10db3769dd9edfa38ac8d900ca400fdfb514d9a7 gperez2 Wed Jul 29 22:41:46 2026 -0700 An in-place update for gnomad v4.1 to v4.1.1 that swaps bigDataUrl, labels, dataVersion, detailsTabUrls, search descriptions, and removes the alpha-only gnomadVariantsV4.1.1 composite. Updates to gnomad.html, gnomadV4.1.html, and gnomadPLI.html regarding the addition of the gnomad v4.1.1 data, refs #37351 diff --git src/hg/makeDb/trackDb/human/hg38/gnomad.html src/hg/makeDb/trackDb/human/hg38/gnomad.html index fbcf956d017..88aa93d0db9 100644 --- src/hg/makeDb/trackDb/human/hg38/gnomad.html +++ src/hg/makeDb/trackDb/human/hg38/gnomad.html @@ -1,132 +1,132 @@ <h2>Description</h2> <p> The <a target="_blank" href="https://gnomad.broadinstitute.org/">Genome Aggregation Database (gnomAD)</a> is a resource developed by an international coalition of investigators at the Broad Institute and collaborating institutions, with the goal of aggregating and harmonizing exome and whole-genome sequencing data from large-scale sequencing projects spanning disease-specific cohorts and population genetics studies. Individuals affected by severe pediatric diseases and first-degree relatives were excluded from the studies. However, some individuals with severe disease may still have remained in the datasets, although probably at an equivalent or lower frequency than observed in the general population. For each variant, gnomAD provides allele frequencies stratified by genetic ancestry group, alongside quality metrics such as depth of coverage and genotype quality scores. The database also supplies sequencing coverage, structural variants, CNVs, and short tandem repeats. Additionally, gnomAD provides non-coding constraint and gene-level constraint metrics — including pLI scores, observed/expected (oe) ratios, and LOEUF values — that quantify intolerance to loss-of-function variation and are widely used to prioritize candidate disease genes. The most -current release on hg38 is v4.1, but the older v3 and v2 versions are also available. +current release on hg38 is v4.1.1, but the older v3 and v2 versions are also available. </p> <p> The available data tracks are: <ul> <li><a href="/cgi-bin/hgTrackUi?db=hg38&g=gnomadVariantsV4.1#TRACK_HTML"><strong>gnomAD -v4.1</strong></a> — Shows single nucleotide variants (SNVs) and small insertion/deletion +v4.1.1</strong></a> — Shows single nucleotide variants (SNVs) and small insertion/deletion variants of 807,162 individuals, including 730,947 exomes and 76,215 genomes.</li> <li><a href="/cgi-bin/hgTrackUi?db=hg38&g=gnomadGenomesVariantsV3_1_1#TRACK_HTML"><strong>gnomAD v3.1.1</strong></a> — Shows variants from 76,156 whole genomes (and no exomes), all mapped to GRCh38/hg38.</li> <li><a href="/cgi-bin/hgTrackUi?db=hg38&g=gnomadGenomesVariantsV3_1#TRACK_HTML"><strong>Deprecated: gnomAD v3.1</strong></a> — Same underlying data as v3.1.1 with older annotations. Do not use; will be removed soon.</li> <li><a href="/cgi-bin/hgTrackUi?db=hg38&g=gnomadGenomesVariantsV3#TRACK_HTML"><strong>gnomAD v3</strong></a> — Shows variants from 71,702 whole genomes from the v3.0 release.</li> <li><a href="/cgi-bin/hgTrackUi?db=hg38&g=gnomadVariantsV2#TRACK_HTML"><strong>gnomAD v2</strong></a> — Shows variants from 125,748 exomes and 15,708 whole genomes, lifted from GRCh37/hg19 to GRCh38/hg38.</li> <li><a href="/cgi-bin/hgTrackUi?db=hg38&g=gnomadConstraint#TRACK_HTML"><strong>gnomAD Mut Constraint</strong></a> — Shows the reduced variation caused by purifying natural selection for 1kbp windows across the genome (based on v3.1.2).</li> <li><a href="/cgi-bin/hgTrackUi?db=hg38&g=gnomadPLI#TRACK_HTML"><strong>gnomAD Constraint Metrics</strong></a> — Contains per-gene and per-transcript metrics of pathogenicity (LOEUF, pLI, and Z-scores) for v2.1.1, v4, and v4.1.</li> <li><a href="/cgi-bin/hgTrackUi?db=hg38&g=gnomad3Coverage#TRACK_HTML"><strong>gnomAD v3 Genome Coverage</strong></a> — Shows various read depth metrics for genome samples from v3.0.1.</li> <li><a href="/cgi-bin/hgTrackUi?db=hg38&g=gnomad4ExomeCoverage#TRACK_HTML"><strong>gnomAD v4 Exome Coverage</strong></a> — Shows various read depth metrics for exome samples from v4.0.</li> <li><a href="/cgi-bin/hgTrackUi?db=hg38&g=gnomadStructuralVariants#TRACK_HTML"><strong>gnomAD Structural Variants</strong></a> — Shows structural variant calls (variants >=50 nucleotides) from gnomAD v4.1.</li> <li><a href="/cgi-bin/hgTrackUi?db=hg38&g=gnomadCopyNumberVariants#TRACK_HTML"><strong>gnomAD Rare CNV Variants</strong></a> — Shows rare copy number variants (<1% overall site frequency) from gnomAD v4.1.</li> <li><a href="/cgi-bin/hgTrackUi?db=hg38&g=gnomadStr#TRACK_HTML"><strong>gnomAD STR</strong></a> — Shows short tandem repeat genotypes at disease-associated loci from gnomAD v3.1.3.</li> </ul> </p> <p> For questions on the gnomAD data, also see the <a target="_blank" href="https://gnomad.broadinstitute.org/faq">gnomAD FAQ</a>.</p> <p> More details on the Variant type(s) can be found on the <a target="_blank" href="https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/master/Ontology_Files/subsets/SOFA.obo">Sequence Ontology page</a>.</p> <h2>Data Access</h2> <p> The raw data can be explored interactively with the <a target="_blank" href="../cgi-bin/hgTables"> Table Browser</a>, or the <a target="_blank" href="../cgi-bin/hgIntegrator">Data Integrator</a>. For automated analysis, the data may be queried from our <a target="_blank" href="/goldenPath/help/api.html">REST API</a>, and the genome annotations are stored in files that can be downloaded from our <a href="https://hgdownload.soe.ucsc.edu/gbdb/$db/gnomAD/" target="_blank">download server</a>, subject to the conditions set forth by the gnomAD consortium (see below).</p> <p> The data can also be found directly from the gnomAD <a target="_blank" href="https://gnomad.broadinstitute.org/downloads">downloads page</a>. Please refer to our <a href="https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome" target="_blank">mailing list archives</a> for questions, or our <a target="_blank" href="../FAQ/FAQdownloads.html#download36">Data Access FAQ</a> for more information.</p> <h2>Credits</h2> <p> Thanks to the <a href="https://gnomad.broadinstitute.org/about" target="_blank">Genome Aggregation Database Consortium</a> for making these data available. The data are released under the <a href="https://creativecommons.org/publicdomain/zero/1.0/" target="_blank">Creative Commons Zero Public Domain Dedication</a> as described <a href="https://gnomad.broadinstitute.org/policies" target="_blank">here</a>. </p> <p> Please note that some annotations within the provided files may have restrictions on usage. See <a href="https://gnomad.broadinstitute.org/policies" target="_blank">here</a> for more information. </p> <h2>References</h2> <p> Karczewski KJ, Francioli LC, Tiao G, Cummings BB, Alföldi J, Wang Q, Collins RL, Laricchia KM, Ganna A, Birnbaum DP <em>et al</em>. <a href="https://doi.org/10.1038/s41586-020-2308-7" target="_blank"> The mutational constraint spectrum quantified from variation in 141,456 humans</a>. <em>Nature</em>. 2020 May;581(7809):434-443. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/32461654" target="_blank">32461654</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7334197/" target="_blank">PMC7334197</a> </p> <p> Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, O'Donnell-Luria AH, Ware JS, Hill AJ, Cummings BB <em>et al</em>. <a href="https://www.nature.com/articles/nature19057" target="_blank">Analysis of protein-coding genetic variation in 60,706 humans</a>. <em>Nature</em>. 2016 Aug 17;536(7616):285-91. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/27535533" target="_blank">27535533</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5018207/" target="_blank">PMC5018207</a> </p> <p> Collins RL, Brand H, Karczewski KJ, Zhao X, Alföldi J, Francioli LC, Khera AV, Lowther C, Gauthier LD, Wang H <em>et al</em>. <a href="https://www.ncbi.nlm.nih.gov/pubmed/32461652" target="_blank"> A structural variation reference for medical and population genetics</a>. <em>Nature</em>. 2020 May;581(7809):444-451. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/32461652" target="_blank">32461652</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7334194/" target="_blank">PMC7334194</a> </p> <p> Chen S, Francioli LC, Goodrich JK, Collins RL, Kanai M, Wang Q, Alföldi J, Watts NA, Vittal C, Gauthier LD <em>et al</em>. <a href="https://doi.org/10.1038/s41586-023-06045-0" target="_blank"> A genomic mutational constraint map using variation in 76,156 human genomes</a>. <em>Nature</em>. 2024 Jan;625(7993):92-100. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/38057664" target="_blank">38057664</a> </p>