Abstract
The 1000 Genomes Project (1000GP) represents the most comprehensive world-wide nucleotide variation data set so far in humans, providing the sequencing and analysis of 2504 genomes from 26 populations and reporting >84 million variants. The availability of this sequence data provides the human lineage with an invaluable resource for population genomics studies, allowing the testing of molecular population genetics hypotheses and eventually the understanding of the evolutionary dynamics of genetic variation in human populations. Here we present PopHuman, a new population genomics-oriented genome browser based on JBrowse that allows the interactive visualization and retrieval of an extensive inventory of population genetics metrics. Efficient and reliable parameter estimates have been computed using a novel pipeline that faces the unique features and limitations of the 1000GP data, and include a battery of nucleotide variation measures, divergence and linkage disequilibrium parameters, as well as different tests of neutrality, estimated in non-overlapping windows along the chromosomes and in annotated genes for all 26 populations of the 1000GP. PopHuman is open and freely available at http://pophuman.uab.cat.
Highlights
Soon after the elucidation of the entire human genome [1,2,3], the description of genetic variation in human populations and the identification of those variants that affect health and disease became the challenges of genomics research [4]
The 1000 Genomes Project (1000GP) represents the most comprehensive world-wide nucleotide variation data set so far in humans, providing the sequencing and analysis of 2504 genomes from 26 populations and reporting >84 million variants. The availability of this sequence data provides the human lineage with an invaluable resource for population genomics studies, allowing the testing of molecular population genetics hypotheses and eventually the understanding of the evolutionary dynamics of genetic variation in human populations
In addition to numerous genome-wide association studies (GWAS) [7], the HapMap data allowed the detection of positive natural selection across the human genome [8,9], as well as the development of new tests to infer recent episodes of selective sweeps based on the length of haplotypes, such as the Long-Range Haplotype (LRH) [10], the integrated Haplotype Score [11], and the Cross Population Extended Haplotype Homozygosity (XP-EHH) [8]
Summary
Soon after the elucidation of the entire human genome [1,2,3], the description of genetic variation in human populations and the identification of those variants that affect health and disease became the challenges of genomics research [4]. PopHuman represents an update to the 1000GP Phase III (2504 individuals, 26 populations, 84.7 million SNPs), and dramatic improvements in the amount of data analyzed and browser performance, compared to the 1000 Genomes Selection Browser 1.0.
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