HUPAN: a pan-genome analysis pipeline for human genomes

被引：51

作者：

Duan, Zhongqu ^{[1
,2
]}

Qiao, Yuyang ^{[1
]}

Lu, Jinyuan ^{[1
]}

Lu, Huimin ^{[1
]}

Zhang, Wenmin ^{[1
]}

Yan, Fazhe ^{[1
]}

Sun, Chen ^{[1
]}

Hu, Zhiqiang ^{[1
]}

Zhang, Zhen ^{[3
,4
]}

Li, Guichao ^{[3
,4
]}

Chen, Hongzhuan ^{[5
]}

Xiang, Zhen ^{[6
]}

Zhu, Zhenggang ^{[6
]}

Zhao, Hongyu ^{[2
,7
]}

Yu, Yingyan ^{[6
]}

Wei, Chaochun ^{[1
,2
,8
]}

机构：

[1] Shanghai Jiao Tong Univ, Sch Life Sci & Biotechnol, 800 Dongchuan Rd, Shanghai 200240, Peoples R China

[2] Shanghai Jiao Tong Univ, SJTU Yale Joint Ctr Biostat & Data Sci, 800 Dongchuan Rd, Shanghai 200240, Peoples R China

[3] Fudan Univ, Shanghai Canc Ctr, Shanghai Med Coll, Dept Radiat Oncol, 270 Dong An Rd, Shanghai 200032, Peoples R China

[4] Fudan Univ, Shanghai Canc Ctr, Shanghai Med Coll, Dept Oncol, 270 Dong An Rd, Shanghai 200032, Peoples R China

[5] Shanghai Jiao Tong Univ, Sch Med, Shanghai Key Lab Translat Med, Dept Pharmacol, 227 South Chongqing Rd, Shanghai 200025, Peoples R China

[6] Shanghai Jiao Tong Univ, Shanghai Key Lab Gastr Neoplasms, Sch Med, Dept Surg,Ruijin Hosp, 197 Ruijin Rd, Shanghai 200025, Peoples R China

[7] Yale Univ, Dept Biostat, 60 Coll St, New Haven, CT 06520 USA

[8] Shanghai Ctr Bioinformat Technol, 1278 Keyuan Rd, Shanghai 201203, Peoples R China

来源：

GENOME BIOLOGY | 2019年 / 20卷 / 1期

基金：

中国国家自然科学基金; 国家重点研发计划;

关键词：

Pan-genome; Core genome; Presence-absence variation (PAV); Genome assembly; Population-specific variation; READ ALIGNMENT; SEQUENCE; DIVERSITY; ANNOTATION; CHIMPANZEE; INSIGHTS;

D O I：

10.1186/s13059-019-1751-y

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

The human reference genome is still incomplete, especially for those population-specific or individual-specific regions, which may have important functions. Here, we developed a HUman Pan-genome ANalysis (HUPAN) system to build the human pan-genome. We applied it to 185 deep sequencing and 90 assembled Han Chinese genomes and detected 29.5Mb novel genomic sequences and at least 188 novel protein-coding genes missing in the human reference genome (GRCh38). It can be an important resource for the human genome-related biomedical studies, such as cancer genome analysis. HUPAN is freely available at http://cgm.sjtu.edu.cn/hupan/ and https://github.com/SJTU-CGM/HUPAN.

引用

页数：11

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