The polymorphism of HLA-A, -C, -B, -DRB3/4/5, -DRB1, -DQB1 loci in Zhejiang Han population, China using NGS technology.
HLA
high resolution
next-generation sequencing
Journal
International journal of immunogenetics
ISSN: 1744-313X
Titre abrégé: Int J Immunogenet
Pays: England
ID NLM: 101232337
Informations de publication
Date de publication:
Dec 2021
Dec 2021
Historique:
revised:
09
08
2021
received:
27
01
2021
accepted:
11
08
2021
pubmed:
24
9
2021
medline:
14
1
2022
entrez:
23
9
2021
Statut:
ppublish
Résumé
The distributions of HLA allele and haplotype are various in the populations. Currently, the data for HLA alleles and haplotypes at three fields resolution level in Chinese Han population is rare. Here, the HLA alleles and haplotypes of the 1734 cord blood samples from Zhejiang Han population, China were reported at three fields resolution. All samples were randomly collected from the Zhejiang Cord Blood Bank, China. HLA-A, -B, -C, -DRB1, -DQB1, -DRB3/4/5 loci was genotyped using next generation sequencing method. The genotypes of the samples were assigned using the HLA TypeStream Visual Software version 1.2.0. The frequency of alleles, haplotype estimation and linkage disequilibrium analysis were performed with the Arlequin software 3.5.2.2. It was found that the top three frequent alleles of HLA-A, -B, -C, -DRB1, -DQB1, -DRB3/4/5 loci were A*11:01:01 (25.81%), A*24:02:01 (16.70%), A*02:01:01 (10.61%); B*40:01:02 (15.97%), B*46:01:01 (11.48%), B*58:01:01 (7.96%); C*07:02:01 (19.03%), C*01:02:01 (17.65%), C*03:04:01 (10.41%); DRB1*09:01:02G (17.96%), DRB1*12:02:01 (9.57%), DRB1*08:03:02 (9.54%); DQB1*03:01:01G (21.05%), DQB1*03:03:02 (19.15%), DQB1*06:01:01G (12.08%); DRB4*01:03:01 (25.72%), DRB3*02:02:01 (20.27%), DRB5*01:01:01 (10.96%), respectively. A total of 1528 distinct A∼C∼B∼DRB3/4/5∼DRB1∼DQB1 haplotypes were estimated, and the top three most common haplotypes were A*33:03:01∼C*03:02:02∼B*58:01:01∼DRB3*02:02:01∼DRB1*03:01:01∼ DQB1*02:01:01 (4.02%), A*30:01:01∼C*06:02:01∼B*13:02:01∼DRB4*01:03:01∼ DRB1*07:01:01 ∼DQB1*02:02:01 (3.11%) and A*02:07:01∼C*01:02:01∼B*46:01:01 ∼DRB4*01:03:01∼DRB1*09:01:02G∼DQB1*03:03:02 (3.05%). Some alleles of different HLA loci were shown strong linkage disequilibrium. In conclusion, the data of allele and haplotype of HLA-A, -B, -C, -DRB1, -DQB1 and -DRB3/4/5 loci at three fields resolution level were obtained in Zhejiang Han population, thus contributing to analyze the HLA ploymorphism in the populations.
Substances chimiques
HLA-A Antigens
0
HLA-DRB1 Chains
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
485-489Subventions
Organisme : Science Research Foundation of Zhejiang Province
ID : LGF19H100001
Organisme : Science Research Foundation of Zhejiang Healthy Bureau
ID : 2020RC053
Informations de copyright
© 2021 John Wiley & Sons Ltd.
Références
Barquera, R., Zuniga, J., Flores-Rivera, J., Corona, T., Penman, B. S., Hernández-Zaragoza, D. I., Soler, M., Jonapá-Gómez, L., Mallempati, K. C., Yescas, P., Ochoa-Morales, A., Barsakis, K., Aguilar-Vázquez, J. A., García-Lechuga, M., Mindrinos, M., Yunis, M., Jiménez-Alvarez, L., Mena-Hernández, L., Ortega, E., …, Yunis, E. (2020). Diversity HLA Class I and Class II blocks and conserved extended haplotypes in Lacandon Mayans. Scientific Reports, 10(1), 3248.
Cargou, M., Ralazamahaleo, M., Blouin, L., Top, I., Elsermans, V., Andreani, M., Guidicelli, G., & Visentin, J. (2020). Evaluation of the AllType kit for HLA typing using the Ion Torrent S5 XL platform. HLA, 95(1), 30-39.
Chen, N., Wang, W., Wang, F., Dong, L., Zhao, S., Zhang, W., He, J., Huang, H., & Zhu, F. (2019). The distributions of HLA-A, HLA-B, HLA-C, HLA-DRB1 and HLA-DQB1 allele and haplotype at high-resolution level in Zhejiang Han population of China. International Journal of Immunogenetics, 46(1), 7-16.
Creary, L. E., Gangavarapu, S., Mallempati, K. C., Montero-Martín, G., Caillier, S. J., Santaniello, A., Hollenbach, J. A., Oksenberg, J. R., & Fernández-Viña, M. A. (2019). Next-generation sequencing reveals new information about HLA allele and haplotype diversity in a large European American population. Human Immunology, 80(10), 807-822.
Degenhardt, F., Wendorff, M., Wittig, M., Ellinghaus, E., Datta, L. W., Schembri, J., Ng, S. C., Rosati, E., Hübenthal, M., Ellinghaus, D., Jung, E. S., Lieb, W., Abedian, S., Malekzadeh, R., Cheon, J. H., Ellul, P., Sood, A., Midha, V., Thelma, B. K., …, Franke, A. (2019). Construction and benchmarking of a multi-ethnic reference panel for the imputation of HLA class I and II alleles. Human Molecular Genetics, 28(12), 2078-2092.
Gonzalez-Galarza, F. F., McCabe, A., Santos, E. J. M. D., Jones, J., Takeshita, L., Ortega-Rivera, N. D., Cid-Pavon, G. M. D., Ramsbottom, K., Ghattaoraya, G., Alfirevic, A., Middleton, D., & Jones, A. R. (2020). Allele frequency net database (AFND) 2020 update: Gold-standard data classification, open access genotype data and new query tools. Nucleic Acids Research, 48(D1), D783-D788.
González-Quezada, B. A., Creary, L. E., Munguia-Saldaña, A. J., Flores-Aguilar, H., Fernández-Viña, M. A., & Gorodezky, C. (2019). Exploring the ancestry and admixture of Mexican Oaxaca Mestizos from Southeast Mexico using next-generation sequencing of 11 HLA loci. Human Immunology, 80(3), 157-162.
He, Y., Zhang, W., Chen, N., Wang, W., He, J., Han, Z., Tao, S., Dong, L., He, J., Zhu, F., & Lv, H. (2016). HLA-A, -B and -DRB1 allele and haplotype frequencies of 8333 Chinese Han from the Zhejiang province, China. International Journal of Immunogenetics, 43(2), 86-95.
He, Y., Li, J., Mao, W., Zhang, D., Liu, M., Shan, X., Zhang, B., Zhu, C., Shen, J., Deng, Z., Wang, Z., Yu, W., Chen, Q., Guo, W., Su, P., Lv, R., Li, G., Li, G., Pei, B., …, Du, D. (2018). HLA common and well-documented alleles in China. HLA, 92(4), 199-205.
Howell, W. M., Carter, V., & Clark, B. (2010). The HLA system: Immunobiology, HLA typing, antibody screening and crossmatching techniques. Journal of Clinical Pathology, 63(5), 387-390.
Kishore, A., & Petrek, M. (2018). Next-generation sequencing based HLA typing: Deciphering immunogenetic aspects of sarcoidosis. Front Gene, 9, 503.
Sverchkova, A., Anzar, I., Stratford, R., & Clancy, T. (2019). Improved HLA typing of Class I and Class II alleles from next-generation sequencing data. HLA, 94(6), 504-513.
Klasberg, S., Surendranath, V., Lange, V., & Schöfl, G. (2019). Bioinformatics strategies, challenges, and opportunities for next generation sequencing based HLA genotyping. Transfus Med Hemother, 46(5), 312-325.
Kojima, Y., Takahara, S., Nonomura, N., Sada, M., Tsuji, T., Hatori, M., Fujioka, H., Kuroda, H., Miki, T., & Okuyama, A. (2000). HLA-DRB genotypes in Japanese patients with renal cell carcinoma. Oncology, 59(1), 57-62.
Liu, R. Q., & Liu, X. Y. (2004). Study of the association of HLA-DR-DQ haplotypes with rheumatoid arthritis. Journal of Ningxia Medical College, 26(5), 323-332.
Sanchez-Mazas, A., & Nunes, J. M. (2019). Does NGS typing highlight our understanding of HLA population diversity?: Some good reasons to say yes and a few to say be careful. Human Immunology, 80(1), 62-66.
Shaw, B. E., Arguello, R., Garcia-Sepulveda, C. A., & Madrigal, J. A. (2010). The impact of HLA genotyping on survival following unrelated donor haematopoietic stem cell transplantation. British Journal of Haematology, 150(3), 251-258.
Shiina, T., Hosomichi, K., Inoko, H., & Kulski, J. K. (2009). The HLA genomic loci map: Expression, interaction, diversity and disease. Journal of Human Genetics, 54(1), 15-39.
Song, E. Y., Park, M. H., Kang, S. J., Park, H. J., Kim, B. C., Tokunaga, K., Akaza, T., & Juji, T. (2002). HLA class II allele and haplotype frequencies in Koreans based on 107 families. Tissue Antigens, 59(6), 475-486.
Tiercy, J. M. (2016). How to select the best available related or unrelated donor of hematopoietic stem cells? Haematologica, 101(6), 680-687.
Copelan, E. A. (2006). Hematopoietic stem-cell transplantation. New England Journal of Medicine, 354(17), 1813-1826.
Wang, F., He, J., Chen, S., Qin, F., Dai, B., Zhang, W., Zhu, F. M., & Lv, H. J. (2014). HLA-A, HLA-B, HLA-DRB1 allele and haplotype frequencies in 6384 umbilical cord blood units and transplantation matching and engraftment statistics in the Zhejiang cord bloodbank of China. International Journal of Immunogenetics, 41(1), 13-19.
Wang, Z. P., Guo, S. S., & Yu, P. (2005). Correlative study on HLA-DR allelic polymorphisms and nasopharyngeal carcinoma in the Han nationality in Hunan province. Chinese Journal of Pathophysiology, 21(5), 1014-1015.
Wang, W., Zhang, W., Zhang, J., He, J., & Zhu, F.M. (2020). Distribution of HLA allele frequencies in 82 Chinese individuals with coronavirus disease-2019 (COVID-19). HLA, 96(2), 194-196.