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/lrSv.html src/hg/makeDb/trackDb/human/lrSv.html new file mode 100644 index 00000000000..7517ed38730 --- /dev/null +++ src/hg/makeDb/trackDb/human/lrSv.html @@ -0,0 +1,308 @@ +<h2>Description</h2> +<p> +This track collection contains structural variant (SV) calls derived from long-read sequencing +studies. Structural variants are genomic rearrangements larger than ~50 bp, including +deletions, insertions, duplications, inversions, and translocations. Long-read sequencing +technologies can span repetitive regions and resolve complex rearrangements +that are difficult to detect with short-read methods. +</p> + +<h3>Available Datasets</h3> +<p> +SV length statistics (min / median / max) are computed from the <tt>svLen</tt> +field of each track, in base pairs. Some tracks include sites with +<tt>svLen=0</tt> (complex events where the reference and alternate alleles +differ in sequence but not in length). +</p> +<table class="stdTbl"> +<tr> + <th>Dataset</th> + <th>N samples</th> + <th>Cohort / disease</th> + <th>Sequencing</th> + <th>SVs</th> + <th>Min</th> + <th>Median</th> + <th>Max</th> +</tr> +<tr> + <td><a href="hgTrackUi?g=han945Sv">Han 945</a></td> + <td>945</td> + <td>Han Chinese, general population</td> + <td>ONT (PromethION)</td> + <td>111,288</td> + <td>0</td> + <td>254</td> + <td>99,743</td> +</tr> +<tr> + <td><a href="hgTrackUi?g=lrSv1kgOnt">1KG ONT</a></td> + <td>1,019</td> + <td>1000 Genomes, globally diverse</td> + <td>ONT</td> + <td>148,375</td> + <td>2</td> + <td>177</td> + <td>49,171</td> +</tr> +<tr> + <td><a href="hgTrackUi?g=tommoJpSv">ToMMo Japanese</a></td> + <td>333 (111 trios)</td> + <td>Japanese, general population</td> + <td>ONT</td> + <td>74,201</td> + <td>51</td> + <td>162</td> + <td>99,980</td> +</tr> +<tr> + <td><a href="hgTrackUi?g=aou1kSv">AoU 1K</a></td> + <td>1,027</td> + <td>All of Us, self-identified Black/African American</td> + <td>PacBio HiFi</td> + <td>541,049</td> + <td>50</td> + <td>152</td> + <td>9,998</td> +</tr> +<tr> + <td><a href="hgTrackUi?g=ga4kSv">GA4K</a></td> + <td>502</td> + <td>Children's Mercy, pediatric rare disease probands + families</td> + <td>PacBio HiFi</td> + <td>115,554</td> + <td>50</td> + <td>186</td> + <td>809,711</td> +</tr> +<tr> + <td><a href="hgTrackUi?g=decodeSv">deCODE 3,622</a></td> + <td>3,622</td> + <td>Icelandic general population</td> + <td>ONT</td> + <td>133,886</td> + <td>0</td> + <td>127</td> + <td>861,080</td> +</tr> +<tr> + <td><a href="hgTrackUi?g=hgsvc3Sv">HGSVC3</a></td> + <td>65</td> + <td>HGSVC3 diverse reference assemblies</td> + <td>PacBio HiFi + ONT</td> + <td>176,531</td> + <td>50</td> + <td>154</td> + <td>30,176,500</td> +</tr> +<tr> + <td><a href="hgTrackUi?g=kwanhoSv">Kim PD Brain</a></td> + <td>100</td> + <td>Parkinson's disease, ILBD, controls (post-mortem brain)</td> + <td>PacBio HiFi</td> + <td>74,552</td> + <td>50</td> + <td>160</td> + <td>190,088,222</td> +</tr> +<tr> + <td><a href="hgTrackUi?g=chirmade101Sv">SVatalog 101</a></td> + <td>101</td> + <td>Long-read WGS cohort for GWAS LD fine-mapping (SickKids)</td> + <td>long-read</td> + <td>87,183</td> + <td>4</td> + <td>160</td> + <td>1,321,484</td> +</tr> +</table> + +<h3>Han 945 SVs (<a href="hgTrackUi?g=han945Sv">han945Sv</a>)</h3> +<p> +Structural variants from 945 Han Chinese individuals. 111,288 SVs +(deletions, insertions, duplications, inversions, translocations) merged with SURVIVOR. +Includes allele frequencies and per-sample support. +</p> + +<h3>1KG ONT SVs (<a href="hgTrackUi?g=lrSv1kgOnt">lrSv1kgOnt</a>)</h3> +<p> +Structural variants from 1,019 individuals across 26 populations (1000 Genomes ONT). +161,332 SVs annotated with SVAN, classifying insertions and deletions by mechanism +of origin (mobile elements, VNTRs, processed pseudogenes, etc.). +Original coordinates are on T2T-CHM13 (hs1); the hg38 version was created via liftOver. +</p> + +<h3>ToMMo Japanese SVs (<a href="hgTrackUi?g=tommoJpSv">tommoJpSv</a>)</h3> +<p> +Structural variants from 333 Japanese individuals (111 trios) from the Tohoku Medical +Megabank (ToMMo). 74,201 SVs (deletions and insertions) with trio-based Mendelian +error rates and allele frequencies. +</p> + +<h3>AoU 1K SVs (<a href="hgTrackUi?g=aou1kSv">aou1kSv</a>)</h3> +<p> +Structural variants from 1,027 individuals from the All of Us (AoU) Research Program, +sequenced with PacBio HiFi long reads. 541,049 SVs (insertions and deletions) +with population-specific allele frequencies, gene annotations, and clinical +trait associations. +</p> + +<h3>GA4K SVs (<a href="hgTrackUi?g=ga4kSv">ga4kSv</a>)</h3> +<p> +Structural variants from 502 probands and family members enrolled in the +Genomic Answers for Kids (GA4K) pediatric rare-disease program at Children's +Mercy Research Institute, sequenced with PacBio HiFi long reads. 115,554 +replicated SVs (deletions, insertions, duplications, inversions) called with +pbsv and merged with JASMINE. The matched GA4K small-variant callset (SNVs +and short indels) lives alongside other population allele-frequency resources +as <a href="hgTrackUi?g=ga4kSnv">GA4K 552 PacBio LR</a> in the Variant +Frequencies track collection. +</p> + +<h3>deCODE 3,622 SVs (<a href="hgTrackUi?g=decodeSv">decodeSv</a>)</h3> +<p> +High-confidence structural variants from 3,622 Icelanders (deCODE genetics), +sequenced with Oxford Nanopore long reads. 133,886 SVs (deletions, insertions +and combined insertion/deletion events). Site-only callset with annotated +surrounding tandem-repeat regions. +</p> + +<h3>HGSVC3 65 SVs (<a href="hgTrackUi?g=hgsvc3Sv">hgsvc3Sv</a>)</h3> +<p> +Structural variants from 65 diverse individuals sequenced and de novo +assembled by the Human Genome Structural Variation Consortium phase 3 +(HGSVC3). 176,532 haplotype-resolved SVs (deletions, insertions and +inversions) called with PAV and cross-validated with ten additional callers, +with per-site carrier haplotype lists and structural annotations. +</p> + +<h3>Kim PD Brain SVs (<a href="hgTrackUi?g=kwanhoSv">kwanhoSv</a>)</h3> +<p> +Structural variants from 100 post-mortem brain samples (Parkinson's disease, +incidental Lewy body disease, and healthy controls) sequenced with PacBio +HiFi long reads. 74,552 high-confidence SVs (deletions, insertions, +duplications, inversions) with per-cohort allele frequencies and +case-control carrier-rate differentials, from Kim et al. 2026. +</p> + +<h3>SVatalog 101 SVs (<a href="hgTrackUi?g=chirmade101Sv">chirmade101Sv</a>)</h3> +<p> +Structural variants from 101 long-read whole-genome sequences released +alongside the GWAS SVatalog tool (Chirmade et al. 2026). 87,183 SVs +(deletions, insertions, duplications, inversions and complex events) +annotated with gene overlaps, ClinGen / gnomAD constraint scores, +OMIM / ClinVar / DGV / Decipher regional annotations. +</p> + +<h2>Data Access</h2> +<p> +Each subtrack has its own documentation page with details on how to download +and intersect the underlying annotations. +</p> + +<h2>References</h2> + +<p> +Gong J, Sun H, Wang K, Zhao Y, Huang Y, Chen Q, Qiao H, Gao Y, Zhao J, Ling Y <em>et al</em>. +<a href="https://doi.org/10.1038/s41467-025-56661-9" target="_blank"> +Long-read sequencing of 945 Han individuals identifies structural variants associated with +phenotypic diversity and disease susceptibility</a>. +<em>Nat Commun</em>. 2025 Feb 10;16(1):1494. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/39929826" target="_blank">39929826</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11811171/" target="_blank">PMC11811171</a> +</p> + +<p> +Schloissnig S, Pani S, Ebler J, Hain C, Tsapalou V, Söylev A, Hüther P, Ashraf H, Prodanov T, +Asparuhova M <em>et al</em>. +<a href="https://doi.org/10.1038/s41586-025-09290-7" target="_blank"> +Structural variation in 1,019 diverse humans based on long-read sequencing</a>. +<em>Nature</em>. 2025 Aug;644(8076):442-452. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/40702182" target="_blank">40702182</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12350158/" target="_blank">PMC12350158</a> +</p> + + +<p> +Otsuki A, Okamura Y, Ishida N, Tadaka S, Takayama J, Kumada K, Kawashima J, Taguchi K, Minegishi N, +Kuriyama S <em>et al</em>. +<a href="https://doi.org/10.1038/s42003-022-03953-1" target="_blank"> +Construction of a trio-based structural variation panel utilizing activated T lymphocytes and long- +read sequencing technology</a>. +<em>Commun Biol</em>. 2022 Sep 20;5(1):991. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/36127505" target="_blank">36127505</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9489684/" target="_blank">PMC9489684</a> +</p> + + + +<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> + + + +<p> +Cohen ASA, Farrow EG, Abdelmoity AT, Alaimo JT, Amudhavalli SM, Anderson JT, Bansal L, Bartik L, +Baybayan P, Belden B <em>et al</em>. +<a href="https://linkinghub.elsevier.com/retrieve/pii/S1098-3600(22)00653-0" target="_blank"> +Genomic answers for children: Dynamic analyses of >1000 pediatric rare disease genomes</a>. +<em>Genet Med</em>. 2022 Jun;24(6):1336-1348. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/35305867" target="_blank">35305867</a> +</p> + + + +<p> +Beyter D, Ingimundardottir H, Oddsson A, Eggertsson HP, Bjornsson E, Jonsson H, Atlason BA, +Kristmundsdottir S, Mehringer S, Hardarson MT <em>et al</em>. +<a href="https://doi.org/10.1038/s41588-021-00865-4" target="_blank"> +Long-read sequencing of 3,622 Icelanders provides insight into the role of structural variants in +human diseases and other traits</a>. +<em>Nat Genet</em>. 2021 Jun;53(6):779-786. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/33972781" target="_blank">33972781</a> +</p> + + + +<p> +Logsdon GA, Ebert P, Audano PA, Loftus M, Porubsky D, Ebler J, Yilmaz F, Hallast P, Prodanov T, Yoo +D <em>et al</em>. +<a href="https://doi.org/10.1038/s41586-025-09140-6" target="_blank"> +Complex genetic variation in nearly complete human genomes</a>. +<em>Nature</em>. 2025 Aug;644(8076):430-441. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/40702183" target="_blank">40702183</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12350169/" target="_blank">PMC12350169</a> +</p> + + + +<p> +Kim K, Lin Z, Simmons SK, Parker J, Kearney M, Liao Z, Haywood N, Zhang J, Cline MP, Tuncali I +<em>et al</em>. +<a href="https://doi.org/10.64898/2026.03.20.713192" target="_blank"> +Integrating Long-Read Structural Variant Analysis with single-nucleus RNA-seq to Elucidate Gene +Expression Effects in Disease</a>. +<em>bioRxiv</em>. 2026 Mar 23;. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/41929179" target="_blank">41929179</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13041997/" target="_blank">PMC13041997</a> +</p> + + + +<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> +