Predicting HLA genotypes using unphased and flanking single-nucleotide polymorphisms in Han Chinese population

BMC Genomics

Volumn 15, Issue 1, 2014, Pages

  Hsieh, Ai Ru ^a,f   Chang, Su Wei ^b   Chen, Pei Lung ^c,d,i   Chu, Chen Chung ^h   Hsiao, Ching Lin ^a   Yang, Wei Shiung ^c,d,i   Chang, Chien Ching ^a   Wu, Jer Yuarn ^a,e,f   Chen, Yuan Tsong ^a,e,g   Chang, Tien Chun ^c,d   Fann, Cathy S J ^a  

^a INSTITUTE OF BIOMEDICAL SCIENCES   (Taiwan)

^b CHANG GUNG UNIVERSITY COLLEGE OF MEDICINE   (Taiwan)

^c NATIONAL TAIWAN UNIVERSITY HOSPITAL   (Taiwan)

^d NATIONAL TAIWAN UNIVERSITY   (Taiwan)

^e ACADEMIA SINICA   (Taiwan)

^f CHINA MEDICAL UNIVERSITY   (Taiwan)

^g DUKE UNIVERSITY MEDICAL CENTER   (United States)

^h MACKAY MEMORIAL HOSPITAL   (Taiwan)

ⁱ NATIONAL TAIWAN UNIVERSITY   (Taiwan)

Author keywords

Human leukocyte antigen (HLA); Major histocompatibility complex (MHC); Single nucleotide polymorphisms (SNPs)

Indexed keywords

3' FLANKING REGION; 5' FLANKING REGION; ALLELES; ASIAN CONTINENTAL ANCESTRY GROUP; CHINA; GENE FREQUENCY; GENOTYPE; HAPMAP PROJECT; HLA ANTIGENS; HLA-B ANTIGENS; HLA-DQ BETA-CHAINS; HUMANS; LINKAGE DISEQUILIBRIUM; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 84893019493     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-81     Document Type: Article

References (41)

1. Claas FH, Duquesnoy RJ. The polymorphic alloimmune response in clinical transplantation. Curr Opin Immunol 2008, 20(5):566-567. 10.1016/j.coi.2008.08.001, 18703140.
2. Lee SJ, Klein J, Haagenson M, Baxter-Lowe LA, Confer DL, Eapen M, Fernandez-Vina M, Flomenberg N, Horowitz M, Hurley CK, et al. High-resolution donor-recipient HLA matching contributes to the success of unrelated donor marrow transplantation. Blood 2007, 110(13):4576-4583. 10.1182/blood-2007-06-097386, 17785583.
3. Asano K, Matsushita T, Umeno J, Hosono N, Takahashi A, Kawaguchi T, Matsumoto T, Matsui T, Kakuta Y, Kinouchi Y, et al. A genome-wide association study identifies three new susceptibility loci for ulcerative colitis in the Japanese population. Nat Genet 2009, 41(12):1325-1329. 10.1038/ng.482, 19915573.
4. Hirschfield GM, Liu X, Xu C, Lu Y, Xie G, Gu X, Walker EJ, Jing K, Juran BD, Mason AL, et al. Primary biliary cirrhosis associated with HLA, IL12A, and IL12RB2 variants. N Engl J Med 2009, 360(24):2544-2555. 10.1056/NEJMoa0810440, 2857316, 19458352.
5. Evseeva I, Nicodemus KK, Bonilla C, Tonks S, Bodmer WF. Linkage disequilibrium and age of HLA region SNPs in relation to classic HLA gene alleles within Europe. Eur J Hum Genet 2010, 18(8):924-932. 10.1038/ejhg.2010.32, 2987379, 20354563.
6. Barreiro LB, Quintana-Murci L. From evolutionary genetics to human immunology: how selection shapes host defence genes. Nat Rev Genet 2010, 11(1):17-30. 10.1038/nrg2698, 19953080.
7. Zhang XC, Li SS, Wang H, Hansen JA, Zhao LP. Empirical evaluations of analytical issues arising from predicting HLA alleles using multiple SNPs. BMC Genet 2011, 12:39. 3111398, 21518453.
8. Tang M, Lautenberger JA, Gao X, Sezgin E, Hendrickson SL, Troyer JL, David VA, Guan L, McIntosh CE, Guo X, et al. The principal genetic determinants for nasopharyngeal carcinoma in China involve the HLA class I antigen recognition groove. PLoS Genet 2012, 8(11):e1003103. 10.1371/journal.pgen.1003103, 3510037, 23209447.
9. Lin M, Chu CC, Chang SL, Lee HL, Loo JH, Akaza T, Juji T, Ohashi J, Tokunaga K. The origin of Minnan and Hakka, the so-called " Taiwanese" , inferred by HLA study. Tissue Antigens 2001, 57(3):192-199. 10.1034/j.1399-0039.2001.057003192.x, 11285126.
10. Wang LM, Kimura A, Satoh M, Mineshita S. HLA linked with leprosy in southern China: HLA-linked resistance alleles to leprosy. Int J Lepr Other Mycobact Dis 1999, 67(4):403-408.
11. Jia X, Han B, Onengut-Gumuscu S, Chen WM, Concannon PJ, Rich SS, Raychaudhuri S, de Bakker PI. Imputing amino acid polymorphisms in human leukocyte antigens. PLoS One 2013, 8(6):e64683. 10.1371/journal.pone.0064683, 3675122, 23762245.
12. Xie M, Li J, Jiang T. Accurate HLA type inference using a weighted similarity graph. BMC Bioinforma 2010, 11(Suppl 11):S10.
13. Li SS, Wang H, Smith A, Zhang B, Zhang XC, Schoch G, Geraghty D, Hansen JA, Zhao LP. Predicting multiallelic genes using unphased and flanking single nucleotide polymorphisms. Genet Epidemiol 2011, 35(2):85-92. 10.1002/gepi.20549, 3057054, 21254215.
14. Leslie S, Donnelly P, McVean G. A statistical method for predicting classical HLA alleles from SNP data. Am J Hum Genet 2008, 82(1):48-56. 10.1016/j.ajhg.2007.09.001, 2253983, 18179884.
15. Fasil TA, Hailu E, Finan C, Aseffa A, Davey G, Newport MJ, Rotimi CN, Adeyemo A. Prediction of HLA class II alleles using SNPs in an African population. PLoS One 2012, 7(6):pg e40206.
16. Pan WH, Fann CS, Wu JY, Hung YT, Ho MS, Tai TH, Chen YJ, Liao CJ, Yang ML, Cheng AT, et al. Han Chinese cell and genome bank in Taiwan: purpose, design and ethical considerations. Hum Hered 2006, 61(1):27-30. 10.1159/000091834, 16534213.
17. Yang HC, Lin CH, Hsu CL, Hung SI, Wu JY, Pan WH, Chen YT, Fann CS. A comparison of major histocompatibility complex SNPs in Han Chinese residing in Taiwan and Caucasians. J Biomed Sci 2006, 13(4):489-498. 10.1007/s11373-006-9077-7, 16544196.
18. Chen PL, Fann CS, Chu CC, Chang CC, Chang SW, Hsieh HY, Lin M, Yang WS, Chang TC. Comprehensive genotyping in two homogeneous Graves' disease samples reveals major and novel HLA association alleles. PLoS One 2011, 6(1):e16635. 10.1371/journal.pone.0016635, 3030609, 21307958.
19. Koehler AB, Murphree ES. A comparison of the akaike and schwarz criteria for selecting model order. Appl Stat-J Roy St C 1988, 37(2):187-195.
20. Fernandez Vina MA, Hollenbach JA, Lyke KE, Sztein MB, Maiers M, Klitz W, Cano P, Mack S, Single R, Brautbar C, et al. Tracking human migrations by the analysis of the distribution of HLA alleles, lineages and haplotypes in closed and open populations. Phil Trans R Soc Lond B Biol Sci 2012, 367(1590):820-829.
21. International HapMap C, Frazer KA, Ballinger DG, Cox DR, Hinds DA, Stuve LL, Gibbs RA, Belmont JW, Boudreau A, Hardenbol P, et al. A second generation human haplotype map of over 3.1 million SNPs. Nature 2007, 449(7164):851-861. 10.1038/nature06258, 2689609, 17943122.
22. Matsuzaki H, Dong S, Loi H, Di X, Liu G, Hubbell E, Law J, Berntsen T, Chadha M, Hui H, et al. Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays. Nat Methods 2004, 1(2):109-111. 10.1038/nmeth718, 15782172.
23. Kennedy GC, Matsuzaki H, Dong S, Liu WM, Huang J, Liu G, Su X, Cao M, Chen W, Zhang J, et al. Large-scale genotyping of complex DNA. Nat Biotechnol 2003, 21(10):1233-1237. 10.1038/nbt869, 12960966.
24. Steemers FJ, Chang W, Lee G, Barker DL, Shen R, Gunderson KL. Whole-genome genotyping with the single-base extension assay. Nat Methods 2006, 3(1):31-33. 10.1038/nmeth842, 16369550.
25. Steemers FJ, Gunderson KL. Whole genome genotyping technologies on the BeadArray platform. Biotechnol J 2007, 2(1):41-49. 10.1002/biot.200600213, 17225249.
26. Cohen J. A coefficient of agreement for nominal scales. Educ Psychol Meas 1960, 20(1):37-46.
27. Almeria S, Vidal D, Ferrer D, Pabon M, Fernandez-de-Mera MI, Ruiz-Fons F, Alzaga V, Marco I, Calvete C, Lavin S, et al. Seroprevalence of Neospora caninum in non-carnivorous wildlife from Spain. Vet Parasitol 2007, 143(1):21-28. 10.1016/j.vetpar.2006.07.027, 16962706.
28. Howie B, Fuchsberger C, Stephens M, Marchini J, Abecasis GR. Fast and accurate genotype imputation in genome-wide association studies through pre-phasing. Nat Genet 2012, 44:955-959. 10.1038/ng.2354, 3696580, 22820512.
29. Howie B, Marchini J, Stephens M. Genotype imputation with thousands of genomes. G3 2011, 1(6):457-470. 2011, 3276165, 22384356.
30. Mijatovic V, Iacobucci I, Sazzini M, Xumerle L, Mori A, Pignatti PF, Martinelli G, Malerba G. Imputation reliability on DNA biallelic markers for drug metabolism studies. BMC Bioinforma 2012, 13(Suppl 14):S7.
31. Li Y, Willer CJ, Ding J, Scheet P, Abecasis GR. MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genet Epidemiol 2010, 34(8):816-834. 10.1002/gepi.20533, 3175618, 21058334.
32. International HapMap C Integrating ethics and science in the International HapMap Project. Nat Rev Genet 2004, 5(6):467-475. 10.1038/nrg1351, 2271136, 15153999, International HapMap C.
33. Southam L, Panoutsopoulou K, Rayner NW, Chapman K, Durrant C, Ferreira T, Arden N, Carr A, Deloukas P, Doherty M, et al. The effect of genome-wide association scan quality control on imputation outcome for common variants. Eur J Hum Genet 2011, 19(5):610-614. 10.1038/ejhg.2010.242, 3083623, 21267008.
34. Marchini J, Howie B. Genotype imputation for genome-wide association studies. Nat Rev Genet 2010, 11(7):499-511. 10.1038/nrg2796, 20517342.
35. Lin P, Hartz SM, Zhang Z, Saccone SF, Wang J, Tischfield JA, Edenberg HJ, Kramer JR AMG, Bierut LJ, et al. A new statistic to evaluate imputation reliability. PLoS One 2010, 5(3):e9697. 10.1371/journal.pone.0009697, 2837741, 20300623.
36. Ng AY. Preventing " Overfitting" of Cross-Validation Data. Proceedings of the Fourteenth International Conference on Machine Learning 1997, 245-253. http://ai.stanford.edu/~ang/papers/cv-final.pdf.
37. Sham PC, Curtis D. Monte Carlo tests for associations between disease and alleles at highly polymorphic loci. Ann Hum Genet 1995, 59(Pt 1):97-105.
38. Yang CW, Hung SI, Juo CG, Lin YP, Fang WH, Lu IH, Chen ST, Chen YT. HLA-B*1502-bound peptides: implications for the pathogenesis of carbamazepine-induced Stevens-Johnson syndrome. J Allergy Clin Immunol 2007, 120(4):870-877. 10.1016/j.jaci.2007.06.017, 17697703.
39. Wei CY, Chung WH, Huang HW, Chen YT, Hung SI. Direct interaction between HLA-B and carbamazepine activates T cells in patients with Stevens-Johnson syndrome. J Allergy Clin Immunol 2012, 129(6):1562-1569. e1565, 10.1016/j.jaci.2011.12.990, 22322005.
40. Chung WH, Hung SI, Hong HS, Hsih MS, Yang LC, Ho HC, Wu JY, Chen YT. Medical genetics: a marker for Stevens-Johnson syndrome. Nature 2004, 428(6982):486. 10.1038/428486a, 15057820.
41. Chen P, Lin JJ, Lu CS, Ong CT, Hsieh PF, Yang CC, Tai CT, Wu SL, Lu CH, Hsu YC, et al. Carbamazepine-induced toxic effects and HLA-B*1502 screening in Taiwan. N Engl J Med 2011, 364(12):1126-1133. 10.1056/NEJMoa1009717, 21428768.