Genomic Analyses from Non-invasive Prenatal Testing Reveal Genetic Associations, Patterns of Viral Infections, and Chinese Population History

Siyang Liu; Shujia Huang; Fang Chen; Lijian Zhao; Yuying Yuan; Stephen Starko Francis; Lin Fang; Zilong Li; Long Lin; Rong Liu; Yong Zhang; Huixin Xu; Shengkang Li; Yuwen Zhou; Robert W. Davies; Qiang Liu; Robin G. Walters; Kuang Lin; Jia Ju; Thorfinn Korneliussen; Melinda A. Yang; Qiaomei Fu; Jun Wang; Lijun Zhou; Anders Krogh; Hongyun Zhang; Wei Wang; Zhengming Chen; Zhiming Cai; Ye Yin; Huanming Yang; Mao Mao; Jay Shendure; Jian Wang; Anders Albrechtsen; Xin Jin; Rasmus Nielsen; Xun Xu

doi:10.1016/j.cell.2018.08.016

Genomic Analyses from Non-invasive Prenatal Testing Reveal Genetic Associations, Patterns of Viral Infections, and Chinese Population History

Siyang Liu
, Shujia Huang
, Fang Chen
, Lijian Zhao
, Yuying Yuan
, Stephen Starko Francis
, Lin Fang
, Zilong Li
, Long Lin
, Rong Liu
, Yong Zhang
, Huixin Xu
, Shengkang Li
, Yuwen Zhou
, Robert W. Davies
, Qiang Liu
, Robin G. Walters
, Kuang Lin
, Jia Ju
, Thorfinn Korneliussen

Melinda A. Yang, Qiaomei Fu, Jun Wang, Lijun Zhou, Anders Krogh, Hongyun Zhang, Wei Wang, Zhengming Chen, Zhiming Cai, Ye Yin, Huanming Yang, Mao Mao, Jay Shendure, Jian Wang, Anders Albrechtsen, Xin Jin, Rasmus Nielsen, Xun Xu

Research output: Contribution to journal › Article › peer-review

228 Scopus citations

Abstract

We analyze whole-genome sequencing data from 141,431 Chinese women generated for non-invasive prenatal testing (NIPT). We use these data to characterize the population genetic structure and to investigate genetic associations with maternal and infectious traits. We show that the present day distribution of alleles is a function of both ancient migration and very recent population movements. We reveal novel phenotype-genotype associations, including several replicated associations with height and BMI, an association between maternal age and EMB, and between twin pregnancy and NRG1. Finally, we identify a unique pattern of circulating viral DNA in plasma with high prevalence of hepatitis B and other clinically relevant maternal infections. A GWAS for viral infections identifies an exceptionally strong association between integrated herpesvirus 6 and MOV10L1, which affects piwi-interacting RNA (piRNA) processing and PIWI protein function. These findings demonstrate the great value and potential of accumulating NIPT data for worldwide medical and genetic analyses. Large-scale analysis of genome sequences from non-invasive prenatal testing in Chinese women yields insights into phenotypic trait associations, viral infection patterns, and population history.

Original language	English
Pages (from-to)	347-359.e14
Journal	Cell
Volume	175
Issue number	2
DOIs	https://doi.org/10.1016/j.cell.2018.08.016
State	Published - 4 Oct 2018
Externally published	Yes

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

Keywords

genome-wide association study
low-pass sequencing
non-invasive prenatal testing
plasma virome
population genetics

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10.1016/j.cell.2018.08.016

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Liu, S., Huang, S., Chen, F., Zhao, L., Yuan, Y., Francis, S. S., Fang, L., Li, Z., Lin, L., Liu, R., Zhang, Y., Xu, H., Li, S., Zhou, Y., Davies, R. W., Liu, Q., Walters, R. G., Lin, K., Ju, J., ... Xu, X. (2018). Genomic Analyses from Non-invasive Prenatal Testing Reveal Genetic Associations, Patterns of Viral Infections, and Chinese Population History. Cell, 175(2), 347-359.e14. https://doi.org/10.1016/j.cell.2018.08.016

@article{256e3365d71b4f9981df1433e7a336dd,

title = "Genomic Analyses from Non-invasive Prenatal Testing Reveal Genetic Associations, Patterns of Viral Infections, and Chinese Population History",

abstract = "We analyze whole-genome sequencing data from 141,431 Chinese women generated for non-invasive prenatal testing (NIPT). We use these data to characterize the population genetic structure and to investigate genetic associations with maternal and infectious traits. We show that the present day distribution of alleles is a function of both ancient migration and very recent population movements. We reveal novel phenotype-genotype associations, including several replicated associations with height and BMI, an association between maternal age and EMB, and between twin pregnancy and NRG1. Finally, we identify a unique pattern of circulating viral DNA in plasma with high prevalence of hepatitis B and other clinically relevant maternal infections. A GWAS for viral infections identifies an exceptionally strong association between integrated herpesvirus 6 and MOV10L1, which affects piwi-interacting RNA (piRNA) processing and PIWI protein function. These findings demonstrate the great value and potential of accumulating NIPT data for worldwide medical and genetic analyses. Large-scale analysis of genome sequences from non-invasive prenatal testing in Chinese women yields insights into phenotypic trait associations, viral infection patterns, and population history.",

keywords = "genome-wide association study, low-pass sequencing, non-invasive prenatal testing, plasma virome, population genetics",

author = "Siyang Liu and Shujia Huang and Fang Chen and Lijian Zhao and Yuying Yuan and Francis, \{Stephen Starko\} and Lin Fang and Zilong Li and Long Lin and Rong Liu and Yong Zhang and Huixin Xu and Shengkang Li and Yuwen Zhou and Davies, \{Robert W.\} and Qiang Liu and Walters, \{Robin G.\} and Kuang Lin and Jia Ju and Thorfinn Korneliussen and Yang, \{Melinda A.\} and Qiaomei Fu and Jun Wang and Lijun Zhou and Anders Krogh and Hongyun Zhang and Wei Wang and Zhengming Chen and Zhiming Cai and Ye Yin and Huanming Yang and Mao Mao and Jay Shendure and Jian Wang and Anders Albrechtsen and Xin Jin and Rasmus Nielsen and Xun Xu",

note = "Publisher Copyright: {\textcopyright} 2018 Elsevier Inc.",

year = "2018",

month = oct,

day = "4",

doi = "10.1016/j.cell.2018.08.016",

language = "英语",

volume = "175",

pages = "347--359.e14",

journal = "Cell",

issn = "0092-8674",

publisher = "Elsevier B.V.",

number = "2",

}

Liu, S, Huang, S, Chen, F, Zhao, L, Yuan, Y, Francis, SS, Fang, L, Li, Z, Lin, L, Liu, R, Zhang, Y, Xu, H, Li, S, Zhou, Y, Davies, RW, Liu, Q, Walters, RG, Lin, K, Ju, J, Korneliussen, T, Yang, MA, Fu, Q, Wang, J, Zhou, L, Krogh, A, Zhang, H, Wang, W, Chen, Z, Cai, Z, Yin, Y, Yang, H, Mao, M, Shendure, J, Wang, J, Albrechtsen, A, Jin, X, Nielsen, R & Xu, X 2018, 'Genomic Analyses from Non-invasive Prenatal Testing Reveal Genetic Associations, Patterns of Viral Infections, and Chinese Population History', Cell, vol. 175, no. 2, pp. 347-359.e14. https://doi.org/10.1016/j.cell.2018.08.016

TY - JOUR

T1 - Genomic Analyses from Non-invasive Prenatal Testing Reveal Genetic Associations, Patterns of Viral Infections, and Chinese Population History

AU - Liu, Siyang

AU - Huang, Shujia

AU - Chen, Fang

AU - Zhao, Lijian

AU - Yuan, Yuying

AU - Francis, Stephen Starko

AU - Fang, Lin

AU - Li, Zilong

AU - Lin, Long

AU - Liu, Rong

AU - Zhang, Yong

AU - Xu, Huixin

AU - Li, Shengkang

AU - Zhou, Yuwen

AU - Davies, Robert W.

AU - Liu, Qiang

AU - Walters, Robin G.

AU - Lin, Kuang

AU - Ju, Jia

AU - Korneliussen, Thorfinn

AU - Yang, Melinda A.

AU - Fu, Qiaomei

AU - Wang, Jun

AU - Zhou, Lijun

AU - Krogh, Anders

AU - Zhang, Hongyun

AU - Wang, Wei

AU - Chen, Zhengming

AU - Cai, Zhiming

AU - Yin, Ye

AU - Yang, Huanming

AU - Mao, Mao

AU - Shendure, Jay

AU - Wang, Jian

AU - Albrechtsen, Anders

AU - Jin, Xin

AU - Nielsen, Rasmus

AU - Xu, Xun

PY - 2018/10/4

Y1 - 2018/10/4

N2 - We analyze whole-genome sequencing data from 141,431 Chinese women generated for non-invasive prenatal testing (NIPT). We use these data to characterize the population genetic structure and to investigate genetic associations with maternal and infectious traits. We show that the present day distribution of alleles is a function of both ancient migration and very recent population movements. We reveal novel phenotype-genotype associations, including several replicated associations with height and BMI, an association between maternal age and EMB, and between twin pregnancy and NRG1. Finally, we identify a unique pattern of circulating viral DNA in plasma with high prevalence of hepatitis B and other clinically relevant maternal infections. A GWAS for viral infections identifies an exceptionally strong association between integrated herpesvirus 6 and MOV10L1, which affects piwi-interacting RNA (piRNA) processing and PIWI protein function. These findings demonstrate the great value and potential of accumulating NIPT data for worldwide medical and genetic analyses. Large-scale analysis of genome sequences from non-invasive prenatal testing in Chinese women yields insights into phenotypic trait associations, viral infection patterns, and population history.

AB - We analyze whole-genome sequencing data from 141,431 Chinese women generated for non-invasive prenatal testing (NIPT). We use these data to characterize the population genetic structure and to investigate genetic associations with maternal and infectious traits. We show that the present day distribution of alleles is a function of both ancient migration and very recent population movements. We reveal novel phenotype-genotype associations, including several replicated associations with height and BMI, an association between maternal age and EMB, and between twin pregnancy and NRG1. Finally, we identify a unique pattern of circulating viral DNA in plasma with high prevalence of hepatitis B and other clinically relevant maternal infections. A GWAS for viral infections identifies an exceptionally strong association between integrated herpesvirus 6 and MOV10L1, which affects piwi-interacting RNA (piRNA) processing and PIWI protein function. These findings demonstrate the great value and potential of accumulating NIPT data for worldwide medical and genetic analyses. Large-scale analysis of genome sequences from non-invasive prenatal testing in Chinese women yields insights into phenotypic trait associations, viral infection patterns, and population history.

KW - genome-wide association study

KW - low-pass sequencing

KW - non-invasive prenatal testing

KW - plasma virome

KW - population genetics

UR - https://www.scopus.com/pages/publications/85054028714

U2 - 10.1016/j.cell.2018.08.016

DO - 10.1016/j.cell.2018.08.016

M3 - 文章

C2 - 30290141

AN - SCOPUS:85054028714

SN - 0092-8674

VL - 175

SP - 347-359.e14

JO - Cell

JF - Cell

IS - 2

ER -

Genomic Analyses from Non-invasive Prenatal Testing Reveal Genetic Associations, Patterns of Viral Infections, and Chinese Population History

Abstract

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Keywords

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