A highly specific microarray method for point mutation detection

BioTechniques

Volumn 44, Issue 1, 2008, Pages 119-126

  Baaj, Yasser ^a   Magdelaine, Corinne ^a   Ubertelli, Virginie ^b   Valat, Christophe ^b   Talini, Luc ^c   Soussaline, Françoise ^d   Khomyakova, Elena ^d   Funalot, Benoît ^e   Vallat, Jean Michel ^e   Sturtz, Franck G ^a  

^a UNIVERSITY OF LIMOGES   (France)

^b Serial Genetics   (France)

^c PSL RESEARCH UNIVERSITY   (France)

^d IMSTAR   (France)

^e LIMOGES UNIVERSITY HOSPITAL   (France)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA;

ARTICLE; CONTROLLED STUDY; DNA HYBRIDIZATION; DNA MICROARRAY; GENE AMPLIFICATION; GENE MUTATION; GENE SEQUENCE; GENOTYPE; HEREDITARY MOTOR SENSORY NEUROPATHY; HUMAN; HUMAN CELL; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION;

BASE SEQUENCE; CASE-CONTROL STUDIES; CHARCOT-MARIE-TOOTH DISEASE; DNA MUTATIONAL ANALYSIS; HUMANS; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OLIGONUCLEOTIDES; POINT MUTATION; SENSITIVITY AND SPECIFICITY;

EID: 39149131406     PISSN: 07366205     EISSN: None     Source Type: Journal    
DOI: 10.2144/000112630     Document Type: Article

References (30)

1. Fodor, S.P., J.L. Read, M.C. Pirrung, L. Stryer, A.T. Lu, and D. Solas. 1991. Light-directed, spatially addressable parallel chemical synthesis. Science 251:767-773.
2. Pease, A.C., D. Solas, E.J. Sullivan, M.T. Cronin, C.P. Holmes, and S.P. Fodor. 1994. Light-generated oligonucleotide arrays for rapid DNA sequence analysis. Proc. Natl. Acad. Sci. USA 91:5022-5026.
3. Hirschhorn, J.N., P. Sklar, K. Lindblad-Toh, Y.M. Lim, M. Ruiz-Gutierrez, S. Bolk, B. Langhorst, S. Schaffner, et al. 2000. SBE-TAGS: an array-based method for efficient single-nucleotide polymorphism genotyping. Proc. Natl. Acad. Sci. USA 97:12164-12169.
4. Lindroos, K., S. Sigurdsson, K. Johansson, L. Ronnblom, and A.C. Syvanen. 2002. Multiplex SNP genotyping in pooled DNA samples by a four-colour microarray system. Nucleic Acids Res. 30:e70.
5. Shumaker, J.M., A. Metspalu, and C.T. Caskey. 1996. Mutation detection by solid phase primer extension. Hum. Mutat. 7:346-354.
6. Pastinen, T., J. Partanen, and A.C. Syvanen. 1996. Multiplex, fluorescent, solid-phase minisequencing for efficient screening of DNA sequence variation. Clin. Chem. 42:1391-1397.
7. Pastinen, T., A. Kurg, A. Metspalu, L. Peltonen, and A.C. Syvanen. 1997. Minisequencing: a specific tool for DNA analysis and diagnostics on oligonucleotide arrays. Genome Res. 7:606-614.
8. Head, S.R., Y.H. Rogers, K. Parikh, G. Lan, S. Anderson, P. Goelet, and M.T. Boyce-Jacino. 1997. Nested genetic bit analysis (N-GBA) for mutation detection in the p53 tumor suppressor gene. Nucleic Acids Res. 25:5065-5071.
9. Pastinen, T., M. Raitio, K. Lindroos, P. Tainola, L. Peltonen, and A.C. Syvanen. 2000. A system for specific, high-throughput genotyping by allele-specific primer extension on microarrays. Genome Res. 10:1031-1042.
10. Tyagi, S. and F.R. Kramer. 1996. Molecular beacons: probes that fluoresce upon hybridization. Nat. Biotechnol. 14:303-308.
11. Tyagi, S., D.P. Bratu, and F.R. Kramer. 1998. Multicolor molecular beacons for allele discrimination. Nat. Biotechnol. 16:49-53.
12. Steemers, F.J., J.A. Ferguson, and D.R. Walt. 2000. Screening unlabeled DNA targets with randomly ordered fiber-optic gene arrays. Nat. Biotechnol. 18:91-94.
13. Khomyakova, E.B., E.V. Dreval, M. Tran-Dang, M.C. Potier, and F.P. Soussaline. 2004. Innovative instrumentation for microarray scanning and analysis: application for characterization of oligonucleotide duplexes behavior. Cell Mol. Biol. (Noisy-le-grand) 50:217-224.
14. Bonnet, G., S. Tyagi, A. Libchaber, and F.R. Kramer. 1999. Thermodynamic basis of the enhanced specificity of structured DNA probes. Proc. Natl. Acad. Sci. USA 96:6171-6176.
15. Riccelli, P.V., F. Merante, K.T. Leung, S. Bortolin, R.L. Zastawny, R. Janeczko, and A.S. Benight. 2001. Hybridization of single-stranded DNA targets to immobilized complementary DNA probes: comparison of hairpin versus linear capture probes. Nucleic Acids Res. 29:996-1004.
16. Marras, S.A., F.R. Kramer, and S. Tyagi. 1999. Multiplex detection of single-nucleotide variations using molecular beacons. Genet. Anal. 14:151-156.
17. Ramachandran, A., J. Flinchbaugh, P. Ayoubi, G.A. Olah, and J.R. Malayer. 2004. Target discrimination by surface-immobilized molecular beacons designed to detect Francisella tularensis. Biosens. Bioelectron. 19:727-736.
18. Du, H., C.M. Strohsahl, J. Camera, B.L. Miller, and T.D. Krauss. 2005. Sensitivity and specificity of metal surface-immobilized "molecular beacon" biosensors. J. Am. Chem. Soc. 127:7932-7940.
19. Schrijver, I., E. Oitmaa, A. Metspalu, and P. Gardner. 2005. Genotyping microarray for the detection of more than 200 CFTR mutations in ethnically diverse populations. J. Mol. Diagn. 7:375-387.
20. Le Calvez, F., A. Ahman, N. Tonisson, J. Lambert, S. Temam, P. Brennan, D.G. Zaridze, A. Metspalu, et al. 2005. Arrayed primer extension resequencing of mutations in the TP53 tumor suppressor gene: comparison with denaturing HPLC and direct sequencing. Clin. Chem. 51:1284-1287.
21. Tonisson, N., A. Kurg, K. Kaasik, E. Lohmussaar, and A. Metspalu. 2000. Unravelling genetic data by arrayed primer extension. Clin. Chem. Lab. Med. 38:165-170.
22. Nikiforov, T.T., R.B. Rendle, P. Goelet, Y.H. Rogers, M.L. Kotewicz, S. Anderson, G.L. Trainor, and M.R. Knapp. 1994. Genetic Bit Analysis: a solid phase method for typing single nucleotide polymorphisms. Nucleic Acids Res. 22:4167-4175.
23. Matsuzaki, H., S. Dong, H. Loi, X. Di, G. Liu, E. Hubbell, J. Law, T. Berntsen, et al. 2004. Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays. Nat. Methods 1:109-111.
24. Matsuzaki, H., H. Loi, S. Dong, Y.Y. Tsai, J. Fang, J. Law, X. Di, W.M. Liu, et al. 2004. Parallel genotyping of over 10,000 SNPs using a one-primer assay on a high-density oligonucleotide array. Genome Res. 14:414-425.
25. Borevitz, J. 2006. Genotyping and mapping with high-density oligonucleotide arrays. Methods Mol. Biol. 323:137-145.
26. Lamy, P., C.L. Andersen, F.P. Wikman, and C. Wiuf. 2006. Genotyping and annotation of Affymetrix SNP arrays. Nucleic Acids Res. 34:e100.
27. Conner, B.J., A.A. Reyes, C. Morin, K. Itakura, R.L. Teplitz, and R.B. Wallace. 1983. Detection of sickle cell beta S-globin allele by hybridization with synthetic oligonucleotides. Proc. Natl. Acad. Sci. USA 80:278-282.
28. Southern, E.M., U. Maskos, and J.K. Elder. 1992. Analyzing and comparing nucleic acid sequences by hybridization to arrays of oligonucleotides: evaluation using experimental models. Genomics 13:1008-1017.
29. Cronin, M.T., R.V. Fucini, S.M. Kim, R.S. Masino, R.M. Wespi, and C.G. Miyada. 1996. Cystic fibrosis mutation detection by hybridization to light-generated DNA probe arrays. Hum. Mutat. 7:244-255.
30. Mir, K.U. and E.M. Southern. 2000. Sequence variation in genes and genomic DNA: methods for large-scale analysis. Annu. Rev. Genomics Hum. Genet. 1:329-360.