Selecting single-nucleotide polymorphisms for association studies with SNPbrowserTM software

Methods in Molecular Biology

Volumn 376, Issue , 2007, Pages 177-193

  De La Vega, Francisco M ^a  

^a NONE

Author keywords

Association study; Genotyping; SNP selection; Statistical power; Tagging SNPs

Indexed keywords

ARTICLE; BIOLOGY; CASE CONTROL STUDY; COMPUTER PROGRAM; GENE LINKAGE DISEQUILIBRIUM; GENETIC DATABASE; GENETIC MARKER; GENETIC PREDISPOSITION; GENETICS; GENOTYPE; HUMAN; METHODOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM;

CASE-CONTROL STUDIES; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENETIC MARKERS; GENETIC PREDISPOSITION TO DISEASE; GENOTYPE; HUMANS; LINKAGE DISEQUILIBRIUM; POLYMORPHISM, SINGLE NUCLEOTIDE; SOFTWARE;

EID: 36549071483     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1385/1-59745-389-7:177     Document Type: Article

References (25)

1. Reich, D. E., Cargill, M., BoIk, S., et al. (2001) Linkage disequilibrium in the human genome. Nature 411, 199-204.
2. De La Vega, F. M., Isaac, H., Collins, A., et al. (2005) The linkage disequilibrium maps of three human chromosomes across four populations reflect their demographic history and a common underlying recombination pattern. Genome Res. 15, 454-462.
3. Consortium, T. I. H. (2005) A haplotype map of the human genome. Nature 437, 1299-1320.
4. Gabriel, S. B., Schaffner, S. F., Nguyen, H., et al. (2002) The structure of haplotype blocks in the human genome. Science 196, 2225-2229.
5. Avi-Itzhak, H. I., Su, X., and De La Vega, F. M. (2003) Selection of minimum subsets of single nucleotide polymorphisms to capture haplotype block diversity. In: Pacific Symposium on Biocomputing, (Altaian, R. B., et al., eds.), World Scientific Press, Lihue, Hawaii, pp. 466-477.
6. Byng, M. C., Whittaker, J. C., Cuthbert, A. P., Mathew, C. G., and Lewis, C. M. (2003) SNP subset selection for genetic association studies. Ann. Hum. Genet. 67, 543-556.
7. Carlson, C.S., Eberle, M. A., Rieder, M. J.,Yi,Q., Kruglyak, L., and Nickerson, D. A. (2004) Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium. Am. J. Hum. Genet. 74, 106-120.
8. Hampe, J., Schreiber, S., and Krawczak, M. (2003) Entropy-based SNP selection for genetic association studies. Hum. Genet. 114, 36-43.
9. Johnson, G. C., Esposito, L., Barratt, B. J., et al. (2001) Haplotype tagging for the identification of common disease genes. Nat. Genet. 29, 233-237.
10. Ke, X. and Cardon, L. R. (2003) Efficient selective screening of haplotype tag SNPs. Bioinformatics 19, 287-288.
11. Sebastiani, P., Lazarus, R., Weiss, S. T., Kunkel, L. M., Kohane, I. S., and Ramoni, M. F. (2003) Minimal haplotype tagging. Proc. Natl. Acad. Sci. USA 100, 9900-9905.
12. Stram, D. O., Haiman, C. A., Hischhorn, J. N., et al. (2003) Choosing haplotype-tagging SNPS based on unphased genotype data using a preliminary sample of unrelated subjects with an example from the Multiethnic Cohort Study. Hum. Hered. 55, 27-36.
13. Weale, M. E., Depondt, C., Macdonald, S. J., et al. (2003) Selection and evaluation of tagging SNPs in the neuronal-sodium-channel gene SCN1A: implications for linkage-disequilibriimi gene mapping. Am. J. Hum. Genet, 73, 551-565.
14. Zhang, K., Sim, F., Watennan, M. S., and Chen, T. (2003) Haplotype block partition with limited resources and applications to human chromosome 21 haplotype data. Am. J. Hum. Genet. 73, 63-73.
15. Home, B. D. and Camp, N. J. (2004) Principal component analysis for selection of optimal SNP-sets that capture intragenic genetic variation. Genet, Epidemiol. 26, 11-21.
16. Hu, X., Schrodi, S. J., Ross, D. A., and Cargill, M. (2004) Selecting tagging SNPs for association studies using power calculations from genotype data. Hum. Hered. 57, 156-70.
17. Lohmueller, K. E., Pearce, C. L., Pike, M., Lander, E. S., and Hirschhorn, J. N. (2003) Meta-analysis of genetic association studies supports a contribution of common variants to susceptibility to common disease. Nat. Genet. 33, 177-182.
18. De La Vega, F. M., Dailey, D., Ziegle, J., Williams, J., Madden, D., and Gilbert, D. A. (2002) New generation phannacogenomic tools: a SNP linkage disequilibrium map, validated SNP assay resource, and high-throughput instrumentation system for large-scale genetic studies. Biotechniques Suppl, 48-50.
19. De la Vega, F. M., Lazanik, K. D., Rhodes, M. D., and Wenz, M. H. (2005) Assessment of two flexible and compatible SNP genotyping platfonns: TaqMan SNP Genotyping Assays and the SNPlex Genotyping System. Mutat. Res. 513, 111-135.
20. Maniatis, N., Collins, A., Xu, C. F., et al. (2002) The first linkage disequilibrium (LD) maps: delineation of hot and cold blocks by diplotype analysis. Proc. Natl. Acad. Sci. USA 99, 2228-2233.
21. Schwartz, R., Halldorsson, B. V., Bafna, V., Clark, A. G., and Istrail, S. (2003) Robustness of inference of haplotype block stnicture. J. Compta. Biol. 10, 13-19.
22. Halldorsson, B. V., Istrail, S., and De La Vega, F. M. (2004) Optimal selection of SNP markers for disease association studies. Hum. Hered. 58, 190-202.
23. De La Vega, F. M., Gordon, D., Su, X., et al. (2005) Gene-centric power and sample size calculations for genetic case/control studies using empirical genotype data from dense SNP maps. Hum. Hered. 60, 46-60.
24. Collins, A., Lau, W., and De La Vega, F. M. (2004) Mapping genes for common diseases: the case for genetic (LD) maps. Hum. Hered. 58, 2-9.
25. Thomas, P. D. and Kejariwal, A. (2004) Coding single-nucleotide polymorphisms associated with complex vs. Mendelian disease: evolutionary evidence for differences in molecular effects. Proc. Natl. Acad. Sci. USA 101, 15,398-15,403.