bac95a147f49cd331052e597006e04b3deee40fc max Wed Apr 22 10:43:20 2026 -0700 lrSv/srSv: human-readable SV type filter labels, script cleanups Add human-readable labels to the supertrack-level svType filter on both the lrSv and srSv supertracks using the "CODE|CODE (Long name)" filterValues syntax: DEL -> "DEL (Deletion)", INS -> "INS (Insertion)", etc. Labels keep the short code up front so users can match what hgTracks shows next to each feature. Also sweep in the in-progress converter/as-file cleanups under scripts/lrSv/ and scripts/srSv/ (introduction of lrSvCommon.py helpers, consistent insLen / svLen / AC column naming, tightened field-description text) that had been piling up as an unstaged working tree. refs #36258 diff --git src/hg/makeDb/trackDb/human/kwanhoSv.html src/hg/makeDb/trackDb/human/kwanhoSv.html index 4c641c20175..76c2050aabd 100644 --- src/hg/makeDb/trackDb/human/kwanhoSv.html +++ src/hg/makeDb/trackDb/human/kwanhoSv.html @@ -1,115 +1,140 @@ <h2>Description</h2> <p style="background-color:#fff3cd; border-left:4px solid #856404; padding:10px 14px; margin-bottom:18px;"> <b>Preliminary data.</b> This callset is a pre-publication release that will be updated before the final publication. Before using these data for analysis or in a paper, please contact the authors at the Aligning Science Across Parkinson's (ASAP) consortium / the Kim lab to check for the latest version and for guidance on appropriate use. </p> <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. +Kim et al. 2026 performed PacBio HiFi long-read whole-genome sequencing on +100 post-mortem cerebellum samples from the Arizona Study of Aging and +Neurodegenerative Disorders / Brain and Body Donation Program cohort +(35 Parkinson's disease, 31 incidental Lewy body disease, 34 healthy +controls). gDNA was isolated with either the Qiagen DNeasy or PacBio +Nanobind PanDNA kit, sheared on a Megaruptor 3 to 10-23.5 kb, built into +SMRTbell libraries (Prep Kit 3.0) and sequenced on PacBio Revio (25M +SMRT cells, 2-h pre-extension, 24-h movies) to ~17x per-sample coverage. +Reads were processed with the Broad long-read WDL pipelines (CCS v6.2.0, +pbmm2 v1.4.0 aligned to GRCh38, SAMtools v1.13 merge/sort) and an +ensemble of three callers was run per sample: Sniffles2 v2.0.6, +<a href="https://github.com/PacificBiosciences/pbsv" target="_blank"> +PBSV</a> v2.9.0 (with GRCh38 tandem-repeat context) and Cue2 v2.0.0 +(deep-learning image-based long-read caller). Per-caller VCFs were +FILTER-PASS / ≥40 bp filtered, split by SV type with BCFtools, and +merged by type across the 100 individuals and across the three callers +with <a href="https://github.com/fritzsedlazeck/SURVIVOR" target="_blank"> +SURVIVOR</a> v1.0.7 (1 kb distance, strand-match, min 50 bp). Centromere, +reference-gap, segmental-duplication and sex-chromosome SVs were excluded. +The high-confidence catalog contains 74,552 SVs (34,056 insertions, +29,545 deletions, 9,707 duplications and 1,244 inversions) released in +Supplementary Table 13 (<tt>media-13.txt</tt>), with per-cohort AF / AC / +AN, Hardy-Weinberg statistics and case/control carrier differentials. +</p> +<p> +The supplementary table <tt>media-13.txt</tt> was downloaded from the Kim +et al. 2026 bioRxiv preprint (<a href="https://doi.org/10.64898/2026.03.20.713192" target="_blank"> +doi:10.64898/2026.03.20.713192</a>). +</p> +<p> +The step-by-step build commands (download, TSV parsing, bigBed build) are +recorded in the UCSC makeDoc for this track container: +<a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/lrSv.txt" target="_blank"> +doc/hg38/lrSv.txt</a>. The conversion scripts and autoSql schemas live in +<a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/lrSv" target="_blank"> +makeDb/scripts/lrSv</a>. </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>