Ann Lab Med.  2021 May;41(3):310-317. 10.3343/alm.2021.41.3.310.

Identification of 8-Digit HLA-A, -B, -C, and -DRB1 Allele and Haplotype Frequencies in Koreans Using the One Lambda AllType Next-Generation Sequencing Kit

• Choe W
• Chae JD
• Yang JJ
• Hwang SH
• Choi SE
• Oh HB

• KMID: 2512689
• DOI: http://doi.org/10.3343/alm.2021.41.3.310

Abstract

Background
Recent studies have successfully implemented next-generation sequencing (NGS) in HLA typing. We performed HLA NGS in a Korean population to estimate HLA-A, -B, -C, and -DRB1 allele and haplotype frequencies up to an 8-digit resolution, which might be useful for an extended application of HLA results.
Methods
A total of 128 samples collected from healthy unrelated Korean adults, previously subjected to Sanger sequencing for 6-digit HLA analysis, were used. NGS was performed for HLA-A, -B, -C, and -DRB1 using the AllType NGS kit (One Lambda, West Hills, CA, USA), Ion Torrent S5 platform (Thermo Fisher Scientific, Waltham, MA, USA), and Type Steam Visual NGS analysis software (One Lambda).
Results
Eight HLA alleles showed frequencies of ≥ 10% in the Korean population, namely, A*24:02:01:01 (19.5%), A*33:03:01 (15.6%), A*02:01:01:01 (14.5%), A*11:01:01:01 (13.3%), B*15:01:01:01 (10.2%), C*01:02:01 (19.9%), C*03:04:01:02 (11.3%), and DRB1*09:01:02 (10.2%). Nine previous 6-digit HLA alleles were further identified as two or more 8-digit HLA alleles. Of these, eight alleles (A*24:02:01, B*35:01:01, B*40:01:02, B*55:02:01, B*58:01:01, C*03:02:02, C*07:02:01, and DRB1*07:01:01) were identified as two 8-digit HLA alleles, and one allele (B*51:01:01) was identified as three 8-digit HLA alleles. The most frequent four-loci haplotype was HLA-A*33:03:01-B*44:03:01:01-C*14: 03-DRB1*13:02:01.
Conclusions
We identified 8-digit HLA-A, -B, -C, and -DRB1 allele and haplotype frequencies in a healthy Korean population using NGS. These new data can be used as a representative Korean data for further disease-related HLA type analysis.

Keyword

Next-generation sequencing; Human leukocyte antigen (HLA); allele frequency; haplotype frequency; 8-digit HLA alleles; Korean population

Figure

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  Fig. 1 Coverage of the HLA-A, -B, -C, and -DRB1 loci. Abbreviations: HLA, human leukocyte antigen; UTR, untranslated region.

Reference

1. Borghans JAM, Keşmir C, et al. Flower D, Timmis J, editors. 2007. MHC diversity in individuals and populations. In silico immunology. Springer;Boston, MA: p. 177–95. DOI: 10.1007/978-0-387-39241-7_10.

2. Cao K, Chopek M, Fernández-Viña MA. 1999; High and intermediate resolution DNA typing systems for class I HLA-A, B, C genes by hybridization with sequence-specific oligonucleotide probes (SSOP). Rev Immunogenet. 1:177–208. PMID: 11253946.

3. Olerup O, Zetterquist H. 1992; HLA-DR typing by PCR amplification with sequence-specific primers (PCR-SSP) in 2 hours: an alternative to serological DR typing in clinical practice including donor-recipient matching in cadaveric transplantation. Tissue Antigens. 39:225–35. DOI: 10.1111/j.1399-0039.1992.tb01940.x. PMID: 1357775.

4. Saiki RK, Walsh PS, Levenson CH, Erlich HA. 1989; Genetic analysis of amplified DNA with immobilized sequence-specific oligonucleotide probes. Proc Natl Acad Sci U S A. 86:6230–4. DOI: 10.1073/pnas.86.16.6230. PMID: 2762325. PMCID: PMC297811.

5. Lind C, Ferriola D, Mackiewicz K, Heron S, Rogers M, Slavich L, et al. 2010; Next-generation sequencing: the solution for high-resolution, unambiguous human leukocyte antigen typing. Hum Immunol. 71:1033–42. DOI: 10.1016/j.humimm.2010.06.016. PMID: 20603174.

6. Bentley G, Higuchi R, Hoglund B, Goodridge D, Sayer D, Trachtenberg EA, et al. 2009; High-resolution, high-throughput HLA genotyping by next-generation sequencing. Tissue Antigens. 74:393–403. DOI: 10.1111/j.1399-0039.2009.01345.x. PMID: 19845894. PMCID: PMC4205125.

7. Erlich RL, Jia X, Anderson S, Banks E, Gao X, Carrington M, et al. 2011; Next-generation sequencing for HLA typing of class I loci. BMC Genomics. 12:42. DOI: 10.1186/1471-2164-12-42. PMID: 21244689. PMCID: PMC3033818.

8. Holcomb CL, Höglund B, Anderson MW, Blake LA, Böhme I, Egholm M, et al. 2011; A multi-site study using high-resolution HLA genotyping by next generation sequencing. Tissue Antigens. 77:206–17. DOI: 10.1111/j.1399-0039.2010.01606.x. PMID: 21299525. PMCID: PMC4205124.

9. Shiina T, Suzuki S, Ozaki Y, Taira H, Kikkawa E, Shigenari A, et al. 2012; Super high resolution for single molecule-sequence-based typing of classical HLA loci at the 8-digit level using next generation sequencers. Tissue Antigens. 80:305–16. DOI: 10.1111/j.1399-0039.2012.01941.x. PMID: 22861646.

10. Hosomichi K, Jinam TA, Mitsunaga S, Nakaoka H, Inoue I. 2013; Phase-defined complete sequencing of the HLA genes by next-generation sequencing. BMC Genomics. 14:355. DOI: 10.1186/1471-2164-14-355. PMID: 23714642. PMCID: PMC3671147.

11. Ehrenberg PK, Geretz A, Baldwin KM, Apps R, Polonis VR, Robb ML, et al. 2014; High-throughput multiplex HLA genotyping by next-generation sequencing using multi-locus individual tagging. BMC Genomics. 15:864. DOI: 10.1186/1471-2164-15-864. PMID: 25283548. PMCID: PMC4196003.

12. Jun JH, Hwang K, Kim SK, Oh HB, Cho MC, Lee KJ. 2014; Estimation of the 6-digit level allele and haplotype frequencies of HLA-A, −B, and -C in Koreans using ambiguity-solving DNA typing. Tissue Antigens. 84:277–84. DOI: 10.1111/tan.12368. PMID: 24851935.

13. IPD-IMGT/HLA Statistics. https://www.ebi.ac.uk/ipd/imgt/hla/stats.html. updated on Nov 2019.

14. In JW, Roh EY, Oh S, Shin S, Park KU, Song EY. 2015; Allele and haplotype frequencies of Human Leukocyte Antigen-A, -B, -C, -DRB1, and -DQB1 from sequence-based DNA typing data in Koreans. Ann Lab Med. 35:429–35. DOI: 10.3343/alm.2015.35.4.429. PMID: 26131415. PMCID: PMC4446582.

15. Chung HY, Yoon JA, Han BY, Song EY, Park MH. 2010; Allelic and haplotypic diversity of HLA-A, -B, -C, and -DRB1 genes in Koreans defined by high-resolution DNA typing. Korean J Lab Med. 30:685–96. DOI: 10.3343/kjlm.2010.30.6.685. PMID: 21157157.

16. 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. 56:522–9. DOI: 10.1034/j.1399-0039.2000.560606.x. PMID: 11169242.

17. Kwok J, Guo M, Yang W, Lee CK, Ho J, Tang WH, et al. 2016; HLA-A, -B, -C, and -DRB1 genotyping and haplotype frequencies for a Hong Kong Chinese population of 7595 individuals. Hum Immunol. 77:1111–2. DOI: 10.1016/j.humimm.2016.10.005. PMID: 27769748.

18. Skibola CF, Akers NK, Conde L, Ladner M, Hawbecker SK, Cohen F, et al. 2012; Multi-locus HLA class I and II allele and haplotype associations with follicular lymphoma. Tissue Antigens. 79:279–86. DOI: 10.1111/j.1399-0039.2012.01845.x. PMID: 22296171. PMCID: PMC3293942.

19. Alfirevic A, Gonzalez-Galarza F, Bell C, Martinsson K, Platt V, Bretland G, et al. 2012; In silico analysis of HLA associations with drug-induced liver injury: use of a HLA-genotyped DNA archive from healthy volunteers. Genome Med. 4:51. DOI: 10.1186/gm350. PMID: 22732016. PMCID: PMC3698530.

20. Hajeer AH, Al Balwi MA, Aytül Uyar F, Alhaidan Y, Alabdulrahman A, Al Abdulkareem I, et al. 2013; HLA-A, -B, -C, -DRB1 and -DQB1 allele and haplotype frequencies in Saudis using next generation sequencing technique. Tissue Antigens. 82:252–8. DOI: 10.1111/tan.12200. PMID: 24461004.

21. Qu H, Fang X. 2013; A brief review on the Human Encyclopedia of DNA Elements (ENCODE) project. Genomics Proteomics Bioinformatics. 11:135–41. DOI: 10.1016/j.gpb.2013.05.001. PMID: 23722115. PMCID: PMC4357814.

22. Cocco E, Meloni A, Murru MR, Corongiu D, Tranquilli S, Fadda E, et al. 2012; Vitamin D responsive elements within the HLA-DRB1 promoter region in Sardinian multiple sclerosis associated alleles. PLoS One. 7:e41678. DOI: 10.1371/journal.pone.0041678. PMID: 22848563. PMCID: PMC3404969.

23. Thomas R, Apps R, Qi Y, Gao X, Male V, O'hUigin C, et al. 2009; HLA-C cell surface expression and control of HIV/AIDS correlate with a variant upstream of HLA-C. Nat Genet. 41:1290–4. DOI: 10.1038/ng.486. PMID: 19935663. PMCID: PMC2887091.

24. Dubois V, Tiercy JM, Labonne MP, Dormoy A, Gebuhrer L. 2004; A new HLA-B44 allele (B*44020102S) with a splicing mutation leading to a complete deletion of exon 5. Tissue Antigens. 63:173–80. DOI: 10.1111/j.1399-0039.2004.00134.x. PMID: 14705988.

25. Elsner HA, Bernard G, Eiz-Vesper B, de Matteis M, Bernard A, Blasczyk R. 2002; Non-expression of HLA-A*2901102 N is caused by a nucleotide exchange in the mRNA splicing site at the beginning of intron 4. Tissue Antigens. 59:139–41. DOI: 10.1034/j.1399-0039.2002.590212.x. PMID: 12028543.

26. Laforet M, Froelich N, Parissiadis A, Bausinger H, Pfeiffer B, Tongio MM. 1997; An intronic mutation responsible for a low level of expression of an HLA-A*24 allele. Tissue Antigens. 50:340–6. DOI: 10.1111/j.1399-0039.1997.tb02884.x. PMID: 9349616.

27. Tamouza R, El Kassar N, Schaeffer V, Carbonnelle E, Tatari Z, Marzais F, et al. 2000; A novel HLA-B*39 allele (HLA-B*3916) due to a rare mutation causing cryptic splice site activation. Hum Immunol. 61:467–73. DOI: 10.1016/S0198-8859(00)00108-7. PMID: 10773349.