2e0addd016cfcbf61485b90d8980a8d75be622c2 lrnassar Sun Jun 14 00:10:06 2026 -0700 lrSv: sync description-page counts to the deduped data; drop Kim PD from the supertrack page. refs #36258 After the QA dedup, update the SV counts cited on the description pages to the unique (post-dedup) totals for the tracks served, while leaving the upstream release/paper counts in the Methods sections: decodeSv 133,886 -> 119,453 displayed gustafsonSv 113,696 -> 113,159 displayed chirmade101 87,183 -> 87,068 displayed aou1k 541,049 -> 540,155 displayed hprc2v21Sv 596,063 -> 549,649 (hg38) and 608,435 -> 541,176 (hs1), throughout (no upstream publication), incl. recomputed nested-snarl counts lrSv.html: update the Available Datasets table count cells to match, set the lrSvAll merged cell to 2,317,508 (post Kim PD removal), and remove the Kim PD Brain row, blurb and reference from the supertrack page (the track is staged on dev/alpha only, kept out of the merge and the description, and is not released). diff --git src/hg/makeDb/trackDb/human/aou1kSv.html src/hg/makeDb/trackDb/human/aou1kSv.html index 523c2be0439..cd3af17f400 100644 --- src/hg/makeDb/trackDb/human/aou1kSv.html +++ src/hg/makeDb/trackDb/human/aou1kSv.html @@ -1,114 +1,115 @@ <h2>Description</h2> <p> This track shows structural variants (SVs) identified by PacBio HiFi long-read sequencing of 1,027 individuals from the All of Us (AoU) Research Program. Participants self-identified as Black or African American and were sequenced -to ~8x coverage. The dataset contains 541,049 SVs (444,524 insertions and -96,525 deletions) on autosomes. +to ~8x coverage. The track contains 540,155 SVs (443,630 insertions and +96,525 deletions) on autosomes, after removing byte-identical duplicate records +from the 541,049-row release. </p> <p> SVs are annotated with population-specific allele frequencies across five ancestry groups (African, Admixed American, East Asian, European, South Asian), gene intersections from curated disease gene lists (OMIM, ACMG, cancer genes), regulatory element overlaps, and associations with eQTLs, GWAS loci, and clinical phenotypes from the AoU electronic health records. </p> <h2>Display Conventions and Configuration</h2> <p> Items are colored by SV type: <ul> <li><span style="color: rgb(200,0,0);">Deletions (DEL)</span> - red</li> <li><span style="color: rgb(0,0,200);">Insertions (INS)</span> - blue</li> </ul> </p> <p> Filters are available for SV type, SV length, and population-specific allele frequencies. For insertions, the item is placed at the insertion site with a width of 1 bp; for deletions, the item spans the deleted region. </p> <p> The detail page shows the following annotations when available: <ul> <li><b>Population Allele Frequencies</b>: separate frequencies for AFR, AMR, EAS, EUR, and SAS ancestry groups</li> <li><b>Fst</b>: fixation index between African and non-African populations</li> <li><b>Gene Intersections</b>: overlapping OMIM, disease, cancer, and ACMG genes with constraint scores (pLI and LOEUF)</li> <li><b>Regulatory Elements</b>: intersected regulatory elements (e.g. enhancer, promoter)</li> <li><b>Other LR Datasets</b>: whether the SV was also detected in HPRC, HGSVC, or 1KG-ONT long-read datasets</li> <li><b>eQTLs</b>: expression QTL associations with q-values</li> <li><b>GWAS Associations</b>: overlapping GWAS loci with trait, gene, rsID, and LD information</li> <li><b>SV-Trait Associations</b>: associations with clinical phenotypes from AoU electronic health records, including odds ratios and confidence intervals</li> </ul> </p> <h2>Methods</h2> <p> Garimella et al. 2025 performed PacBio HiFi long-read sequencing on 1,027 All of Us participants self-identifying as Black or African American, to ~8x per-sample coverage at HudsonAlpha Discovery. SVs (≥50 bp) were called per sample with an ensemble of three methods: two alignment-based callers, <a href="https://github.com/PacificBiosciences/pbsv" target="_blank"> PBSV</a> v2.6.0 (with Tandem Repeat Finder context) and <a href="https://github.com/fritzsedlazeck/Sniffles" target="_blank">Sniffles2</a> v2.0.6, plus the assembly-based <a href="https://github.com/EichlerLab/pav" target="_blank">PAV</a> v1.2.1 (hifiasm haplotype-resolved contigs aligned to GRCh38 with minimap2 <tt>-x asm20</tt>). Per-caller VCFs were normalized, merged within and across samples and filtered into stringent and lenient tiers, and the callset was re-genotyped across the cohort to produce the final release: 541,049 autosomal SVs (444,524 insertions, 96,525 deletions) with per-ancestry allele frequencies (AFR, AMR, EAS, EUR, SAS) and gene, regulatory, eQTL, GWAS and EHR-phenotype annotations. </p> <p> This track was built from the supplementary media-2 table of the AoU long-read sequencing preprint (<a href="https://doi.org/10.1101/2025.10.02.25336942" target="_blank"> doi:10.1101/2025.10.02.25336942</a>). Access to the underlying AoU long-read data requires registration through the <a href="https://www.researchallofus.org/" target="_blank">All of Us Research Hub</a>. </p> <p> The step-by-step build commands (download, format conversion, bigBed build) are recorded in the UCSC makeDoc for this track container: <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/lrSv.txt" target="_blank"> doc/hg38/lrSv.txt</a>. The conversion scripts and autoSql schemas live in <a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/lrSv" target="_blank"> makeDb/scripts/lrSv</a>. </p> <h2>Data Access</h2> <p> This track was built from supplementary data (media-2) of the AoU long-read sequencing preprint. Access to the full AoU dataset requires registration through the <a href="https://www.researchallofus.org/" target="_blank">All of Us Research Hub</a>. </p> <h2>Credits</h2> <p> Thanks to Garimella et al. and the All of Us Research Program for making their structural variant annotations publicly available. </p> <h2>References</h2> <p> Garimella KV, Li Q, Wertz J, Lee SK, Cunial F, Huang Y, Mostovoy Y, Lorig-Roach R, English A, Su H <em>et al</em>. <a href="https://doi.org/10.1101/2025.10.02.25336942" target="_blank"> Population-scale Long-read Sequencing in the All of Us Research Program</a>. <em>medRxiv</em>. 2025 Oct 5;. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/41256123" target="_blank">41256123</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12622093/" target="_blank">PMC12622093</a> </p>