This container track contains annotation tracks with variant frequencies, aka allele frequencies, from these projects:
Most tracks only show the variant and allele frequencies on mouseover or clicks. +When zoomed in, tracks display alleles with base-specific coloring. Homozygote +data are shown as one letter, while heterozygotes will be displayed with both +letters. +
+-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 the MXB track: In "pack" mode, this 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 Haplotype Display help page. 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.
--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. -
Most of the data in these tracks are not available for download from UCSC. +Only individual variants can be browsed on our website. +But the data can be downloaded +for free from the original projects. Accessing the +data usually requires a click-through license on the respectice websites: +
+MXB: Allele frequencies by geographical state and ancestry are available via the MexVar platform. Raw genotype data are available under controlled access at the -EGA (Study: EGAS00001005797; Dataset: EGAD00010002361). +EGA (Study: EGAS00001005797; Dataset: EGAD00010002361). For the VCFs, email andres.moreno@cinvestav.mx.
-MCPS: Summarized allele frequencies are available from +MCPS: VCFs with summarized allele frequencies are available from the MCPS website.
++Regeneron one million exomes: VCFs with summarized allele frequencies are available from +the RGC ME website. +
++TOPMED: VCFs with summarized allele frequencies are available from +the TOPMED BRAVO website. They require a login. +
++GenomeAsia Pilot: VCFs are available from UCSC and also from the +the GenomeAsia 100K website. No license nor login. +
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.
@@ -77,30 +125,39 @@ the ENSA-Genomics Consortium for their contributions to sample collection and data processing that made possible the construction of the MXB genomic resource.
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.
++Regeneron Million Exomes: The Regeneron Genetics Center, and its collaborators +(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. This research has been conducted using the UK Biobank Resource +under application number 26041. +
+Barberena-Jonas, C. et al. (2025). MexVar database: Clinical genetic variation beyond the Hispanic label in the Mexican Biobank. Nature Medicine (in press).
Sohail M, Moreno-Estrada A. The Mexican Biobank Project promotes genetic discovery, inclusive science and local capacity building. Dis Model Mech. 2024 Jan 1;17(1). PMID: 38299665; PMC: PMC10855211 @@ -114,15 +171,34 @@ Nature. 2023 Oct;622(7984):775-783. PMID: 37821706; PMC: PMC10600006
Ziyatdinov A, Torres J, Alegre-Díaz J, Backman J, Mbatchou J, Turner M, Gaynor SM, Joseph T, Zou Y, Liu D et al. Genotyping, sequencing and analysis of 140,000 adults from Mexico City. Nature. 2023 Oct;622(7984):784-793. PMID: 37821707; PMC: PMC10600010
++GenomeAsia100K Consortium. + +The GenomeAsia 100K Project enables genetic discoveries across Asia. +Nature. 2019 Dec;576(7785):106-111. +PMID: 31802016; PMC: PMC7054211 +
+ ++Sun KY, Bai X, Chen S, Bao S, Zhang C, Kapoor M, Backman J, Joseph T, Maxwell E, Mitra G et +al. + +A deep catalogue of protein-coding variation in 983,578 individuals. +Nature. 2024 Jul;631(8021):583-592. +PMID: 38768635; PMC: PMC11254753 +
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