SNP discovery in pooled samples with mismatch repair detection

Genome Research

Volumn 14, Issue 7, 2004, Pages 1404-1412

  Fakhrai Rad, Hossein ^a   Zheng, Jianbiao ^a   Willis, Thomas D ^a   Wong, Kee ^a   Suyenaga, Kent ^a   Moorhead, Martin ^a   Eberle, Jim ^a   Thorstenson, Yvonne R ^b   Jones, Ted ^b   Davis, Ronald W ^b   Namsaraev, Eugeni ^a   Faham, Malek ^a  

^a ParAllele BioScience   (United States)

^b STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA FRAGMENT; GENOMIC DNA;

ALLELE; ANALYTIC METHOD; ARTICLE; CONTROLLED STUDY; DNA DETERMINATION; GENE AMPLIFICATION; GENE FREQUENCY; GENETIC PROCEDURES; GENETIC VARIABILITY; HUMAN; MISMATCH REPAIR; NONHUMAN; POPULATION RESEARCH; PRIORITY JOURNAL; REPRODUCIBILITY; SENSITIVITY ANALYSIS; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; TERMINAL SEQUENCE;

ANIMALS; BASE PAIR MISMATCH; CHROMOSOME MAPPING; CHROMOSOMES, HUMAN, PAIR 21; CLONING, MOLECULAR; DNA REPAIR; FALSE NEGATIVE REACTIONS; FALSE POSITIVE REACTIONS; GENE FREQUENCY; GENES, BRCA1; GENES, BRCA2; GENETICS, POPULATION; HUMANS; HYBRID CELLS; MICE; NUCLEIC ACID AMPLIFICATION TECHNIQUES; POLYMORPHISM, SINGLE NUCLEOTIDE; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; VARIATION (GENETICS);

EID: 3543085719     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.2373904     Document Type: Article

References (23)

1. Amos, C.I., Frazier, M.L., and Wang, W. 2000. DNA pooling in mutation detection with reference to sequence analysis. Am. J. Hum. Genet. 66: 1689-1692.
2. Ausubel, F.M., Brent, R., Kingston, R.L., Moore, D.D., Seidman, J.G., Smith, J.A., and Struhl, K. 1999. Current protocols in molecular biology. John Wiley and Sons, New York.
3. Cargill, M., Altshuler, D., Ireland, J., Sklar, P., Ardlie, K., Patil, N., Shaw, N., Lane, C.R., Lim, E.P., Kalyanaraman, N., et al. 1999. Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nat. Genet. 22: 231-238.
4. Carlson, C.S., Eberle, M.A., Rieder, M.J., Smith, J.D., Kruglyak, L., and Nickerson, D.A. 2003. Additional SNPs and linkage-disequilibrium analyses are necessary for whole-genome association studies in humans. Nat. Genet. 33: 518-521.
5. Dawson, E., Abecasis, C.R., Bumpstead, S., Chen, Y., Hunt, S., Beare, D.M., Pabial, J., Dibling, T., Tinsley, E., Kirby, S., et al. 2002. A first-generation linkage disequilibrium map of human chromosome 22. Nature 418: 544-548.
6. Faham, M., Baharloo, S., Tomitaka, S., DeYoung, J., and Freimer N. 2001. Mismatch repair detection (MRD): High throughput scanning for DNA variations. Hum. Mol. Genet. 10: 1657-1664.
7. Gabriel, S., Schaffner, S.F., Nguyen, H., Moore, J.M., Roy, J., Blumenstiel, B., Higgins, J., DeFelice, M., Lochner, A., Faggart, M., et al. 2002. The structure of haplotype blocks in the human genome. Science 296: 2225-2229.
8. Haga, H., Yamada, R., Ohnishi, Y., Nakamura, Y., and Tanaka, T. 2002. Gene-based SNP discovery as part of the Japanese Millennium Genome Project 2002: Identification of 190,562 genetic variations in the human genome. J. Hum. Genet. 47: 605-610.
9. Halushka, M.K., Fan, J.B., Bentley, K., Hsie, L., Shen, N., Weder, A., Cooper, R., Lipshutz, R., and Chakravarti, A. 1999. Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis. Nat. Genet. 22: 239-247.
10. International HapMap Consortium. 2003. The international HapMap project. Nature 426: 789-796.
11. Johnson, G.C.L., Esposito, L., Barratt, B.J., Smith, A.N., Heward, J., Di Genova, G., Ueda, H., Cordell, H.J., Eaves, I.A., Dudbridge, F., et al. 2001. Haplotype tagging for the identification of common disease genes. Nat. Genet. 29: 233-237.
12. Krook, A., Stratton, I.M., and O'Rahilly, S. 1992. Rapid and simultaneous detection of multiple mutations by pooled and multiplex single nucleotide primer extension: Application to the study of insulin-responsive glucose transporter and insulin receptor mutations in non-insulin dependent diabetes. Hum. Mol. Genet. 1: 391-395.
13. Kruglyak, L. and Nickerson, D.A. 2001. Variation is the spice of life. Nat. Genet. 27: 234-236.
14. Kwok, P-Y., Carlson, C., Yager, T.D., Ankener, W., and Nickerson, D.A. 1994. Comparative analysis of human DNA variations by fluorescence-based sequencing of PCR products. Genomics 23: 138-144.
15. McKinzie, P.B and Parsons, B.L. 2002. Detection of rare K-ras codon 12 mutations using allele-specific competitive blocker PCR. Mutat. Res. 27: 209-220.
16. Modrich, P. 1991. Mismatch repair. Ann. Rev. Genet. 25: 229-248.
17. -7 by combining two genotypic selection methods, MutEx enrichment and allele-specific competitive blocker PCR. Environ. Mol. Mutagen. 32: 200-211.
18. Patil, N., Berno, A.J., Hinds, D.A., Barrett, W.A., Doshi, J.M., Hacker, C.R., Kautzer, C.R., Lee, D.H., Marjoribanks, C., McDonough, D.P., et al. 2001. Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science 294: 1719-1723.
19. Reich, D.E., Schaffner, S.F., Daly, M.J., McVean, G., Mullikin, J.C., Higgins, J.M., Richter, D.J., Lander, E.S., and Altshuler, D. 2002. Human genome sequence variation and the influence of gene history, mutation and recombination. Nat. Genet. 32: 135-142.
20. Rozen, S. and Skaletsky, H.J. 1996, 1997, and 1998. Primer3. Code available at: http://www-genome.wi.mit.edu/genome_software/other/primer3.html.
21. Sachidanandam, R., Weissman, D., Schmidt, S.C., Kakol, J.M., Stein, L.D., Marth, G., Sherry, S., Mullikin, J.C., Mortimore, B.J., Willey, D.L., et al. 2001. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409: 928-933.
22. Werner, M., Sych, M., Herbon, N., Illig, T., Konig, I.R., and Wist, M. 2002. Large-scale determination of SNP allele frequencies in DNA pools using MALDI-TOF mass spectrometry. Hum. Mutat. 20: 57-64.
23. Wolford, J.K., Blunt, D., Ballecer, C., and Prochazka, M. 2000. High-throughput SNP detection by using DNA pooling and denaturing high performance liquid chromatography (DHPLC). Hum. Genet. 107: 483-487.