Allele polymorphism and haplotype diversity of HLA-A, -B and -DRB1 loci in sequence-based typing for Chinese Uyghur ethnic group

PLoS ONE

Volumn 5, Issue 11, 2010, Pages

  Shen, Chun Mei ^a,b   Zhu, Bo Feng ^a,b   Deng, Ya Jun ^c   Ye, Shi Hui ^b   Yan, Jiang Wei ^d   Yang, Guang ^e   Wang, Hong Dan ^a   Qin, Hai Xia ^e   Huang, Qi Zhao ^f   Zhang, Jing Jing ^c  

^a XI'AN JIAOTONG UNIVERSITY   (China)

^b Shaanxi Blood Center   (China)

^c BGI SHENZHEN   (China)

^d Chinese Academy of Sciences   (China)

^e MEDICAL COLLEGE OF GEORGIA   (United States)

^f THIRD MILITARY MEDICAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

HLA A ANTIGEN; HLA B ANTIGEN; HLA DR ANTIGEN; HLA-DRB1 ANTIGEN;

ARTICLE; CHINESE; CONTROLLED STUDY; ETHNICITY; FORENSIC GENETICS; GENE FREQUENCY; GENE IDENTIFICATION; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC DISTANCE; GENETIC POLYMORPHISM; GENETIC VARIABILITY; HAPLOTYPE; HETEROZYGOSITY; HLA TYPING; HUMAN; MOLECULAR PHYLOGENY; PHYLOGENETIC TREE; POLYMERASE CHAIN REACTION; ALLELE; ASIAN; CHINA; CLASSIFICATION; GENETICS; GENOTYPE; PHYLOGENY;

ALLELES; ASIAN CONTINENTAL ANCESTRY GROUP; CHINA; GENE FREQUENCY; GENETIC VARIATION; GENOTYPE; HAPLOTYPES; HLA-A ANTIGENS; HLA-B ANTIGENS; HLA-DR ANTIGENS; HUMANS; LINKAGE DISEQUILIBRIUM; PHYLOGENY; POLYMORPHISM, GENETIC;

EID: 78149488802     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0013458     Document Type: Article

References (69)

1. Hahn, Reinhard F., "Uyghur", in Johanson, Lars; Csató, Éva Ágnes, The Turkic Languages, Routledge, 1998; 379-396, ISBN 978-0-415082-00-6.
2. Yakup, Abdurishid, The Turfan Dialect of Uyghur, 2005; Turcologica, 63, Wiesbaden: Harrassowitz Verlag, ISBN 3-447-05233-3.
3. Volz A, Boyle JM, Cann HM, Cottingham RW, Orr HT, et al. (1994) port of the Second International Workshop on Human Chromosome 6. Genomics 21: 464-472.
4. Cao K, Hollenbach J, Shi X, Shi W, Chopek M, et al. (2001) Analysis of the frequencies of HLA-A, B, and C alleles and haplotypes in the five major ethnic groups of the United States reveals high levels of diversity in these loci and contrasting distribution patterns in these populations. Hum Immunol 62: 1009-1030.
5. Imanishi T, Wakisaka A, Gojobori T (1992) Genetic relationships among various human populations indicated by MHC polymorphisms. In: Tsuji K, AizawaM, Sasazuki T, eds. HLA 1991. Oxford: Oxford University Press 627-632.
6. Chen S, Ren X, Liu Y, Hu Q, Hong W, et al. (2007) Human leukocyte antigen class I polymorphism in Miao, Bouyei, and Shui ethnic minorities of Guizhou, China. Hum Immunol 68: 928-933.
7. Jinam TA, Saitou N, Edo J, Mahmood A, Phipps ME (2010) Molecular analysis of HLA Class I and Class II genes in four indigenous Malaysian populations. Tissue Antigens 75: 151-158.
8. Shen C, Zhu B, Liu M, Li S (2008) Genetic polymorphisms at HLA-A, -B, and - DRB1 loci in Han population of Xi'an city in China. Croat Med J 49: 476-482.
9. Yao Y, Shi L, Shi L, Matsushita M, Yu L, et al. (2009) Distribution of HLA-A,-B, -Cw, and -DRB1 alleles and haplotypes in an isolated Han population in Southwest China. Tissue Antigens 73: 561-568.
10. Hu SP, Luan JA, Li B, Chen JX, Cai KL, et al. (2007) Genetic link between Chaoshan and other Chinese Han populations: Evidence from HLA-A and HLA-B allele frequency distribution. Am J Phys Anthropol 132: 140-150.
11. Edinur HA, Zafarina Z, Spínola H, Nurhaslindawaty AR, Panneerchelvam S, et al. (2009) HLA polymorphism in six Malay subethnic groups in Malaysia. Hum Immunol 70: 518-526.
12. Shen CM, Zhu BF, Ye SH, Liu ML, Yang G, et al. (2010) Allelic diversity and haplotype structure of HLA loci in the Chinese Han population living in the Guanzhong region of the Shaanxi province. Hum Immunol 71: 627-633.
13. Zhu BF, Yang G, Shen CM, Qin HX, Liu SZ, et al. (2010) Distributions of HLA-A and -B alleles and haplotypes in the Yi ethnic minority of Yunnan, China: relationship to other populations. J Zhejiang Univ Sci B 11: 127-135.
14. Yan CX, Song YP, Lai SP, Lai JH, Zhang HB, et al. (2002) Analysis of DNA polymorphism at HLA-A locus by PCR amplification with sequence specific oligonucleotide probe in Chinese Han and Uygur populations. Yi Chuan Xue Bao 29: 384-389 (in Chinese).
15. Mizuki N, Ohno S, Ando H, Sato T, Imanishi T, et al. (1998) Major histocompatibility complex class II alleles in an Uygur population in the Silk Route of Northwest China. Tissue Antigens 51: 287-292.
16. Xu MY, Hong KX, Ma J, Deng XL, Li J, et al. (2006) Analysis of HLA-B locus gene polymorphism in Sichuan Yi ethnic group and Xinjiang Uygur ethnic group. Yi Chuan 28: 913-7 (in Chinese).
17. Schipper RF, Oudshoorn M, D'Amaro J, van der Zanden HG, de Lange P, et al. (1996) Validation of large data sets, an essential prerequisite for data analysis: an analytical survey of the Bone Marrow Donors Worldwide. Tissue Antigens 47: 169-178.
18. Shi L, Ogata S, Yu JK, Ohashi J, Yu L, et al. (2008) Distribution of HLA alleles and haplotypes in Jinuo and Wa populations in Southwest China. Hum Immunol 69: 58-65.
19. Ogata S, Shi L, Matsushita M, Yu L, Huang XQ, et al. (2007) Polymorphisms of human leucocyte antigen genes in Maonan people in China. Tissue Antigens 69: 154-160.
20. Qiu XP, Tan Y, Zuo ZH, Wei Y, Wu XX (2006) Distribution of HLA-A, -B allele and haplotype polymorphism in the Tujia nationality of Hubei province in China. Zhonghua Yi Xue Yi Chuan Xue Za Zhi 23: 219-21 (in Chinese).
21. Shi L, Yao YF, Shi L, Matsushita M, Yu L, et al. (2010) HLA alleles and haplotypes distribution in Dai population in Yunnan province, Southwest China. Tissue Antigens 75: 159-165.
22. Chen S, Hong W, Shao H, Fu Y, Liu X, et al. (2006) Allelic distribution of HLA class I genes in the Tibetan ethnic population of China. Int J Immunogenet 33: 439-445.
23. Hong W, Chen S, Shao H, Fu Y, Hu Z, et al. (2007) HLA class I polymorphism in Mongolian and Hui ethnic groups from Northern China. Hum Immunol 68: 439-448.
24. Middleton D, Hawkins BR, Williams F, Meenagh A, Moscoso J, et al. (2004) HLA class I allele distribution of a Hong Kong Chinese population based on high-resolution PCR-SSOP typing. Tissue Antigens 63: 555-561.
25. Trachtenberg E, Vinson M, Hayes E, Hsu YM, Houtchens K, et al. (2007) HLA class I (A, B, C) and class II (DRB1, DQA1, DQB1, DPB1) alleles and haplotypes in the Han from southern China. Tissue Antigens 70: 455-463.
26. Yang G, Deng YJ, Hu SN, Wu DY, Li SB, et al. (2006) HLA-A, -B, and -DRB1 polymorphism defined by sequence-based typing of the Han population in Northern China. Tissue Antigens 67: 146-152.
27. Wen SH, Lai MJ, Yang KL (2008) Human leukocyte antigen-A, -B, and -DRB1 haplotypes of cord blood units in the Tzu Chi Taiwan Cord Blood Bank. Hum Immunol 69: 430-436.
28. Williams F, Meenagh A, Darke C, Acosta A, Daar AS, et al. (2001) Analysis of the distribution of HLA-B alleles in populations from five continents. Hum Immunol 62: 645-650.
29. Yuliwulandari R, Kashiwase K, Nakajima H, Uddin J, Susmiarsih TP, et al. (2009) Polymorphisms of HLA genes in Western Javanese (Indonesia): close affinities to Southeast Asian populations. Tissue Antigens 73: 46-53.
30. Hoa BK, Hang NT, Kashiwase K, Ohashi J, Lien LT, et al. (2008) HLA-A, -B, -C, -DRB1 and -DQB1 alleles and haplotypes in the Kinh population in Vietnam. Tissue Antigens 71: 127-134.
31. Lee KW, Oh DH, Lee C, Yang SY (2005) Allelic and haplotypic diversity of HLA-A, -B, -C, -DRB1, and -DQB1 genes in the Korean population. Tissue Antigens 65: 437-447.
32. Saito S, Ota S, Yamada E, Inoko H, Ota M (2000) Allele frequencies and haplotypic associations defined by allelic DNA typing at HLA class I and class II loci in the Japanese population. Tissue Antigens 56: 522-529.
33. Zhu B, Wang Z, Wu Q, Sedike ME, Zhu J, et al. (2005) Genetic analysis of 15 STR loci of Chinese Uigur ethnic population. J Forensic Sci 50: 1235-1236.
34. Zhu BF, Wang ZY, Yang CH, Li XS, Zhu J, et al. (2005) Y-chromosomal STR haplotypes in Chinese Uigur ethnic group. Int J Legal Med 119: 306-309.
35. Shen CM, Zhu BF, Li SB (2008) HLA-A, B, and DRB1 gene polymorphisms in Mongol ethnic group of Inner Mongolia, China. Yi Chuan 30: 164-168 (in Chinese).
36. Shen CM, Zhu BF, Liu ML, Zhang HD, Li SB (2008) HLA-A, B, and DRB1 genes and haplotype polymorphisms in Hui nationality group of Ningxia Hui autonomous region in China. Journal of the fourth military medical university 29: 1540-1543 (in Chinese).
37. Deng YJ, Yang G, Wu DY, Hu SN, Li SB, et al. (2006) HLA-A, B, DRB1 gene polymorphism of Beijing population was studied by high-resolution polymerase chain reaction sequence-based typing. Zhonghua Yi Xue Yi Chuan Xue Za Zhi 23: 103-106 (in Chinese).
38. Chen S, Hu Q, Liu Z, Fu Y, Lin J, et al. (2007) The distribution of HLA alleles revealed a founder effect in the geographically isolated Chinese population, Drung. Mol Immunol 44: 2017-2022.
39. Yao Y, Shi L, Shi L, Matsushita M, Yu L, et al. (2009) Distribution of HLA-A, -B, -Cw, and -DRB1 alleles and haplotypes in an isolated Han population in Southwest China. Tissue Antigens 73: 561-568.
40. Chen S, Li W, Hu Q, Liu Z, Xu Y, et al. (2007) Polymorphism of HLA class I genes in Meizhou Han population of Guangdong, China. Int J Immunogenet 34: 131-136.
41. Spínola H, Bruges-Armas J, Mora MG, Middleton D, Brehm A (2006) HLA genes in Madeira Island (Portugal) inferred from sequence-based typing: footprints from different origins. Mol Immunol 43: 1726-1728.
42. Schmidt AH, Baier D, Solloch UV, Stahr A, Cereb N, et al. (2009) Estimation of high-resolution HLA-A, -B, -C, -DRB1 allele and haplotype frequencies based on 8862 German stem cell donors and implications for strategic donor registry planning. Hum Immunol 70: 895-902.
43. Mack SJ, Tu B, Lazaro A, Yang R, Lancaster AK, et al. (2009) HLA-A, -B, -C, and -DRB1 allele and haplotype frequencies distinguish Eastern European Americans from the general European American population. Tissue Antigens 73: 17-32.
44. Klitz W, Gragert L, Maiers M, Tu B, Lazaro A, et al. (2009) Four-locus highresolution HLA typing in a sample of Mexican Americans. Tissue Antigens 74: 508-513.
45. Mizuki M, Ohno S, Ando H, Sato T, Imanishi T, et al. (1997) Major histocompatibility complex class II alleles in Kazak and Han populations in the Silk Route of northwestern China. Tissue Antigens 50: 527-534.
46. Williams F, Meenagh A, Single R, McNally M, Kelly P, et al. (2004) High resolution HLA-DRB1 identification of a Caucasian population. Hum Immunol 65: 66-77.
47. Single RM, Meyer D, Hollenbach JA, Nelson MP, Noble JA, et al. (2002) Haplotype frequency estimation in patient populations: the effect of departures from Hardy-Weinberg proportions and collapsing over a locus in the HLA region. Genet Epidemiol 22: 186-195.
48. Hattemer HH (1982) Genetic Distance between Populations. Theor Appl Genet 62: 219-223.
49. Zhou R, Yang D, Zhang H, Yu W, An L, et al. (2008) Origin and evolution of two Yugur sub-clans in Northwest China: a case study in paternal genetic landscape. Ann Hum Biol 35: 198-211.
50. Katsuyama Y, Inoko H, Imanishi T, Mizuki N, Gojobori T, et al. (1998) Genetic relationships among Japanese, northern Han, Hui, Uygur, Kazakh, Greek, Saudi Arabian, and Italian populations based on allelic frequencies at four VNTR (D1S80, D4S43, COL2A1, D17S5) and one STR (ACTBP2) loci. Hum Hered 48: 126-137.
51. Yu MS, Qiu XF, Xue JG, Liu ZD, Tan JZ, et al. (1988) Mitochondrial DNA polymorphism in Chinese. Sci Sin B 31: 860-872 (in Chinese).
52. Powell GT, Yang H, Tyler-Smith C, Xue Y (2007) The population history of the Xibe in northern China: a comparison of autosomal, mtDNA and Ychromosomal analyses of migration and gene flow. Forensic Sci Int Genet 1: 115-119.
53. Bai RF, Shi MS, Yu XJ, Na ZY (2008) The Y-STR polymorphisms and phylogenetic relationships of two minority populations in Liaoning province. Zhonghua Yi Xue Yi Chuan Xue Za Zhi 25: 469-472 (in Chinese).
54. Zhu B, Li X, Wang Z, Wu H, He Y, et al. (2005) Y-STRs haplotypes of Chinese Mongol ethnic group using Y-PLEX 12. Forensic Sci Int 153: 260-263.
55. Zhu BF, Lv GP, Shen CM, Yao GF, Zhu J, et al. (2005) Genetic Polymorphism of Six Y Chromosomal STR in Chinese Hui Ethnic Group. Academic Journal of Xi'an Jiaotong University 17: 49-52 (in Chinese).
56. Zhu B, Liu S, Ci D, Huang J, Wang Y, et al. (2006) Population genetics for Ychromosomal STRs haplotypes of Chinese Tibetan ethnic minority group in Tibet. Forensic Sci Int 161: 78-83.
57. Shete S, Tiwari H, Elston RC (2000) On estimating the heterozygosity and polymorphism information content value. Theor Popul Biol 57: 265-271.
58. Miller SA, Dykes DD, Polesky HF (1988) A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res 16: 1215.
59. Kurz B, Steiert I, Heuchert G, Müller CA (1999) New high resolution typing strategy for HLA-A locus alleles based on dye terminator sequencing of haplotypic group-specific PCR-amplicons of exon 2 and exon 3. Tissue Antigens 53: 81-96.
60. Pozzi S, Longo A, Ferrara GB (1999) HLA-B locus sequence-based typing. Tissue Antigens 53: 275-81.
61. Jia ZJ, Fu YG, Pan DJ, Liu ZH, Chen WM, et al. (2002) Determination of HLADRB1 gene polymorphism by PCR-SBT in Lahu ethnic group of Yunnan, China. Yi Chuan 24: 131-136 (in Chinese).
62. Deng YJ, Yang G, Wu DY, Hu SN, Li SB, et al. (2005) Study on the HLADRB1 Polymorphism Determined by High-resolution PCR-SBT in a Population of Beijing Region. Journal of Forensic Medicine 21: 280-285 (in Chinese).
63. Excoffier L, Laval G, Schneider S (2005) Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online 1: 47-50.
64. John Lee, J Lee, Leon WHoyer (1990) The HLA system: a new approach. New York: Springer-Verlag Press 6: 141-151.
65. Nei M (1987) Molecilar Evolutionary Genetics. New York: Columbia University Press.
66. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406-425.
67. Guo SW, Thompson EA (1992) Performing the exact test of Hardy-Weinberg proportion for multiple alleles. Biometrics 48: 361-372.
68. Tereba A (1999) Tools for analysis of population statistics. Profiles DNA 2: 3.
69. Salmon DB, Brocteur J (1978) Probability of paternity exclusion when relatives are involved. Am J Hum Genet 30: 65-75.