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Volumn 175, Issue 2, 2018, Pages 347-359.e14

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

(38)  Liu, Siyang a,b   Huang, Shujia a,c   Chen, Fang a,b,u   Zhao, Lijian a   Yuan, Yuying a   Francis, Stephen Starko d,e   Fang, Lin a   Li, Zilong f   Lin, Long f   Liu, Rong a   Zhang, Yong a   Xu, Huixin a   Li, Shengkang a   Zhou, Yuwen a,f   Davies, Robert W g   Liu, Qiang a   Walters, Robin G h   Lin, Kuang h   Ju, Jia a   Korneliussen, Thorfinn i   more..


Author keywords

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

Indexed keywords

PIWI INTERACTING RNA; DNA;

EID: 85054028714     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2018.08.016     Document Type: Article
Times cited : (198)

References (70)
  • 7
    • 84923946495 scopus 로고    scopus 로고
    • LD Score regression distinguishes confounding from polygenicity in genome-wide association studies
    • Bulik-Sullivan, B.K., Loh, P.-R., Finucane, H.K., Ripke, S., Yang, J., Patterson, N., Daly, M.J., Price, A.L., Neale, B.M., Schizophrenia Working Group of the Psychiatric Genomics Consortium. LD Score regression distinguishes confounding from polygenicity in genome-wide association studies. Nat. Genet. 47 (2015), 291–295.
    • (2015) Nat. Genet. , vol.47 , pp. 291-295
    • Bulik-Sullivan, B.K.1    Loh, P.-R.2    Finucane, H.K.3    Ripke, S.4    Yang, J.5    Patterson, N.6    Daly, M.J.7    Price, A.L.8    Neale, B.M.9
  • 8
    • 84945309867 scopus 로고    scopus 로고
    • The Genotype-Tissue Expression (GTEx) Project
    • Carithers, L.J., Moore, H.M., The Genotype-Tissue Expression (GTEx) Project. Biopreserv. Biobank. 13 (2015), 307–308.
    • (2015) Biopreserv. Biobank. , vol.13 , pp. 307-308
    • Carithers, L.J.1    Moore, H.M.2
  • 9
    • 59649086482 scopus 로고    scopus 로고
    • Neuropathogenesis of congenital cytomegalovirus infection: disease mechanisms and prospects for intervention
    • Cheeran, M.C.J., Lokensgard, J.R., Schleiss, M.R., Neuropathogenesis of congenital cytomegalovirus infection: disease mechanisms and prospects for intervention. Clin. Microbiol. Rev. 22 (2009), 99–126.
    • (2009) Clin. Microbiol. Rev. , vol.22 , pp. 99-126
    • Cheeran, M.C.J.1    Lokensgard, J.R.2    Schleiss, M.R.3
  • 11
    • 83455213326 scopus 로고    scopus 로고
    • China Kadoorie Biobank of 0.5 million people: survey methods, baseline characteristics and long-term follow-up
    • Chen, Z., Chen, J., Collins, R., Guo, Y., Peto, R., Wu, F., Li, L., China Kadoorie Biobank (CKB) collaborative group. China Kadoorie Biobank of 0.5 million people: survey methods, baseline characteristics and long-term follow-up. Int. J. Epidemiol. 40 (2011), 1652–1666.
    • (2011) Int. J. Epidemiol. , vol.40 , pp. 1652-1666
    • Chen, Z.1    Chen, J.2    Collins, R.3    Guo, Y.4    Peto, R.5    Wu, F.6    Li, L.7
  • 12
    • 85044575558 scopus 로고    scopus 로고
    • SOAPnuke: A MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data
    • Chen, Y., Chen, Y., Shi, C., Huang, Z., Zhang, Y., Li, S., Li, Y., Ye, J., Yu, C., Li, Z., et al. SOAPnuke: A MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data. Gigascience 7 (2018), 1–6.
    • (2018) Gigascience , vol.7 , pp. 1-6
    • Chen, Y.1    Chen, Y.2    Shi, C.3    Huang, Z.4    Zhang, Y.5    Li, S.6    Li, Y.7    Ye, J.8    Yu, C.9    Li, Z.10
  • 13
    • 84976908696 scopus 로고    scopus 로고
    • Rapid genotype imputation from sequence without reference panels
    • Davies, R.W., Flint, J., Myers, S., Mott, R., Rapid genotype imputation from sequence without reference panels. Nat. Genet. 48 (2016), 965–969.
    • (2016) Nat. Genet. , vol.48 , pp. 965-969
    • Davies, R.W.1    Flint, J.2    Myers, S.3    Mott, R.4
  • 16
    • 84894161596 scopus 로고    scopus 로고
    • Assessing the effect of sequencing depth and sample size in population genetics inferences
    • Fumagalli, M., Assessing the effect of sequencing depth and sample size in population genetics inferences. PLoS ONE, 8, 2013, e79667.
    • (2013) PLoS ONE , vol.8 , pp. e79667
    • Fumagalli, M.1
  • 20
    • 0027398935 scopus 로고
    • Embigin, a member of the immunoglobulin superfamily expressed in embryonic cells, enhances cell-substratum adhesion
    • Huang, R.P., Ozawa, M., Kadomatsu, K., Muramatsu, T., Embigin, a member of the immunoglobulin superfamily expressed in embryonic cells, enhances cell-substratum adhesion. Dev. Biol. 155 (1993), 307–314.
    • (1993) Dev. Biol. , vol.155 , pp. 307-314
    • Huang, R.P.1    Ozawa, M.2    Kadomatsu, K.3    Muramatsu, T.4
  • 21
    • 84870175220 scopus 로고    scopus 로고
    • Noninvasive Fetal Trisomy (NIFTY) test: an advanced noninvasive prenatal diagnosis methodology for fetal autosomal and sex chromosomal aneuploidies
    • Jiang, F., Ren, J., Chen, F., Zhou, Y., Xie, J., Dan, S., Su, Y., Xie, J., Yin, B., Su, W., et al. Noninvasive Fetal Trisomy (NIFTY) test: an advanced noninvasive prenatal diagnosis methodology for fetal autosomal and sex chromosomal aneuploidies. BMC Med. Genomics, 5, 2012, 57.
    • (2012) BMC Med. Genomics , vol.5 , pp. 57
    • Jiang, F.1    Ren, J.2    Chen, F.3    Zhou, Y.4    Xie, J.5    Dan, S.6    Su, Y.7    Xie, J.8    Yin, B.9    Su, W.10
  • 22
    • 84927691835 scopus 로고    scopus 로고
    • Clinical usefulness of mean platelet volume and red blood cell distribution width to platelet ratio for predicting the severity of hepatic fibrosis in chronic hepatitis B virus patients
    • Karagoz, E., Ulcay, A., Tanoglu, A., Kara, M., Turhan, V., Erdem, H., Oncul, O., Gorenek, L., Clinical usefulness of mean platelet volume and red blood cell distribution width to platelet ratio for predicting the severity of hepatic fibrosis in chronic hepatitis B virus patients. Eur. J. Gastroenterol. Hepatol. 26 (2014), 1320–1324.
    • (2014) Eur. J. Gastroenterol. Hepatol. , vol.26 , pp. 1320-1324
    • Karagoz, E.1    Ulcay, A.2    Tanoglu, A.3    Kara, M.4    Turhan, V.5    Erdem, H.6    Oncul, O.7    Gorenek, L.8
  • 25
    • 84990847026 scopus 로고    scopus 로고
    • Positive selection on a regulatory insertion-deletion polymorphism in FADS2 influences apparent endogenous synthesis of arachidonic acid
    • Kothapalli, K.S.D., Ye, K., Gadgil, M.S., Carlson, S.E., O'Brien, K.O., Zhang, J.Y., Park, H.G., Ojukwu, K., Zou, J., Hyon, S.S., et al. Positive selection on a regulatory insertion-deletion polymorphism in FADS2 influences apparent endogenous synthesis of arachidonic acid. Mol. Biol. Evol. 33 (2016), 1726–1739.
    • (2016) Mol. Biol. Evol. , vol.33 , pp. 1726-1739
    • Kothapalli, K.S.D.1    Ye, K.2    Gadgil, M.S.3    Carlson, S.E.4    O'Brien, K.O.5    Zhang, J.Y.6    Park, H.G.7    Ojukwu, K.8    Zou, J.9    Hyon, S.S.10
  • 27
    • 50149083663 scopus 로고    scopus 로고
    • Hypermutation of an ancient human retrovirus by APOBEC3G
    • Lee, Y.N., Malim, M.H., Bieniasz, P.D., Hypermutation of an ancient human retrovirus by APOBEC3G. J. Virol. 82 (2008), 8762–8770.
    • (2008) J. Virol. , vol.82 , pp. 8762-8770
    • Lee, Y.N.1    Malim, M.H.2    Bieniasz, P.D.3
  • 29
    • 80054915847 scopus 로고    scopus 로고
    • A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data
    • Li, H., A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27 (2011), 2987–2993.
    • (2011) Bioinformatics , vol.27 , pp. 2987-2993
    • Li, H.1
  • 30
    • 84947756393 scopus 로고    scopus 로고
    • FermiKit: assembly-based variant calling for Illumina resequencing data
    • Li, H., FermiKit: assembly-based variant calling for Illumina resequencing data. Bioinformatics 31 (2015), 3694–3696.
    • (2015) Bioinformatics , vol.31 , pp. 3694-3696
    • Li, H.1
  • 31
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li, H., Durbin, R., Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25 (2009), 1754–1760.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 33
    • 79957951017 scopus 로고    scopus 로고
    • Low-coverage sequencing: implications for design of complex trait association studies
    • Li, Y., Sidore, C., Kang, H.M., Boehnke, M., Abecasis, G.R., Low-coverage sequencing: implications for design of complex trait association studies. Genome Res. 21 (2011), 940–951.
    • (2011) Genome Res. , vol.21 , pp. 940-951
    • Li, Y.1    Sidore, C.2    Kang, H.M.3    Boehnke, M.4    Abecasis, G.R.5
  • 34
    • 7444255651 scopus 로고    scopus 로고
    • China's floating population: new evidence from the 2000 Census
    • Liang, Z., Ma, Z., China's floating population: new evidence from the 2000 Census. Popul. Dev. Rev. 30 (2004), 467–488.
    • (2004) Popul. Dev. Rev. , vol.30 , pp. 467-488
    • Liang, Z.1    Ma, Z.2
  • 35
    • 0030203913 scopus 로고    scopus 로고
    • Internal migration in China, 1950-1988
    • Liang, Z., White, M.J., Internal migration in China, 1950-1988. Demography 33 (1996), 375–384.
    • (1996) Demography , vol.33 , pp. 375-384
    • Liang, Z.1    White, M.J.2
  • 39
    • 77953808087 scopus 로고    scopus 로고
    • Genotype imputation for genome-wide association studies
    • Marchini, J., Howie, B., Genotype imputation for genome-wide association studies. Nat. Rev. Genet. 11 (2010), 499–511.
    • (2010) Nat. Rev. Genet. , vol.11 , pp. 499-511
    • Marchini, J.1    Howie, B.2
  • 44
    • 64649096636 scopus 로고    scopus 로고
    • The global prevalence of glucose-6-phosphate dehydrogenase deficiency: a systematic review and meta-analysis
    • Nkhoma, E.T., Poole, C., Vannappagari, V., Hall, S.A., Beutler, E., The global prevalence of glucose-6-phosphate dehydrogenase deficiency: a systematic review and meta-analysis. Blood Cells Mol. Dis. 42 (2009), 267–278.
    • (2009) Blood Cells Mol. Dis. , vol.42 , pp. 267-278
    • Nkhoma, E.T.1    Poole, C.2    Vannappagari, V.3    Hall, S.A.4    Beutler, E.5
  • 45
    • 78650498921 scopus 로고    scopus 로고
    • The impact of natural selection on an ABCC11 SNP determining earwax type
    • Ohashi, J., Naka, I., Tsuchiya, N., The impact of natural selection on an ABCC11 SNP determining earwax type. Mol. Biol. Evol. 28 (2011), 849–857.
    • (2011) Mol. Biol. Evol. , vol.28 , pp. 849-857
    • Ohashi, J.1    Naka, I.2    Tsuchiya, N.3
  • 47
    • 84978827983 scopus 로고    scopus 로고
    • Admixture, population structure, and f-statistics
    • Peter, B.M., Admixture, population structure, and f-statistics. Genetics 202 (2016), 1485–1501.
    • (2016) Genetics , vol.202 , pp. 1485-1501
    • Peter, B.M.1
  • 50
    • 16344379606 scopus 로고    scopus 로고
    • Manchus and Han: Ethnic Relations and Political Power in Late Qing and Early Republican China, 1861-1928
    • University of Washington Press
    • Rhoads, E.J.M., Manchus and Han: Ethnic Relations and Political Power in Late Qing and Early Republican China, 1861-1928. 2000, University of Washington Press.
    • (2000)
    • Rhoads, E.J.M.1
  • 52
    • 84862249935 scopus 로고    scopus 로고
    • Association testing for next-generation sequencing data using score statistics
    • Skotte, L., Korneliussen, T.S., Albrechtsen, A., Association testing for next-generation sequencing data using score statistics. Genet. Epidemiol. 36 (2012), 430–437.
    • (2012) Genet. Epidemiol. , vol.36 , pp. 430-437
    • Skotte, L.1    Korneliussen, T.S.2    Albrechtsen, A.3
  • 53
    • 33745502326 scopus 로고    scopus 로고
    • Thyroid function testing in pregnancy and thyroid disease: trimester-specific reference intervals
    • Soldin, O.P., Thyroid function testing in pregnancy and thyroid disease: trimester-specific reference intervals. Ther. Drug Monit. 28 (2006), 8–11.
    • (2006) Ther. Drug Monit. , vol.28 , pp. 8-11
    • Soldin, O.P.1
  • 54
    • 84926430250 scopus 로고    scopus 로고
    • UK biobank: an open access resource for identifying the causes of a wide range of complex diseases of middle and old age
    • Sudlow, C., Gallacher, J., Allen, N., Beral, V., Burton, P., Danesh, J., Downey, P., Elliott, P., Green, J., Landray, M., et al. UK biobank: an open access resource for identifying the causes of a wide range of complex diseases of middle and old age. PLoS Med., 12, 2015, e1001779.
    • (2015) PLoS Med. , vol.12 , pp. e1001779
    • Sudlow, C.1    Gallacher, J.2    Allen, N.3    Beral, V.4    Burton, P.5    Danesh, J.6    Downey, P.7    Elliott, P.8    Green, J.9    Landray, M.10
  • 60
  • 62
    • 84908890496 scopus 로고    scopus 로고
    • Defining the role of common variation in the genomic and biological architecture of adult human height
    • Wood, A.R., Esko, T., Yang, J., Vedantam, S., Pers, T.H., Gustafsson, S., Chu, A.Y., Estrada, K., Luan, J., Kutalik, Z., et al. Electronic Medical Records and Genomics (eMEMERGEGE) Consortium MIGen Consortium PAGEGE Consortium, LifeLines Cohort Study. Defining the role of common variation in the genomic and biological architecture of adult human height. Nat. Genet. 46 (2014), 1173–1186.
    • (2014) Nat. Genet. , vol.46 , pp. 1173-1186
    • Wood, A.R.1    Esko, T.2    Yang, J.3    Vedantam, S.4    Pers, T.H.5    Gustafsson, S.6    Chu, A.Y.7    Estrada, K.8    Luan, J.9    Kutalik, Z.10
  • 63
    • 71449083275 scopus 로고    scopus 로고
    • Genomic dissection of population substructure of Han Chinese and its implication in association studies
    • Xu, S., Yin, X., Li, S., Jin, W., Lou, H., Yang, L., Gong, X., Wang, H., Shen, Y., Pan, X., et al. Genomic dissection of population substructure of Han Chinese and its implication in association studies. Am. J. Hum. Genet. 85 (2009), 762–774.
    • (2009) Am. J. Hum. Genet. , vol.85 , pp. 762-774
    • Xu, S.1    Yin, X.2    Li, S.3    Jin, W.4    Lou, H.5    Yang, L.6    Gong, X.7    Wang, H.8    Shen, Y.9    Pan, X.10
  • 64
    • 84919825510 scopus 로고    scopus 로고
    • Epidemiology of hepatitis B virus infection in China: current status and challenges
    • Yan, Y.P., Su, H.X., Ji, Z.H., Shao, Z.J., Pu, Z.S., Epidemiology of hepatitis B virus infection in China: current status and challenges. J. Clin. Transl. Hepatol. 2 (2014), 15–22.
    • (2014) J. Clin. Transl. Hepatol. , vol.2 , pp. 15-22
    • Yan, Y.P.1    Su, H.X.2    Ji, Z.H.3    Shao, Z.J.4    Pu, Z.S.5
  • 65
    • 43149108855 scopus 로고    scopus 로고
    • Gene admixture in ethnic populations in upper part of Silk Road revealed by mtDNA polymorphism
    • Yang, L., Tan, S., Yu, H., Zheng, B., Qiao, E., Dong, Y., Zan, R., Xiao, C., Gene admixture in ethnic populations in upper part of Silk Road revealed by mtDNA polymorphism. Sci. China C Life Sci. 51 (2008), 435–444.
    • (2008) Sci. China C Life Sci. , vol.51 , pp. 435-444
    • Yang, L.1    Tan, S.2    Yu, H.3    Zheng, B.4    Qiao, E.5    Dong, Y.6    Zan, R.7    Xiao, C.8
  • 68
    • 84928601078 scopus 로고    scopus 로고
    • Non-invasive prenatal testing for trisomies 21, 18 and 13: clinical experience from 146,958 pregnancies
    • Zhang, H., Gao, Y., Jiang, F., Fu, M., Yuan, Y., Guo, Y., Zhu, Z., Lin, M., Liu, Q., Tian, Z., et al. Non-invasive prenatal testing for trisomies 21, 18 and 13: clinical experience from 146,958 pregnancies. Ultrasound Obstet. Gynecol. 45 (2015), 530–538.
    • (2015) Ultrasound Obstet. Gynecol. , vol.45 , pp. 530-538
    • Zhang, H.1    Gao, Y.2    Jiang, F.3    Fu, M.4    Yuan, Y.5    Guo, Y.6    Zhu, Z.7    Lin, M.8    Liu, Q.9    Tian, Z.10
  • 69
    • 84855822878 scopus 로고    scopus 로고
    • Virologic factors associated with failure to passive-active immunoprophylaxis in infants born to HBsAg-positive mothers
    • Zou, H., Chen, Y., Duan, Z., Zhang, H., Pan, C., Virologic factors associated with failure to passive-active immunoprophylaxis in infants born to HBsAg-positive mothers. J. Viral Hepat. 19 (2012), e18–e25.
    • (2012) J. Viral Hepat. , vol.19 , pp. e18-e25
    • Zou, H.1    Chen, Y.2    Duan, Z.3    Zhang, H.4    Pan, C.5
  • 70
    • 84886616544 scopus 로고    scopus 로고
    • Frequency of human endogenous retroviral sequences (HERV) K113 and K115 in the Polish population, and their effect on HIV infection
    • Zwolińska, K., Knysz, B., Gąsiorowski, J., Pazgan-Simon, M., Gładysz, A., Sobczyński, M., Piasecki, E., Frequency of human endogenous retroviral sequences (HERV) K113 and K115 in the Polish population, and their effect on HIV infection. PLoS ONE, 8, 2013, e77820.
    • (2013) PLoS ONE , vol.8 , pp. e77820
    • Zwolińska, K.1    Knysz, B.2    Gąsiorowski, J.3    Pazgan-Simon, M.4    Gładysz, A.5    Sobczyński, M.6    Piasecki, E.7


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