PGG.Han: the Han Chinese genome database and analysis platform

被引：61

作者：

Gao, Yang ^{[1
,2
]}

Zhang, Chao ^{[1
]}

Yuan, Liyun ^{[1
]}

Ling, YunChao ^{[1
]}

Wang, Xiaoji ^{[1
]}

Liu, Chang ^{[1
]}

Pan, Yuwen ^{[1
]}

Zhang, Xiaoxi ^{[1
,2
]}

Ma, Xixian ^{[1
]}

Wang, Yuchen ^{[1
]}

Lu, Yan ^{[1
,3
]}

Yuan, Kai ^{[1
]}

Ye, Wei ^{[1
]}

Qian, Jiaqiang ^{[1
]}

Chang, Huidan ^{[1
]}

Cao, Ruifang ^{[1
]}

Yang, Xiao ^{[1
]}

Ma, Ling ^{[1
]}

Ju, Yuanhu ^{[1
]}

Dai, Long ^{[1
]}

Tang, Yuanyuan ^{[1
]}

Zhang, Guoqing ^{[1
]}

Xu, Shuhua ^{[1
,2
,3
,4
]}

机构：

[1] Univ Chinese Acad Sci, Chinese Acad Sci,Key Lab Computat Biol, Biomed Big Data Ctr,CAS MPG Partner Inst Computat, Shanghai Inst Nutr & Hlth,Shanghai Inst Biol Sci, Shanghai 200031, Peoples R China

[2] ShanghaiTech Univ, Sch Life Sci & Technol, Shanghai 201210, Peoples R China

[3] Collaborat Innovat Ctr Genet & Dev, Shanghai 200438, Peoples R China

[4] Chinese Acad Sci, Ctr Excellence Anim Evolut & Genet, Kunming 650223, Yunnan, Peoples R China

来源：

NUCLEIC ACIDS RESEARCH | 2020年 / 48卷 / D1期

基金：

中国国家自然科学基金;

关键词：

POPULATION; VARIANTS; ANCESTRY; PANEL; RARE;

D O I：

10.1093/nar/gkz829

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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) populationstructure-aware shared control data for genotypephenotype 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.

引用

页码：D971 / D976

页数：6

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