Ultra-high resolution HLA genotyping and allele discovery by highly multiplexed cDNA amplicon pyrosequencing

BMC Genomics

Volumn 13, Issue 1, 2012, Pages

  Lank, Simon M ^a   Golbach, Brittney A ^a   Creager, Hannah M ^a   Wiseman, Roger W ^a   Keskin, Derin B ^b,c   Reinherz, Ellis L ^b,c   Brusic, Vladimir ^b,c   O'Connor, David H ^a,d  

^a UNIVERSITY OF WISCONSIN   (United States)

^b DANA FARBER CANCER INSTITUTE   (United States)

^c HARVARD MEDICAL SCHOOL   (United States)

^d UNIVERSITY OF WISCONSIN SCHOOL OF MEDICINE AND PUBLIC HEALTH   (United States)

Author keywords

Cellular immunity; Galaxy; Genotyping; HLA; Multiplexing; Pyrosequencing; Roche 454; Tissue typing

Indexed keywords

COMPLEMENTARY DNA; HLA ANTIGEN; HLA ANTIGEN CLASS 1; HLA ANTIGEN CLASS 2; HLA DR ANTIGEN;

ACCURACY; ALLELE; AMPLICON; ARTICLE; COMPUTER ANALYSIS; COMPUTER PROGRAM; GENE LOCUS; GENOTYPE; HIGH THROUGHPUT SEQUENCING; HLA TYPING; HUMAN; HUMAN CELL; OPEN READING FRAME; POLYMERASE CHAIN REACTION; PYROSEQUENCING; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

ALLELES; BASE SEQUENCE; CELL LINE; DNA PRIMERS; DNA, COMPLEMENTARY; GENES, MHC CLASS I; GENES, MHC CLASS II; GENOTYPE; GENOTYPING TECHNIQUES; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HLA ANTIGENS; HUMANS; NUCLEIC ACID AMPLIFICATION TECHNIQUES; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

EID: 84864497082     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-378     Document Type: Article

References (34)

1. Caillat-Zucman S. Molecular mechanisms of HLA association with autoimmune diseases. Tissue Antigens 2009, 73:1-8. 10.1111/j.1399-0039.2008.01167.x, 19017300.
2. Capittini C, Martinetti M, Cuccia M. MHC variation, mate choice and natural selection: the scent of evolution. Riv Biol 2008, 101:463-480.
3. Kulpa DA, Collins KL. The emerging role of HLA-C in HIV-1 infection. Immunology 2011, 134:116-122. 10.1111/j.1365-2567.2011.03474.x, 3194220, 21896007.
4. Rodriguez-Novoa S, Cuenca L, Morello J, Cordoba M, Blanco F, Jimenez-Nacher I, Soriano V. Use of the HCP5 single nucleotide polymorphism to predict hypersensitivity reactions to abacavir: correlation with HLA-B*5701. J Antimicrob Chemother 2010, 65:1567-1569. 10.1093/jac/dkq204, 20534626.
5. Seliger B, Stoehr R, Handke D, Mueller A, Ferrone S, Wullich B, Tannapfel A, Hofstaedter F, Hartmann A. Association of HLA class I antigen abnormalities with disease progression and early recurrence in prostate cancer. Cancer Immunol Immunother 2010, 59:529-540. 10.1007/s00262-009-0769-5, 3426221, 19820934.
6. Robinson J, Mistry K, McWilliam H, Lopez R, Parham P, Marsh SG. The IMGT/HLA database. Nucleic Acids Res 2011, 39:D1171-D1176. 10.1093/nar/gkq998, 3013815, 21071412.
7. Balazs I, Beekman J, Neuweiler J, Liu H, Watson E, Ray B. Molecular typing of HLA-A, -B, and DRB using a high throughput micro array format. Hum Immunol 2001, 62:850-857. 10.1016/S0198-8859(01)00274-9, 11476908.
8. Pereyra F, Jia X, McLaren PJ, Telenti A, de Bakker PI, Walker BD, Ripke S, Brumme CJ, Pulit SL, Carrington M, Kadie CM, Carlson JM, Heckerman D, Graham RR, Plenge RM, Deeks SG, Gianniny L, Crawford G, Sullivan J, Gonzalez E, Davies L, Camargo A, Moore JM, Beattie N, Gupta S, Crenshaw A, Burtt NP, Guiducci C, Gupta N, Gao X, Qi Y, et al. The major genetic determinants of HIV-1 control affect HLA class I peptide presentation. Science 2010, 330:1551-1557. 3235490, 21051598.
9. Marsh SG. Nomenclature for factors of the HLA system, update June 2011. Tissue Antigens 2011, 78:314-319. 10.1111/j.1399-0039.2011.01760.x, 21929577.
10. Liao WW, Arthur JW. Predicting Peptide binding affinities to MHC molecules using a modified semi-empirical scoring function. PLoS One 2011, 6:e25055. 10.1371/journal.pone.0025055, 3178607, 21966412.
11. Friedrich D, Jalbert E, Dinges WL, Sidney J, Sette A, Huang Y, McElrath MJ, Horton H. Vaccine-induced HIV-specific CD8+ T cells utilize preferential HLA alleles and target specific regions of HIV-1. J Acquir Immune Defic Syndr 2011,
12. Greene JM, Wiseman RW, Lank SM, Bimber BN, Karl JA, Burwitz BJ, Lhost JJ, Hawkins OE, Kunstman KJ, Broman KW, Wolinsky SM, Hildebrand WH, O'Connor DH. Differential MHC class I expression in distinct leukocyte subsets. BMC Immunol 2011, 12:39. 10.1186/1471-2172-12-39, 3155488, 21762519.
13. Kim OY, Monsel A, Bertrand M, Coriat P, Cavaillon JM, Adib-Conquy M. Differential down-regulation of HLA-DR on monocyte subpopulations during systemic inflammation. Crit Care 2010, 14:R61. 10.1186/cc8959, 2887183, 20385017.
14. Khanna R, Silins SL, Weng Z, Gatchell D, Burrows SR, Cooper L. Cytotoxic T cell recognition of allelic variants of HLA B35 bound to an Epstein-Barr virus epitope: influence of peptide conformation and TCR-peptide interaction. Eur J Immunol 1999, 29:1587-1597. 10.1002/(SICI)1521-4141(199905)29:05<1587::AID-IMMU1587>3.0.CO;2-W, 10359113.
15. Parham P. MHC class I molecules and KIRs in human history, health and survival. Nat Rev Immunol 2005, 5:201-214. 10.1038/nri1570, 15719024.
16. Sampah ME, Ceccato CM, Blankson JN. HIV type 1-mediated downregulation of HLA-B*57/B*5801 proteins on elite suppressor CD4+ T cells. AIDS Res Hum Retroviruses 2011, 27:183-186. 10.1089/aid.2010.0144, 3064525, 20919920.
17. Kloverpris HN, Stryhn A, Harndahl M, van der Stok M, Payne RP, Matthews PC, Chen F, Riddell L, Walker BD, Ndung'u T, Buus S, Goulder P. HLA-B*57 Micropolymorphism shapes HLA allele-specific epitope immunogenicity, selection pressure, and HIV immune control. J Virol 2012, 86:919-929. 10.1128/JVI.06150-11, 3255844, 22090105.
18. Lebedeva TV, Mastromarino SA, Lee E, Ohashi M, Alosco SM, Yu N. Resolution of HLA class I sequence-based typing ambiguities by group-specific sequencing primers. Tissue Antigens 2011, 77:247-250. 10.1111/j.1399-0039.2010.01616.x, 21299532.
19. Bettencourt BF, Santos MR, Fialho RN, Couto AR, Peixoto MJ, Pinheiro JP, Spinola H, Mora MG, Santos C, Brehm A, Bruges-Armas J. Evaluation of two methods for computational HLA haplotypes inference using a real dataset. BMC Bioinformatics 2008, 9:68. 10.1186/1471-2105-9-68, 2268655, 18230173.
20. Listgarten J, Brumme Z, Kadie C, Xiaojiang G, Walker B, Carrington M, Goulder P, Heckerman D. Statistical resolution of ambiguous HLA typing data. PLoS Comput Biol 2008, 4:e1000016. 10.1371/journal.pcbi.1000016, 2289775, 18392148.
21. Nunes JM, Riccio ME, Tiercy JM, Sanchez-Mazas A. Allele frequency estimation from ambiguous data: using resampling schema in validating frequency estimates and in selective neutrality testing. Hum Biol 2011, 83:437-447. 10.3378/027.083.0307, 21740157.
22. Bentley G, Higuchi R, Hoglund B, Goodridge D, Sayer D, Trachtenberg EA, Erlich HA. High-resolution, high-throughput HLA genotyping by next-generation sequencing. Tissue Antigens 2009, 74:393-403. 10.1111/j.1399-0039.2009.01345.x, 19845894.
23. Erlich RL, Jia X, Anderson S, Banks E, Gao X, Carrington M, Gupta N, DePristo MA, Henn MR, Lennon NJ, de Bakker PI. Next-generation sequencing for HLA typing of class I loci. BMC Genomics 2011, 12:42. 10.1186/1471-2164-12-42, 3033818, 21244689.
24. Lank SM, Wiseman RW, Dudley DM, O'Connor DH. A novel single cDNA amplicon pyrosequencing method for high-throughput, cost-effective sequence-based HLA class I genotyping. Hum Immunol 2010, 71:1011-1017. 10.1016/j.humimm.2010.07.012, 3191540, 20650293.
25. Korlach J, Bjornson KP, Chaudhuri BP, Cicero RL, Flusberg BA, Gray JJ, Holden D, Saxena R, Wegener J, Turner SW. Real-time DNA sequencing from single polymerase molecules. Methods Enzymol 2010, 472:431-455.
26. Min SK, Kim WY, Cho Y, Kim KS. Fast DNA sequencing with a graphene-based nanochannel device. Nat Nanotechnol 2011, 6:162-165. 10.1038/nnano.2010.283, 21297626.
27. Gilles A, Meglecz E, Pech N, Ferreira S, Malausa T, Martin JF. Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing. BMC Genomics 2011, 12:245. 10.1186/1471-2164-12-245, 3116506, 21592414.
28. Holcomb CL, Hoglund B, Anderson MW, Blake LA, Bohme I, Egholm M, Ferriola D, Gabriel C, Gelber SE, Goodridge D, Hawbecker S, Klein R, Ladner M, Lind C, Monos D, Pando MJ, Proll J, Sayer DC, Schmitz-Agheguian G, Simen BB, Thiele B, Trachtenberg EA, Tyan DB, Wassmuth R, White S, Erlich HA. A multi-site study using high-resolution HLA genotyping by next generation sequencing. Tissue Antigens 2011, 77:206-217. 10.1111/j.1399-0039.2010.01606.x, 21299525.
29. Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R, Mangan M, Nekrutenko A, Taylor J. Galaxy: a web-based genome analysis tool for experimentalists. Curr Protoc Mol Biol 2010, 19:1-21.
30. Kent WJ. BLAT-the BLAST-like alignment tool. Genome Res 2002, 12:656-664. 187518, 11932250.
31. Marsh SG, Albert ED, Bodmer WF, Bontrop RE, Dupont B, Erlich HA, Fernandez-Vina M, Geraghty DE, Holdsworth R, Hurley CK, Lau M, Lee KW, Mach B, Maiers M, Mayr WR, Muller CR, Parham P, Petersdorf EW, Sasazuki T, Strominger JL, Svejgaard A, Terasaki PI, Tiercy JM, Trowsdale J. Nomenclature for factors of the HLA system, 2010. Tissue Antigens 2010, 75:291-455. 10.1111/j.1399-0039.2010.01466.x, 2848993, 20356336.
32. Koehler RN, Walsh AM, Sanders-Buell EE, Eller LA, Eller M, Currier JR, Bautista CT, Wabwire-Mangen F, Hoelscher M, Maboko L, Kim J, Michael NL, Robb ML, McCutchan FE, Kijak GH. High-throughput high-resolution class I HLA genotyping in East Africa. PLoS One 2010, 5:e10751. 10.1371/journal.pone.0010751, 2873994, 20505773.
33. Keskin DB, Reinhold B, Lee SY, Zhang G, Lank S, O'Connor D, Berkowitz RS, Brusic V, Kim SJ, Reinherz EL. Direct identification of an HPV-16 tumor antigen from cervical cancer biopsy specimens. Frontiers in Immunology 2011, 2.
34. Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 2004, 5:113. 10.1186/1471-2105-5-113, 517706, 15318951.