsCard/AutosomalFreqs.vue @@ -19,6 +19,7 @@ import { CohortAlleleCounts as Gnomad4CohortAlleleCounts, Record as Gnomad4Record } from '../../pbs/annonars/gnomad/gnomad4' +import { chromIsXY, isInParRegion } from './lib' const props = defineProps<{ /** Annotated sequence variant. */ @@ -71,7 +72,7 @@ const allPopLabels = { asj: 'Ashkenazy Jewish', eas: 'East Asian', fin: 'European (Finnish)', - nfe: 'European (North-Western)', + nfe: 'European (Non-Finnish)', amr: 'Latino/Admixed American', sas: 'South Asian', oth: 'Other', @@ -83,6 +84,7 @@ const idKey = (token: string): string => { } const sexExpanded = ref<{ [key: string]: boolean }>({}) +const variantIsInParRegion = isInParRegion(props.seqvar)