Fundamentals of pyrosequencing

Archives of Pathology and Laboratory Medicine

Volumn 137, Issue 9, 2013, Pages 1296-1303

  Harrington, Colleen T ^a   Lin, Elaine I ^a   Olson, Matthew T ^a   Eshleman, James R ^a  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; PYROPHOSPHORIC ACID DERIVATIVE;

CHEMISTRY; COMPUTER PROGRAM; DNA SEQUENCE; GENETICS; GENOTYPE; HIGH THROUGHPUT SEQUENCING; HUMAN; METHODOLOGY; MUTATION; NEOPLASM; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; REVIEW;

BASE SEQUENCE; DIPHOSPHATES; DNA MUTATIONAL ANALYSIS; DNA, NEOPLASM; GENOTYPE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MUTATION; NEOPLASMS; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 84885111805     PISSN: 00039985     EISSN: 15432165     Source Type: Journal    
DOI: 10.5858/arpa.2012-0463-RA     Document Type: Review

References (23)

1. Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA. 1977;74(12):5463-5467.
2. Maxam AM, Gilbert W. A new method for sequencing DNA. Proc Natl Acad Sci USA. 1977;74(2):560-564. (Pubitemid 8038842)
3. Prober JM, Trainor GL, Dam RJ, et al. A system for rapid DNA sequencing with fluorescent chain-terminating dideoxynucleotides. Science. 1987; 238(4825):336-341. (Pubitemid 17151722)
4. Murphy KM, Berg KD, Eshleman JR. Sequencing of genomic DNA by combined amplification and cycle sequencing reaction. Clin Chem. 2005;51(1): 35-39. (Pubitemid 40024011)
5. Murphy KM, Eshleman JR. Simultaneous sequencing of multiple polymer-ase chain reaction products and combined polymerase chain reaction with cycle sequencing in single reactions. Am J Pathol. 2002;161(1):27-33. (Pubitemid 34760767)
6. Halling SM, Peterson-Burch BD, Bricker BJ, et al. Completion of the genome sequence of Brucella abortus and comparison to the highly similar genomes of Brucella melitensis and Brucella suis. J Bacteriol. 2005;187(8):2715-2726. (Pubitemid 40490376)
7. Nyren P. Enzymatic method for continuous monitoring of DNA polymerase activity. Anal Biochem. 1987;167(2):235-238 (Pubitemid 18022937)
8. Hyman ED. A new method of sequencing DNA. Anal Biochem. 1988; 174(2):423-436.
9. Alderborn A, Kristofferson A, Hammerling U. Determination of single-nucleotide polymorphisms by real-time pyrophosphate DNA sequencing. Genome Res. 2000;10(8):1249-1258.
10. Ahmadian A, Gharizadeh B, Gustafsson AC, et al. Single-nucleotide polymorphism analysis by pyrosequencing. Anal Biochem. 2000;280(1):103-110. (Pubitemid 30210818)
11. Ahmadian A, Ehn M, Hober S. Pyrosequencing: history, biochemistry and future. Clin Chim Acta. 2006;363(1-2):83-94. (Pubitemid 41748205)
12. Ahmadian A, Gharizadeh B, O'Meara D, Odeberg J, Lundeberg J. Genotyping by apyrase-mediated allele-specific extension. Nucleic Acids Res. 2001;29(24):E121. doi:10.1093/nar/29.24.e121.
13. Ronaghi M, Shokralla S, Gharizadeh B. Pyrosequencing for discovery and analysis of DNA sequence variations. Pharmacogenomics. 2007;8(10):1437-1441. (Pubitemid 350162855)
14. Diamandis EP, Christopoulos TK. The biotin-(strept)avidin system: principles and applications in biotechnology. Clin Chem. 1991;37(5):625-636. (Pubitemid 21892699)
15. Klenow H, Overgaard-Hansen K, Patkar SA. Proteolytic cleavage of native DNA polymerase into two different catalytic fragments: influence of assay conditions on the change of exonuclease activity and polymerase activity accompanying cleavage. Eur J Biochem. 1971;22(3):371-381.
16. Nordström T, Nourizad K, Ronaghi M, Nyren P. Method enabling pyrosequencing on double-stranded DNA. Anal Biochem. 2000;282(2):186-193. (Pubitemid 30439490)
17. Tsiatis AC, Norris-Kirby A, Rich RG, et al. Comparison of Sanger sequencing, pyrosequencing, and melting curve analysis for the detection of KRAS mutations: diagnostic and clinical implications. J Mol Diagn. 2010;12(4): 425-432.
18. Ogino S, Kawasaki T, Brahmandam M, et al. Sensitive sequencing method for KRAS mutation detection by pyrosequencing. J Mol Diagn. 2005;7(3):413-421. (Pubitemid 41149657)
19. Rothberg JM, Hinz W, Rearick TM, et al. An integrated semiconductor device enabling non-optical genome sequencing. Nature. 2011;475(7356):348-352. doi:10.1038/nature10242.
20. Chen G, Olson MT, O'Neill A, et al. A virtual pyrogram generator to resolve complex pyrosequencing results. J Mol Diagn. 2012;14(2):149-159.
21. Ronaghi M. Pyrosequencing sheds light on DNA sequencing. Genome Res. 2001;11(1):3-11. (Pubitemid 32117949)
22. Langaee T, Ronaghi M. Genetic variation analyses by pyrosequencing. Mutat Res. 2005;573(1-2):96-102.
23. Ronaghi M, Uhlen M, Nyren P. A sequencing method based on real-time pyrophosphate. Science. 1998;281(5375):363, 365.