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Published in: European Journal of Medical Research 1/2017

Open Access 01-12-2017 | Review

Advances in the genome-wide association study of chronic hepatitis B susceptibility in Asian population

Authors: Bing Qiu, Wei Jiang, Mojtaba Olyaee, Kenji Shimura, Akihiro Miyakawa, Huijing Hu, Yongcui Zhu, Lixin Tang

Published in: European Journal of Medical Research | Issue 1/2017

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Abstract

Chronic hepatitis B (CHB) is the most common chronic liver disease resulting from viral infection and has become a serious threat to human health. Each year, about 1.2 million people in the world die from diseases caused by chronic infection of hepatitis B virus. The genetic polymorphism is significantly associated with the susceptibility to chronic hepatitis B. Genome-wide association study was recently developed and has become an important tool to detect susceptibility genes of CHB. To date, a number of CHB-associated susceptibility loci and regions have been identified by scientists over the world. To clearly understand the role of susceptibility loci in the occurrence of CHB is important for the early diagnosis and prevention of CHB.
Literature
1.
go back to reference Bhat M, Ghali P, Deschenes M, Wong P. Prevention and management of chronic hepatitis B. Int J Prev Med. 2014;5(Suppl 3):S200–7.PubMedPubMedCentral Bhat M, Ghali P, Deschenes M, Wong P. Prevention and management of chronic hepatitis B. Int J Prev Med. 2014;5(Suppl 3):S200–7.PubMedPubMedCentral
2.
go back to reference Liaw YF, Kao JH, Piratvisuth T, Chan HL, Chien RN, Liu CJ, Gane E, Locarnini S, Lim SG, Han KH, Amarapurkar D, Cooksley G, Jafri W, Mohamed R, Hou JL, Chuang WL, et al. Asian-Pacific consensus statement on the management of chronic hepatitis B: a 2012 update. Hep Int. 2012;6(3):531–61.CrossRef Liaw YF, Kao JH, Piratvisuth T, Chan HL, Chien RN, Liu CJ, Gane E, Locarnini S, Lim SG, Han KH, Amarapurkar D, Cooksley G, Jafri W, Mohamed R, Hou JL, Chuang WL, et al. Asian-Pacific consensus statement on the management of chronic hepatitis B: a 2012 update. Hep Int. 2012;6(3):531–61.CrossRef
4.
go back to reference Cui Y, Jia J. Update on epidemiology of hepatitis B and C in China. J Gastroenterol Hepatol. 2013;28(Suppl 1):7–10.CrossRefPubMed Cui Y, Jia J. Update on epidemiology of hepatitis B and C in China. J Gastroenterol Hepatol. 2013;28(Suppl 1):7–10.CrossRefPubMed
5.
go back to reference Ezzikouri S, Ozawa M, Kohara M, Elmdaghri N, Benjelloun S, Tsukiyama-Kohara K. Recent insights into hepatitis B virus-host interactions. J Med Virol. 2014;86(6):925–32.CrossRefPubMed Ezzikouri S, Ozawa M, Kohara M, Elmdaghri N, Benjelloun S, Tsukiyama-Kohara K. Recent insights into hepatitis B virus-host interactions. J Med Virol. 2014;86(6):925–32.CrossRefPubMed
6.
go back to reference Thorat M. Tuning into the genetic orchestra using microarrays: limitations of DNA microarrays in clinical practice. Nat Clin Pract Oncol. 2006;3(12):E1.CrossRefPubMed Thorat M. Tuning into the genetic orchestra using microarrays: limitations of DNA microarrays in clinical practice. Nat Clin Pract Oncol. 2006;3(12):E1.CrossRefPubMed
7.
go back to reference Lacey S, Chung JY, Lin H. A comparison of whole genome sequencing with exome sequencing for family-based association studies. BMC Proc. 2014;8(Suppl 1 Genetic Analysis Workshop 18Vanessa Olmo):S38.CrossRefPubMedPubMedCentral Lacey S, Chung JY, Lin H. A comparison of whole genome sequencing with exome sequencing for family-based association studies. BMC Proc. 2014;8(Suppl 1 Genetic Analysis Workshop 18Vanessa Olmo):S38.CrossRefPubMedPubMedCentral
8.
go back to reference Lalonde E, Albrecht S, Ha KC, Jacob K, Bolduc N, Polychronakos C, Dechelotte P, Majewski J, Jabado N. Unexpected allelic heterogeneity and spectrum of mutations in Fowler syndrome revealed by next-generation exome sequencing. Hum Mutat. 2010;31(8):918–23.CrossRefPubMed Lalonde E, Albrecht S, Ha KC, Jacob K, Bolduc N, Polychronakos C, Dechelotte P, Majewski J, Jabado N. Unexpected allelic heterogeneity and spectrum of mutations in Fowler syndrome revealed by next-generation exome sequencing. Hum Mutat. 2010;31(8):918–23.CrossRefPubMed
9.
go back to reference Petersen BS, Fredrich B, Hoeppner MP, Ellinghaus D, Franke A. Opportunities and challenges of whole-genome and -exome sequencing. BMC Genet. 2017;18(1):14.CrossRefPubMedPubMedCentral Petersen BS, Fredrich B, Hoeppner MP, Ellinghaus D, Franke A. Opportunities and challenges of whole-genome and -exome sequencing. BMC Genet. 2017;18(1):14.CrossRefPubMedPubMedCentral
10.
go back to reference Kim SY, Li Y, Guo Y, Li R, Holmkvist J, Hansen T, Pedersen O, Wang J, Nielsen R. Design of association studies with pooled or un-pooled next-generation sequencing data. Genet Epidemiol. 2010;34(5):479–91.CrossRefPubMedPubMedCentral Kim SY, Li Y, Guo Y, Li R, Holmkvist J, Hansen T, Pedersen O, Wang J, Nielsen R. Design of association studies with pooled or un-pooled next-generation sequencing data. Genet Epidemiol. 2010;34(5):479–91.CrossRefPubMedPubMedCentral
11.
go back to reference Seal A, Gupta A, Mahalaxmi M, Aykkal R, Singh TR, Arunachalam V. Tools, resources and databases for SNPs and indels in sequences: a review. Int J Bioinform Res Appl. 2014;10(3):264–96.CrossRefPubMed Seal A, Gupta A, Mahalaxmi M, Aykkal R, Singh TR, Arunachalam V. Tools, resources and databases for SNPs and indels in sequences: a review. Int J Bioinform Res Appl. 2014;10(3):264–96.CrossRefPubMed
12.
go back to reference Klein RJ, Zeiss C, Chew EY, Tsai JY, Sackler RS, Haynes C, Henning AK, SanGiovanni JP, Mane SM, Mayne ST, Bracken MB, Ferris FL, Ott J, Barnstable C, Hoh J. Complement factor H polymorphism in age-related macular degeneration. Science. 2005;308(5720):385–9.CrossRefPubMedPubMedCentral Klein RJ, Zeiss C, Chew EY, Tsai JY, Sackler RS, Haynes C, Henning AK, SanGiovanni JP, Mane SM, Mayne ST, Bracken MB, Ferris FL, Ott J, Barnstable C, Hoh J. Complement factor H polymorphism in age-related macular degeneration. Science. 2005;308(5720):385–9.CrossRefPubMedPubMedCentral
13.
go back to reference Arking D, Rommens J. Editorial overview: molecular and genetic bases of disease: Enter the post-GWAS era. Curr Opin Genet Dev. 2015;33:77–9.CrossRefPubMed Arking D, Rommens J. Editorial overview: molecular and genetic bases of disease: Enter the post-GWAS era. Curr Opin Genet Dev. 2015;33:77–9.CrossRefPubMed
14.
go back to reference van der Sijde MR, Ng A, Fu J. Systems genetics: from GWAS to disease pathways. Biochem Biophys Acta. 2014;1842(10):1903–9.PubMed van der Sijde MR, Ng A, Fu J. Systems genetics: from GWAS to disease pathways. Biochem Biophys Acta. 2014;1842(10):1903–9.PubMed
15.
go back to reference Kamatani Y, Wattanapokayakit S, Ochi H, Kawaguchi T, Takahashi A, Hosono N, Kubo M, Tsunoda T, Kamatani N, Kumada H, Puseenam A, Sura T, Daigo Y, Chayama K, Chantratita W, Nakamura Y, et al. A genome-wide association study identifies variants in the HLA-DP locus associated with chronic hepatitis B in Asians. Nat Genet. 2009;41(5):591–5.CrossRefPubMed Kamatani Y, Wattanapokayakit S, Ochi H, Kawaguchi T, Takahashi A, Hosono N, Kubo M, Tsunoda T, Kamatani N, Kumada H, Puseenam A, Sura T, Daigo Y, Chayama K, Chantratita W, Nakamura Y, et al. A genome-wide association study identifies variants in the HLA-DP locus associated with chronic hepatitis B in Asians. Nat Genet. 2009;41(5):591–5.CrossRefPubMed
16.
go back to reference Mbarek H, Ochi H, Urabe Y, Kumar V, Kubo M, Hosono N, Takahashi A, Kamatani Y, Miki D, Abe H, Tsunoda T, Kamatani N, Chayama K, Nakamura Y, Matsuda K. A genome-wide association study of chronic hepatitis B identified novel risk locus in a Japanese population. Hum Mol Genet. 2011;20(19):3884–92.CrossRefPubMed Mbarek H, Ochi H, Urabe Y, Kumar V, Kubo M, Hosono N, Takahashi A, Kamatani Y, Miki D, Abe H, Tsunoda T, Kamatani N, Chayama K, Nakamura Y, Matsuda K. A genome-wide association study of chronic hepatitis B identified novel risk locus in a Japanese population. Hum Mol Genet. 2011;20(19):3884–92.CrossRefPubMed
17.
go back to reference Kim YJ, Kim HY, Lee JH, Yu SJ, Yoon JH, Lee HS, Kim CY, Cheong JY, Cho SW, Park NH, Park BL, Namgoong S, Kim LH, Cheong HS, Shin HD. A genome-wide association study identified new variants associated with the risk of chronic hepatitis B. Hum Mol Genet. 2013;22(20):4233–8.CrossRefPubMed Kim YJ, Kim HY, Lee JH, Yu SJ, Yoon JH, Lee HS, Kim CY, Cheong JY, Cho SW, Park NH, Park BL, Namgoong S, Kim LH, Cheong HS, Shin HD. A genome-wide association study identified new variants associated with the risk of chronic hepatitis B. Hum Mol Genet. 2013;22(20):4233–8.CrossRefPubMed
18.
go back to reference Cheong HS, Lee JH, Yu SJ, Yoon JH, Lee HS, Cheong JY, Cho SW, Park NH, Park BL, Namgoong S, Kim LH, Shin HD, Kim YJ. Association of VARS2-SFTA2 polymorphisms with the risk of chronic hepatitis B in a Korean population. Liver Int. 2015;35(8):1934–40.CrossRefPubMed Cheong HS, Lee JH, Yu SJ, Yoon JH, Lee HS, Cheong JY, Cho SW, Park NH, Park BL, Namgoong S, Kim LH, Shin HD, Kim YJ. Association of VARS2-SFTA2 polymorphisms with the risk of chronic hepatitis B in a Korean population. Liver Int. 2015;35(8):1934–40.CrossRefPubMed
19.
go back to reference Nishida N, Sawai H, Matsuura K, Sugiyama M, Ahn SH, Park JY, Hige S, Kang JH, Suzuki K, Kurosaki M, Asahina Y, Mochida S, Watanabe M, Tanaka E, Honda M, Kaneko S, et al. Genome-wide association study confirming association of HLA-DP with protection against chronic hepatitis B and viral clearance in Japanese and Korean. PLoS ONE. 2012;7(6):e39175.CrossRefPubMedPubMedCentral Nishida N, Sawai H, Matsuura K, Sugiyama M, Ahn SH, Park JY, Hige S, Kang JH, Suzuki K, Kurosaki M, Asahina Y, Mochida S, Watanabe M, Tanaka E, Honda M, Kaneko S, et al. Genome-wide association study confirming association of HLA-DP with protection against chronic hepatitis B and viral clearance in Japanese and Korean. PLoS ONE. 2012;7(6):e39175.CrossRefPubMedPubMedCentral
20.
go back to reference Liu L, Li J, Yao J, Yu J, Zhang J, Ning Q, Wen Z, Yang D, He Y, Kong X, Song Q, Chen M, Yang H, Liu Q, Li S, Lin J. A genome-wide association study with DNA pooling identifies the variant rs11866328 in the GRIN2A gene that affects disease progression of chronic HBV infection. Viral Immunol. 2011;24(5):397–402.CrossRefPubMed Liu L, Li J, Yao J, Yu J, Zhang J, Ning Q, Wen Z, Yang D, He Y, Kong X, Song Q, Chen M, Yang H, Liu Q, Li S, Lin J. A genome-wide association study with DNA pooling identifies the variant rs11866328 in the GRIN2A gene that affects disease progression of chronic HBV infection. Viral Immunol. 2011;24(5):397–402.CrossRefPubMed
21.
go back to reference Hu Z, Liu Y, Zhai X, Dai J, Jin G, Wang L, Zhu L, Yang Y, Liu J, Chu M, Wen J, Xie K, Du G, Wang Q, Zhou Y, Cao M, et al. New loci associated with chronic hepatitis B virus infection in Han Chinese. Nat Genet. 2013;45(12):1499–503.CrossRefPubMed Hu Z, Liu Y, Zhai X, Dai J, Jin G, Wang L, Zhu L, Yang Y, Liu J, Chu M, Wen J, Xie K, Du G, Wang Q, Zhou Y, Cao M, et al. New loci associated with chronic hepatitis B virus infection in Han Chinese. Nat Genet. 2013;45(12):1499–503.CrossRefPubMed
22.
go back to reference He D, Tao S, Guo S, Li M, Wu J, Huang H, Guo X, Yan G, Zhu P, Wang Y. Interaction of TLR-IFN and HLA polymorphisms on susceptibility of chronic HBV infection in Southwest Han Chinese. Liver Int. 2015;35(8):1941–9.CrossRefPubMed He D, Tao S, Guo S, Li M, Wu J, Huang H, Guo X, Yan G, Zhu P, Wang Y. Interaction of TLR-IFN and HLA polymorphisms on susceptibility of chronic HBV infection in Southwest Han Chinese. Liver Int. 2015;35(8):1941–9.CrossRefPubMed
23.
go back to reference Jiang DK, Ma XP, Yu H, Cao G, Ding DL, Chen H, Huang HX, Gao YZ, Wu XP, Long XD, Zhang H, Zhang Y, Gao Y, Chen TY, Ren WH, Zhang P, et al. Genetic variants in five novel loci including CFB and CD40 predispose to chronic hepatitis B. Hepatology. 2015;62(1):118–28.CrossRefPubMed Jiang DK, Ma XP, Yu H, Cao G, Ding DL, Chen H, Huang HX, Gao YZ, Wu XP, Long XD, Zhang H, Zhang Y, Gao Y, Chen TY, Ren WH, Zhang P, et al. Genetic variants in five novel loci including CFB and CD40 predispose to chronic hepatitis B. Hepatology. 2015;62(1):118–28.CrossRefPubMed
24.
go back to reference Zhu M, Dai J, Wang C, Wang Y, Qin N, Ma H, Song C, Zhai X, Yang Y, Liu J, Liu L, Li S, Yang H, Zhu F, Shi Y, Shen H, et al. Fine mapping the MHC region identified four independent variants modifying susceptibility to chronic hepatitis B in Han Chinese. Hum Mol Genet. 2016;25(6):1225–32.CrossRefPubMed Zhu M, Dai J, Wang C, Wang Y, Qin N, Ma H, Song C, Zhai X, Yang Y, Liu J, Liu L, Li S, Yang H, Zhu F, Shi Y, Shen H, et al. Fine mapping the MHC region identified four independent variants modifying susceptibility to chronic hepatitis B in Han Chinese. Hum Mol Genet. 2016;25(6):1225–32.CrossRefPubMed
25.
go back to reference Nishida N, Ohashi J, Khor SS, Sugiyama M, Tsuchiura T, Sawai H, Hino K, Honda M, Kaneko S, Yatsuhashi H, Yokosuka O, Koike K, Kurosaki M, Izumi N, Korenaga M, Kang JH, et al. Understanding of HLA-conferred susceptibility to chronic hepatitis B infection requires HLA genotyping-based association analysis. Sci Rep. 2016;6:24767.CrossRefPubMedPubMedCentral Nishida N, Ohashi J, Khor SS, Sugiyama M, Tsuchiura T, Sawai H, Hino K, Honda M, Kaneko S, Yatsuhashi H, Yokosuka O, Koike K, Kurosaki M, Izumi N, Korenaga M, Kang JH, et al. Understanding of HLA-conferred susceptibility to chronic hepatitis B infection requires HLA genotyping-based association analysis. Sci Rep. 2016;6:24767.CrossRefPubMedPubMedCentral
26.
go back to reference Xiang X, Guo Y, Yang L, Ge Q, Mijit S, Xu F. Association of human leukocyte antigen DP/DQ gene polymorphisms with chronic hepatitis B in Chinese Han and Uygur populations. Infect Genet Evol J Mol Epidemiol Evolut Genet Infect Dis. 2016;43:407–11. Xiang X, Guo Y, Yang L, Ge Q, Mijit S, Xu F. Association of human leukocyte antigen DP/DQ gene polymorphisms with chronic hepatitis B in Chinese Han and Uygur populations. Infect Genet Evol J Mol Epidemiol Evolut Genet Infect Dis. 2016;43:407–11.
27.
go back to reference Shin JG, Cheong HS, Lee K, Ju BG, Lee JH, Yu SJ, Yoon JH, Cheong JY, Cho SW, Park NH, Namgoong S, Kim LH, Kim YJ, Shin HD. Identification of novel OCT4 genetic variant associated with the risk of chronic hepatitis B in a Korean population. Liver Int. 2017;37(3):354–61.CrossRefPubMed Shin JG, Cheong HS, Lee K, Ju BG, Lee JH, Yu SJ, Yoon JH, Cheong JY, Cho SW, Park NH, Namgoong S, Kim LH, Kim YJ, Shin HD. Identification of novel OCT4 genetic variant associated with the risk of chronic hepatitis B in a Korean population. Liver Int. 2017;37(3):354–61.CrossRefPubMed
28.
go back to reference Png E, Thalamuthu A, Ong RT, Snippe H, Boland GJ, Seielstad M. A genome-wide association study of hepatitis B vaccine response in an Indonesian population reveals multiple independent risk variants in the HLA region. Hum Mol Genet. 2011;20(19):3893–8.CrossRefPubMed Png E, Thalamuthu A, Ong RT, Snippe H, Boland GJ, Seielstad M. A genome-wide association study of hepatitis B vaccine response in an Indonesian population reveals multiple independent risk variants in the HLA region. Hum Mol Genet. 2011;20(19):3893–8.CrossRefPubMed
29.
go back to reference Pan L, Zhang L, Zhang W, Wu X, Li Y, Yan B, Zhu X, Liu X, Yang C, Xu J, Zhou G, Xu A, Li H, Liu Y. A genome-wide association study identifies polymorphisms in the HLA-DR region associated with non-response to hepatitis B vaccination in Chinese Han populations. Hum Mol Genet. 2014;23(8):2210–9.CrossRefPubMed Pan L, Zhang L, Zhang W, Wu X, Li Y, Yan B, Zhu X, Liu X, Yang C, Xu J, Zhou G, Xu A, Li H, Liu Y. A genome-wide association study identifies polymorphisms in the HLA-DR region associated with non-response to hepatitis B vaccination in Chinese Han populations. Hum Mol Genet. 2014;23(8):2210–9.CrossRefPubMed
30.
go back to reference Begum F, Sharker MH, Sherman SL, Tseng GC, Feingold E. Regionally Smoothed Meta-Analysis Methods for GWAS Datasets. Genet Epidemiol. 2016;40(2):154–60.CrossRefPubMed Begum F, Sharker MH, Sherman SL, Tseng GC, Feingold E. Regionally Smoothed Meta-Analysis Methods for GWAS Datasets. Genet Epidemiol. 2016;40(2):154–60.CrossRefPubMed
31.
go back to reference Mak TS, Best N, Rushton L. Robust bayesian sensitivity analysis for case-control studies with uncertain exposure misclassification probabilities. Int J Biostat. 2015;11(1):135–49.CrossRefPubMed Mak TS, Best N, Rushton L. Robust bayesian sensitivity analysis for case-control studies with uncertain exposure misclassification probabilities. Int J Biostat. 2015;11(1):135–49.CrossRefPubMed
32.
go back to reference Henrard S, Speybroeck N, Hermans C. Classification and regression tree analysis vs. multivariable linear and logistic regression methods as statistical tools for studying haemophilia. Haemophilia. 2015;21(6):715–22.CrossRefPubMed Henrard S, Speybroeck N, Hermans C. Classification and regression tree analysis vs. multivariable linear and logistic regression methods as statistical tools for studying haemophilia. Haemophilia. 2015;21(6):715–22.CrossRefPubMed
33.
go back to reference Pan Q, Hu T, Moore JH. Epistasis, complexity, and multifactor dimensionality reduction. Methods Mol Biol. 2013;1019:465–77.CrossRefPubMed Pan Q, Hu T, Moore JH. Epistasis, complexity, and multifactor dimensionality reduction. Methods Mol Biol. 2013;1019:465–77.CrossRefPubMed
Metadata
Title
Advances in the genome-wide association study of chronic hepatitis B susceptibility in Asian population
Authors
Bing Qiu
Wei Jiang
Mojtaba Olyaee
Kenji Shimura
Akihiro Miyakawa
Huijing Hu
Yongcui Zhu
Lixin Tang
Publication date
01-12-2017
Publisher
BioMed Central
Published in
European Journal of Medical Research / Issue 1/2017
Electronic ISSN: 2047-783X
DOI
https://doi.org/10.1186/s40001-017-0288-3

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