The tagged microarray marker (TAM) method for high-throughput detection of single nucleotide and indel polymorphisms

Nature Protocols

Volumn 2, Issue 1, 2007, Pages 168-177

  Jing, Runchun ^a   Bolshakov, Viacheslav ^a,b   Flavell, Andrew J ^a  

^a UNIVERSITY OF DUNDEE   (United Kingdom)

^b UNIVERSITY OF READING   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BIOTIN; GLASS; MOLECULAR MARKER; STREPTAVIDIN; OLIGONUCLEOTIDE;

ALLELE; ARTICLE; GENE DELETION; GENE INSERTION; GENE LOCUS; GENETIC ANALYSIS; GENETIC POLYMORPHISM; HIGH THROUGHPUT SCREENING; MATERIAL COATING; MICROARRAY ANALYSIS; POLYMERASE CHAIN REACTION; PREDICTION; PRIORITY JOURNAL; SCORING SYSTEM; SINGLE NUCLEOTIDE POLYMORPHISM; TIME; FLUORESCENCE; GENETIC MARKER; GENETICS; METHODOLOGY; TRANSPOSON;

BIOTIN; DNA TRANSPOSABLE ELEMENTS; FLUORESCENCE; GENETIC MARKERS; MICROARRAY ANALYSIS; OLIGONUCLEOTIDES; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 34347232737     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2006.408     Document Type: Article

References (19)

1. Wang, D.G. et al. Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science 280, 1077-1082 (1998).
2. Schena, M., Shalon, D., Davis, R.W. & Brown, P.O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467-470 (1995).
3. Jenkins, S. & Gibson, N. High throughput SNP genotyping. Comp. Funct. Genomics 3, 57-66 (2002).
4. Hirschhorn, J.N. et al. SBE-TAGS: An array-based method for efficient single-nucleotide polymorphism. Proc. Natl. Acad. Sci. USA 97, 12164-12169 (2000).
5. Jaccoud, D., Peng, K., Feinstein, D. & Kilian, A. Diversity arrays: A solid state technology for sequence information independent genotyping. Nucleic Acids Res. 29, e25 (2001).
6. Pastinen, T. et al. A system for specific, high-throughput genotyping by allele-specific primer extension on microarrays. Genome Res. 10, 1031-1042 (2000).
7. Guo, Z., Gatterman, M.S., Hood, L., Hansen, J.A. & Petersdorf, E.W. Oligonucleotide arrays for high-throughput SNPs detection in the MHC class I genes: HLA-B as a model system. Genome Res. 12, 447-457 (2002).
8. Lindroos, K., Sigurdsson, S., Johansson, K., Ronnblom, L. & Syvanen, A.-C. Multiplex SNP genotyping in pooled DNA samples by a four-colour microarray system. Nucleic Acids Res. 30, e70 (2002).
9. Engle, L.J., Simpson, C.L. & Landers, J.E. Using high-throughput SNP technologies to study cancer. Oncogene 25, 1594-1601 (2006).
10. Elder, J.K. et al. Antisense oligonucleotide scanning arrays. in DNA Microarrays: A Practical Approach (ed. Schena, M.) 77-98 (IRL Press, Oxford, UK, 1999).
11. Fan, J.B. et al. Highly parallel SNP genotyping. Cold Spring Harb. Symp. Quant. Biol. 68, 69-78 (2003).
12. Flavell, A.J. et al. A microarray-based high throughput molecular marker genotyping method: The tagged microrray (TAM) marker approach. Nucleic Acids Res. 31, e115 (2003).
13. Rust, S., Funke, H. & Assmann, G. Mutagenically separated PCR (MS-PCR): a highly specific one step procedure for easy mutation detection. Nucleic Acids Res. 21, 3623-3629 (1993).
14. Newton, C.R. et al. Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS). Nucleic Acids Res. 17, 2503-2516 (1989).
15. Kwok, S. et al. Effects of primer-template mismatches on the polymerase chain reaction: Human immunodeficiency virus type 1 model studies. Nucleic Acids Res. 18, 999-1005 (1990).
16. Ye, S., Dhillon, S., Ke, X., Collins, A.R. & Day, I.N.M. An efficient procedure for genotyping single nucleotide polymorphisms. Nucleic Acids Res. 29, e88 (2001).
17. Hayashi, K., Hashimoto, N., Daigen, M. & Ashikawa, I. Development of PCR-based SNP markers for rice blast resistance genes at the Piz locus. Theor. Appl. Genet. 108, 1212-1220 (2004).
18. Flavell, A.J., Knox, M.R., Pearce, S.R. & Ellis, T.H.N. Retrotransposon-based insertion polymorphisms (RBIP) for high throughput marker analysis. Plant J. 16, 643-650 (1998).
19. Nelson, S. & Denny, C.F. Representational difference analysis and microarray hybridization for efficient cloning and screening of differentially expressed genes. in DNA Microarrays: A Practical Approach (ed. Schena, M.) 77-98 (IRL Press, Oxford, UK, 1999).