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>