Next-Generation Sequencing of the HLA locus: Methods and impacts on HLA typing, population genetics and disease association studies

Human Immunology

Volumn 77, Issue 11, 2016, Pages 1016-1023

  Carapito, Raphael ^a,b,c,d   Radosavljevic, Mirjana ^a,b,c,d   Bahram, Seiamak ^a,b,c,d  

^a UNIVERSITÉ DE STRASBOURG   (France)

^b INSERM   (France)

^c UNIVERSITY HOSPITAL OF STRASBOURG   (France)

^d HÔPITAL CIVIL   (France)

Author keywords

HLA; HLA typing; HLA disease association; NGS; Population genetics

Indexed keywords

ARTICLE; BIOINFORMATICS; DISEASE ASSOCIATION; GENE LOCUS; GENE SEQUENCE; GENE TECHNOLOGY; HLA SYSTEM; HLA TYPING; HUMAN; NEXT GENERATION SEQUENCING; POPULATION GENETICS; PRIORITY JOURNAL; GENE LINKAGE DISEQUILIBRIUM; GENETIC POLYMORPHISM; GENETICS; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HIGH THROUGHPUT SEQUENCING; HISTOCOMPATIBILITY TEST; PROCEDURES;

HLA ANTIGEN;

GENETIC LOCI; GENETICS, POPULATION; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HISTOCOMPATIBILITY TESTING; HLA ANTIGENS; HUMANS; LINKAGE DISEQUILIBRIUM; POLYMORPHISM, GENETIC;

EID: 84962690503     PISSN: 01988859     EISSN: 18791166     Source Type: Journal    
DOI: 10.1016/j.humimm.2016.04.002     Document Type: Article

References (59)

1. [1] Dausset, J., Iso-leuco-anticorps. Acta haemat, 20, 1958, 156.
2. [2] Trowsdale, J., The MHC, disease and selection. Immunol. Lett., 137, 2011, 1.
3. [3] Trowsdale, J., Knight, J.C., Major histocompatibility complex genomics and human disease. Annu. Rev. Genomics Hum. Genet., 14, 2013, 301.
4. [4] Vandiedonck, C., Knight, J.C., The human Major Histocompatibility Complex as a paradigm in genomics research. Brief. Funct. Genomic. Proteomic., 8, 2009, 379.
5. [5] Shiina, T., Inoko, H., Kulski, J.K., An update of the HLA genomic region, locus information and disease associations: 2004. Tissue Antigens, 64, 2004, 631.
6. [6] Hetherington, S., Hughes, A.R., Mosteller, M., Shortino, D., Baker, K.L., Spreen, W., et al. Genetic variations in HLA-B region and hypersensitivity reactions to abacavir. Lancet, 359, 2002, 1121.
7. ∗5701 as a marker for immunologically confirmed abacavir hypersensitivity in white and black patients. Clin. Infect. Dis., 46, 2008, 1111.
8. [8] Sanchez-Mazas, A., Meyer, D., The relevance of HLA sequencing in population genetics studies. J. Immunol. Res., 2014, 2014, 971818.
9. [9] Robinson, J., Waller, M.J., Parham, P., de Groot, N., Bontrop, R., Kennedy, L.J., et al. IMGT/HLA and IMGT/MHC: sequence databases for the study of the major histocompatibility complex. Nucleic Acids Res., 31, 2003, 311.
10. [10] Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 43, 2015, D6.
11. [11] Tewhey, R., Warner, J.B., Nakano, M., Libby, B., Medkova, M., David, P.H., et al. Microdroplet-based PCR enrichment for large-scale targeted sequencing. Nat. Biotechnol., 27, 2009, 1025.
12. [12] Lange, V., Bohme, I., Hofmann, J., Lang, K., Sauter, J., Schone, B., et al. Cost-efficient high-throughput HLA typing by MiSeq amplicon sequencing. BMC Genomics, 15, 2014, 63.
13. [13] Zhou, M., Gao, D., Chai, X., Liu, J., Lan, Z., Liu, Q., et al. Application of high-throughput, high-resolution and cost-effective next generation sequencing-based large-scale HLA typing in donor registry. Tissue Antigens, 85, 2015, 20.
14. [14] Cao, H., Wang, Y., Zhang, W., Chai, X., Zhang, X., Chen, S., et al. A short-read multiplex sequencing method for reliable, cost-effective and high-throughput genotyping in large-scale studies. Hum. Mutat., 34, 2013, 1715.
15. [15] Yamamoto, F., Hoglund, B., Fernandez-Vina, M., Tyan, D., Rastrou, M., Williams, T., et al. Very high resolution single pass HLA genotyping using amplicon sequencing on the 454 next generation DNA sequencers: Comparison with Sanger sequencing. Hum. Immunol., 76, 2015, 910.
16. [16] Danzer, M., Niklas, N., Stabentheiner, S., Hofer, K., Proll, J., Stuckler, C., et al. Rapid, scalable and highly automated HLA genotyping using next-generation sequencing: a transition from research to diagnostics. BMC Genomics, 14, 2013, 221.
17. [17] Shiina, T., Suzuki, S., Kulski, J., MHC Genotyping in Human and Nonhuman Species by PCR-based Next-Generation Sequencing. Kulski, J.K., (eds.) Biochemistry, Genetics and Molecular Biology » “Next Generation Sequencing – Advances, Applications and Challenges”, 2016, InTech.
18. [18] Proll, J., Danzer, M., Stabentheiner, S., Niklas, N., Hackl, C., Hofer, K., et al. Sequence capture and next generation resequencing of the MHC region highlights potential transplantation determinants in HLA identical haematopoietic stem cell transplantation. DNA Res., 18, 2011, 201.
19. [19] Wittig, M., Anmarkrud, J.A., Kassens, J.C., Koch, S., Forster, M., Ellinghaus, E., et al. Development of a high-resolution NGS-based HLA-typing and analysis pipeline. Nucleic Acids Res., 43, 2015, e70.
20. [20] Metzker, M.L., Sequencing technologies – the next generation. Nat. Rev. Genet., 11, 2010, 31.
21. [21] Liu, L., Li, Y., Li, S., Hu, N., He, Y., Pong, R., et al. Comparison of next-generation sequencing systems. J. Biomed. Biotechnol., 2012, 2012, 251364.
22. [22] Rothberg, J.M., Hinz, W., Rearick, T.M., Schultz, J., Mileski, W., Davey, M., et al. An integrated semiconductor device enabling non-optical genome sequencing. Nature, 475, 2011, 348.
23. [23] Barone, J.C., Saito, K., Beutner, K., Campo, M., Dong, W., Goswami, C.P., et al. HLA-genotyping of clinical specimens using Ion Torrent-based NGS. Hum. Immunol., 76, 2015, 903.
24. [24] Turcatti, G., Romieu, A., Fedurco, M., Tairi, A.P., A new class of cleavable fluorescent nucleotides: synthesis and optimization as reversible terminators for DNA sequencing by synthesis. Nucleic Acids Res., 36, 2008, e25.
25. [25] Gabriel, C., Furst, D., Fae, I., Wenda, S., Zollikofer, C., Mytilineos, J., et al. HLA typing by next-generation sequencing - getting closer to reality. Tissue Antigens, 83, 2014, 65.
26. [26] Ewing, B., Green, P., Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res., 8, 1998, 186.
27. [27] Margulies, M., Egholm, M., Altman, W.E., Attiya, S., Bader, J.S., Bemben, L.A., et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature, 437, 2005, 376.
28. [28] Eid, J., Fehr, A., Gray, J., Luong, K., Lyle, J., Otto, G., et al. Real-time DNA sequencing from single polymerase molecules. Science, 323, 2009, 133.
29. [29] Chin, C.S., Alexander, D.H., Marks, P., Klammer, A.A., Drake, J., Heiner, C., et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods, 10, 2013, 563.
30. [30] Kim, K.E., Peluso, P., Babayan, P., Yeadon, P.J., Yu, C., Fisher, W.W., et al. Long-read, whole-genome shotgun sequence data for five model organisms. Sci. Data, 1, 2014, 140045.
31. [31] Westbrook, C.J., Karl, J.A., Wiseman, R.W., Mate, S., Koroleva, G., Garcia, K., et al. No assembly required: Full-length MHC class I allele discovery by PacBio circular consensus sequencing. Hum. Immunol., 76, 2015, 891.
32. [32] Goodwin, S., Gurtowski, J., Ethe-Sayers, S., Deshpande, P., Schatz, M.C., McCombie, W.R., Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome. Genome Res., 2015.
33. [33] Quick, J., Quinlan, A.R., Loman, N.J., A reference bacterial genome dataset generated on the MinION portable single-molecule nanopore sequencer. Gigascience, 3, 2014, 22.
34. [34] Ashton, P.M., Nair, S., Dallman, T., Rubino, S., Rabsch, W., Mwaigwisya, S., et al. MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island. Nat. Biotechnol., 33, 2015, 296.
35. [35] Dilthey, A., Cox, C., Iqbal, Z., Nelson, M.R., McVean, G., Improved genome inference in the MHC using a population reference graph. Nat. Genet., 47, 2015, 682.
36. [36] Hosomichi, K., Shiina, T., Tajima, A., Inoue, I., The impact of next-generation sequencing technologies on HLA research. J. Hum. Genet., 2015.
37. [37] Shukla, S.A., Rooney, M.S., Rajasagi, M., Tiao, G., Dixon, P.M., Lawrence, M.S., et al. Comprehensive analysis of cancer-associated somatic mutations in class I HLA genes. Nat. Biotechnol., 2015.
38. [38] Shiina, T., Hosomichi, K., Inoko, H., Kulski, J.K., The HLA genomic loci map: expression, interaction, diversity and disease. J. Hum. Genet., 54, 2009, 15.
39. [39] Vandiedonck, C., Taylor, M.S., Lockstone, H.E., Plant, K., Taylor, J.M., Durrant, C., et al. Pervasive haplotypic variation in the spliceo-transcriptome of the human major histocompatibility complex. Genome Res., 21, 2011, 1042.
40. [40] Qu, H., Fang, X., A brief review on the Human Encyclopedia of DNA Elements (ENCODE) project. Genomics Proteomics Bioinformatics, 11, 2013, 135.
41. [41] Marth, G.T., Yu, F., Indap, A.R., Garimella, K., Gravel, S., Leong, W.F., et al. The functional spectrum of low-frequency coding variation. Genome Biol., 12, 2011, R84.
42. [42] Fernandez Vina, M.A., Hollenbach, J.A., Lyke, K.E., Sztein, M.B., Maiers, M., Klitz, W., et al. Tracking human migrations by the analysis of the distribution of HLA alleles, lineages and haplotypes in closed and open populations. Philos. Trans. R. Soc. Lond. B Biol. Sci., 367, 2012, 820.
43. [43] de Bakker, P.I., McVean, G., Sabeti, P.C., Miretti, M.M., Green, T., Marchini, J., et al. A high-resolution HLA and SNP haplotype map for disease association studies in the extended human MHC. Nat. Genet., 38, 2006, 1166.
44. [44] Lilly, F., Boyse, E.A., Old, L.J., Genetic basis of susceptibility to viral leukaemogenesis. Lancet, 2, 1964, 1207.
45. [45] Amiel, J.L., Study of the leukocyte phenotypes in Hodgkin's disease. Curtoni, E.S., Mattiuz, P.L., Tosi, R.M., (eds.) Histocompatibility Testing 1967, 1967, Williams & Wilkins, Baltimore, 79–81.
46. [46] Thorsby, E., Lie, B.A., HLA associated genetic predisposition to autoimmune diseases: Genes involved and possible mechanisms. Transpl. Immunol., 14, 2005, 175.
47. [47] Elahi, S., Horton, H., Association of HLA-alleles with the immune regulation of chronic viral infections. Int. J. Biochem. Cell Biol., 44, 2012, 1361.
48. [48] Stefansson, H., Ophoff, R.A., Steinberg, S., Andreassen, O.A., Cichon, S., Rujescu, D., et al. Common variants conferring risk of schizophrenia. Nature, 460, 2009, 744.
49. [49] de Bakker, P.I., Raychaudhuri, S., Interrogating the major histocompatibility complex with high-throughput genomics. Hum. Mol. Genet., 21, 2012, R29.
50. [50] Wei, Z., Wang, K., Qu, H.Q., Zhang, H., Bradfield, J., Kim, C., et al. From disease association to risk assessment: an optimistic view from genome-wide association studies on type 1 diabetes. PLoS Genet., 5, 2009, e1000678.
51. [51] Welter, D., MacArthur, J., Morales, J., Burdett, T., Hall, P., Junkins, H., et al. The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. Nucleic Acids Res., 42, 2014, D1001.
52. [52] Noble, J.A., Erlich, H.A., Genetics of type 1 diabetes. Cold Spring Harb. Perspect Med., 2, 2012, a007732.
53. [53] Ricano-Ponce, I., Wijmenga, C., Mapping of immune-mediated disease genes. Annu. Rev. Genomics Hum. Genet., 14, 2013, 325.
54. [54] Ioannidis, J.P., Thomas, G., Daly, M.J., Validating, augmenting and refining genome-wide association signals. Nat. Rev. Genet., 10, 2009, 318.
55. [55] Mack, S.J., A gene feature enumeration approach for describing HLA allele polymorphism. Hum Immunol, 2015.
56. [56] van Dijk, E.L., Auger, H., Jaszczyszyn, Y., Thermes, C., Ten years of next-generation sequencing technology. Trends Genet., 30, 2014, 418.
57. [57] Bahassi el, M., Stambrook, P.J., Next-generation sequencing technologies: breaking the sound barrier of human genetics. Mutagenesis, 29, 2014, 303.
58. [58] Churko, J.M., Mantalas, G.L., Snyder, M.P., Wu, J.C., Overview of high throughput sequencing technologies to elucidate molecular pathways in cardiovascular diseases. Circ. Res., 112, 2013, 1613.
59. [59] Xuan, J., Yu, Y., Qing, T., Guo, L., Shi, L., Next-generation sequencing in the clinic: promises and challenges. Cancer Lett., 340, 2013, 284.