Volume 23, Issue 2 (2020)                   mjms 2020, 23(2): 75-84 | Back to browse issues page

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Ghafari N, Raesi M, Guity K, Daneshpour M. Evaluation and Comparison of New Methods in HLA Typing. mjms 2020; 23 (2) :75-84
URL: http://mjms.modares.ac.ir/article-30-21065-en.html
1- Cellular and Molecular Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
2- Cellular and Molecular Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran , daneshpour@sbmu.ac.ir
Abstract:   (2740 Views)
The human leukocyte antigen (HLA) system has unique genetic and biochemical complexes, so it is important to determine the type of HLA in a clinical and laboratory process. In addition, to its application to assess the risk of various diseases, it also plays a vital role in organ transplants. The determination of HLA in patients requiring transplantation, in addition to the accuracy, also requires the speed of action. So that any delay and error in this work can endanger the patient's life. The need for a precise definition of the HLA type, along with improved speed and cost reduction, has led to the introduction of several methods for this test. Today, the introduction of a new generation of revolutionary sequencing has been carried out in genetic assessments. The HLA determination also uses this technique, and a variety of methods have been introduced for genetic HLA examination using a new generation of sequencing. In the present study, along with the review of traditional methods in HLA diagnosis, two of the most widely used techniques based on a new generation of sequencing methods, Thermal Sequencing method and Illumina Miseq method were evaluated.
Full-Text [PDF 527 kb]   (2018 Downloads)    
Article Type: Analytic Review | Subject: Molecular Biology
Received: 2018/05/20 | Accepted: 2020/06/17

References
1. Samaranayake N, Fernando SD, Neththikumara NF, Rodrigo C, Karunaweera ND, Dissanayake VH. Association of HLA class I and II genes with cutaneous leishmaniasis: A case control study from Sri Lanka and a systematic review. BMC Infect Dis. 2016;16(1):292. [Link] [DOI:10.1186/s12879-016-1626-8]
2. Trowsdale J. Genetic and functional relationships between MHC and NK receptor genes. Immunity. 2001;15(3):363-74. [Link] [DOI:10.1016/S1074-7613(01)00197-2]
3. Corvin A, Morris DW. Genome-wide association studies: findings at the major histocompatibility complex locus in psychosis. Biol Psychiatry. 2014;75(4):276-83. [Link] [DOI:10.1016/j.biopsych.2013.09.018]
4. Shiina T, Hosomichi K, Inoko H, Kulski JK. The HLA genomic loci map: expression, interaction, diversity and disease. J Hum Genet. 2009;54(1):15-39. [Link] [DOI:10.1038/jhg.2008.5]
5. Zheng X, Shen J, Cox C, Wakefield JC, Ehm MG, Nelson MR, et al. HIBAG-HLA genotype imputation with attribute bagging. Pharmacogenom J. 2014;14(2):192-200. [Link] [DOI:10.1038/tpj.2013.18]
6. Marsh SG, Albert ED, Bodmer WF, Bontrop RE, Dupont B, Erlich HA, et al. Nomenclature for factors of the HLA system. Hum Immunol. 2005;66(5):571-636. [Link] [DOI:10.1016/j.humimm.2005.02.002]
7. Robinson J, Halliwell JA, McWilliam H, Lopez R, Parham P, Marsh SG. IMGT/HLA database. Nucleic Acids Res. 2013;41(Database issue):D1222-7. [Link] [DOI:10.1093/nar/gks949]
8. Thomson G, Valdes AM, Noble JA, Kockum I, Grote MN, Najman J, et al. Relative predispositional effects of HLA class II DRB1-DQB1 haplotypes and genotypes on type 1 diabetes: A meta-analysis. Tissue Antigens. 2007;70(2):110-27. [Link] [DOI:10.1111/j.1399-0039.2007.00867.x]
9. Brown MA, Kenna T, Wordsworth BP. Genetics of ankylosing spondylitis-insights into pathogenesis. Nat Rev Rheumatol. 2016;12(2):81-91. [Link] [DOI:10.1038/nrrheum.2015.133]
10. Weeks CL, Batra A, Tighe MP. QUESTION 2: Is HLA typing for coeliac disease helpful in children with type 1 diabetes mellitus?. Arch Dis Child. 2016;101(6):590-1. [Link] [DOI:10.1136/archdischild-2016-311070]
11. Hachiya Y, Kawasaki A, Oka Sh, Kondo Y, Ito S, Matsumoto I, et al. Association of HLA-G 3'Untranslated region polymorphisms with systemic lupus erythematosus in a Japanese population: A case-control association study. PLoS One. 2016;11(6):e0158065. [Link] [DOI:10.1371/journal.pone.0158065]
12. Saruhan-Direskeneli G, Hughes T, Yilmaz V, Durmus H, Adler A, Alahgholi-Hajibehzad M, et al. Genetic heterogeneity within the HLA region in three distinct clinical subgroups of myasthenia gravis. Clin Immunol. 2016;166-167:81-8. [Link] [DOI:10.1016/j.clim.2016.05.003]
13. Huang R, Yin J, Chen Y, Deng F, Chen J, Gao X, et al. The amino acid variation within the binding pocket 7 and 9 of HLA-DRB1 molecules are associated with primary Sjögren's syndrome. J Autoimmun. 2015;57:53-9. [Link] [DOI:10.1016/j.jaut.2014.11.006]
14. Tafti M, Lammers GJ, Dauvilliers Y, Overeem S, Mayer G, Nowak J, et al. Narcolepsy-associated HLA class I alleles implicate cell-mediated cytotoxicity. Sleep. 2016;39(3):581-7. [Link] [DOI:10.5665/sleep.5532]
15. Liu J, Ye Z, Mayer JG, Hoch BA, Green C, Rolak L, et al. Phenome-wide association study maps new diseases to the human major histocompatibility complex region. J Med Genet. 2016;53(10):681-9. [Link] [DOI:10.1136/jmedgenet-2016-103867]
16. Daneshpour MS, Faam B, Mansournia MA, Hedayati M, Halalkhor S, Mesbah-Namin SA, et al. Haplotype analysis of Apo AI-CIII-AIV gene cluster and lipids level: Tehran lipid and glucose study. Endocrine. 2012;41(1):103-10. [Link] [DOI:10.1007/s12020-011-9526-6]
17. Daneshpour MS, Hosseinzadeh N, Zarkesh M, Azizi F. Haplotype frequency distribution for 7 microsatellites in chromosome 8 and 11 in relation to the metabolic syndrome in four ethnic groups: Tehran lipid and glucose study. Gene. 2012;495(1):62-4. [Link] [DOI:10.1016/j.gene.2011.12.011]
18. Daneshpour MS, Alfadhli S, Houshmand M, Zeinali S, Hedayati M, Zarkesh M, et al. Allele frequency distribution data for D8S1132, D8S1779, D8S514, and D8S1743 in four ethnic groups in relation to metabolic syndrome: Tehran lipid and glucose study. Biochem Genet. 2009;47(9-10):680-7. [Link] [DOI:10.1007/s10528-009-9265-z]
19. Hebbring SJ. The challenges, advantages and future of phenome-wide association studies. Immunology. 2014;141(2):157-65. [Link] [DOI:10.1111/imm.12195]
20. Bacigalupo A, Sica S. HLA haplotype mismatch transplants and posttransplant cyclophosphamide. Adv Hematol. 2016;2016:7802967. [Link] [DOI:10.1155/2016/7802967]
21. Reisner Y, Kapoor N, Kirkpatrick D, Pollack MS, Cunningham-Rundles S, Dupont B, et al. Transplantation for severe combined immunodeficiency with HLA-A, B, D, DR incompatible parental marrow cells fractionated by soybean agglutinin and sheep red blood cells. Blood. 1983;61(2):341-8. [Link] [DOI:10.1182/blood.V61.2.341.341]
22. Daneshpour MA, Fallah MS, Eshraghi P. Revolution of DNA sequencing method from the past until today. Pathobiol Res. 2014;16(4):1-13. [Persian] [Link]
23. Daneshpour MS, Rebai A, Houshmand M, Alfadhli S, Zeinali S, Hedayati M, et al. 8q24. 3 and 11q25 chromosomal loci association with low HDL‐C in metabolic syndrome. Eur J Clin Investig. 2011;41(10):1105-12. [Link] [DOI:10.1111/j.1365-2362.2011.02516.x]
24. Tiercy JM. How to select the best available related or unrelated donor of hematopoietic stem cells?. Haematologica. 2016;101(6):680-7. [Link] [DOI:10.3324/haematol.2015.141119]
25. Cereb N, Kim HR, Ryu J, Yang SY. Advances in DNA sequencing technologies for high resolution HLA typing. Hum Immunol. 2015;76(12):923-7. [Link] [DOI:10.1016/j.humimm.2015.09.015]
26. Valluei V, Mustafa M, Santhosh A, Middleton D, Alvales M, El Haj E, et al. Frequencies of HLA-A, HLA-B, HLA-DR, and HLA-DQ phenotypes in the United Arab Emirates population. Tissue Antigens. 2005;66(2):107-13. [Link] [DOI:10.1111/j.1399-0039.2005.00441.x]
27. Farjadian S, Naruse T, Kawata H, Ghaderi A, Bahram S, Inoko H. Molecular analysis of HLA allele frequencies and haplotypes in Baloch of Iran compared with related populations of Pakistan. Tissue Antigens. 2004;64(5):581-7. [Link] [DOI:10.1111/j.1399-0039.2004.00302.x]
28. Shankarkumar U, Prasanavar D, Ghosh K, Mohanty D. HLA A* 02 allele frequencies and B haplotype associations in Western Indians. Hum Immunol. 2003;64(5):562-6. [Link] [DOI:10.1016/S0198-8859(03)00032-6]
29. Jung HL. Shedding a new light on the HLA matching. Korean J Hematol. 2011;46(1):1-2. [Link] [DOI:10.5045/kjh.2011.46.1.1]
30. Erlich H. HLA DNA typing: Past, present, and future. Tissue Antigens. 2012;80(1):1-11. [Link] [DOI:10.1111/j.1399-0039.2012.01881.x]
31. Parham P. Histocompatibility typing-Mac is back in town. Immunol Today. 1988;9(5):127-30. [Link] [DOI:10.1016/0167-5699(88)91190-5]
32. Saiki RK, Bugawan TL, Horn GT, Mullis KB, Erlich HA. Analysis of enzymatically amplified β-globin and HLA-DQα DNA with allele-specific oligonucleotide probes. Nature. 1986;324(6093):163-6. [Link] [DOI:10.1038/324163a0]
33. Olerup O, Zetterquist H. 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. 1992;39(5):225-35. [Link] [DOI:10.1111/j.1399-0039.1992.tb01940.x]
34. Nunes E, Heslop H, Fernandez-Vina M, Taves C, Wagenknecht DR, Eisenbrey AB, et al. Definitions of histocompatibility typing terms. Blood. 2011;118(23):e180-3. [Link] [DOI:10.1182/blood-2011-05-353490]
35. Santamaria P, Lindstrom AL, Boyce-Jacino MT, Myster SH, Barbosa JJ, Faras AJ, et al. HLA class I sequence-based typing. Hum Immunol. 1993;37(1):39-50. [Link] [DOI:10.1016/0198-8859(93)90141-M]
36. Gabriel C, Fürst D, Faé I, Wenda S, Zollikofer C, Mytilineos J, et al. HLA typing by next-generation sequencing-getting closer to reality. Tissue Antigens. 2014;83(2):65-75. [Link] [DOI:10.1111/tan.12298]
37. Nielsen R, Paul JS, Albrechtsen A, Song YS. Genotype and SNP calling from next-generation sequencing data. Nat Rev Genet. 2011;12(6):443-51. [Link] [DOI:10.1038/nrg2986]
38. Weimer ET. Clinical validation of NGS technology for HLA: An early adopter's perspective. Hum Immunol. 2016;77(10):820-3. [Link] [DOI:10.1016/j.humimm.2016.06.014]
39. Dunn PP. Human leucocyte antigen typing: Techniques and technology, a critical appraisal. Int J Immunogenet. 2011;38(6):463-73. [Link] [DOI:10.1111/j.1744-313X.2011.01040.x]
40. Liu L, Li Y, Li S, Hu N, He Y, Pong R, et al. Comparison of next-generation sequencing systems. BioMed Res Int. 2012;2012:251364. [Link] [DOI:10.1155/2012/251364]
41. De Santis D, Dinauer D, Duke J, Erlich HA, Holcomb CL, Lind C, et al. 16th IHIW: Review of HLA typing by NGS. Int J Immunogenet. 2013;40(1):72-6. [Link] [DOI:10.1111/iji.12024]
42. Boyd SD, Gaëta BA, Jackson KJ, Fire AZ, Marshall EL, Merker JD, et al. Individual variation in the germline Ig gene repertoire inferred from variable region gene rearrangements. J Immunol. 2010;184(12):6986-92. [Link] [DOI:10.4049/jimmunol.1000445]
43. Robins HS, Campregher PV, Srivastava SK, Wacher A, Turtle CJ, Kahsai O, et al. Comprehensive assessment of T-cell receptor β-chain diversity in αβ T cells. Blood. 2009;114(19):4099-107. [Link] [DOI:10.1182/blood-2009-04-217604]
44. Daneshpour M, Masjoodi S, Ghafari N, Raesi M, Fallah M. Performance of Illumina Next Generation Sequencing. Pathobiol Res. 2018;21(3):153-61. [Persian] [Link]
45. Simen BB, Simons JF, Hullsiek KH, Novak RM, MacArthur RD, Baxter JD, et al. Low-abundance drug-resistant viral variants in chronically HIV-infected, antiretroviral treatment-naive patients significantly impact treatment outcomes. J Infect Dis. 2009;199(5):693-701. [Link] [DOI:10.1086/596736]
46. Lataillade M, Chiarella J, Yang R, Schnittman S, Wirtz V, Uy J, et al. Prevalence and clinical significance of HIV drug resistance mutations by ultra-deep sequencing in antiretroviral-naive subjects in the CASTLE study. PloS One. 2010;5(6):e10952. [Link] [DOI:10.1371/journal.pone.0010952]
47. Kohlmann A, Grossmann V, Haferlach C, Kazak B, Schindela S, Klein HU, et al. Next-generation sequencing technology reveals a characteristic pattern of molecular mutations in 75% of Chronic Myelomonocytic Leukemia (CMML) by detecting frequent alterations in TET2, RUNX1, CBL, and RAS. Blood. 2009;114(22):417. [Link] [DOI:10.1182/blood.V114.22.417.417]
48. Bentley G, Higuchi R, Hoglund B, Goodridge D, Sayer D, Trachtenberg EA, et al. High-resolution, high-throughput HLA genotyping by next-generation sequencing. Tissue Antigens. 2009;74(5):393-403. [Link] [DOI:10.1111/j.1399-0039.2009.01345.x]
49. Gabriel Ch, Danzer M, Hackl Ch, Kopal G, Hufnagl P, Hofer K, et al. Rapid high-throughput human leukocyte antigen typing by massively parallel pyrosequencing for high-resolution allele identification. Hum Immunol. 2009;70(11):960-4. [Link] [DOI:10.1016/j.humimm.2009.08.009]
50. Danzer M, Niklas N, Stabentheiner S, Hofer K, Pröll J, Stückler Ch, et al. Rapid, scalable and highly automated HLA genotyping using next-generation sequencing: A transition from research to diagnostics. BMC Genom. 2013;14(1):221. [Link] [DOI:10.1186/1471-2164-14-221]
51. Holcomb CL, Höglund B, Anderson MW, Blake LA, Böhme I, Egholm M, et al. A multi-site study using high-resolution HLA genotyping by next generation sequencing. Tissue Antigens. 2011;77(3):206-17. [Link] [DOI:10.1111/j.1399-0039.2010.01606.x]
52. Parameswaran P, Jalili R, Tao L, Shokralla S, Gharizadeh B, Ronaghi M, et al. A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing. Nucleic Acids Res. 2007;35(19):e130. [Link] [DOI:10.1093/nar/gkm760]
53. Andersson AF, Lindberg M, Jakobsson H, Bäckhed F, Nyrén P, Engstrand L. Comparative analysis of human gut microbiota by barcoded pyrosequencing. PLoS One. 2008;3(7):e2836. [Link] [DOI:10.1371/journal.pone.0002836]
54. Moonsamy PV, Williams T, Bonella P, Holcomb CL, Höglund BN, Hillman G, et al. High throughput HLA genotyping using 454 sequencing and the Fluidigm Access Array™ system for simplified amplicon library preparation. Tissue Antigens. 2013;81(3):141-9. [Link] [DOI:10.1111/tan.12071]

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