Understanding of HLA-conferred susceptibility to chronic hepatitis B infection requires HLA genotyping-based association analysis

Scientific Reports

Volumn 6, Issue , 2016, Pages

  Nishida, Nao ^a,b   Ohashi, Jun ^c   Khor, Seik Soon ^b   Sugiyama, Masaya ^a   Tsuchiura, Takayo ^a   Sawai, Hiromi ^b   Hino, Keisuke ^d   Honda, Masao ^e   Kaneko, Shuichi ^e   Yatsuhashi, Hiroshi ^f   Yokosuka, Osamu ^g   Koike, Kazuhiko ^b   Kurosaki, Masayuki ^h   Izumi, Namiki ^h   Korenaga, Masaaki ^a   Kang, Jong Hon ⁱ   Tanaka, Eiji ^j   Taketomi, Akinobu ^k   Eguchi, Yuichiro ^l   Sakamoto, Naoya ^k   Yamamoto, Kazuhide ^m   Tamori, Akihiro ⁿ   Sakaida, Isao ^o   Hige, Shuhei ^p   Itoh, Yoshito ^q   Mochida, Satoshi ^r   Mita, Eiji ^s   Takikawa, Yasuhiro ^t   Ide, Tatsuya ^u   Hiasa, Yoichi ^v   Kojima, Hiroto ^w   Yamamoto, Ken ^u   Nakamura, Minoru ^f   Saji, Hiroh ^w   Sasazuki, Takehiko ^x   Kanto, Tatsuya ^a   Tokunaga, Katsushi ^b   Mizokami, Masashi ^a   more..

^a National Center for Global Health and Medicine   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

^c UNIVERSITY OF TOKYO   (Japan)

^d KAWASAKI MEDICAL SCHOOL   (Japan)

^e KANAZAWA UNIVERSITY GRADUATE SCHOOL OF MEDICAL SCIENCE   (Japan)

^f NATIONAL HOSPITAL ORGANIZATION NAGASAKI MEDICAL CENTER   (Japan)

^g CHIBA UNIVERSITY   (Japan)

^h MUSASHINO RED CROSS HOSPITAL   (Japan)

ⁱ TEINE KEIJINKAI HOSPITAL   (Japan)

^j SHINSHU UNIVERSITY SCHOOL OF MEDICINE   (Japan)

^k HOKKAIDO UNIVERSITY GRADUATE SCHOOL OF MEDICINE   (Japan)

^l SAGA UNIVERSITY   (Japan)

^m OKAYAMA UNIVERSITY   (Japan)

ⁿ OSAKA CITY UNIVERSITY GRADUATE SCHOOL OF MEDICINE   (Japan)

^o YAMAGUCHI UNIVERSITY GRADUATE SCHOOL OF MEDICINE   (Japan)

^p Sapporo Kosei General Hospital   (Japan)

^q KYOTO PREFECTURAL UNIVERSITY OF MEDICINE   (Japan)

^r SAITAMA MEDICAL UNIVERSITY   (Japan)

^s OSAKA NATIONAL HOSPITAL   (Japan)

^t IWATE MEDICAL UNIVERSITY   (Japan)

^u KURUME UNIVERSITY SCHOOL OF MEDICINE   (Japan)

^v EHIME UNIVERSITY GRADUATE SCHOOL OF MEDICINE   (Japan)

^w Japanese Red Cross Kanto Koshinetsu Block Blood Center   (Japan)

^x KYUSHU UNIVERSITY   (Japan)

more..

Author keywords

[No Author keywords available]

Indexed keywords

HLA ANTIGEN;

CHRONIC HEPATITIS B; DISEASE PREDISPOSITION; GENE LINKAGE DISEQUILIBRIUM; GENETICS; GENOTYPE; HAPLOTYPE; HUMAN; IMMUNOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM;

DISEASE SUSCEPTIBILITY; GENOTYPE; HAPLOTYPES; HEPATITIS B, CHRONIC; HLA ANTIGENS; HUMANS; LINKAGE DISEQUILIBRIUM; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 84973367412     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep24767     Document Type: Article

References (22)

1. Kamatani, Y. et al. A genome-wide association study identifies variants in the HLA-DP locus associated with chronic hepatitis B in Asians. Nature genetics 41, 591-595, doi: 10.1038/ng.348 (2009).
2. Mbarek, H. et al. A genome-wide association study of chronic hepatitis B identified novel risk locus in a Japanese population. Human molecular genetics 20, 3884-3892, doi: 10.1093/hmg/ddr301 (2011).
3. Nishida, N. 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 7, e39175, doi: 10.1371/journal.pone.0039175 (2012).
4. Kim, Y. J. et al. A genome-wide association study identified new variants associated with the risk of chronic hepatitis B. Human molecular genetics 22, 4233-4238, doi: 10.1093/hmg/ddt266 (2013).
5. Hu, Z. et al. New loci associated with chronic hepatitis B virus infection in Han Chinese. Nature genetics 45, 1499-1503, doi: 10.1038/ng.2809 (2013).
6. Nishida, N., Tokunaga, K. & Mizokami, M. Genome-Wide Association Study Reveals Host Genetic Factors for Liver Diseases. Journal of clinical and translational hepatology 1, 45-50, doi: 10.14218/JCTH.2013.010XX (2013).
7. Al-Qahtani, A. A. et al. Association between HLA variations and chronic hepatitis B virus infection in Saudi Arabian patients. Plos one 9, e80445, doi: 10.1371/journal.pone.0080445 (2014).
8. Khor, S. S. et al. High-accuracy imputation for HLA class I and II genes based on high-resolution SNP data of population-specific references. The pharmacogenomics journal doi: 10.1038/tpj.2015.4 (2015).
9. Nishida, N. et al. Evaluating the performance of Affymetrix SNP Array 6.0 platform with 400 Japanese individuals. BMC genomics 9, 431, doi: 10.1186/1471-2164-9-431 (2008).
10. Okada, Y. et al. Construction of a population-specific HLA imputation reference panel and its application to Graves' disease risk in Japanese. Nature genetics 47, 798-802, doi: 10.1038/ng.3310 (2015).
11. Pillai, N. E. et al. Predicting HLA alleles from high-resolution SNP data in three Southeast Asian populations. Human molecular genetics 23, 4443-4451, doi: 10.1093/hmg/ddu149 (2014).
12. Trachtenberg, E. A., Erlich, H. A., Rickards, O., DeStefano, G. F. & Klitz, W. HLA class II linkage disequilibrium and haplotype evolution in the Cayapa Indians of Ecuador. American journal of human genetics 57, 415-424 (1995).
13. Ronningen, K. S. et al. Distribution of HLA class II alleles among Norwegian Caucasians. Human immunology 29, 275-281 (1990).
14. Tokunaga, K. et al. Sequence-based association analysis of HLA class I and II alleles in Japanese supports conservation of common haplotypes. Immunogenetics 46, 199-205 (1997).
15. Ueda, S. et al. Identification of independent susceptible and protective HLA alleles in Japanese autoimmune thyroid disease and their epistasis. The Journal of clinical endocrinology and metabolism 99, E379-383, doi: 10.1210/jc.2013-2841 (2014).
16. Ikeda, N. et al. Determination of HLA-A,-C,-B,-DRB1 allele and haplotype frequency in Japanese population based on family study. Tissue antigens 85, 252-259, doi: 10.1111/tan.12536 (2015).
17. Miyagawa, T. et al. Appropriate data cleaning methods for genome-wide association study. Journal of human genetics 53, 886-893, doi: 10.1007/s10038-008-0322-y (2008).
18. Zheng, X. et al. HIBAG-HLA genotype imputation with attribute bagging. The pharmacogenomics journal 14, 192-200, doi: 10.1038/tpj.2013.18 (2014).
19. Stephens, M. & Scheet, P. Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation. American journal of human genetics 76, 449-462, doi: 10.1086/428594 (2005).
20. Stephens, M., Smith, N. J. & Donnelly, P. A new statistical method for haplotype reconstruction from population data. American journal of human genetics 68, 978-989, doi: 10.1086/319501 (2001).
21. Lewontin, R. C. The Interaction of Selection and Linkage. I. General Considerations; Heterotic Models. Genetics 49, 49-67 (1964).
22. Excoffier, L. & Slatkin, M. Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Molecular biology and evolution 12, 921-927 (1995).