3bf9e1a841206d3bf5902e06791ef5be2dbdbd39 max Fri Jul 17 09:09:47 2026 -0700 lrSv: add Noyvert multi-ancestry long-read SV subtrack (noyvertSv) #Preview2 week - bugs introduced now will need a build patch to fix 888 Oxford Nanopore 1000 Genomes genomes, Sniffles2 v2.0.7, 107,445 SVs with per-superpopulation allele frequencies, imputation-accuracy metrics and UK Biobank SV-WAS associations. Converter approximates AC/AN from AF and the genotype missing rate (source has no allele count), stores BND mate breakends, and follows the shared lrSv svType/svLen/insLen/AC field convention so the container-level filters apply. refs #36258 diff --git src/hg/makeDb/trackDb/human/lrSv.html src/hg/makeDb/trackDb/human/lrSv.html index 615e2c4fd8e..a9ff3beb234 100644 --- src/hg/makeDb/trackDb/human/lrSv.html +++ src/hg/makeDb/trackDb/human/lrSv.html @@ -203,30 +203,41 @@ <td>4</td> <td>160</td> <td>1,321,484</td> </tr> <tr> <td><a href="hgTrackUi?g=cardSv">NIH CARD 351</a></td> <td>351</td> <td>NIH CARD post-mortem brain (prefrontal cortex); NABEC (European) + HBCC (African/African-admixed), neurologically normal controls</td> <td>No</td> <td>~40x ONT (R9.4.1 / R10.4.1)</td> <td>228,855</td> <td>1</td> <td>1</td> <td>30,282,742</td> </tr> +<tr> + <td><a href="hgTrackUi?g=noyvertSv">Noyvert 888</a></td> + <td>888</td> + <td>1000 Genomes, 5 superpopulations; used to impute SVs into ~500,000 UK Biobank participants</td> + <td>No</td> + <td>~15x ONT (R9.4.1)</td> + <td>107,445</td> + <td>1</td> + <td>1</td> + <td>28,634,664</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. ~426k SVs (insertions, deletions, inversions) called with pbsv and merged with Jasmine, with allele frequencies, genotype counts and Hardy-Weinberg statistics across the cohort. </p> @@ -357,30 +368,44 @@ OMIM / ClinVar / DGV / Decipher regional annotations. </p> <h3><a href="hgTrackUi?g=cardSv">NIH CARD 351 SVs</a></h3> <p> Structural variants from Oxford Nanopore long-read sequencing of post-mortem brain tissue (prefrontal cortex) from 351 neurologically normal individuals, generated by the NIH Center for Alzheimer's and Related Dementias (NIH CARD) Long-Read Initiative (Billingsley et al. 2024). The cohort combines 205 European-ancestry samples (North American Brain Expression Consortium, NABEC) and 146 African / African-admixed samples (NIMH Human Brain Collection Core, HBCC). ~229k SVs (insertions, deletions, inversions) with per-cohort carrier counts and allele frequencies. </p> +<h3><a href="hgTrackUi?g=noyvertSv">Noyvert 888 SVs</a></h3> +<p> +Structural variants from Oxford Nanopore long-read sequencing of 888 +individuals from the 1000 Genomes Project, spanning five ancestry groups +(European, Admixed American, East Asian, South Asian, African; Noyvert et al. +2025). ~107k SVs (insertions, deletions, inversions, breakends and +duplications) called with Sniffles2, with overall and per-superpopulation +allele frequencies, Sniffles2 and Hardy-Weinberg quality metrics, and +imputation accuracy. The panel was used to impute SVs into about 500,000 UK +Biobank participants and test them for association with disease traits and +protein levels; genome-wide significant UK Biobank associations are listed on +each variant's details page. +</p> + <h2>Data Access</h2> <p> Each subtrack has its own documentation page with details on how to download and intersect the underlying annotations. The build process for all subtracks is recorded in the UCSC makeDoc, <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/lrSv.txt" target="_blank">doc/hg38/lrSv.txt</a> (and <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hs1/lrSv.txt" target="_blank">doc/hs1/lrSv.txt</a> for T2T-CHM13); the conversion scripts are in <a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/lrSv" target="_blank">makeDb/scripts/lrSv</a>, and the track configuration is in <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/trackDb/human/lrSv.ra" target="_blank">trackDb/human/lrSv.ra</a>. </p> <h2>References</h2> @@ -518,15 +543,23 @@ </p> <p> Billingsley KJ, Meredith M, Daida K, Jerez PA, Negi S, Malik L, Genner RM, Moller A, Zheng X, Gibson SB <em>et al</em>. <a href="https://doi.org/10.1101/2024.12.16.628723" target="_blank"> Long-read sequencing of hundreds of diverse brains provides insight into the impact of structural variation on gene expression and DNA methylation</a>. <em>bioRxiv</em>. 2024 Dec 17;. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/39764002" target="_blank">39764002</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11702628/" target="_blank">PMC11702628</a> </p> + +<p> +Noyvert B, Erzurumluoglu AM, Drichel D, Omland S, Andlauer TFM <em>et al</em>. +<a href="https://doi.org/10.7554/eLife.106115.1" target="_blank"> +Imputation of structural variants using a multi-ancestry long-read sequencing panel enables +identification of disease associations</a>. +<em>eLife</em>. 2025. doi:10.7554/eLife.106115.1 +</p>