De novo assembly of a haplotype-resolved human genome

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

De novo assembly of a haplotype-resolved human genome. / Cao, Hongzhi; Wu, Honglong; Luo, Ruibang; Huang, Shujia; Sun, Yuhui; Tong, Xin; Xie, Yinlong; Liu, Binghang; Yang, Hailong; Zheng, Hancheng; Li, Jian; Li, Bo; Wang, Yu; Yang, Fang; Sun, Peng; Liu, Siyang; Gao, Peng; Huang, Haodong; Sun, Jing; Chen, Dan; He, Guangzhu; Huang, Weihua; Huang, Zheng; Li, Yue; Tellier, Laurent C.A.M.; Liu, Xiao; Feng, Qiang; Xu, Xun; Zhang, Xiuqing; Bolund, Lars; Krogh, Anders; Kristiansen, Karsten; Drmanac, Radoje; Drmanac, Snezana; Nielsen, Rasmus; Li, Songgang; Wang, Jian; Yang, Huanming; Li, Yingrui; Wong, Gane Ka-Shu; Wang, Jun.

In: Nature Biotechnology, Vol. 33, No. 6, 2015, p. 617-626.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Cao, H, Wu, H, Luo, R, Huang, S, Sun, Y, Tong, X, Xie, Y, Liu, B, Yang, H, Zheng, H, Li, J, Li, B, Wang, Y, Yang, F, Sun, P, Liu, S, Gao, P, Huang, H, Sun, J, Chen, D, He, G, Huang, W, Huang, Z, Li, Y, Tellier, LCAM, Liu, X, Feng, Q, Xu, X, Zhang, X, Bolund, L, Krogh, A, Kristiansen, K, Drmanac, R, Drmanac, S, Nielsen, R, Li, S, Wang, J, Yang, H, Li, Y, Wong, GK-S & Wang, J 2015, 'De novo assembly of a haplotype-resolved human genome', Nature Biotechnology, vol. 33, no. 6, pp. 617-626. https://doi.org/10.1038/nbt.3200

APA

Cao, H., Wu, H., Luo, R., Huang, S., Sun, Y., Tong, X., Xie, Y., Liu, B., Yang, H., Zheng, H., Li, J., Li, B., Wang, Y., Yang, F., Sun, P., Liu, S., Gao, P., Huang, H., Sun, J., ... Wang, J. (2015). De novo assembly of a haplotype-resolved human genome. Nature Biotechnology, 33(6), 617-626. https://doi.org/10.1038/nbt.3200

Vancouver

Cao H, Wu H, Luo R, Huang S, Sun Y, Tong X et al. De novo assembly of a haplotype-resolved human genome. Nature Biotechnology. 2015;33(6):617-626. https://doi.org/10.1038/nbt.3200

Author

Cao, Hongzhi ; Wu, Honglong ; Luo, Ruibang ; Huang, Shujia ; Sun, Yuhui ; Tong, Xin ; Xie, Yinlong ; Liu, Binghang ; Yang, Hailong ; Zheng, Hancheng ; Li, Jian ; Li, Bo ; Wang, Yu ; Yang, Fang ; Sun, Peng ; Liu, Siyang ; Gao, Peng ; Huang, Haodong ; Sun, Jing ; Chen, Dan ; He, Guangzhu ; Huang, Weihua ; Huang, Zheng ; Li, Yue ; Tellier, Laurent C.A.M. ; Liu, Xiao ; Feng, Qiang ; Xu, Xun ; Zhang, Xiuqing ; Bolund, Lars ; Krogh, Anders ; Kristiansen, Karsten ; Drmanac, Radoje ; Drmanac, Snezana ; Nielsen, Rasmus ; Li, Songgang ; Wang, Jian ; Yang, Huanming ; Li, Yingrui ; Wong, Gane Ka-Shu ; Wang, Jun. / De novo assembly of a haplotype-resolved human genome. In: Nature Biotechnology. 2015 ; Vol. 33, No. 6. pp. 617-626.

Bibtex

@article{2aa5344d7b9f47ad9962f75864c25c83,
title = "De novo assembly of a haplotype-resolved human genome",
abstract = "The human genome is diploid, and knowledge of the variants on each chromosome is important for the interpretation of genomic information. Here we report the assembly of a haplotype-resolved diploid genome without using a reference genome. Our pipeline relies on fosmid pooling together with whole-genome shotgun strategies, based solely on next-generation sequencing and hierarchical assembly methods. We applied our sequencing method to the genome of an Asian individual and generated a 5.15-Gb assembled genome with a haplotype N50 of 484 kb. Our analysis identified previously undetected indels and 7.49 Mb of novel coding sequences that could not be aligned to the human reference genome, which include at least six predicted genes. This haplotype-resolved genome represents the most complete de novo human genome assembly to date. Application of our approach to identify individual haplotype differences should aid in translating genotypes to phenotypes for the development of personalized medicine.",
author = "Hongzhi Cao and Honglong Wu and Ruibang Luo and Shujia Huang and Yuhui Sun and Xin Tong and Yinlong Xie and Binghang Liu and Hailong Yang and Hancheng Zheng and Jian Li and Bo Li and Yu Wang and Fang Yang and Peng Sun and Siyang Liu and Peng Gao and Haodong Huang and Jing Sun and Dan Chen and Guangzhu He and Weihua Huang and Zheng Huang and Yue Li and Tellier, {Laurent C.A.M.} and Xiao Liu and Qiang Feng and Xun Xu and Xiuqing Zhang and Lars Bolund and Anders Krogh and Karsten Kristiansen and Radoje Drmanac and Snezana Drmanac and Rasmus Nielsen and Songgang Li and Jian Wang and Huanming Yang and Yingrui Li and Wong, {Gane Ka-Shu} and Jun Wang",
year = "2015",
doi = "10.1038/nbt.3200",
language = "English",
volume = "33",
pages = "617--626",
journal = "Nature Biotechnology",
issn = "1087-0156",
publisher = "nature publishing group",
number = "6",

}

RIS

TY - JOUR

T1 - De novo assembly of a haplotype-resolved human genome

AU - Cao, Hongzhi

AU - Wu, Honglong

AU - Luo, Ruibang

AU - Huang, Shujia

AU - Sun, Yuhui

AU - Tong, Xin

AU - Xie, Yinlong

AU - Liu, Binghang

AU - Yang, Hailong

AU - Zheng, Hancheng

AU - Li, Jian

AU - Li, Bo

AU - Wang, Yu

AU - Yang, Fang

AU - Sun, Peng

AU - Liu, Siyang

AU - Gao, Peng

AU - Huang, Haodong

AU - Sun, Jing

AU - Chen, Dan

AU - He, Guangzhu

AU - Huang, Weihua

AU - Huang, Zheng

AU - Li, Yue

AU - Tellier, Laurent C.A.M.

AU - Liu, Xiao

AU - Feng, Qiang

AU - Xu, Xun

AU - Zhang, Xiuqing

AU - Bolund, Lars

AU - Krogh, Anders

AU - Kristiansen, Karsten

AU - Drmanac, Radoje

AU - Drmanac, Snezana

AU - Nielsen, Rasmus

AU - Li, Songgang

AU - Wang, Jian

AU - Yang, Huanming

AU - Li, Yingrui

AU - Wong, Gane Ka-Shu

AU - Wang, Jun

PY - 2015

Y1 - 2015

N2 - The human genome is diploid, and knowledge of the variants on each chromosome is important for the interpretation of genomic information. Here we report the assembly of a haplotype-resolved diploid genome without using a reference genome. Our pipeline relies on fosmid pooling together with whole-genome shotgun strategies, based solely on next-generation sequencing and hierarchical assembly methods. We applied our sequencing method to the genome of an Asian individual and generated a 5.15-Gb assembled genome with a haplotype N50 of 484 kb. Our analysis identified previously undetected indels and 7.49 Mb of novel coding sequences that could not be aligned to the human reference genome, which include at least six predicted genes. This haplotype-resolved genome represents the most complete de novo human genome assembly to date. Application of our approach to identify individual haplotype differences should aid in translating genotypes to phenotypes for the development of personalized medicine.

AB - The human genome is diploid, and knowledge of the variants on each chromosome is important for the interpretation of genomic information. Here we report the assembly of a haplotype-resolved diploid genome without using a reference genome. Our pipeline relies on fosmid pooling together with whole-genome shotgun strategies, based solely on next-generation sequencing and hierarchical assembly methods. We applied our sequencing method to the genome of an Asian individual and generated a 5.15-Gb assembled genome with a haplotype N50 of 484 kb. Our analysis identified previously undetected indels and 7.49 Mb of novel coding sequences that could not be aligned to the human reference genome, which include at least six predicted genes. This haplotype-resolved genome represents the most complete de novo human genome assembly to date. Application of our approach to identify individual haplotype differences should aid in translating genotypes to phenotypes for the development of personalized medicine.

U2 - 10.1038/nbt.3200

DO - 10.1038/nbt.3200

M3 - Journal article

C2 - 26006006

VL - 33

SP - 617

EP - 626

JO - Nature Biotechnology

JF - Nature Biotechnology

SN - 1087-0156

IS - 6

ER -

ID: 138373867