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>

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+<h2>Description</h2>
+<p>
+This track shows structural variants (SVs) identified by PacBio HiFi long-read
+whole-genome sequencing of 100 post-mortem human brain samples, split across
+three diagnostic groups: Parkinson's disease (PD), incidental Lewy body
+disease (ILBD) and healthy controls (HC). The high-confidence catalog
+contains 74,552 SVs: 34,056 insertions, 29,545 deletions, 9,707 duplications
+and 1,244 inversions.
+</p>
+<p>
+The dataset accompanies Kim et al. (2026), which combines the long-read SV
+catalog with single-nucleus RNA-seq from the same donors to identify SVs
+associated with cell-type-specific gene expression, including variants
+near genes nominated as causal targets of PD GWAS loci.
+</p>
+
+<h2>Display Conventions and Configuration</h2>
+<p>
+Items are colored by SV type:
+<ul>
+<li><span style="color: rgb(200,0,0);">Deletions (DEL)</span> - red</li>
+<li><span style="color: rgb(0,0,200);">Insertions (INS)</span> - blue</li>
+<li><span style="color: rgb(0,160,0);">Duplications (DUP)</span> - green</li>
+<li><span style="color: rgb(230,140,0);">Inversions (INV)</span> - orange</li>
+</ul>
+</p>
+<p>
+Insertions are placed at the insertion site with a width of 1 bp; deletions,
+duplications and inversions span the affected reference interval. Filters are
+available for SV type, SV length, variant quality and allele frequencies in
+each of the three cohorts (PD, HC, ILBD), as well as the case-minus-control
+carrier-rate differential.
+</p>
+<p>
+The detail page shows, for each variant:
+<ul>
+<li><b>Cohort support vector</b>: three-bit flag (PD/ILBD/HC) indicating
+which cohorts include at least one carrier.</li>
+<li><b>Carrier rates</b>: fraction of cases (PD+ILBD) and controls (HC)
+carrying the variant, and the case-minus-control differential.</li>
+<li><b>Per-cohort AF / AC / AN</b>: alternate allele frequency, alternate
+allele count, and total called alleles in PD, HC and ILBD samples.</li>
+<li><b>Carrier lists</b>: sample IDs carrying the variant in each cohort.</li>
+<li><b>Nearby SNP context</b>: number of SNPs nearby and the number in
+linkage disequilibrium with the SV (from the paper's LD analyses).</li>
+<li><b>Read support</b>: average mapping quality and average supporting
+reads per sample at the variant site.</li>
+</ul>
+</p>
+
+<h2>Methods</h2>
+<p>
+Long-read whole-genome sequencing was performed on 100 post-mortem brain
+samples (35 PD, 31 ILBD, 34 HC) with PacBio HiFi chemistry. Per-sample SV
+calls from multiple callers were merged into a joint callset; the
+high-confidence filtered catalog released in Supplementary Table 13
+(<tt>media-13.txt</tt>) of the Kim et al. 2026 preprint is used directly
+here. Per-cohort allele frequencies, Hardy-Weinberg statistics and case /
+control carrier rates are reported in the source table; the track exposes
+the allele counts and the case-control differential as filterable fields.
+The paper also integrates single-nucleus RNA-seq from two brain regions
+of the same donors to test SV-expression associations in specific cell
+types, but that layer is not shown in this track.
+</p>
+
+<h2>Data Access</h2>
+<p>
+The data can be explored interactively in table format with the
+<a href="../cgi-bin/hgTables">Table Browser</a> or the
+<a href="../cgi-bin/hgIntegrator">Data Integrator</a>, and accessed
+programmatically through our <a href="https://api.genome.ucsc.edu">API</a>,
+track=<i>kwanhoSv</i>.
+</p>
+<p>
+The bigBed is available from
+<a href="http://hgdownload.soe.ucsc.edu/gbdb/hg38/lrSv/" target="_blank">our
+download server</a> as <tt>kwanho.bb</tt>. Example:
+<tt>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/lrSv/kwanho.bb -chrom=chr21 -start=0 -end=100000000 stdout</tt>.
+</p>
+<p>
+The full supplementary data for the paper (including <tt>media-13.txt</tt>)
+is available from the Kim et al. 2026 preprint.
+</p>
+
+<h2>Credits</h2>
+<p>
+Thanks to Kim, Levin and colleagues at the Aligning Science Across
+Parkinson's (ASAP) Collaborative Research Network, the Broad Institute,
+Yale School of Medicine, Banner Sun Health Research Institute and their
+collaborators for releasing this dataset.
+</p>
+
+<h2>References</h2>
+
+
+<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>
+