Building the Sequence Map of the Human Pan-genome

Overview

Journal Nat Biotechnol

Specialty Biotechnology

Date 2009 Dec 10

PMID 19997067

Citations 130

Authors

Ruiqiang Li

Yingrui Li

Hancheng Zheng

Ruibang Luo

Hongmei Zhu

Qibin Li

Wubin Qian

Yuanyuan Ren

Geng Tian

Jinxiang Li

Guangyu Zhou

Xuan Zhu

Honglong Wu

Junjie Qin

Xin Jin

Dongfang Li

Hongzhi Cao

Xueda Hu

Helene Blanche

Howard Cann

Xiuqing Zhang

Songgang Li

Lars Bolund

Karsten Kristiansen

Huanming Yang

Jun Wang

Jian Wang

Affiliations

Soon will be listed here.

Abstract

Here we integrate the de novo assembly of an Asian and an African genome with the NCBI reference human genome, as a step toward constructing the human pan-genome. We identified approximately 5 Mb of novel sequences not present in the reference genome in each of these assemblies. Most novel sequences are individual or population specific, as revealed by their comparison to all available human DNA sequence and by PCR validation using the human genome diversity cell line panel. We found novel sequences present in patterns consistent with known human migration paths. Cross-species conservation analysis of predicted genes indicated that the novel sequences contain potentially functional coding regions. We estimate that a complete human pan-genome would contain approximately 19-40 Mb of novel sequence not present in the extant reference genome. The extensive amount of novel sequence contributing to the genetic variation of the pan-genome indicates the importance of using complete genome sequencing and de novo assembly.

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