Transferability of tag SNPs to capture common genetic variation in DNA repair genes across multiple populations

Proceedings of the Pacific Symposium on Biocomputing 2006, PSB 2006

Volumn , Issue , 2006, Pages 478-486

  De Barker, Paul I W ^a   Graham, Robert R ^a   Altshuler, David ^a   Henderson, Brian E ^b   Haiman, Christopher A ^b  

^a BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^b UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPARATIVE ANALYSIS; COMPLEX TRAITS; DNA REPAIR; GENETIC VARIATION; GENOTYPING; HAPLOTYPES; HUMAN GENOMES; LINKAGE DISEQUILIBRIUM; MARGINAL LOSS; MULTIPLE POPULATIONS; SINGLE NUCLEOTIDE POLYMORPHISMS; TAG SNP; TAG SNPS;

GENES;

ARTICLE; BIOLOGY; DNA REPAIR; GENE LINKAGE DISEQUILIBRIUM; GENETIC DATABASE; GENETIC VARIABILITY; GENETICS; GENOTYPE; HAPLOTYPE; HUMAN; POPULATION GENETICS; RACE; SINGLE NUCLEOTIDE POLYMORPHISM;

COMPUTATIONAL BIOLOGY; CONTINENTAL POPULATION GROUPS; DATABASES, GENETIC; DNA REPAIR; GENETICS, POPULATION; GENOTYPE; HAPLOTYPES; HUMANS; LINKAGE DISEQUILIBRIUM; POLYMORPHISM, SINGLE NUCLEOTIDE; VARIATION (GENETICS);

EID: 39049193219     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (20)

1. Altmuller, J., et al., Genomewide scans of complex human diseases: true linkage is hard to find. Am J Hum Genet, 2001. 69(5): p. 936-50.
2. Lohmueller, K.E., et al., Meta-analysis of genetic association studies supports a contribution of common variants to susceptibility to common disease. Nat Genet, 2003. 33(2): p. 177-82.
3. The International HapMap Consortium, The International HapMap Project. Nature, 2003. 426(6968): p. 789-96.
4. Johnson, G.C., et al., Haplotype tagging for the identification of common disease genes. Nat Genet, 2001. 29(2): p. 233-7.
5. Hinds, D. A., et al., Whole-genome patterns of common DNA variation in three human populations. Science, 2005. 307(5712): p. 1072-9.
6. Nejentsev, S., et al., Comparative high-resolution analysis of linkage disequilibrium and tag single nucleotide polymorphisms between populations in the vitamin D receptor gene. Hum Mol Genet, 2004, 13(15): p. 1633-9.
7. Ahmadi, K.R., et al., A single-nucleotidepolymorphism tagging set for human drug metabolism and transport. Nat Genet, 2005. 37(1): p. 84-9.
8. Mueller, J.C., et al., Linkage disequilibrium patterns and tagSNP transferability among European populations. Am J Hum Genet, 2005. 76(3): p. 387-98.
9. Kolonel, L.N., et al., A multiethnic cohort in Hawaii and Los Angeles: baseline characteristics. Am J Epidemiol, 2000. 151(4): p. 346-57.
10. Hankin, J.H., et al., Singapore Chinese Health Study: development, validation, and calibration of the quantitative food frequency questionnaire. Nutr Cancer, 2001. 39(2): p. 187-95, .
11. Excoffier, L. and M. Slatkin, Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Mol Biol Evol, 1995. 12(5): p. 921-7.
12. Stram, D.O., et al., 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, 2003. 55(1): p. 27-36.
13. Weale, M.E., et al., Selection and evaluation of tagging SNPs in the neuronal-sodium-channe! gene SCN1A: implications for linkagedisequilibrium gene mapping. AmJ Hum Genet, 2003. 73(3): p. 551- 65.
14. Meng, Z., et al., Selection of genetic markers for association analyses, using linkage disequilibrium and haplotypes. Am J Hum Genet, 2003. 73(1): p. 115-30.
15. Carlson, C.S., et al., Selecting a maximally informative set of singlenucleotide polymorphisms for association analyses using linkage disequilibrium. Am J Hum Genet, 2004. 74(1): p. 106-20.
16. Lin, Z. and R.B. Altaian, Finding haplotype tagging SNPs by use of principal components analysis. Am J Hum Genet, 2004. 75(5): p. 850- 61.
17. de Bakker, P.I.W., et al., Efficiency and power in genetic association studies. Nat Genet, 2005. In the press.
18. Barrett, J.C., et al., Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics, 2005. 21(2): p. 263-5.
19. Reich, D.E., et al., Linkage disequilibrium in the human genome. Nature, 2001. 411(6834): p. 199-204.
20. Wall, J.D. and J.K. Pritchard, Haplotype blocks and linkage disequilibrium in the human genome. Nat Rev Genet, 2003. 4(8): p. 587-97.