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/lrSv.html src/hg/makeDb/trackDb/human/lrSv.html index 4b396be3b91..e55ac8a085f 100644 --- src/hg/makeDb/trackDb/human/lrSv.html +++ src/hg/makeDb/trackDb/human/lrSv.html @@ -33,31 +33,31 @@ <th>N samples</th> <th>Cohort / disease</th> <th>Disease cases</th> <th>Coverage</th> <th>SV count</th> <th>Min</th> <th>Median</th> <th>Max</th> </tr> <tr> <td><a href="hgTrackUi?g=lrSvAll"><b>All merged</b></a></td> <td>—</td> <td>All long-read SV datasets merged on identical position+type+length, with per-database AC</td> <td>mixed</td> <td>mixed (PacBio HiFi, ONT)</td> - <td>2,359,011</td> + <td>2,317,508</td> <td>0</td> <td>147</td> <td>190,088,223</td> </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>No</td> <td>mixed (HiFi)</td> <td>426,239</td> <td>20</td> <td>33</td> <td>101,381</td> </tr> @@ -66,31 +66,31 @@ <td>945</td> <td>Han Chinese, general population</td> <td>No</td> <td>~17x ONT</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>No</td> <td>~37x ONT (R9.4.1)</td> - <td>113,696</td> + <td>113,159</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, diverse</td> <td>No</td> <td>~17x ONT</td> <td>148,375</td> <td>2</td> <td>177</td> <td>49,171</td> </tr> @@ -99,64 +99,64 @@ <td>333 (111 trios)</td> <td>Japanese, general population</td> <td>No</td> <td>~22x 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; biobank includes a variety of conditions (diabetes, hearing loss, etc.)</td> <td>Yes (mixed)</td> <td>~8x HiFi</td> - <td>541,049</td> + <td>540,155</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>Yes (probands)</td> <td>~27x 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>No</td> <td>~17x ONT</td> - <td>133,886</td> + <td>119,453</td> <td>0</td> <td>127</td> <td>861,080</td> </tr> <tr> <td><a href="hgTrackUi?g=hprc2v21Sv">HPRC v2.1</a></td> <td>233</td> <td>HPRC release-2 pangenome (CHM13 + diverse 1KG assemblies)</td> <td>No</td> <td>~60x HiFi + ~30x ONT (pangenome graph)</td> - <td>596,063</td> + <td>549,649</td> <td>50</td> <td>276</td> <td>1,064,897</td> </tr> <tr> <td><a href="hgTrackUi?g=hgsvc2Sv">HGSVC2</a></td> <td>32</td> <td>HGSVC2 haplotype-resolved assemblies (5 superpopulations)</td> <td>No</td> <td>>40x PacBio CLR + >20x HiFi (+ Strand-seq)</td> <td>111,746</td> <td>50</td> <td>168</td> <td>57,207,414</td> </tr> @@ -181,48 +181,37 @@ <td>1</td> <td>21</td> <td>99,885</td> </tr> <tr> <td><a href="hgTrackUi?g=cpc1Sv">CPC</a></td> <td>58</td> <td>Chinese Pangenome Consortium, 36 minority ethnic groups (HPRC-specific SVs removed)</td> <td>No</td> <td>~30x HiFi (pangenome graph)</td> <td>36,030</td> <td>1</td> <td>53</td> <td>8,998,096</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>Yes (PD + ILBD)</td> - <td>~17x 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>Cystic fibrosis (CF) patients from the CF Canada-Sick Kids Program in Individual CF Therapy (CFIT). Long-read WGS used for GWAS LD fine-mapping</td> <td>Yes (all CF)</td> <td>~50x PacBio CLR (34, Sequel I) + ~76x HiFi (67, Sequel II)</td> - <td>87,183</td> + <td>87,068</td> <td>4</td> <td>160</td> <td>1,321,484</td> </tr> </table> <p> Note: there is likely some overlap in sample composition across these collections. For example, 1000 Genomes samples are also included in HPRC and CoLoRSdb. </p> <h3><a href="hgTrackUi?g=colorsDbSv">CoLoRSdb SVs</a></h3> <p> Structural variants from the Consortium of Long-Read Sequencing database (CoLoRSdb), from 1,427 PacBio HiFi long-read whole-genome sequences. @@ -331,39 +320,30 @@ drawn from eight countries (PacBio HiFi + ultralong ONT + Hi-C; Nassir et al. 2025). ~73k SVs on hg38 (deletions, insertions, complex and mixed snarls), lifted from the native T2T-CHM13 assembly; the hs1 track uses the native coordinates. </p> <h3><a href="hgTrackUi?g=cpc1Sv">CPC 58 SVs</a></h3> <p> Structural variants from the Chinese Pangenome Consortium (CPC), 58 samples spanning 36 minority ethnic groups (PacBio HiFi pangenome graph; Gao et al. 2023). This track shows the CPC contribution to the joint CPC+HPRC graph with HPRC-specific SVs removed. ~36k SVs on hg38 (deletions, insertions and mixed snarls), lifted from the native T2T-CHM13 assembly; the hs1 track is native. </p> -<h3><a href="hgTrackUi?g=kwanhoSv">Kim PD Brain SVs</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. ~75k 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><a href="hgTrackUi?g=chirmade101Sv">SVatalog 101 SVs</a></h3> <p> Structural variants from 101 long-read whole-genome sequences released alongside the GWAS SVatalog tool (Chirmade et al. 2026). The samples come from the CF Canada-Sick Kids Program in Individual CF Therapy (CFIT), a cystic-fibrosis (CF) patient cohort assembled to model patient-specific responses to CFTR modulator therapies (most participants are F508del homozygotes or F508del / minimal-function compound heterozygotes; a smaller number carry rare nonsense or missense CFTR mutations). ~87k SVs (deletions, insertions, duplications, inversions and complex events) annotated with gene overlaps, ClinGen / gnomAD constraint scores, OMIM / ClinVar / DGV / Decipher regional annotations. </p> @@ -444,40 +424,30 @@ <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>