Super high resolution for single molecule-sequence-based typing of classical HLA loci at the 8-digit level using next generation sequencers

Tissue Antigens

Volumn 80, Issue 4, 2012, Pages 305-316

  Shiina, T ^a   Suzuki, S ^a   Ozaki, Y ^a   Taira, H ^b   Kikkawa, E ^a   Shigenari, A ^a   Oka, A ^a   Umemura, T ^c   Joshita, S ^c   Takahashi, O ^b   Hayashi, Y ^d   Paumen, M ^d   Katsuyama, Y ^e   Mitsunaga, S ^a   Ota, M ^c   Kulski, J K ^f   Inoko, H ^a  

^a TOKAI UNIVERSITY SCHOOL OF MEDICINE   (Japan)

^b Technical Support Life Technologies Japan Ltd   (Japan)

^c SHINSHU UNIVERSITY SCHOOL OF MEDICINE   (Japan)

^d Scientific Affairs Life Technologies Japan Ltd   (Japan)

^e SHINSHU UNIVERSITY HOSPITAL   (Japan)

^f UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

Author keywords

DNA typing; Human leukocyte antigen; Next generation sequencing; Polymerase chain reaction; Super high resolution single molecule sequence based typing

Indexed keywords

DNA; HLA A ANTIGEN; HLA ANTIGEN; HLA B ANTIGEN; HLA C ANTIGEN; HLA DQB1 ANTIGEN; HLA DR1 ANTIGEN;

3' UNTRANSLATED REGION; ALLELE; ANTIGEN DETECTION; ANTIGEN EXPRESSION; ANTIGEN FUNCTION; ARTICLE; CONTROLLED STUDY; COST EFFECTIVENESS ANALYSIS; GENE AMPLIFICATION; GENE LOCUS; GENE SEQUENCE; HLA TYPING; HUMAN; MOLECULE; NEXT GENERATION SEQUENCING; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROMOTER REGION; SEQUENCE ANALYSIS; SUPER HIGH RESOLUTION SINGLE MOLECULE SEQUENCE BASED TYPING;

3' UNTRANSLATED REGIONS; ALLELES; DNA PRIMERS; GENETIC LOCI; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HLA ANTIGENS; HUMANS; MULTILOCUS SEQUENCE TYPING; POLYMERASE CHAIN REACTION; PROMOTER REGIONS, GENETIC; SEQUENCE ANALYSIS, DNA;

EID: 84866632618     PISSN: 00012815     EISSN: 13990039     Source Type: Journal    
DOI: 10.1111/j.1399-0039.2012.01941.x     Document Type: Article

References (24)

1. The MHC sequencing consortium. Complete sequence and gene map of a human major histocompatibility complex. Nature 1999: 401: 921-3.
2. Shiina T, Inoko H, Kulski JK. An update of the HLA genomic region, locus information and disease associations: 2004. Tissue Antigens 2004: 64: 631-49.
3. Shiina T, Hosomichi K, Inoko H, Kulski JK. The HLA genomic loci map: expression, interaction, diversity and disease. J Hum Genet 2009: 54: 15-39.
4. Robinson J, Mistry K, McWilliam H, Lopez R, Parham P, Marsh SG. The IMGT/HLA database. Nucleic Acids Res 2011: 39: D1171-6.
5. Ota M, Seki T, Fukushima H, Tsuji K, Inoko H. HLA-DRB1 genotyping by modified PCR-RFLP method combined with group-specific primers. Tissue Antigens 1992: 39: 187-202.
6. Hoshino S, Kimura A, Fukuda Y, Dohi K, Sasazuki T. Polymerase chain reaction--single-strand conformation polymorphism analysis of polymorphism in DPA1 and DPB1 genes: a simple, economical, and rapid method for histocompatibility testing. Hum Immunol 1992: 33: 98-107.
7. 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: 225-35.
8. Santamaria P, Boyce-Jacino MT, Lindstrom AL, Barbosa JJ, Faras AJ, Rich SS. HLA class II 'typing': direct sequencing of DRB, DQB, and DQA genes. Hum Immunol 1992: 33: 69-81.
9. Bettinotti MP, Mitsuishi Y, Bibee K, Lau M, Terasaki PI. Comprehensive method for the typing of HLA-A, B, and C alleles by direct sequencing of PCR products obtained from genomic DNA. J Immunother 1997: 20: 425-30.
10. Itoh Y, Mizuki N, Shimada T et al. High-throughput DNA typing of HLA-A, -B, -C, and -DRB1 loci by a PCR-SSOP-Luminex method in the Japanese population. Immunogenetics 2005: 57: 717-29.
11. Rozemuller EH. Collection and analysis of SBT results data. In: Hansen JA, ed. 13th IHWS Technology Joint Report. Seattle: Immunobiology of Human MHC, 2006, 413-6.
12. Lind C, Ferriola D, Mackiewicz K et al. Next-generation sequencing: the solution for high-resolution, unambiguous human leukocyte antigen typing. Hum Immunol 2010: 71: 1033-42.
13. Adams SD, Barracchini KC, Chen D et al. Ambiguous allele combinations in HLA class I and class II sequence-based typing: when precise nucleotide sequencing leads to imprecise allele identification. J Transl Med 2004: 2: 30.
14. Gabriel C, Danzer M, Hackl C et al. Rapid high-throughput human leukocyte antigen typing by massively parallel pyrosequencing for high-resolution allele identification. Hum Immunol 2009: 70: 960-4.
15. 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: 1011-7.
16. Holcomb CL, Hoglund B, Anderson MW et al. A multi-site study using high-resolution HLA genotyping by next generation sequencing. Tissue Antigens 2011: 77: 206-17.
17. Wiseman RW, Karl JA, Bimber BN et al. Major histocompatibility complex genotyping with massively parallel pyrosequencing. Nat Med 2009: 15: 1322-6.
18. Lind C, Ferriola D, Monos D. Next generation sequencing: entering a new era in HLA sequence-based typing. ASHI 2010: 34: 8-14.
19. Bentley G, Higuchi R, Hoglund B et al. High-resolution, high-throughput HLA genotyping by next-generation sequencing. Tissue Antigens 2009: 74: 393-403.
20. Kita YF, Ando A, Tanaka K et al. Application of high-resolution, massively parallel pyrosequencing for estimation of haplotypes and gene expression levels of swine leukocyte antigen (SLA) class I genes. Immunogenetics 2012: 64: 187-99.
21. Vogel U, Szczepanowski R, Claus H, Junemann S, Prior K, Harmsen D. Ion Torrent PGM sequencing for genomic typing of Neisseria meningitidis for rapid determination of multiple layers of typing information. J Clin Microbiol 2012.
22. Galan M, Guivier E, Caraux G, Charbonnel N, Cosson JF. A 454 multiplex sequencing method for rapid and reliable genotyping of highly polymorphic genes in large-scale studies. BMC Genomics 2010: 11: 296.
23. Eid J, Fehr A, Gray J et al. Real-time DNA sequencing from single polymerase molecules. Science 2009: 323: 133-8.
24. Pleasance ED, Cheetham RK, Stephens PJ et al. A comprehensive catalogue of somatic mutations from a human cancer genome. Nature 2010: 463: 191-6.