Version: Nov 2025 (hg38 lift) Assembly: Human Dec. 2013 (GRCh38/hg38)
Description
The Mexico Biobank (MXB) project
genotyped 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).
Genotyping used the Illumina Multi-Ethnic Global Array (MEGA, ~1.8M SNPs), which is
optimized for admixed populations and enriched for ancestry-informative and medically relevant
variants. Only autosomal, biallelic SNPs that passed quality control are included. Samples
came from 898 recruitment sites, and indigenous language speakers were prioritized.
This track shows allele frequencies computed from the phased genotypes. The full
phased genotype data with haplotype clustering display is available in the
Mexico Biobank track under Phased Variants.
Frequencies can also be plotted onto a map on the
MexVar platform.
The hg38 data was lifted from hg19 by UCSC (see below).
Data Access
Due to license restrictions, the data for this track cannot be downloaded from the UCSC
Genome Browser. The Table Browser, Data Integrator, and download server are not available
for this track.
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). For the VCFs, email
andres.moreno@cinvestav.mx to obtain the data.
Methods
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.
At UCSC, the phased VCF was lifted from hg19 to hg38 with CrossMap, then allele counts
(AC, AF, AN) were computed using bcftools fill-tags and genotypes were stripped to produce
a sites-only frequency VCF.
The makeDoc file documents how the source files of the varFreqs track were converted.
For some tracks, python scripts were needed and are also available from GitHub.
Credits
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.