a catalog of biological databases
|Description:||The Han Chinese Genomes Database (PGG.Han) serves as the central repository of the genomic data of the Han Chinese Genomes Project.|
|University/Institution:||CAS-MPG Partner Institute for Computational Biology|
|Address:||320 Yue Yang Road, Shanghai, China 200031|
|Contact name (PI/Team):||Shuhua Xu|
|Contact email (PI/Helpdesk):||firstname.lastname@example.org|
PGG.Han: the Han Chinese genome database and analysis platform. [PMID: 31584086]
As the largest ethnic group in the world, the Han Chinese population is nonetheless underrepresented in global efforts to catalogue the genomic variability of natural populations. Here, we developed the PGG.Han, a population genome database to serve as the central repository for the genomic data of the Han Chinese Genome Initiative (Phase I). In its current version, the PGG.Han archives whole-genome sequences or high-density genome-wide single-nucleotide variants (SNVs) of 114 783 Han Chinese individuals (a.k.a. the Han100K), representing geographical sub-populations covering 33 of the 34 administrative divisions of China, as well as Singapore. The PGG.Han provides: (i) an interactive interface for visualization of the fine-scale genetic structure of the Han Chinese population; (ii) genome-wide allele frequencies of hierarchical sub-populations; (iii) ancestry inference for individual samples and controlling population stratification based on nested ancestry informative markers (AIMs) panels; (iv) population-structure-aware shared control data for genotype-phenotype association studies (e.g. GWASs) and (v) a Han-Chinese-specific reference panel for genotype imputation. Computational tools are implemented into the PGG.Han, and an online user-friendly interface is provided for data analysis and results visualization. The PGG.Han database is freely accessible via http://www.pgghan.org or https://www.hanchinesegenomes.org.