cc6ef4c74d072de9c22e8bb88ab0e0983e6f2f47
max
  Wed Jul 22 18:09:16 2026 -0700
lrSv cardSv: switch CARD count fields from carrier counts to allele counts

The NIH CARD provider republished the display bigBed with the count columns
changed to diploid allele counts (alleleCount = nabecAlleleCount +
hbccAlleleCount). Re-downloaded and rebuilt; renamed the schema fields to AC /
nabecAc / hbccAc, updated filter ranges (0:702, 0:410, 0:292) and labels to
allele counts, and reworded cardSv.html and the lrSv.html summary. Also noted
there are no Alzheimer's cases in these cohorts. Re-ran the merge so lrSvAll
carries CARD's allele counts. refs #36258

diff --git src/hg/makeDb/trackDb/human/lrSv.html src/hg/makeDb/trackDb/human/lrSv.html
index 6621e40f46a..c2ad0693e4a 100644
--- src/hg/makeDb/trackDb/human/lrSv.html
+++ src/hg/makeDb/trackDb/human/lrSv.html
@@ -195,31 +195,31 @@
 </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>87,068</td>
   <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>NIH CARD post-mortem brain (prefrontal cortex); NABEC (European) + HBCC (African/African-admixed), no Alzheimer's disease cases</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>
@@ -355,40 +355,41 @@
 
 <h3><a href="hgTrackUi?g=chirmade101Sv">SVatalog 101 SVs - Cystic Fibrosis</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>
 
-<h3><a href="hgTrackUi?g=cardSv">NIH CARD 351 SVs - Alzheimer's and related dementias</a></h3>
+<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.
+brain tissue (prefrontal cortex) from 351 individuals, generated by the NIH
+Center for Alzheimer's and Related Dementias (NIH CARD) Long-Read Initiative
+(Billingsley et al. 2024). These are population brain-tissue cohorts with no
+Alzheimer's disease cases. 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 allele 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>