Version: 2016-12-07 public (hg38 lift) Assembly: Human Dec. 2013 (GRCh38/hg38)
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.
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.
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.