Posted by: shrikantmantri | December 11, 2009

Nature Biotechnology Paper:Building the sequence map of the human pan-genome

Building the sequence map of the human pan-genome

Ruiqiang Li1,2,7, Yingrui Li1,7, Hancheng Zheng1,3,7, Ruibang Luo1,3,7, Hongmei Zhu1, Qibin Li1, Wubin Qian1, Yuanyuan Ren1, Geng Tian1, Jinxiang Li1, Guangyu Zhou1, Xuan Zhu1, Honglong Wu1,6, Junjie Qin1, Xin Jin1,3, Dongfang Li1,6, Hongzhi Cao1,6, Xueda Hu1, Hélène Blanche4, Howard Cann4, Xiuqing Zhang1, Songgang Li1, Lars Bolund1,5, Karsten Kristiansen1,2, Huanming Yang1, Jun Wang1,2 & Jian Wang1


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 approx5 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 approx19–40 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.


  1. BGI-Shenzhen, Shenzhen 518083, China.
  2. Department of Biology, University of Copenhagen, Copenhagen, Denmark.
  3. School of Bioscience and Biotechnology, South China University of Technology, Guangzhou, China.
  4. Fondation Jean Dausset, Centre d'Étude du Polymorphisme Humain (CEPH), Paris, France.
  5. Institute of Human Genetics, University of Aarhus, Aarhus, Denmark.
  6. Genome Research Institute, Shenzhen University Medical School, Shenzhen, China.
  7. These authors contributed equally to this work.

Correspondence to: Jun Wang1,2 e-mail: wangj@genomics.org.cn

Correspondence to: Jian Wang1 e-mail: wangjian@genomics.org.cn

 

Posted via email from Sharing significant bytes —(Shrikant Mantri)

Advertisements

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s

Categories

%d bloggers like this: