c16022c991b55ffe9bb620746a6101346c920a67 lrnassar Tue May 5 14:23:44 2026 -0700 QA: claim cross-checks on varFreqs description pages; correct 1 internal contradiction and update 3 supertrack references to current/canonical papers. refs #36642 alfaVcf.html: the Description claimed "15.5 million rs sites" while the Methods (and the actual VCF, 163,487,286 records) reflected the post-conversion content. Updated the Description to "163 million variants (146 million SNPs and 17 million indels)" so Description and Methods now agree, and removed the outdated ClinVar count. varFreqs.html (supertrack References): - ABraOM: replaced Naslavsky 2017 Hum Mutat (the 609-individual exome paper) with Naslavsky 2022 Nat Commun (the 1,171-WGS paper), which is the flagship for the data we actually serve and is what abraom.html cites. - Mexico Biobank: added Sohail 2023 Nature ("Mexican Biobank advances population and medical genomics of diverse ancestries"), which is the descriptor paper for the 6,011-individual MEGA-array dataset; the supertrack page previously had no MexBB citation. - ToMMo: replaced Tadaka 2021 NAR (jMorp updates in 2020) with Tadaka 2024 NAR (jMorp Multi-Omics Reference Panel update report 2023), the more recent jMorp release note that tommo60kjpn.html already cites. Other claims spot-checked against the VCF and verified consistent: TopMed (header NS=150,899 matches the page; 868,581,653 records matches exactly), GenomeAsia (~65M / actual 66.2M; 1,739 individuals from 219 populations confirmed), GA4K (552 samples / AN=1,104 / 36.2M variants all verified), SVatalog (8.8M / actual 8,814,835), Tishkoff (33.6M / actual 33,600,472), Saudi (302 individuals / 25.5M variants). diff --git src/hg/makeDb/trackDb/human/varFreqs.html src/hg/makeDb/trackDb/human/varFreqs.html index e46c2c2fcdd..34a4119aca8 100644 --- src/hg/makeDb/trackDb/human/varFreqs.html +++ src/hg/makeDb/trackDb/human/varFreqs.html @@ -513,57 +513,68 @@ PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/27654912" target="_blank">27654912</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5161557/" target="_blank">PMC5161557</a> </p> <p> McCarthy S, Das S, Kretzschmar W, Delaneau O, Wood AR, Teumer A, Kang HM, Fuchsberger C, Danecek P, Sharp K <em>et al</em>. <a href="https://doi.org/10.1038/ng.3643" target="_blank"> A reference panel of 64,976 haplotypes for genotype imputation</a>. <em>Nat Genet</em>. 2016 Oct;48(10):1279-83. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/27548312" target="_blank">27548312</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5388176/" target="_blank">PMC5388176</a> </p> <p> -Naslavsky MS, Yamamoto GL, de Almeida TF, Ezquina SAM, Sunaga DY, Pho N, Bozoklian D, Sandberg TOM, -Brito LA, Lazar M <em>et al</em>. -<a href="https://doi.org/10.1002/humu.23220" target="_blank"> -Exomic variants of an elderly cohort of Brazilians in the ABraOM database</a>. -<em>Hum Mutat</em>. 2017 Jul;38(7):751-763. -PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/28332257" target="_blank">28332257</a> +Naslavsky MS, Scliar MO, Yamamoto GL, Wang JYT, Zverinova S, Karp T, Nunes K, Ceroni JRM, +de Carvalho DL, da Silva Simões CE <em>et al</em>. +<a href="https://doi.org/10.1038/s41467-022-28648-3" target="_blank"> +Whole-genome sequencing of 1,171 elderly admixed individuals from São Paulo, Brazil</a>. +<em>Nat Commun</em>. 2022 Mar 4;13(1):1004. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/35246524" target="_blank">35246524</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8897431/" target="_blank">PMC8897431</a> +</p> + +<p> +Sohail M, Palma-Martínez MJ, Chong AY, Quinto-Cortés CD, Barberena-Jonas C, +Medina-Muñoz SG, Ragsdale A, Delgado-Sánchez G, Cruz-Hervert LP, Ferreyra-Reyes L +<em>et al</em>. +<a href="https://doi.org/10.1038/s41586-023-06560-0" target="_blank"> +Mexican Biobank advances population and medical genomics of diverse ancestries</a>. +<em>Nature</em>. 2023 Oct;622(7984):775-783. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/37821706" target="_blank">37821706</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10600006/" target="_blank">PMC10600006</a> </p> <p> Singh T, Poterba T, Curtis D, Akil H, Al Eissa M, Barchas JD, Bass N, Bigdeli TB, Breen G, Bromet EJ <em>et al</em>. <a href="https://doi.org/10.1038/s41586-022-04556-w" target="_blank"> Rare coding variants in ten genes confer substantial risk for schizophrenia</a>. <em>Nature</em>. 2022 Apr;604(7906):509-516. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/35396579" target="_blank">35396579</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9805802/" target="_blank">PMC9805802</a> </p> <p> -Tadaka S, Hishinuma E, Komaki S, Motoike IN, Kawashima J, Saigusa D, Inoue J, Takayama J, Okamura Y, -Aoki Y <em>et al</em>. -<a href="https://doi.org/10.1093/nar/gkaa1034" target="_blank"> -jMorp updates in 2020: large enhancement of multi-omics data resources on the general Japanese -population</a>. -<em>Nucleic Acids Res</em>. 2021 Jan 8;49(D1):D536-D544. -PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/33179747" target="_blank">33179747</a>; PMC: <a -href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7779038/" target="_blank">PMC7779038</a> +Tadaka S, Kawashima J, Hishinuma E, Saito S, Okamura Y, Otsuki A, Kojima K, Komaki S, Aoki Y, +Kanno T <em>et al</em>. +<a href="https://doi.org/10.1093/nar/gkad978" target="_blank"> +jMorp: Japanese Multi-Omics Reference Panel update report 2023</a>. +<em>Nucleic Acids Res</em>. 2024 Jan 5;52(D1):D622-D632. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/37930845" target="_blank">37930845</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10767895/" target="_blank">PMC10767895</a> </p> <p> Taliun D, Harris DN, Kessler MD, Carlson J, Szpiech ZA, Torres R, Taliun SAG, Corvelo A, Gogarten SM, Kang HM <em>et al</em>. <a href="https://doi.org/10.1038/s41586-021-03205-y" target="_blank"> Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program</a>. <em>Nature</em>. 2021 Feb;590(7845):290-299. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/33568819" target="_blank">33568819</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7875770/" target="_blank">PMC7875770</a> </p> <p> Wong E, Bertin N, Hebrard M, Tirado-Magallanes R, Bellis C, Lim WK, Chua CY, Tong PML, Chua R, Mak K <em>et al</em>.