7594507ca126d5242346787e42e13c52ea7709b1 max Fri Apr 17 08:40:31 2026 -0700 Add lrSv supertrack: long-read structural variants from 9 studies (hg38). #Preview2 week - bugs introduced now will need a build patch to fix Sub-tracks (all bigBed 9+): han945Sv - 945 Han Chinese, ONT (Gong 2025, PMID 39929826) lrSv1kgOnt - 1019 1000 Genomes, ONT, SVAN-annotated (Schloissnig 2025, PMID 40702182; lifted from hs1) tommoJpSv - 333 Japanese (111 trios), ONT (Otsuki 2022, PMID 36127505) aou1kSv - 1027 All of Us, PacBio HiFi (Garimella 2025, PMID 41256123) ga4kSv - 502 GA4K pediatric rare disease, PacBio HiFi (Cohen 2022, PMID 35305867) decodeSv - 3622 Icelanders, ONT (Beyter 2021, PMID 33972781) hgsvc3Sv - 65 HGSVC3 diverse haplotype-resolved assemblies, HiFi+ONT (Logsdon 2025, PMID 40702183; merges insdel+inv tables) kwanhoSv - 100 post-mortem brains (PD/ILBD/HC), PacBio HiFi (Kim 2026, PMID 41929179) chirmade101Sv - 101 long-read WGS GWAS SVatalog cohort (Chirmade 2026, PMID 41203876) Includes per-track conversion scripts and autoSql under scripts/lrSv/, the supertrack summary table in lrSv.html, and a consolidated makeDoc at doc/hg38/lrSv.txt. refs #36258 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> diff --git src/hg/makeDb/trackDb/human/chirmade101Sv.html src/hg/makeDb/trackDb/human/chirmade101Sv.html new file mode 100644 index 00000000000..3f78a6c24dc --- /dev/null +++ src/hg/makeDb/trackDb/human/chirmade101Sv.html @@ -0,0 +1,97 @@ +<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 +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> +SVs were called from 101 long-read whole-genome sequencing samples and +annotated as described in Chirmade et al. 2026. The annotation table used +here (<tt>sv_annotations.tsv</tt>) is the companion data release for GWAS +SVatalog, available from the Zenodo record linked below. Coordinates in +the source TSV are 1-based closed and were converted to 0-based half-open +BED for this track. +</p> +<p> +Note that the SVatalog tool's pre-computed LD analyses use a common-SV +subset (35,732 sites); the underlying long-read callset released in this +TSV (87,183 SVs) is larger and includes rarer variants not used for LD +visualisation. +</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> +