d7817fcecf25ab8669176afc941cadd468729f4a max Tue Nov 25 08:57:14 2025 -0800 adding Singapore to variant frequencies track diff --git src/hg/makeDb/trackDb/human/phasedVars.html src/hg/makeDb/trackDb/human/phasedVars.html new file mode 100644 index 00000000000..52beedc8e7a --- /dev/null +++ src/hg/makeDb/trackDb/human/phasedVars.html @@ -0,0 +1,183 @@ +

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 "Variant 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. + (Publication?) +
+ 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. +

+ +

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. 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 +

+ +

+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 +