2eb76dc0d29bb19615c354880a3a58830664b05d max Thu Oct 30 07:16:23 2025 -0700 adding MCPS Mexico city variants, refs #36628 diff --git src/hg/makeDb/trackDb/human/hg38/varFreqs.html src/hg/makeDb/trackDb/human/hg38/varFreqs.html index b827610b738..7f0f1473060 100644 --- src/hg/makeDb/trackDb/human/hg38/varFreqs.html +++ src/hg/makeDb/trackDb/human/hg38/varFreqs.html @@ -1,94 +1,122 @@ <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 allele frequencies from the Mexico Biobank + <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). + 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. </li> </ul> <h2>Display Conventions</h2> <p> -The track sorts the haplotypes. This can be useful for determining the +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> -We thank the Center for Research and Advanced Studies (Cinvestav) of Mexico for +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> +