Connector Inversion Probe technology: A powerful one-primer multiplex DAN amplification system for numerous scientific application

PLoS ONE

Volumn 2, Issue 9, 2007, Pages

  Akhras, Michael S ^a,b   Unemo, Magnus ^c   Thiyagarajan, Sreedevi ^a   Nyrén, Pål ^b   Davis, Ronald W ^a   Fire, Andrew Z ^a   Pourmand, Nader ^a,d  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

^c ÖREBRO UNIVERSITY HOSPITAL   (Sweden)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBIOTIC RESISTANCE; ARTICLE; COMPUTER INTERFACE; COMPUTER PROGRAM; CONNECTOR INVERSION PROBE; CONTROLLED STUDY; GENE AMPLIFICATION; GENE MUTATION; GENE TECHNOLOGY; GENOTYPE; METHODOLOGY; NEISSERIA GONORRHOEAE; NONHUMAN; ONLINE SYSTEM; PATHOGENESIS; SEQUENCE ANALYSIS; WART VIRUS; DNA PROBE; GENETICS; MUTATION;

BACTERIA (MICROORGANISMS); HUMAN PAPILLOMAVIRUS; NEISSERIA GONORRHOEAE;

DNA;

DNA; DNA PROBES; DRUG RESISTANCE, MICROBIAL; MUTATION;

EID: 41249094334     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0000915     Document Type: Article

References (45)

1. Saiki RK, Scharf S, Faloona F, Mullis KB, Horn GT, et al. (1985) Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science 230: 1350-1354.
2. Csako G (2006) Present and future of rapid and/or high-throughput methods for nucleic acid testing. Clin Chim, Acta 363: 6-31.
3. Chamberlain JS, Gibbs RA, RanierJE, Nguyen PN, Caskey CT (1988) Deletion screening of the Duchenne muscular dystrophy locus via multiplex DNA amplification. Nucleic Acids Res 16: 11141-11156.
4. Elnitio EM, Ashshi AM, Cooper RJ, Klapper PE (2000) Multiplex PCR: optimization and application in diagnostic virology. Clin Microbiol Rev 13: 559-570.
5. Nilsson M, Dahl F, Larsson C, Gullberg M, Stenberg J (2006) Analyzing genes using closing and replicating circles. Trends Biotechnol 24: 83-88.
6. Fredriksson S, Baner J, Dahl F, Chu A, Ji H, et al. (2007) Multiplex amplification of all coding sequences within 10 cancer genes by Gene-Collector. Nucleic Acids Res 35: e47.
7. Dahl F, Stenberg J, Fredriksson S, Welch K, Zhang M, et al. (2007) Multigene amplification and massively parallel sequencing for cancer mutation discovery. Proc Nad Acad Sci U S A.
8. Barany F (199 1) Genetic disease detection and DNA amplification using cloned thermostable ligase. Proc Natl Acad Sci U S A 88: 189-193.
9. Abravaya K, Carrino JJ, Muldoon S, Lee HH (1995) Detection of point mutations with a modified ligase chain reaction (Gap-LCR). Nucleic Acids Res 23:675-682.
10. Okazaki R, Okazaki T, Sakabe K, Sugimoto K, Sugino A (1968) Mechanism of DNA chain growth. I. Possible discontinuity and unusual secondary structure of newly synthesized chains. Proc Natl Acad Sci U S A 59: 598-605.
11. Nilsson M, Malmgren H, Samiotaki M, Kwiatkowski M, Chowdhary BP, et al. (1994) Padlock probes: circularizing oligonucleotides for localized DNA detection. Science 265: 2085-2088.
12. Fire A, Xu SQ (1995) Rolling replication of short DNA circles. Proc Natl Acad Sci U S A 92: 4641-4645.
13. Lizardi PM, Huang X, Zhu Z, Bray-Ward P, Thomas DC, et al. (1998) Mutation detection and single-molecule counting using isothermal roUing-circle amplification. Nat Genet 19: 225-232.
14. Hardenbol P, Baner J, Jain M, Nilsson M, Namsaraev EA, et al. (2003) Multiplexed genotyping with sequence-tagged molecular inversion probes. Nat Biotechnol 21: 673-678.
15. Hardenbol P, Yu F, Belmont J, Mackenzie J, Bruckner C, et al. (2005) Highly multiplexed molecular inversion probe genotyping: over 10,000 targeted SNPs genotyped in a single tube assay. Genome Res 15: 269-275.
16. Wang Y, Moorhead M, Karlin-Neumann G, Falkowski M, Chen C, et al. (2005) Allele quantification using molecular inversion probes (MIP). Nucleic Acids Res. 33: e183.
17. Akhras MS, Thiyagarajan S, Villablanca AC, Davis RW, Nyrén P, et al. (2007) PathogenMip Assay: A Multiplex Pathogen Detection Assay. PLoS ONE 2: e223.
18. Thiyagarajan S, Karhanek M, Akhras M, Davis RW, Pourmand N (2006) PathogenMIPer: a tool for the design of molecular inversion probes to detect multiple pathogens. BMC Bioinformatics 7: 500.
19. de Villiers EM Fauquet C, Broker TR, Bernard HU, zur Hausen H (2004) Classification of papillomaviruses. Virology 324: 17-27.
20. Doorbar J (2006) Molecular biology of human papillomavirus infection and cervical cancer. Clin Sci (Lond) 110: 525-541.
21. Lindbäck E, Gharizadeh B, Ataker F, Airell A, Jalal S, et al. (2005) DNA gyrase gene in Neisseria gonorrhoeae as indicator for resistance to ciprofloxacin and species verification. Int J STD AIDS 16: 142-147.
22. Lindbäck E, Unemo M, Akhras M, Gharizadeh B, Fredlund H, et al. (2006) Pyrosequencing of the DNA gyrase gene in Neisseria species: effective indicator of ciprofloxacin resistance in Neisseria gonorrhoeae. Apmis 114: 837-841.
23. Unemo M, Sjöstrand A, Akhras M, Gharizadeh B, Lindback E, et al. (2007) Molecular characterization of Neisseria gonorrhoeae identifies tansmission and resistance of one ciprofloxacin-resistant strain. Apmis 115: 231-241.
24. Gharizadeh B, Akhras M, Unemo M, Wretlind B, Nyren P, et al. (2005) Detection of gyrA mutations associated with ciprofloxacin resistance in Neisseria gonorrhoeae by rapid and reliable pre-programmed short DNA sequencing. Int J Antimicrob Agents 26: 486-490.
25. Gharizadeh B, Zheng B, Akhras M, Ghaderi M, Jejelowo, O, et al. (2006) Sentinel-base DNA genotyping using multiple sequencing primers for high-risk human papillomaviruses. Mol Cell Probes 20: 230-238.
26. Gharizadeh B, Akhras M, Nourizad N, Ghaderi M, Yasuda K, et al. (2006) Methodological improvements of pyrosequencing technology. J Biotechnol 124: 504-511.
27. de Roda Husman AM, Walboomers JM, van den Brule AJ, Meijer CJ, Snijders PJ (1995) The use of general primers GP5 and GP6 elongated at their 3′ ends with adjacent highly conserved sequences improves human papillomavirus detection by PCR. J Gen Virol 76 ( Pt 4): 1057-1062.
28. Gravitt PE, Peyton CL, Alessi TQ, Wheeler CM, Coutlee F, et al. (2000) Improved amplification of genital human papillomaviruses. J Clin Microbiol 38: 357-361.
29. Chavali S, Mahajan A, Tabassum R, Maiti S, Bharadwaj D (2005) Oligonucleotide properties determination and primer designing: a critical examination of predictions. Bioinformatics 21: 3918-3925.
30. Ben-Dov E, Shapiro OH, Siboni N, Kushmaro A (2006) Advantage of using inosine at the 3′ termini of 16S rRNA gene universal primers for the study of microbial diversity. Appl Environ Microbiol 72: 6902-6906.
31. Alekshun MN, Levy SB (2007) Molecular mechanisms of antibacterial multidrug resistance. Cell 128: 1037-1050.
32. Ji H, Kumm J, Zhang M, Farnam K, Salari K, et al. (2006) Molecular inversion probe analysis of gene copy alterations reveals distinct categories of colorectal carcinoma. Cancer Res 66: 7910-7919.
33. Hartley JL, Temple GF, Brasch MA (2000) DNA cloning using in vitro site-specific recombination. Genome Res 10: 1788-1795.
34. Dressman D, Yan H, Traverso G, Kinzler KW, Vogelstein B (2003) Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of generic variations. Proc Natl Acad Sci U S A 100: 8817-8822.
35. Dafforn A, Chen P, Deng G, Herrler M, Iglehart D, et al. (2004) Linear mRNA amplification from as little as 5 ng total RNA for global gene expression analysis. Biotechniques 37: 854-857.
36. Notomi T, Okayama H, Masubuchi H, Yonekawa T, Watanabe K, et al. (2000) Loop-mediated isothermal amplification of DNA. Nucleic Acids Res 28: E63.
37. Mitani Y, Lezhava A, Kawai Y, Kikuchi T, Oguchi-Katayama A, et al. (2007) Rapid SNP diagnostics using asymmetric isothermal amplification and a new mismatch-suppression technology. Nat Methods 4: 257-262.
38. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380.
39. Li M, Diehl F, Dressman D, Vogelstein B, Kinzler KW (2006) BEAMing up for detection and quantification of rare sequence variants. Nat Methods 3: 95-97.
40. Bennett ST, Barnes C, Cox A, Davies L, Brown C (2005) Toward the 1,000 dollars human genome. Pharmacogenomics 6: 373-382.
41. Shendure J, Porreca, GJ, Reppas NB, Lin X, McCutcheon JP, et al. (2005) Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309: 1728-1732.
42. Braslavsky I, Hebert B, Kartalov E, Quake SR (2003) Sequence information can be obtained from single DNA molecules. Proc Natl Acad Sci U S A 100: 3960-3964.
43. Jarvius J, Melin J, Goransson J, Stenberg J, Fredriksson S, et al. (2006) Digital quantification using amplified single-molecule detection. Nat Methods 3: 725-727.
44. Binladen J, Gilbert MT, Bollback JP, Panitz F, Bendixen C, et al. (2007) The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. PLoS ONE 2: e197.
45. Borodina TA, Lehrach H, Soldatov, AV (2003) Ligation-based synthesis of oligonucleotides with block structure. Anal Biochem 318: 309-313.