High-throughput SNP genotyping by single-tube PCR with Tm-shift primers

BioTechniques

Volumn 39, Issue 6, 2005, Pages 885-892

  Wang, Jun ^a   Chuang, Karen ^a   Ahluwalia, Mandeep ^a   Patel, Sarika ^b   Umblas, Manette ^a   Mirel, Daniel ^a   Higuchi, Russell ^a   Germer, Soren ^a,b  

^a ROCHE MOLECULAR SYSTEMS   (United States)

^b HOFFMANN LA ROCHE INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SOFTWARE; MELTING; NUCLEIC ACIDS; REAL TIME SYSTEMS; THERMAL CYCLING;

ALLELE-SPECIFIC PCR PRIMERS; GENOME-WIDE SCANS; SINGLE NUCLEOTIDE POLYMORPHISM (SNP); SNP GENOTYPING;

GENETIC ENGINEERING;

GENOMIC DNA; PRIMER DNA;

ALLELE; ARTICLE; COMPUTER PROGRAM; GENE AMPLIFICATION; GENOTYPE; HUMAN; POLYMERASE CHAIN REACTION; SINGLE NUCLEOTIDE POLYMORPHISM; TEMPERATURE MEASUREMENT; METHODOLOGY; TRANSITION TEMPERATURE;

DNA PRIMERS; GENOTYPE; HUMANS; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; TRANSITION TEMPERATURE;

EID: 33644814591     PISSN: 07366205     EISSN: None     Source Type: Journal    
DOI: 10.2144/000112028     Document Type: Article

References (32)

1. Mackay, T.F. 2001. The genetic architecture of quantitative traits. Annu. Rev. Genet. 35:303-339.
2. Botstein, D. and N. Risch. 2003. Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease. Nat. Genet. 33(Suppl):228-237.
3. Carlson, C.S., M.A. Eberle, L. Kruglyak, and D.A. Nickerson. 2004. Mapping complex disease loci in whole-genome association studies. Nature 429:446-452.
4. Kwok, P.Y. 2001. Methods for genotyping single nucleotide polymorphisms. Annu. Rev. Genomics Hum. Genet. 2:235-258.
5. Twyman, R.M. and S.B. Primrose. 2003. Techniques patents for SNP genotyping. Pharmacogenomics 4:67-79.
6. Chen, X. and P.F. Sullivan. 2003. Single nucleotide polymorphism genotyping: biochemistry, protocol, cost and throughput. Pharmacogenomics J. 3:77-96.
7. Fu, D.J., K. Tang, A. Braun, D. Reuter, B. Darnhofer-Demar, D.P. Little, M.J. O'Donnell, C.R. Cantor, and H. Koster. 1998. Sequencing exons 5 to 8 of the p53 gene by MALDI-TOF mass spectrometry. Nat. Biotechnol. 16:381-384.
8. Buetow, K.H., M. Edmonson, R. MacDonald, R. Clifford, P. Yip, J. Kelley, D.P. Little, R. Strausberg, et al. 2001. High-throughput development and characterization of a genomewide collection of gene-based single nucleotide polymorphism markers by chip-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Proc. Natl. Acad. Sci. USA 98:581-584.
9. Mohlke, K.L., M.R. Erdos, L.J. Scott, T.E. Fingerlin, A.U. Jackson, K. Silander, P. Hollstein, M. Boehnke, and F.S. Collins. 2002. High-throughput screening for evidence of association by using mass spectrometry genotyping on DNA pools. Proc. Natl. Acad. Sci. USA 99:16928-16933.
10. Hacia, J.G., J.B. Fan, O. Ryder, L. Jin, K. Edgemon, G. Ghandour, R.A. Mayer, B. Sun, et al. 1999. Determination of ancestral alleles for human single-nucleotide polymorphisms using high-density oligonucleotide arrays. Nat. Genet. 22:164-167.
11. Fan, J.B., X. Chen, M.K. Halushka, A. Berno, X. Huang, T. Ryder, R.J. Lipshutz, D.J. Lockhart, and A. Chakravarti. 2000. Parallel genotyping of human SNPs using generic high-density oligonucleotide tag arrays. Genome Res. 10:853-860.
12. Hardenbol, P., J. Baner, M. Jain, M. Nilsson, E.A. Namsaraev, G.A. Karlin-Neumann, H. Fakhrai-Rad, M. Ronaghi, et al. 2003. Multiplexed genotyping with sequence-tagged molecular inversion probes. Nat. Biotechnol. 21:673-678.
13. Ferguson, J.A., F.J. Steemers, and D.R. Walt. 2000. High-density fiber-optic DNA random microsphere array. Anal. Chem. 72:5618-5624.
14. Medintz, I., W.W. Wong, L. Berti, L. Shiow, J. Tom, J. Scherer, G. Sensabaugh, and R.A. Mathies. 2001. High-performance multiplex SNP analysis of three hemochromatosis-related mutations with capillary array electrophoresis microplates. Genome Res. 11:413-421.
15. De Angelis, D.A. 1999. Why FRET over genomics? Physiol. Genomics 7:93-99.
16. Livak, K.J., J. Marmaro, and J.A. Todd. 1995. Towards fully automated genome-wide polymorphism screening. Nat. Genet. 9:341-342.
17. Tyagi, S., D.P. Bratu, and F.R. Kramer. 1998. Multicolor molecular beacons for allele discrimination. Nat. Biotechnol. 76:49-53.
18. Piatek, A.S., S. Tyagi, A.C. Pol, A. Telenti, L.P. Miller, F.R. Kramer, and D. Alland. 1998. Molecular beacon sequence analysis for detecting drug resistance in Mycobacterium tuberculosis. Nat. Biotechnol. 76:359-363.
19. Germer, S., M.J. Holland, and R. Higuchi. 2000. High-throughput SNP allele-frequency determination in pooled DNA samples by kinetic PCR. Genome Res. 10:258-266.
20. Newton, C.R., A. Graham, L.E. Heptinstall, S.J. Powell, C. Summers, N. Kalsheker, J.C. Smith, and A.F. Markham. 1989. Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS). Nucleic Acids Res. 17:2503-2516.
21. Wu, D.Y., L. Ugozzoli, B.K. Pal, and R.B. Wallace. 1989. Allele-specific enzymatic amplification of beta-globin genomic DNA for diagnosis of sickle cell anemia. Proc. Natl. Acad. Sci. USA 86:2757-2760.
22. 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.
23. Hardenbol, P., F. Yu, J. Belmont, J. Mackenzie, C. Bruckner, T. Brundage, A. Boudreau, S. Chow, 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.
24. Murray, S.S., A. Oliphant, R. Shen, C. McBride, R.J. Steeke, S.G. Shannon, T. Rubano, B.G. Kermani, et al. 2004. A highly informative SNP linkage panel for human genetic studies. Nat. Methods 1:113-117.
25. Germer, S. and R. Higuchi. 1999. Single-tube genotyping without oligonucleotide probes. Genome Res. 9:72-78.
26. Ardlie, K.G., K.L. Lunetta, and M. Seielstad. 2002. Testing for population subdivision and association in four case-control studies. Am. J. Hum. Genet. 71:304-311.
27. Birch, D.E. 1996. Simplified hot start PCR. Nature 381:445-446.
28. Germer, S. and R. Higuchi. 2002. Homogeneous allele-specific PCR in SNP genotyping. In P.-Y. Kwok (Ed.), Methods in Molecular Biology, vol. 212: Single Nucleotide Polymorphisms: Methods and Protocols. Humana Press, Totowa, NJ.
29. Lawyer, F.C., S. Stoffel, R.K. Saiki, S.Y. Chang, P.A. Landre, R.D. Abramson, and D.H. Gelfand. 1993. High-level expression, purification, and enzymatic characterization of full-length Thermus aquaticus DNA polymerase and a truncated form deficient in 5′ to 3′ exonuclease activity. PCR Methods Appl. 2:275-287.
30. Tada, M., M. Omata, S. Kawai, H. Saisho, M. Ohto, R.K. Saiki, and J.J. Sninsky. 1993. Detection of ras gene mutations in pancreatic juice and peripheral blood of patients with pancreatic adenocarcinoma. Cancer Res. 53:2472-2474.
31. Chou, Q., M. Russell, D.E. Birch, J. Raymond, and W. Bloch. 1992. Prevention of pre-PCR mis-priming and primer dimerization improves low-copy-number amplifications. Nucleic Acids Res. 20:1717-1723.
32. Sharma, S. 1996. Cluster analysis, p. 185-236. In Applied Multivariate Techniques. John Wiley & Sons, New York.