65091fe6f6487c23d650a144e947fc1c582d3f40 max Tue Apr 21 02:16:16 2026 -0700 abelSv: move under lrSv supertrack as short-read comparison subtrack Move the Abel et al. 2020 CCDG 17,795-genome SV callset from a top-level hg38 track to a subtrack of the lrSv supertrack (parallel to onekg3202Sr) and relabel shortLabel/longLabel to flag Illumina short-read provenance. The same bigBed is now visible on hg38 in the long-read SV browsing context. Also: - Clarify abelSv.html variant counts: 738,624 upstream unique SVs across both callsets, 737,998 after B37->hg38 liftOver (626 unmapped). B38=458,106, B37lift=279,892. - lrSv.html: fix triple-slash https:/// in the Ebert et al. Science reference URL. - bigBed.html: add closing </li> on the extra-fields pipe-separator bullet and tighten a comma in the same sentence. refs #36258, refs #37376 diff --git src/hg/makeDb/trackDb/human/lrSv.html src/hg/makeDb/trackDb/human/lrSv.html index e2d16939843..1eec6373f17 100644 --- src/hg/makeDb/trackDb/human/lrSv.html +++ src/hg/makeDb/trackDb/human/lrSv.html @@ -1,449 +1,449 @@ <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> <p> All subtracks below are long-read callsets, except the last row (1KG 3202, Illumina short-read), which is included as a short-read comparator. </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=colorsDbSv">CoLoRSdb</a></td> <td>1,427</td> <td>Consortium of Long-Read Sequencing, joint callset</td> <td>PacBio HiFi</td> <td>426,239</td> <td>20</td> <td>33</td> <td>101,381</td> </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=gustafsonSv">1KG ONT 100</a></td> <td>100</td> <td>1000 Genomes, 5 superpopulations / 19 subpopulations</td> <td>ONT (R9.4.1)</td> <td>113,696</td> <td>0</td> <td>164</td> <td>98,289</td> </tr> <tr> <td><a href="hgTrackUi?g=lrSv1kgOnt">1KG ONT Vienna</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=hprc2Sv">HPRC v2</a></td> <td>233</td> <td>HPRC release-2 pangenome (CHM13 + diverse 1KG assemblies)</td> <td>PacBio HiFi (pangenome graph)</td> <td>1,483,114</td> <td>50</td> <td>280</td> <td>97,718</td> </tr> <tr> <td><a href="hgTrackUi?g=hgsvc2Sv">HGSVC2</a></td> <td>32</td> <td>HGSVC2 haplotype-resolved assemblies (5 superpopulations)</td> <td>PacBio CLR + HiFi + Strand-seq</td> <td>111,746</td> <td>50</td> <td>168</td> <td>57,207,414</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> <tr> <td><a href="hgTrackUi?g=onekg3202Sr">1KG 3202 (short-read)</a></td> <td>3,202</td> <td>1000 Genomes expanded cohort (<b>short-read comparator</b>)</td> <td><b>Illumina short-read</b></td> <td>173,366</td> <td>1</td> <td>314</td> <td>154,807,729</td> </tr> </table> <h3>CoLoRSdb SVs (<a href="hgTrackUi?g=colorsDbSv">colorsDbSv</a>)</h3> <p> Structural variants from the Consortium of Long-Read Sequencing database (CoLoRSdb), from 1,427 PacBio HiFi long-read whole-genome sequences. 426,239 SVs (insertions, deletions, inversions) called with pbsv and merged with Jasmine, with allele frequencies, genotype counts and Hardy-Weinberg statistics across the cohort. </p> <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 100 SVs (<a href="hgTrackUi?g=gustafsonSv">gustafsonSv</a>)</h3> <p> Structural variants from Oxford Nanopore long-read sequencing of 100 1000 Genomes samples (5 superpopulations, 19 subpopulations) released by the 1000 Genomes ONT Sequencing Consortium and described in Gustafson et al. 2024. 113,696 SVs (insertions, deletions, duplications, inversions) called with five callers and merged with Jasmine. This is a separate dataset from the Vienna 1KG-ONT release below. </p> <h3>1KG ONT Vienna 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>HPRC v2 SVs (<a href="hgTrackUi?g=hprc2Sv">hprc2Sv</a>)</h3> <p> Structural variants derived from the Human Pangenome Reference Consortium release-2 minigraph-cactus pangenome graph, built from 233 PacBio HiFi haplotype-resolved assemblies (CHM13 + diverse 1000 Genomes samples). 1,483,114 SV-sized alleles (INS, DEL, COMPLEX, INV) extracted with <tt>vg deconstruct</tt> and decomposed with <tt>vcfwave</tt> (WFA2). </p> <h3>HGSVC2 32 SVs (<a href="hgTrackUi?g=hgsvc2Sv">hgsvc2Sv</a>)</h3> <p> Structural variants from 32 haplotype-resolved diploid genomes (HGSVC2 freeze 4, Ebert et al. 2021). 111,746 SVs (deletions, insertions and inversions) called from phased de novo assemblies with PAV, with per-variant 1000 Genomes population allele frequencies (insertions and deletions) and rich structural/gene annotations. An earlier HGSVC release complementary to <a href="hgTrackUi?g=hgsvc3Sv">HGSVC3</a>. </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> <h3>1KG 3202 SVs (<a href="hgTrackUi?g=onekg3202Sr">onekg3202Sr</a>) - short-read comparator</h3> <p> <b>This is a short-read dataset, included for comparison only.</b> Structural variants from the expanded 1000 Genomes cohort of 3,202 Illumina NovaSeq short-read whole genomes (Byrska-Bishop et al. 2022), called with the GATK-SV / svtools pipeline. 173,366 SVs (DEL, INS, DUP, INV, CPX, CNV, CTX) with per-superpopulation allele frequencies. Useful for contrasting short-read vs. long-read SV breakpoints and for spotting variants unique to long-read data. </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> <p> Gustafson JA, Gibson SB, Damaraju N, Zalusky MPG, Hoekzema K, Twesigomwe D, Yang L, Snead AA, Richmond PA, De Coster W <em>et al</em>. <a href="http://genome.cshlp.org/lookup/pmidlookup?view=long&pmid=39358015" target="_blank"> High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation</a>. <em>Genome Res</em>. 2024 Nov 20;34(11):2061-2073. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/39358015" target="_blank">39358015</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11610458/" target="_blank">PMC11610458</a> </p> <p> Ebert P, Audano PA, Zhu Q, Rodriguez-Martin B, Porubsky D, Bonder MJ, Sulovari A, Ebler J, Zhou W, Serra Mari R <em>et al</em>. -<a href="https:///www.science.org/doi/10.1126/science.abf7117" target="_blank"> +<a href="https://www.science.org/doi/10.1126/science.abf7117" target="_blank"> Haplotype-resolved diverse human genomes and integrated analysis of structural variation</a>. <em>Science</em>. 2021 Apr 2;372(6537). PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/33632895" target="_blank">33632895</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8026704/" target="_blank">PMC8026704</a> </p> <p> Byrska-Bishop M, Evani US, Zhao X, Basile AO, Abel HJ, Regier AA, Corvelo A, Clarke WE, Musunuri R, Nagulapalli K <em>et al</em>. <a href="https://linkinghub.elsevier.com/retrieve/pii/S0092-8674(22)00991-6" target="_blank"> High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios</a>. <em>Cell</em>. 2022 Sep 1;185(18):3426-3440.e19. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/36055201" target="_blank">36055201</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9439720/" target="_blank">PMC9439720</a> </p>