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/chirmade101Sv.html src/hg/makeDb/trackDb/human/chirmade101Sv.html index 1ffe94e15a3..dc35b075c66 100644 --- src/hg/makeDb/trackDb/human/chirmade101Sv.html +++ src/hg/makeDb/trackDb/human/chirmade101Sv.html @@ -1,119 +1,120 @@ <h2>Description</h2> <p> This track shows structural variants (SVs) identified by long-read whole-genome sequencing of 101 individuals, released together with the <a href="https://svatalog.research.sickkids.ca/" target="_blank">GWAS SVatalog</a> web tool described in Chirmade et al. 2026. GWAS SVatalog computes and visualizes linkage disequilibrium between these SVs and GWAS-associated SNPs so that investigators can assess whether a SNP association signal may be tagging an underlying SV. </p> <p> -The table contains 87,183 SVs (42,435 deletions, 41,734 insertions, -1,394 duplications, 912 inversions, 708 complex events). Each SV is +The table contains 87,068 SVs (42,435 deletions, 41,619 insertions, +1,394 duplications, 912 inversions, 708 complex events; byte-identical +duplicate records have been removed). Each SV is annotated with gene overlaps, GC content, repeat context, ClinGen haploinsufficiency / triplosensitivity scores, gnomAD per-gene constraint metrics (pLI, LOEUF, missense O/E), OMIM phenotype associations, ClinVar variant IDs, and overlaps with DGV, Decipher and ClinGen regional annotations. </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> <li><span style="color: rgb(0,160,0);">Duplications (dup)</span> - green</li> <li><span style="color: rgb(230,140,0);">Inversions (inv)</span> - orange</li> <li><span style="color: rgb(140,0,200);">Complex</span> - purple</li> </ul> </p> <p> Filters are available for SV type, SV length and the number of overlapping genes. The detail page shows the full annotation row: gene-level constraint scores (per overlapping gene), ClinGen / Decipher / ClinVar region matches, OMIM phenotype annotations and gnomAD SV frequencies at >=90% reciprocal overlap. Because most genomic regions carry no clinical annotation, many columns will be blank for an arbitrary SV. </p> <h2>Methods</h2> <p> Chirmade et al. 2026 called SVs from 101 whole-genome sequenced individuals enrolled in the CF Canada-SickKids Program in Individualized Therapy (CFIT), a predominantly-European cohort of people with cystic fibrosis. Each sample was sequenced with two long-read / linked-read technologies: PacBio continuous long reads on Sequel I (34 samples, 50x) or Sequel II (67 samples, 76x), and 10X Genomics linked reads on Illumina HiSeq X at ~30x. SVs were called per sample with pbsv v2.2.2 (pbmm2 alignments) and Sniffles v1.0.11 (NGMLR alignments) on the PacBio CLR data, and with Long Ranger, CNVnator v0.4, ERDS v1.1 and Manta v1.6.0 on the 10XG data. Per-platform and cross-platform calls were merged in three steps using a 50% reciprocal overlap rule (pbsv anchored, tagged by Sniffles on PacBio; Manta anchored, augmented by CNVnator, ERDS and Long Ranger deletions on 10XG; then a cross-platform merge with PacBio coordinates preferred), and SV records present in fewer than three participants were dropped. The released catalog contains 87,183 SVs (42,435 deletions, 41,734 insertions, 1,394 duplications, 912 inversions and 708 complex events); the pre-computed GWAS SVatalog LD analyses use a common-SV subset of 35,732 sites against 116,870 GWAS-Catalog SNPs. </p> <p> The annotation TSV <tt>sv_annotations.tsv</tt> was downloaded from the Zenodo companion record, <a href="https://zenodo.org/records/13367574" target="_blank"> zenodo.org/records/13367574</a>. Coordinates in the TSV are 1-based closed and were converted to 0-based half-open BED for this track. </p> <p> The step-by-step build commands (download, coordinate shift, 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> The data can be explored interactively in table format with the <a href="../cgi-bin/hgTables">Table Browser</a> or the <a href="../cgi-bin/hgIntegrator">Data Integrator</a>, and accessed programmatically through our <a href="https://api.genome.ucsc.edu">API</a>, track=<i>chirmade101Sv</i>. </p> <p> The bigBed is available from <a href="http://hgdownload.soe.ucsc.edu/gbdb/hg38/lrSv/" target="_blank">our download server</a> as <tt>chirmade101.bb</tt>. Example: <tt>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/lrSv/chirmade101.bb -chrom=chr21 -start=0 -end=100000000 stdout</tt>. </p> <p> The original annotation table is available on Zenodo: <a href="https://zenodo.org/records/13367574" target="_blank">zenodo.org/records/13367574</a>. The GWAS SVatalog web tool itself is at <a href="https://svatalog.research.sickkids.ca/" target="_blank">svatalog.research.sickkids.ca</a>. </p> <h2>Credits</h2> <p> Thanks to Chirmade, Strug and colleagues at The Hospital for Sick Children and the University of Toronto for releasing this annotated long-read SV callset alongside the GWAS SVatalog tool. </p> <h2>References</h2> <p> Chirmade S, Wang Z, Mastromatteo S, Sanders E, Thiruvahindrapuram B, Nalpathamkalam T, Pellecchia G, Lin F, Keenan K, Patel RV <em>et al</em>. <a href="https://doi.org/10.1038/s41437-025-00809-2" target="_blank"> GWAS SVatalog: a visualization tool to aid fine-mapping of GWAS loci with structural variations</a>. <em>Heredity (Edinb)</em>. 2026 Mar;135(3):199-210. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/41203876" target="_blank">41203876</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13031531/" target="_blank">PMC13031531</a> </p>