Tag-extension-based method for sensitive and specific genotyping of single nucleotide polymorphism on microarray

Clinica Chimica Acta

Volumn 409, Issue 1-2, 2009, Pages 11-17

  Shan, Qun ^a   Zheng, Yuanlin ^a   Chen, Guoqing ^a   Zheng, Guihong ^a   Lu, Jun ^a   Lv, Xiaojuan ^a  

^a JIANGSU NORMAL UNIVERSITY   (China)

Author keywords

Genotyping; Microarray; Sensitivity; Single nucleotide polymorphism; Specificity; Tag extension

Indexed keywords

4 AMINOBUTYRIC ACID RECEPTOR; 4 AMINOBUTYRIC ACID RECEPTOR BETA 3; CYTIDINE; GENOMIC DNA; GUANOSINE; UNCLASSIFIED DRUG;

ACCURACY; ARTICLE; CONTROLLED STUDY; DNA MICROARRAY; DNA SEQUENCE; GENOTYPE; HUMAN; NUCLEIC ACID IMMOBILIZATION; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RELIABILITY; SENSITIVITY AND SPECIFICITY; SINGLE NUCLEOTIDE POLYMORPHISM;

BASE SEQUENCE; DNA PRIMERS; FLUORESCENT DYES; GENOTYPE; NUCLEIC ACID HYBRIDIZATION; OLIGODEOXYRIBONUCLEOTIDES; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE; REPRODUCIBILITY OF RESULTS;

EID: 70349814058     PISSN: 00098981     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cca.2009.07.018     Document Type: Article

References (25)

1. Hood L., Heath J.R., Phelps M.E., et al. Systems biology and new technologies enable predictive and preventative medicine. Science 306 (2004) 640-643
2. Lord P.G., and Papoian T. Genomics and drug toxicity. Science 306 (2004) 575
3. Whitcombe D., Theaker J., Guy S.P., et al. Detection of PCR products using self-probing amplicons and fluorescence. Nat. Biotechnol. 17 (1999) 804-807
4. Marras S.A., Kramer F.R., and Tyagi S. Multiplex detection of single-nucleotide variations using molecular beacons. Genet. Anal. 14 (1999) 151-156
5. Pastinen T., Raitio M., Lindroos K., et al. A system for specific, high-throughput genotyping by allele-specific primer extension on microarrays. Genome Res. 10 (2000) 1031-1042
6. Newton C.R., Graham A., Heptinstall L.E., et al. Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS). Nucleic Acids Res. 17 (1989) 2503-2516
7. Hirschhorn J.N., Sklar P., Lindblad-Toh K., et al. SBE-TAGS: an array-based method for efficient single-nucleotide polymorphism genotyping. Proc Natl Acad Sci U S A 97 (2000) 12164-12169
8. Landegren U., Kaiser R., Sanders J., et al. A ligase-mediated gene detection technique. Science 241 (1988) 1077-1080
9. Ahmadian A., Gharizadeh B., Gustafsson A.C., et al. Single-nucleotide polymorphism analysis by pyrosequencing. Anal. Biochem. 280 (2000) 103-110
10. Bishop J., Blair S., and Chagovetz A.M. A competitive kinetic model of nucleic acid surface hybridization in the presence of point mutants. Biophys. J. 90 (2006) 831-840
11. Flavell A.J., Bolshakov V.N., Booth A., et al. A microarray-based high throughput molecular marker genotyping method: the tagged microarray marker (TAM) approach. Nucleic Acids Res. 31 (2003) e115
12. Soler C., Hamilton B., Furey A., et al. Optimization of LC-MS/MS using triple quadrupole mass analyzer for the simultaneous analysis of carbosulfan and its main metabolites in oranges. Anal. Chim. Acta 571 (2006) 1-11
13. Cozza A., Morandin F., Galfre S.G., et al. TAMGeS: a three-array method for genotyping of SNPs by a dual-colour approach. BMC Genomics 8 (2007) 10
14. Tebbutt S.J., Mercer G.D., Do R., et al. Deoxynucleotides can replace dideoxynucleotides in minisequencing by arrayed primer extension. Biotechniques 40 (2006) 331-338
15. Xiao M., Phong A., Lum K.L., et al. Role of excess inorganic pyrophosphate in primer-extension genotyping assays. Genome Res. 14 (2004) 1749-1755
16. Kwok S., Kellogg D.E., McKinney N., et al. Effects of primer-template mismatches on the polymerase chain reaction: human immunodeficiency virus type 1 model studies. Nucleic Acids Res. 18 (1990) 999-1005
17. Huang M.M., Arnheim N., and Goodman M.F. Extension of base mispairs by Taq DNA polymerase: implications for single nucleotide discrimination in PCR. Nucleic Acids Res. 20 (1992) 4567-4573
18. Rehman F.N., Audeh M., Abrams E.S., et al. Immobilization of acrylamide-modified oligonucleotides by co-polymerization. Nucleic Acids Res. 27 (1999) 649-655
19. Lo W.S., Lau C.F., Xuan Z., et al. Association of SNPs and haplotypes in GABAA receptor beta2 gene with schizophrenia. Mol. Psychiatry 9 (2004) 603-608
20. Pan Z., Li Y., Shan Q., et al. Fabrication of 3-D gel microarrays directly with raw polymerase chain reaction products by heat-directed polymerization. Electrophoresis 29 (2008) 2424-2436
21. Pan Z., Li Y., Zhou D., et al. Ultrasonic approach to enhance signal-to-noise in three dimensional microarray. Anal. Biochem. 376 (2008) 280-282
22. Botstein D., and Risch N. Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease. Nat. Genet. 33 (2003) 228-237 Suppl
23. Li X., Luo J., Xiao P., et al. Genotyping of multiple single nucleotide polymorphisms with hyperbranched rolling circle amplification and microarray. Clin. Chim. Acta 399 (2009) 40-44
24. Xiao P., Cheng L., Wan Y., et al. An improved gel-based DNA microarray method for detecting single nucleotide mismatch. Electrophoresis 27 (2006) 3904-3915
25. Pan Z., Li Y., Xiao P., et al. Multiple hybridization-extension sequencing (MHES) on microarray. J. Biochem. 142 (2007) 605-611