diff --git a/docs/content/finding-data/external-integrations.md b/docs/content/finding-data/external-integrations.md index e6005c88..4c914681 100644 --- a/docs/content/finding-data/external-integrations.md +++ b/docs/content/finding-data/external-integrations.md @@ -35,6 +35,8 @@ MaveDB displays ClinVar significance classifications and **star** status alongsi Mapped variants in MaveDB are cross-referenced with the [gnomAD database](https://gnomad.broadinstitute.org/) to retrieve population allele frequency data. This integration provides context about the prevalence of variants in diverse human populations, which is an important factor in clinical variant interpretation alongside functional evidence. +A variant's frequency is displayed on its [variant page](../mavemd/variant-page.md), and is available in bulk through the `gnomad` namespace of the variant data download. Each frequency is matched by ClinGen allele ID, so it is a direct assertion about that variant rather than an aggregate over related variants. Variants absent from gnomAD show no frequency. + ## Ensembl VEP MaveDB uses the [Ensembl Variant Effect Predictor (VEP)](https://www.ensembl.org/info/docs/tools/vep/index.html) to annotate mapped variants with predicted functional consequences, including effects on protein coding sequences, splicing, and regulatory regions. These VEP annotations are displayed alongside variant effect scores on score set pages, providing additional context for interpreting the functional impact of each variant. diff --git a/docs/content/mavemd/variant-page.md b/docs/content/mavemd/variant-page.md index 2a1b20ce..5d52f1f1 100644 --- a/docs/content/mavemd/variant-page.md +++ b/docs/content/mavemd/variant-page.md @@ -36,6 +36,17 @@ Each dataset on the variant page includes an [assay fact](../reference/assay-fac For the full list of assay fact properties and their definitions, see the [assay facts reference](../reference/assay-facts.md). +## Annotations + +Beneath the assay details, an annotations card gathers evidence about the variant itself, independent of any one assay. **Classification** reports the selected measurement's functional score, ACMG code, and OddsPath ratio. + +**Population frequency** reports the variant's frequency in [gnomAD](../finding-data/external-integrations.md#gnomad), where it is present: + +- **AF** -- The allele frequency, followed by the allele count and allele number it was computed from. +- **FAF95** -- The filtering allele frequency at 95% confidence, a conservative sampling-adjusted estimate, with the genetic ancestry group that attains it. A variant whose FAF95 exceeds a disease's maximum credible allele frequency is too common to be pathogenic (ACMG BA1/BS1). + +The gnomAD release the frequencies were drawn from is shown alongside them, with a link to the variant's gnomAD page. Variants absent from gnomAD are reported as having no record rather than as having zero frequency. + ## Interactive histogram The variant page includes the same interactive score histogram shown on score set pages, but with the selected variant's position highlighted within the distribution. 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1a04a075..85df4518 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "mavedb-ui", - "version": "2026.2.4", + "version": "2026.2.4.1", "private": true, "type": "module", "scripts": { diff --git a/src/api/clingen/alleles.test.ts b/src/api/clingen/alleles.test.ts new file mode 100644 index 00000000..c28c8b4e --- /dev/null +++ b/src/api/clingen/alleles.test.ts @@ -0,0 +1,94 @@ +import axios from 'axios' +import {beforeEach, describe, expect, it, vi} from 'vitest' + +import {getAlleleByGnomad} from './alleles' + +vi.mock('axios', () => ({ + default: { + get: vi.fn() + }, + isAxiosError: (error: unknown) => Boolean((error as {isAxiosError?: boolean})?.isAxiosError) +})) + +const mockedAxiosGet = vi.mocked(axios.get) + +/** A ClinGen allele, trimmed to the fields these tests care about. */ +const ALLELE = {'@id': 'http://reg.genome.network/allele/CA412761507'} + +/** The registry rejects a position whose reference allele doesn't match the assembly with a 400. */ +function referenceMismatch() { + return { + isAxiosError: true, + response: {status: 400, data: {errorType: 'IncorrectReferenceAllele'}} + } +} + +/** The HGVS strings axios was asked to resolve, in order. */ +function queriedHgvs() { + return mockedAxiosGet.mock.calls.map((call) => call[1]?.params?.hgvs) +} + +describe('getAlleleByGnomad', () => { + beforeEach(() => { + mockedAxiosGet.mockReset() + }) + + it('resolves a GRCh38 ID without trying GRCh37', async () => { + mockedAxiosGet.mockResolvedValueOnce({data: ALLELE} as never) + + expect(await getAlleleByGnomad('X-41334274-A-C')).toEqual({allele: ALLELE, assembly: 'grch38'}) + expect(queriedHgvs()).toEqual(['NC_000023.11:g.41334274A>C']) + }) + + it('falls back to the GRCh37 accession when the reference allele does not match GRCh38', async () => { + mockedAxiosGet.mockRejectedValueOnce(referenceMismatch()).mockResolvedValueOnce({data: ALLELE} as never) + + expect(await getAlleleByGnomad('17-7579472-G-C')).toEqual({allele: ALLELE, assembly: 'grch37'}) + expect(queriedHgvs()).toEqual(['NC_000017.11:g.7579472G>C', 'NC_000017.10:g.7579472G>C']) + }) + + it('propagates a server error instead of masking it as a wrong-assembly retry', async () => { + const outage = {isAxiosError: true, response: {status: 503, data: {}}} + mockedAxiosGet.mockRejectedValueOnce(outage) + + await expect(getAlleleByGnomad('X-41334274-A-C')).rejects.toBe(outage) + expect(mockedAxiosGet).toHaveBeenCalledTimes(1) + }) + + it('propagates a network failure, which carries no response', async () => { + const offline = {isAxiosError: true, message: 'Network Error'} + mockedAxiosGet.mockRejectedValueOnce(offline) + + await expect(getAlleleByGnomad('X-41334274-A-C')).rejects.toBe(offline) + expect(mockedAxiosGet).toHaveBeenCalledTimes(1) + }) + + it('surfaces the GRCh37 failure when neither assembly resolves', async () => { + const mismatch = referenceMismatch() + mockedAxiosGet.mockRejectedValueOnce(referenceMismatch()).mockRejectedValueOnce(mismatch) + + await expect(getAlleleByGnomad('17-7579472-G-C')).rejects.toBe(mismatch) + expect(mockedAxiosGet).toHaveBeenCalledTimes(2) + }) + + it('reads only the requested assembly when one is forced, without falling back', async () => { + mockedAxiosGet.mockResolvedValueOnce({data: ALLELE} as never) + + expect(await getAlleleByGnomad('17-7676154-G-C', 'grch37')).toEqual({allele: ALLELE, assembly: 'grch37'}) + expect(queriedHgvs()).toEqual(['NC_000017.10:g.7676154G>C']) + }) + + it('surfaces the failure of a forced assembly rather than trying the other one', async () => { + const mismatch = referenceMismatch() + mockedAxiosGet.mockRejectedValueOnce(mismatch) + + await expect(getAlleleByGnomad('17-7676154-G-C', 'grch37')).rejects.toBe(mismatch) + expect(mockedAxiosGet).toHaveBeenCalledTimes(1) + }) + + it('rejects an ID it cannot translate without calling the registry', async () => { + // Passes gnomadIdRegex, but the alleles describe no change. + await expect(getAlleleByGnomad('1-11796321-A-A')).rejects.toThrow('Not a valid gnomAD variant ID') + expect(mockedAxiosGet).not.toHaveBeenCalled() + }) +}) diff --git a/src/api/clingen/alleles.ts b/src/api/clingen/alleles.ts index b67f4a68..b17d00dc 100644 --- a/src/api/clingen/alleles.ts +++ b/src/api/clingen/alleles.ts @@ -1,4 +1,5 @@ -import axios from 'axios' +import axios, {isAxiosError} from 'axios' +import {type GenomeAssembly, gnomadIdToHgvsCandidates} from '@/lib/gnomad' import type {ClinGenAllele, ClinGenGene} from './types' const CLINGEN_BASE_URL = 'https://reg.genome.network' @@ -15,14 +16,14 @@ export async function getAlleleByHgvs(hgvs: string): Promise { return response.data } -export async function getAlleleByDbSnp(rsId: string): Promise { +export async function getAlleleByDbSnp(rsId: string): Promise { const response = await axios.get(`${CLINGEN_BASE_URL}/alleles`, { params: {'dbSNP.rs': rsId} }) return response.data } -export async function getAlleleByClinVar(variationId: string): Promise { +export async function getAlleleByClinVar(variationId: string): Promise { const response = await axios.get(`${CLINGEN_BASE_URL}/alleles`, { params: {'ClinVar.variationId': variationId} }) @@ -35,3 +36,48 @@ export async function getGeneBySymbol(symbol: string): Promise { }) return response.data } + +/** An allele resolved from a gnomAD ID, with the assembly whose coordinates it was read under. */ +export interface GnomadAlleleResult { + allele: ClinGenAllele + assembly: GenomeAssembly +} + +/** + * Look up an allele by gnomAD variant ID (e.g. 1-11796321-G-A). + * + * The ID is translated into genomic HGVS and resolved as such, rather than looked up among the registry's gnomAD + * cross-references: the registry computes an allele from any coordinates that match the reference, whereas its gnomAD + * index only covers variants it has ingested a gnomAD record for. + * + * A gnomAD ID doesn't name the reference genome its coordinates belong to, so by default GRCh38 is tried first and + * GRCh37 second. A 4xx from the first attempt is how coordinates announce they belong to the older assembly — the + * registry rejects a position whose reference allele doesn't match with `IncorrectReferenceAllele`. Note that a + * position can be valid under both assemblies while naming a different variant in each, in which case the earlier + * assembly wins; pass `assembly` to read the ID under a specific one instead, and let any failure propagate. + * + * @returns The allele, and the assembly its coordinates were read under. + */ +export async function getAlleleByGnomad(gnomadId: string, assembly?: GenomeAssembly): Promise { + const candidates = gnomadIdToHgvsCandidates(gnomadId).filter( + (candidate) => assembly == undefined || candidate.assembly === assembly + ) + if (candidates.length === 0) { + throw new Error(`Not a valid gnomAD variant ID: ${gnomadId}`) + } + + for (const [index, candidate] of candidates.entries()) { + const isLastCandidate = index === candidates.length - 1 + try { + return {allele: await getAlleleByHgvs(candidate.hgvs), assembly: candidate.assembly} + } catch (error) { + // Only a rejection of these coordinates warrants trying the next assembly; a network failure or registry outage + // should surface, as should the final attempt's failure. + if (isLastCandidate || !isAxiosError(error) || !error.response || error.response.status >= 500) { + throw error + } + } + } + // Unreachable: the loop either returns or throws on its final iteration. + throw new Error(`Could not resolve gnomAD variant ID: ${gnomadId}`) +} diff --git a/src/api/mavedb/index.ts b/src/api/mavedb/index.ts index c097c748..3a92e5cf 100644 --- a/src/api/mavedb/index.ts +++ b/src/api/mavedb/index.ts @@ -1,18 +1,3 @@ -import {isAxiosError} from 'axios' - -export interface ErrorResponse { - status: number - data?: Record -} - -/** Extract a normalized response from a caught Axios error. */ -export function getErrorResponse(e: unknown): ErrorResponse { - if (isAxiosError(e) && e.response) { - return {status: e.response.status, data: e.response.data as Record} - } - return {status: 500} -} - export * from './access-keys' export * from './calibrations' export * from './collections' diff --git a/src/api/mavedb/score-sets.ts b/src/api/mavedb/score-sets.ts index f2211a84..77cfe891 100644 --- a/src/api/mavedb/score-sets.ts +++ b/src/api/mavedb/score-sets.ts @@ -7,13 +7,17 @@ type ScoreSetSearch = components['schemas']['ScoreSetsSearch'] type ScoreSetsSearchResponse = components['schemas']['ScoreSetsSearchResponse'] export type ScoreSetsSearchFilterOptionsResponse = components['schemas']['ScoreSetsSearchFilterOptionsResponse'] -const HISTOGRAM_VARIANT_DATA_NAMESPACES = ['vep', 'scores', 'clingen'] +// Both screens read a score set's whole variant table from the same endpoint, but they render different +// things from it, so each names the namespaces it actually consumes. Keeping these separate matters at +// scale: a saturation-mutagenesis score set is 100k+ rows, and an unused namespace is 100k+ wasted cells. +const SCORE_SET_CHART_NAMESPACES = ['vep', 'scores', 'clingen', 'mavedb'] -function scoreSetVariantDataParams( - options: {includePostMappedHgvs?: boolean; namespaces?: string[]} = {} -): URLSearchParams { +// The variant page additionally reads the selected measurement's gnomAD frequency out of its row; this +// request is the only source of it. See `gnomadFromVariantRow`. +const VARIANT_PAGE_NAMESPACES = [...SCORE_SET_CHART_NAMESPACES, 'gnomad'] + +function scoreSetVariantDataParams(options: {namespaces?: string[]} = {}): URLSearchParams { const params = new URLSearchParams() - if (options.includePostMappedHgvs) params.append('include_post_mapped_hgvs', 'true') for (const namespace of options.namespaces ?? []) params.append('namespaces', namespace) return params } @@ -24,11 +28,14 @@ function scoreSetVariantDataUrl(urn: string, params: URLSearchParams = new URLSe return query ? `${baseUrl}?${query}` : baseUrl } -export function histogramScoreSetVariantDataUrl(urn: string): string { - return scoreSetVariantDataUrl( - urn, - scoreSetVariantDataParams({includePostMappedHgvs: true, namespaces: HISTOGRAM_VARIANT_DATA_NAMESPACES}) - ) +/** Variant data for a score set page's histogram and heatmap. */ +export function scoreSetChartVariantDataUrl(urn: string): string { + return scoreSetVariantDataUrl(urn, scoreSetVariantDataParams({namespaces: SCORE_SET_CHART_NAMESPACES})) +} + +/** Variant data for the variant page: the score distribution chart plus the selected row's annotations. */ +export function variantPageVariantDataUrl(urn: string): string { + return scoreSetVariantDataUrl(urn, scoreSetVariantDataParams({namespaces: VARIANT_PAGE_NAMESPACES})) } // --------------------------------------------------------------------------- @@ -103,17 +110,32 @@ export async function publishScoreSet(urn: string) { } export async function getScoreSetClinicalControlOptions(urn: string) { - const response = await axios.get(`${config.apiBaseUrl}/score-sets/${encodeURIComponent(urn)}/clinical-controls/options`) + const response = await axios.get( + `${config.apiBaseUrl}/score-sets/${encodeURIComponent(urn)}/clinical-controls/options` + ) return response.data } export async function downloadScoreSetFile(urn: string, type: 'scores' | 'counts'): Promise { const response = await axios.get( - `${config.apiBaseUrl}/score-sets/${encodeURIComponent(urn)}/${type}?drop_na_columns=true` + `${config.apiBaseUrl}/score-sets/${encodeURIComponent(urn)}/${type}?drop_unused_hgvs_columns=true` ) return response.data } +/** + * Fetch the CSV column namespaces this score set has data for. + */ +export async function getScoreSetCsvNamespaces( + urn: string, + signal?: AbortSignal +): Promise { + const response = await axios.get(`${config.apiBaseUrl}/score-sets/${encodeURIComponent(urn)}/csv-namespaces`, { + signal + }) + return response.data +} + export async function downloadScoreSetVariantData(urn: string, params: URLSearchParams): Promise { const response = await axios.get(scoreSetVariantDataUrl(urn, params)) return response.data @@ -121,14 +143,14 @@ export async function downloadScoreSetVariantData(urn: string, params: URLSearch export async function getScoreSetScoresPreview(urn: string): Promise { const response = await axios.get( - `${config.apiBaseUrl}/score-sets/${encodeURIComponent(urn)}/scores?drop_na_columns=true` + `${config.apiBaseUrl}/score-sets/${encodeURIComponent(urn)}/scores?drop_unused_hgvs_columns=true` ) return response.data } export async function getScoreSetCountsPreview(urn: string): Promise { const response = await axios.get( - `${config.apiBaseUrl}/score-sets/${encodeURIComponent(urn)}/counts?drop_na_columns=true` + `${config.apiBaseUrl}/score-sets/${encodeURIComponent(urn)}/counts?drop_unused_hgvs_columns=true` ) return response.data } @@ -138,7 +160,9 @@ export async function downloadMappedVariants(urn: string) { return response.data } -export async function getRecentlyPublishedScoreSets(signal?: AbortSignal): Promise { +export async function getRecentlyPublishedScoreSets( + signal?: AbortSignal +): Promise { const response = await axios.get(`${config.apiBaseUrl}/score-sets/recently-published`, { headers: {accept: 'application/json'}, signal diff --git a/src/api/mavedb/variants.ts b/src/api/mavedb/variants.ts index f0db95a4..185d131c 100644 --- a/src/api/mavedb/variants.ts +++ b/src/api/mavedb/variants.ts @@ -1,13 +1,14 @@ import axios from 'axios' import config from '@/config' -import {histogramScoreSetVariantDataUrl} from '@/api/mavedb/score-sets' +import {variantPageVariantDataUrl} from '@/api/mavedb/score-sets' import {components} from '@/schema/openapi' type ScoreSet = components['schemas']['ScoreSet'] type VariantEffectMeasurementWithScoreSet = components['schemas']['VariantEffectMeasurementWithScoreSet'] type ClingenAlleleIdVariantLookupResponse = components['schemas']['ClingenAlleleIdVariantLookupResponse'] type MappedVariant = components['schemas']['MappedVariant'] +type AvailableCsvNamespace = components['schemas']['AvailableCsvNamespace'] export async function lookupVariantsByClingenId( clingenAlleleIds: string[] @@ -30,8 +31,9 @@ export async function getVariantDetail(urn: string): Promise { - const response = await axios.get(histogramScoreSetVariantDataUrl(scoreSetUrn)) +/** The containing score set's variant table, as read by the variant page. */ +export async function getVariantPageScoreSetData(scoreSetUrn: string): Promise { + const response = await axios.get(variantPageVariantDataUrl(scoreSetUrn)) return response.data } @@ -47,3 +49,24 @@ export async function getScoreSet(urn: string): Promise { const response = await axios.get(`${config.apiBaseUrl}/score-sets/${encodeURIComponent(urn)}`) return response.data } + +/** + * Fetch the CSV column namespaces this variant has data for. + */ +export async function getVariantCsvNamespaces(urn: string, signal?: AbortSignal): Promise { + const response = await axios.get(`${config.apiBaseUrl}/variants/${encodeURIComponent(urn)}/csv-namespaces`, {signal}) + return response.data +} + +export function variantCsvUrl(urn: string, namespaces?: string[]): string { + const params = new URLSearchParams() + for (const namespace of namespaces ?? []) params.append('namespaces', namespace) + const query = params.toString() + const baseUrl = `${config.apiBaseUrl}/variants/${encodeURIComponent(urn)}/csv` + return query ? `${baseUrl}?${query}` : baseUrl +} + +export async function downloadVariantCsv(urn: string, namespaces?: string[]): Promise { + const response = await axios.get(variantCsvUrl(urn, namespaces)) + return response.data +} diff --git a/src/assets/app.css b/src/assets/app.css index 49b1e8b6..589340b1 100644 --- a/src/assets/app.css +++ b/src/assets/app.css @@ -113,12 +113,18 @@ --color-badge-alert: #fef3c7; /* ── Search Types ──────────────────────────────────────────── */ + --color-hgvs: #5c6b7a; + --color-hgvs-light: #eceff2; --color-dbsnp: #e6b84d; --color-dbsnp-light: #fdf3d7; --color-clinvar: #5aafa0; --color-clinvar-light: #c8ece5; --color-ga4gh: #0f6ca4; --color-ga4gh-light: #e3f0f9; + --color-gnomad: #5b4ba8; + --color-gnomad-light: #ece9f7; + --color-gene: #b5446e; + --color-gene-light: #fbeaf1; /* ── Measurement Types (variant screen) ────────────────────── */ --color-nucleotide: #2e7d32; diff --git a/src/components/collection/CollectionDataSetEditor.vue b/src/components/collection/CollectionDataSetEditor.vue index 5e962885..9a4c997f 100644 --- a/src/components/collection/CollectionDataSetEditor.vue +++ b/src/components/collection/CollectionDataSetEditor.vue @@ -101,7 +101,7 @@ import useItem from '@/composition/item.ts' import {addCollectionScoreSet, addCollectionExperiment} from '@/api/mavedb/collections' import {getScoreSet} from '@/api/mavedb/variants' import {getExperiment} from '@/api/mavedb/experiments' -import {getErrorResponse} from '@/api/mavedb' +import {getErrorResponse} from '@/lib/errors' import {type DataSetType, DATA_SET_TYPE_LABELS} from '@/lib/collections' import MvEmailPrompt from '@/components/common/MvEmailPrompt.vue' import {components} from '@/schema/openapi' diff --git a/src/components/common/MvCsvColumnDialog.vue b/src/components/common/MvCsvColumnDialog.vue new file mode 100644 index 00000000..afc2e983 --- /dev/null +++ b/src/components/common/MvCsvColumnDialog.vue @@ -0,0 +1,129 @@ + + + diff --git a/src/components/common/MvVariantPreview.vue b/src/components/common/MvVariantPreview.vue index 85fd7762..e0d2c4b0 100644 --- a/src/components/common/MvVariantPreview.vue +++ b/src/components/common/MvVariantPreview.vue @@ -10,28 +10,32 @@
+ @click="downloadFile('scores')" /> + @click="downloadFile('counts')" /> + @click="customDialogVisible = true" /> + +