Pyrosequencing™: A one-step method for high resolution HLA typing

Journal of Translational Medicine

Volumn 1, Issue , 2003, Pages

  Ramon, Daniel ^a   Braden, Megan ^a   Adams, Sharon ^b   Marincola, Francesco M ^b   Wang, Lu ^a  

^a PEL FREEZ Clinical Systems LLC   (United States)

^b NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HLA ANTIGEN; NUCLEOTIDE;

ALLELE; ARTICLE; AUTOMATION; COMPUTER PROGRAM; DATA ANALYSIS; DEVICE; DNA FINGERPRINTING; DNA SEQUENCE; DNA TEMPLATE; DONOR; HETEROZYGOTE; HLA TYPING; HUMAN; METHODOLOGY; MOLECULAR TYPING; OUTCOMES RESEARCH; SIGNAL PROCESSING;

EID: 4344567914     PISSN: 14795876     EISSN: None     Source Type: Journal    
DOI: 10.1186/1479-5876-1-9     Document Type: Article

References (34)

1. Petersdorf EW, Mickelson EM, Anasetti C, Martin PJ, Wool-frey AE, Hansen JA: Effect of HLA mismatches on the outcome of hematopoietic transplants. Curr Opin Immunol 1999, 11:521-526.
2. Duquesnoy RJ: HLA matchmaker: a molecularly based algorithm for histocompatibility determination. I Description of the algorithm. Hum Immunol 2002, 63:339-352.
3. Duquesnoy RJ, Marrari M: HLA matchmaker: a molecularly based algorithm for histocompatibility determination. II. Verification of the algorithm and determination of the relative immunogenicity of amino acid triplet-defined epitopes. Hum Immunol 2002, 63:353-363.
4. Adams SD, Krausa P, McGinnis M, Simonis TB, Stein J, Marincola FM: Practicality of high-throughput HLA sequencing based typing. ASHI Quarterly 2001, 25:54-57.
5. Erlich HA, Opelz G, Hansen JA: HLA DNA typing and transplantation. Immunity 2001, 14:347-356.
6. Adams SD, Barracchini KC, Chen D, Robbins F-M, Stroncek D, Marincola FM: Ambiguous allele combinations in sequence-based typing. ASHI Quarterly 2003, in press.
7. Sanger F, Nickels S, Coulson AR: DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 1977, 74:5463-5467.
8. Jin P, Wang E: Polymorphism in clinical immunology. From HLA typing to immunogenetic profiling. J Transl Med 2003., 1(18):
9. Ronaghi M, Uhlen M, Nyrén P: A sequencing method based on real-time pyrophosphate. Science 1998, 281:363-365.
10. Ronaghi M: Pyrosequencing sheds light on DNA sequencing. Genome Res 2001, 11:3-11.
11. Wang L, Marincola FM: Applaying Pyrosequencing to HLA-typing. ASHI Quarterly 2003, 27:16-18.
12. Ahmadian A, Gharizadeh B, Gustafsson AC, Sterky F, Nyren P, Uhlen M, Lundeberg J: Single-nucleotide polymorphism analysis by Pyrosequencing. Anal Biochem 2000,280:103-10.
13. Sun YQ, Monstein HJ, Nilsson LE, Petersson F, Borch K: Profiling and identification of eubacteria in the stomach of Mongolian gerbils with and without Helicobacter pylory infection. Helicobacter 2003, 8:149-157.
14. Vozarova B, Fernandez-Real JM, Knowler WC, Gallart L, Hanson RL, Gruber JD, Ricart W, Vendrell J, Richart C, Tataranni PA, Wolford JK.: The interleukin-6 (-174) G/C promoter polymorphism is associated with type-2 diabetes mellitus in Native Americans and Caucasians. Hum Genet 2003, 112:409-413.
15. Hefler LA, Ludwig E, Lampe D, Zeillinger R, Leodolter S, Gitsch G, Koelbl H, Tempfer CB: Polymorphisms of the endothelial nitric oxide synthase gene in ovarian cancer. Gynecol Oncol 2002, 86:134-137.
16. Elahi E, Pourmand N, Chaung R, Rofoogaran A, Boisver J, Samimi-Rad K, Davis RW, Ronaghi M: Determination of hepatitis C virus genotype by Pyrosequencing. J Virol Methods 2003, 109:171-176.
17. Pacey-Miller T, Henry R: Single-nucleotide polymorphism detection in plants using a single stranded Pyrosequencing protocol with a universal biotinylated primer. Analyt Biochem 2003, 317:165-170.
18. De Vivo I, Huggins GS, Hankinson SE, Lescault PJ, Boezen M, Colditz GA, Hunter DJ: A functional polymorphism in the promoter of the progesterone receptor gene associated with endometrial cancer risk. Proc Natl Acad Sci U S A 2002, 99:12263-12268.
19. Wolford JK, Gruber JD, Ossowski VM, Vozarova B, Antonio Tataranni P, Bogardus C, Hanson RL: A C-reactive protein promoter polymorphism is associated with type 2 diabeter mellitus in Pima Indians. Molec Genet Metab 2003, 78:136-144.
20. Barber RC, O'Keefe GE: Characterization of a single nucleotide polymorphism in the lipopolysaccaride binding protein and its association with sepsis. Am J Respir Crit Care Med 2003, 167:1316-1320.
21. Robin C, Lyman RF, Long AD, Langley CH, Mackay TFC: Hairy: a quantitative trait locus for Drosophila Sensory Bristle Number. Genetics 2002, 162:155-164.
22. Olofsson P, Holmberg J, Tordsson J, Lu S, Akerstrom B, Holmdahl R: Positional identification of Ncf1 as a gene that regulates arthritis severity in rats. Nature Genetics 2003, 33:25-32.
23. Nordstrom T, Nourizad K, Ronaghi M, Nyren P: Method enabling Pyrosequencing on double-stranded DNA. Anal Biochem 2000, 282:186-93.
24. Sundstrom M, Vliagoftis H, Karlberg P, Butterfield JH, Nilsson K, Metcalfe DD, Nilsson G: Functional and phenotypic studies of two variants of a human mast cell line with a distinct set of mutations in the c-kit proto-oncogene. Immunology 2003, 108:89-97.
25. Ronaghi M, Karamohamed S, Pettersson B, Uhlen M, Nyren P: Real-time DNA sequencing using detection of pyrophosphate release. Anal Biochem 1996, 242:84-9.
26. Wang E, Adams S, Zhao Y, Panelli MC, Simon R, Klein H, Marincola FM: A strategy for detection of known and unknown SNP using a minimum number of oligonucleotides. J Transl Med 2003, 1:4.
27. Eriksson S, Berg LM, Wadelius M, Aldeborn A: Cttochrome P450 genotyping by multiplex real-time DNA sequencing with Pyrosequencing™ technology. Assay Drug Develop Technol 2002, 1:49-59.
28. Ringquist S, Alexander AM, Rudert WA, Styche A, Trucco M: Pyrosequencing-based typing of alleles of the HLA-DQB1 gene. Biotechniques 2002, 33:166-175.
29. Gharizadeh B, Nordstrom T, Ahmadian A, Ronaghi M, Nyren P: Long-read Pyrosequencing using pure 2'-deoxyadenosine-5'-O'-(1- thiotriphosphate) Sp-isomer. Analyt Biochem 2002, 301:82-90.
30. Gharizadeh B, Ghaderi M, Donnelly D, Amini B, Wallin KL, Nyren P: Multiple-primer DNA sequencing method. Electrophoresis 2003, 24:1145-1151.
31. Lahser FC, Wright-Minogue J, Skelton A, Molcolm BA: Quantitative estimation of viral fitness using Pyrosequencing. Biotechniques 2003, 34:26-28.
32. Ronaghi M, Uhlen M, Nyren P: A sequencing method based on real-time pyrophosphate. Science 1998, 281:363-365.
33. Hochberg EP, Miklos DB, Neuberg D, Eichner DA, McLaughlin SF, Mattes-Ritz A, Alyea EP, Antin JH, Soiffer RJ, Ritz J: A novel rapid single nucleotide polymorphism (SNP)-based method for assessment of hematopoietic chimerism after allogeneic stem cell transplantation. Blood 2003, 101:363-369.
34. Fakhrai-Rad H, Pourmand N, Ronaghi M: Pyrosequencing: an accurate detection platform for single nucleotide polymorphisms. Hum Mutat 2002, 19:479-85.