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Add GTEx and Pext to gnomAD v4.1 #1602

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merged 9 commits into from
Nov 22, 2024
Merged

Add GTEx and Pext to gnomAD v4.1 #1602

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67624a8
feat(data-pipelines): add steps to process v4 gtex/pext
rileyhgrant Jul 30, 2024
e6d3665
feat(graphql-api): adjust api types for new gtex/pext schema
rileyhgrant Aug 15, 2024
ebf26be
feat(metadata): add new top level dataset type
rileyhgrant Sep 23, 2024
ded8ddb
feat(browser): adjust frontend for new gtex/pext schema
rileyhgrant Aug 15, 2024
3dc264a
test(browser): add TissueExpressionTrack tests
rileyhgrant Oct 23, 2024
1eba898
feat(browser): add more labels on transcript tissue expression plot
rileyhgrant Nov 15, 2024
c1e0d6d
feat(data-pipeline): repartition gene model release tables
rileyhgrant Nov 20, 2024
d282dc8
feat(graphql-api): modify Gene ES indices to allow rollbacks
rileyhgrant Nov 15, 2024
d89c134
feat(browser): add v4 pext to data page
rileyhgrant Nov 21, 2024
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46 changes: 46 additions & 0 deletions browser/src/DataPage/GnomadV4Downloads.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -487,6 +487,52 @@ const GnomadV4Downloads = () => {
</FileList>
</DownloadsSection>

<DownloadsSection>
<SectionTitle id="v4-pext">Proportion expressed across transcripts (pext)</SectionTitle>
<p>
For information on pext, see{' '}
{/* @ts-expect-error TS(2769) FIXME: No overload matches this call. */}
<ExternalLink href="https://doi.org/10.1038/s41586-020-2329-2">
<em>Transcript expression-aware annotation improves rare variant interpretation.</em>{' '}
Nature 581, 452–458 (2020)
</ExternalLink>
</p>
<FileList>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<GetUrlButtons
label="Annotation-level pext for all possible SNVs Hail table"
path="/release/4.1/pext/gnomad.pext.gtex_v10.annotation_level.ht"
includeAzure={false}
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<DownloadLinks
label="Annotation-level pext for all possible SNVs TSV"
path="/release/4.1/pext/gnomad.pext.gtex_v10.annotation_level.tsv.gz"
includeAzure={false}
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<GetUrlButtons
label="Base-level pext Hail table"
path="/release/4.1/pext/gnomad.pext.gtex_v10.base_level.ht"
includeAzure={false}
/>
</ListItem>
{/* @ts-expect-error TS(2745) FIXME: This JSX tag's 'children' prop expects type 'never... Remove this comment to see the full error message */}
<ListItem>
<DownloadLinks
label="Base-level pext TSV"
path="/release/4.1/pext/gnomad.pext.gtex_v10.base_level.tsv.gz"
includeAzure={false}
/>
</ListItem>
</FileList>
</DownloadsSection>

<DownloadsSection>
<SectionTitle id="v4-resources">Resources</SectionTitle>
<FileList>
Expand Down
167 changes: 167 additions & 0 deletions browser/src/DataPage/__snapshots__/DataPage.spec.tsx.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -8556,6 +8556,173 @@ exports[`Data Page has no unexpected changes 1`] = `
</li>
</ul>
</section>
<section
className="c15"
>
<span
className="c6"
>
<h2
className="c16"
>
<a
aria-hidden="true"
className="c8 c9"
href="#v4-pext"
id="v4-pext"
>
<img
alt=""
aria-hidden="true"
height={12}
src="test-file-stub"
width={12}
/>
</a>
Proportion expressed across transcripts (pext)
</h2>
</span>
<p>
For information on pext, see

<a
className="c11"
href="https://doi.org/10.1038/s41586-020-2329-2"
rel="noopener noreferrer"
target="_blank"
>
<em>
Transcript expression-aware annotation improves rare variant interpretation.
</em>

Nature 581, 452–458 (2020)
</a>
</p>
<ul
className="c19"
>
<li
className="c20"
>
<span>
Annotation-level pext for all possible SNVs Hail table
</span>
<br />
Show URL for

<button
aria-label="Show Google URL for Annotation-level pext for all possible SNVs Hail table"
className="c21"
onClick={[Function]}
type="button"
>
Google
</button>
/
<button
aria-label="Show Amazon URL for Annotation-level pext for all possible SNVs Hail table"
className="c21"
onClick={[Function]}
type="button"
>
Amazon
</button>
</li>
<li
className="c20"
>
<span>
Annotation-level pext for all possible SNVs TSV
</span>
<br />
<span>
Download from

<a
aria-label="Download Annotation-level pext for all possible SNVs TSV from Google"
className="c11"
href="https://storage.googleapis.com/gcp-public-data--gnomad/release/4.1/pext/gnomad.pext.gtex_v10.annotation_level.tsv.gz"
onClick={[Function]}
rel="noopener noreferrer"
target="_blank"
>
Google
</a>
/
<a
aria-label="Download Annotation-level pext for all possible SNVs TSV from Amazon"
className="c11"
href="https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.1/pext/gnomad.pext.gtex_v10.annotation_level.tsv.gz"
onClick={[Function]}
rel="noopener noreferrer"
target="_blank"
>
Amazon
</a>
</span>
</li>
<li
className="c20"
>
<span>
Base-level pext Hail table
</span>
<br />
Show URL for

<button
aria-label="Show Google URL for Base-level pext Hail table"
className="c21"
onClick={[Function]}
type="button"
>
Google
</button>
/
<button
aria-label="Show Amazon URL for Base-level pext Hail table"
className="c21"
onClick={[Function]}
type="button"
>
Amazon
</button>
</li>
<li
className="c20"
>
<span>
Base-level pext TSV
</span>
<br />
<span>
Download from

<a
aria-label="Download Base-level pext TSV from Google"
className="c11"
href="https://storage.googleapis.com/gcp-public-data--gnomad/release/4.1/pext/gnomad.pext.gtex_v10.base_level.tsv.gz"
onClick={[Function]}
rel="noopener noreferrer"
target="_blank"
>
Google
</a>
/
<a
aria-label="Download Base-level pext TSV from Amazon"
className="c11"
href="https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.1/pext/gnomad.pext.gtex_v10.base_level.tsv.gz"
onClick={[Function]}
rel="noopener noreferrer"
target="_blank"
>
Amazon
</a>
</span>
</li>
</ul>
</section>
<section
className="c15"
>
Expand Down
53 changes: 30 additions & 23 deletions browser/src/GenePage/GenePage.tsx
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Original file line number Diff line number Diff line change
Expand Up @@ -50,7 +50,7 @@ import MitochondrialGeneCoverageTrack from './MitochondrialGeneCoverageTrack'
import MitochondrialVariantsInGene from './MitochondrialVariantsInGene'
import { getPreferredTranscript } from './preferredTranscript'
import StructuralVariantsInGene from './StructuralVariantsInGene'
import TissueExpressionTrack from './TissueExpressionTrack'
import TissueExpressionTrack, { TranscriptWithTissueExpression } from './TissueExpressionTrack'
import VariantsInGene from './VariantsInGene'

import { GnomadConstraint } from '../ConstraintTable/GnomadConstraintTable'
Expand All @@ -71,6 +71,7 @@ import {
LegendSwatch,
} from '../ChartStyles'
import { logButtonClick } from '../analytics'
import { GtexTissueExpression } from './TranscriptsTissueExpression'

export type Strand = '+' | '-'

Expand All @@ -88,6 +89,30 @@ export type GeneMetadata = {
flags: string[]
}

export type GeneTranscript = {
transcript_id: string
transcript_version: string
exons: {
feature_type: string
start: number
stop: number
}[]
gtex_tissue_expression: GtexTissueExpression | null
}

export type Pext = {
regions: {
start: number
stop: number
mean: number
tissues: {
tissue: string
value: number
}[]
}[]
flags: string[]
}

export type Gene = GeneMetadata & {
reference_genome: ReferenceGenome
name?: string
Expand All @@ -100,29 +125,11 @@ export type Gene = GeneMetadata & {
start: number
stop: number
}[]
transcripts: {
transcript_id: string
transcript_version: string
exons: {
feature_type: string
start: number
stop: number
}[]
}[]
transcripts: GeneTranscript[]
flags: string[]
gnomad_constraint?: GnomadConstraint
exac_constraint?: ExacConstraint
pext?: {
regions: {
start: number
stop: number
mean: number
tissues: {
[key: string]: number
}
}[]
flags: string[]
}
pext?: Pext
short_tandem_repeats?: {
id: string
}[]
Expand Down Expand Up @@ -517,6 +524,7 @@ const GenePage = ({ datasetId, gene, geneId }: Props) => {
<TrackWrapper>
<GeneTranscriptsTrack
datasetId={datasetId}
isTissueExpressionAvailable={!!gene.pext}
gene={gene}
includeNonCodingTranscripts={includeNonCodingTranscripts}
includeUTRs={includeUTRs}
Expand All @@ -531,7 +539,7 @@ const GenePage = ({ datasetId, gene, geneId }: Props) => {
exons={cdsCompositeExons}
expressionRegions={gene.pext.regions}
flags={gene.pext.flags}
transcripts={gene.transcripts}
transcripts={gene.transcripts as TranscriptWithTissueExpression[]} // if a gene has pext, it has gtex
preferredTranscriptId={preferredTranscriptId}
preferredTranscriptDescription={preferredTranscriptDescription}
/>
Expand Down Expand Up @@ -563,7 +571,6 @@ const GenePage = ({ datasetId, gene, geneId }: Props) => {
<VariantsInGene
datasetId={datasetId}
gene={gene}
// @ts-expect-error TS(2322) FIXME: Type '{ datasetId: string; gene: { gene_id: string... Remove this comment to see the full error message
includeNonCodingTranscripts={includeNonCodingTranscripts}
includeUTRs={includeUTRs}
zoomRegion={zoomRegion}
Expand Down
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