PopHumanVar

PopHumanVar integrates functional and population genomics data to prioritize candidate causal variants in recent human selective sweeps.

Key Features:

• Integration of Diverse Data Sources: Integrates functional and population genomics data from GEVA, SnpEFF, GWAS Catalog, ClinVar, RegulomeDB, and DisGeNET.
• Graphical Representation of Information: Produces layered graphical summaries that combine natural selection statistics and functional annotations.
• Genealogical Estimations: Provides genealogical estimations of variant age for biallelic single nucleotide variants (SNVs) from the 1000 Genomes Project phase 3.
• Selection Statistics: Computes selection statistics including iHS, nSL, and iSAFE to identify regions under positive selection.

Scientific Applications:

• Detect adaptive selection in human populations: Explore candidate genomic regions that underwent selection during human global expansion by combining selection statistics, age estimates, and functional annotations.
• Prioritize causal variants in selective sweeps: Prioritize variants putatively causal of recent selective sweeps using integrated database annotations and computed selection metrics.
• Case studies: Support analysis of established selection examples such as EDAR in East Asians, ACKR1 (DARC) in Africans, and LCT/MCM6 in Europeans.

Methodology:

Integrates GEVA, SnpEFF, GWAS Catalog, ClinVar, RegulomeDB, and DisGeNET with 1000 Genomes Project phase 3 biallelic SNVs to compute iHS, nSL, and iSAFE, estimate variant age, and prioritize candidate causal variants.