030cc7d4165ee6b37bd4c9ecfb443fb39ac2468d max Mon Nov 3 07:59:26 2025 -0800 updating mexico biobank track, and related tracks, refs #36259 diff --git src/hg/makeDb/trackDb/human/hg38/varFreqs.html src/hg/makeDb/trackDb/human/varFreqs.html similarity index 84% rename from src/hg/makeDb/trackDb/human/hg38/varFreqs.html rename to src/hg/makeDb/trackDb/human/varFreqs.html index 7f0f1473060..b68cab22aa6 100644 --- src/hg/makeDb/trackDb/human/hg38/varFreqs.html +++ src/hg/makeDb/trackDb/human/varFreqs.html @@ -1,122 +1,128 @@ <h2>Description</h2> <p> This container track contains annotation tracks with variant frequencies, aka allele frequencies, from these projects: </p> <ul> <li> <b>Mexico Biobank (MXB)</b>: This track displays alleles and their haplotype linkage from the Mexico Biobank (MXB), based on genotyping of 6,011 individuals sampled across all 32 states of Mexico during the 2000 National Health Survey (ENSA 2000) conducted by the National Institute of Public Health (INSP). </li> <li> <b>Mexico City Prospective Study (MCPS)</b>: This track displays only the allele frequencies from the Mexico City - Prospective Study (MXB). From 9,950 whole genome sequenced individuals and 141,046 exome sequenced and genotyped individuals from the Mexico City Prospective Study (MCPS). For details see Ziyatdinov A, Nature 2023 in the reference section of this page. Data version from January 2023. + Prospective Study (MXB). From 9,950 whole genome sequenced individuals and 141,046 exome sequenced and genotyped individuals from the Mexico City Prospective Study (MCPS). For details see Ziyatdinov A, Nature 2023 in the reference section of this page. + </li> + <li> + <b>Million Exomes Project (ME)</b>: Variant frequencies from whole-exome sequencing data from 983,578 individuals sequenced by the Regeneron Genetics Center (RGC). These data span dozens of collaborations including large biobanks and health systems. All data were generated by the RGC on a single, harmonized sequencing and informatics protocol. The dataset includes individuals across diverse ancestral populations, encompassing outbred and founder populations and cohorts with high rates of consanguinity. + </li> + <li> + <b>NHLBI TOPMED Freeze 8</b>: NHLBI TOPMed (Trans-Omics for Precision Medicine) program, launched by the U.S. National Heart, Lung, and Blood Institute, integrates whole-genome sequencing with molecular, clinical, and environmental data from large, well-phenotyped cohorts. Its goal is to uncover the biological mechanisms underlying heart, lung, blood, and sleep disorders to advance precision medicine and improve population health. Freeze 10 contains 868,581,653 variants from 150,899 whole genomes </li> </ul> <h2>Display Conventions</h2> <p> In "pack" mode, the MXB track sorts the haplotypes. This can be useful for determining the similarity between the samples and inferring inheritance at a particular locus. For a full description of how the display works, please see our <a href="../goldenpath/help/hgVcfTrackHelp.html">Haplotype Display help page</a>. Briefly, each sample's phased and/or homozygous genotypes are split into haplotypes, clustered by similarity around a central variant (in pink), and sorted for display by their position in the clustering tree. Click a variant to center on it. The tree (as space allows) is drawn in the label area next to the track image. Leaf clusters, in which all haplotypes are identical (at least for the variants used in clustering), are colored purple. </p> <p> When zoomed it, it display alleles with base-specific coloring. Homozygote data are shown as one letter, while heterozygotes will be displayed with both letters. </p> <h2>Data Access</h2> <p> MXB: Allele frequencies by geographical state and ancestry are available via the <a target=_blank href="https://morenolab.shinyapps.io/mexvar/">MexVar platform</a>. Raw genotype data are available under controlled access at the EGA (Study: EGAS00001005797; Dataset: EGAD00010002361). </p> <p> MCPS: Summarized allele frequencies are available from the <a target=_blank href="https://rgc-mcps.regeneron.com/">MCPS website</a>. </p> <h2>Methods</h2> <p> MXB: Genotyping was performed with the Illumina Multi-Ethnic Global Array (MEGA, ~1.8M SNPs), optimized for admixed populations and enriched for ancestry-informative and medically relevant variants. Only autosomal, biallelic SNPs passing quality control are included. Samples were selected from 898 recruitment sites, with prioritization of indigenous language speakers. Data processing included GenomeStudio → PLINK conversion, strand alignment, removal of duplicates, update of map positions using dbSNP Build 151 and low-quality variants/individuals, and relatedness filtering. </p> <h2>Credits</h2> <p> MXB: We thank the Center for Research and Advanced Studies (Cinvestav) of Mexico for generating and providing the frequency data, the National Institute of Medical Sciences and Nutrition (INCMNSZ) for DNA extraction, and the Ministry of Health together with the National Institute of Public Health (INSP) for the design and implementation of the National Health Survey 2000 (ENSA 2000). We also thank the ENSA-Genomics Consortium for their contributions to sample collection and data processing that made possible the construction of the MXB genomic resource. </p> <p> MCPS: Data produced by Regeneron RGC and collaborators, which are the University of Oxford, Universidad Nacional Autónoma de México (UNAM) and National Institute of Genomic Medicine in Mexico. The Regeneron Genetics Center, University of Oxford, Universidad Nacional Autónoma de México (UNAM), National Institute of Genomic Medicine in Mexico, Abbvie Inc. and AstraZeneca UK Limited (collectively, the “Collaborators”) bear no responsibility for the analyses or interpretations of the data presented here. Any opinions, insights, or conclusions presented herein are those of the authors and not of the Collaborators. </p> </p> <h2>References</h2> <p> Barberena-Jonas, C. et al. (2025). MexVar database: Clinical genetic variation beyond the Hispanic label in the Mexican Biobank. <em>Nature Medicine (in press)</em>. </p> <p> Sohail M, Moreno-Estrada A. <a href="https://journals.biologists.com/dmm/article-lookup/doi/10.1242/dmm.050522" target="_blank"> The Mexican Biobank Project promotes genetic discovery, inclusive science and local capacity building</a>. <em>Dis Model Mech</em>. 2024 Jan 1;17(1). PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/38299665" target="_blank">38299665</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10855211/" target="_blank">PMC10855211</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> Ziyatdinov A, Torres J, Alegre-Díaz J, Backman J, Mbatchou J, Turner M, Gaynor SM, Joseph T, Zou Y, Liu D <em>et al</em>. <a href="https://doi.org/10.1038/s41586-023-06595-3" target="_blank"> Genotyping, sequencing and analysis of 140,000 adults from Mexico City</a>. <em>Nature</em>. 2023 Oct;622(7984):784-793. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/37821707" target="_blank">37821707</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10600010/" target="_blank">PMC10600010</a> </p>