9cedfa38c14068c79dec89f76c606ee22b3f931a max Wed Sep 30 15:02:37 2026 -0700 phasedVars: new subtrack hgdp1kSnv, a 17GB version of the 3.5TB gnomAD HGDP+1000G genotype VCF with only SNVs with AC>5 and only GT, so haplotype clustering can be shown up to 5Mbp, refs #37306 diff --git src/hg/makeDb/trackDb/human/phasedVars.html src/hg/makeDb/trackDb/human/phasedVars.html index 74fa8148711..80f7a4496df 100644 --- src/hg/makeDb/trackDb/human/phasedVars.html +++ src/hg/makeDb/trackDb/human/phasedVars.html @@ -1,189 +1,201 @@

Description

This tracks contains variants of individual genotypes, usually phased, from the projects Human Diversity Genome Project, Simons Genome Diversity Project, gnomad's HGDP+1000 Genomes callset, and the Mexico Biobank. The original release of 1000 Genomes has its own, separate track. Projects where the released variants are not phased can be found in the container track "SNV Frequencies".

Available on hg19 and hg38:

Mexico Biobank (MXB): This track displays phased alleles from the Mexico Biobank Project (MXB), based on array 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). Frequencies can be plotted onto a map on MexVar. The hg38 track was lifted from hg19.
Simons Genome Diversity Project (SGDP): Funded by the Simons Foundation, the Simons Genome Diversity Project is a large-scale effort that sequenced high-coverage genomes from 300 individuals (279 in this track) representing 142 diverse and often indigenous populations worldwide. Its goal was to capture the full range of human genetic diversity to better understand population history, migration, and adaptation. It is sampling populations in a way that represents as much anthropological, linguistic and cultural diversity as possible, and thus includes many deeply divergent human populations that are not well represented in other datasets. SGDP emphasizes breadth of global representation and population history, whereas HGDP emphasizes continuity and comparability across major population groups. Not all iits data is public, so this track contains only 279 genomes. For details, see (Mallick et al, Nature 2016). The hg38 track was lifted from hg19.

Available only on hg38:

Human Genome Diversity Project (HGDP): 929 high-coverage genome sequences from 54 diverse human populations, 26 of which are physically phased using linked-read sequencing. The Human Genome Diversity Project (HGDP) was launched in the early 1990s to study the genetic variation and evolutionary history of modern humans across global populations. Its goal was to document the full spectrum of human genetic diversity, particularly in indigenous and geographically isolated groups, to better understand population structure, migration, adaptation, and disease susceptibility.The project collected samples from ~1,000 individuals representing over 50 populations worldwide, including groups from Africa, Europe, Asia, Oceania, and the Americas. These data have become a foundational reference for population genetics and human evolution studies. Data can be downloaded from the Sanger Website. For details, see (Bergström et al, Science 2020).
gnomAD HGDP and 1000 Genomes callset: A reprocessed version by the gnomAD project for the 1000 Genomes and Human Genome Diversity Project (HGDP) data, with 4094 genomes from 80 populations. We already have separate, older tracks for 1000 Genomes on the main hg38 browser and for HGDP, just above. This track combines both datasets, with harmonized data quality. For details, see (Koenig et al, 2024).

Display Conventions

Full haplotype display: 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. 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.

For a full description of how the display works, please see our Haplotype Display help page.

Data Access

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). For the VCFs, email andres.moreno@cinvestav.mx.

Methods

SGDP: The version used was https://sharehost.hms.harvard.edu/genetics/reich_lab/sgdp/vcf_variants/, merged with bcftools and lifted to hg38 with CrossMap.

+gnomAD HGDP+1000G, SNVs AC>5: The full gnomAD callset is 3.5 TB and too slow +to display in haplotype clustering mode except in very small windows. For this +second, smaller version we kept only single-nucleotide variants with an allele count +(INFO/AC) higher than five, only the GT genotype field and only the AC, AN and AF +INFO fields, using bcftools. Indels, rare variants and all other fields are only in +the full track. See the +makeDoc and the +script for details. +

Credits

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.

SGDP: This project was funded by the Simons Foundation. Thanks to David Reich and Swapan Mallick for help with importing the data.

References

Barberena-Jonas C, Medina-Muñoz SG, Cedillo-Castelán V, Sepúlveda-Morales T, Gonzaga-Jáuregui C, ENSA Genomics Consortium, García-García L, Ioannidis AG, Moreno-Estrada A. Clinical genetic variation across Hispanic populations in the Mexican Biobank. Nat Med. 2026 Jan 21;. DOI: 10.1038/s41591-025-04100-z; PMID: 41566040

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

Sohail M, Palma-Martínez MJ, Chong AY, Quinto-Corés CD, Barberena-Jonas C, Medina-Muñoz SG, Ragsdale A, Delgado-Sánchez G, Cruz-Hervert LP, Ferreyra-Reyes L et al. Mexican Biobank advances population and medical genomics of diverse ancestries. Nature. 2023 Oct;622(7984):775-783. PMID: 37821706; PMC: PMC10600006

Bergström A, McCarthy SA, Hui R, Almarri MA, Ayub Q, Danecek P, Chen Y, Felkel S, Hallast P, Kamm J et al. Insights into human genetic variation and population history from 929 diverse genomes. Science. 2020 Mar 20;367(6484). PMID: 32193295; PMC: PMC7115999

Koenig Z, Yohannes MT, Nkambule LL, Zhao X, Goodrich JK, Kim HA, Wilson MW, Tiao G, Hao SP, Sahakian N et al. A harmonized public resource of deeply sequenced diverse human genomes. Genome Res. 2024 Jun 25;34(5):796-809. PMID: 38749656; PMC: PMC11216312

Mallick S, Li H, Lipson M, Mathieson I, Gymrek M, Racimo F, Zhao M, Chennagiri N, Nordenfelt S, Tandon A et al. The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature. 2016 Oct 13;538(7624):201-206. PMID: 27654912; PMC: PMC5161557