The impact of missing and erroneous genotypes on tagging SNP selection and power of subsequent association tests

Human Heredity

Volumn 61, Issue 1, 2006, Pages 31-44

  Liu, Wenlei ^a   Zhao, Wei ^a   Chase, Gary A ^a  

^a PENN STATE COLLEGE OF MEDICINE   (United States)

Author keywords

Genotyping error; Haplotype; Missing genotype; Power; Tagging SNPs

Indexed keywords

ALGORITHM; ANALYTICAL ERROR; ARTICLE; COMPUTER PROGRAM; GENE IDENTIFICATION; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC DISORDER; GENETIC LINKAGE; GENETIC MARKER; GENETIC SUSCEPTIBILITY; GENOTYPE; HAPLOTYPE; HUMAN; PERFORMANCE; SINGLE NUCLEOTIDE POLYMORPHISM;

ALGORITHMS; AROMATASE; CHROMOSOME MAPPING; COMPUTER SIMULATION; GENE FREQUENCY; GENOTYPE; HAPLOTYPES; HUMANS; LINKAGE (GENETICS); LINKAGE DISEQUILIBRIUM; MODELS, STATISTICAL; POLYMORPHISM, SINGLE NUCLEOTIDE; RISK; SELECTION (GENETICS);

EID: 33744463384     PISSN: 00015652     EISSN: None     Source Type: Journal    
DOI: 10.1159/000092141     Document Type: Article

References (31)

1. Kruglyak L, Nickerson DA: Variation is the spice of life. Nat Genet 2001;27:234-236.
2. Badano JL, Katsanis N: Beyond Mendel: an evolving view of human genetic disease transmission. Nat Rev Genet 2002;3:779-789.
3. Risch N, Merikangas K: The future of genetic studies of complex human diseases. Science 1996;273:1516-1517.
4. Kruglyak L: Prospects for whole-genome linkage disequilibrium mapping of common disease genes. Nat Genet 1999;22:139-144.
5. Judson R, Stephens JC, Windemuth A: The predictive power of haplotypes in clinical response. Pharmacogenomics 2000;1:15-26.
6. Johnson GC, Esposito L, Barratt BJ, Smith AN, Heward J, Di Genova G, Ueda H, Cordell HJ, Eaves IA, Dudbridge F, Twells RC, Payne F, Hughes W, Nutland S, Stevens H, Carr P, Tuomilehto-Wolf E, Tuomilehto J, Gough SC, Clayton DG, Todd JA: Haplotype tagging for the identification of common disease genes. Nat Genet 2001;29:233-237.
7. Stram DO, Haiman CA, Hirschhorn JN, Altshuler D, Kolonel LN, Henderson BE, Pike MC: 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;55:27-36.
8. Hu X, Schrodi SJ, Ross DA, Cargill M: Selecting tagging SNPs for association studies using power calculations from genotype data. Hum Hered 2004;57:156-170.
9. Carlson CS, Eberle MA, Rieder MJ, Yi Q, Kruglyak L, Nickerson DA: Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium. Am J Hum Genet 2004;74:106-120.
10. Hampe J, Schreiber S, Krawczak M: Entropy-based SNP selection for genetic association studies. Hum Genet 2003;114:36-43.
11. Michalatos-Beloin S, Tishkoff SA, Bentley KL, Kidd KK, Ruano G: Molecular haplotyping of genetic markers 10 kb apart by allele-specific long-range PCR. Nucleic Acids Res 1996;24:4841-4843.
12. Proudnikov D, LaForge KS, Kreek MJ: High-throughput molecular haplotype analysis (allelic assignment) of single-nucleotide polymorphisms by fluorescent polymerase chain reaction. Anal Biochem 2004;335:165-167.
13. Hill WG: Estimation of linkage disequilibrium in randomly mating populations. Heredity 1974;33:229-239.
14. Excoffier L, Slatkin M: Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Mol Biol Evol 1995;12:921-927.
15. Kirk KM, Cardon LR: The impact of genotyping error on haplotype reconstruction and frequency estimation. Eur J Hum Genet 2002;10:616-622.
16. Kelly ED, Sievers F, McManus R: Haplotype frequency estimation error analysis in the presence of missing genotype data. BMC Bioinformatics 2004;5:188.
17. Gabriel SB, Schaffner SF, Nguyen H, Moore JM, Roy J, Blumenstiel B, Higgins J, DeFelice M, Lochner A, Faggart M, Liu-Cordero SN, Rotimi C, Adeyemo A, Cooper R, Ward R, Lander ES, Daly MJ, Altshuler D: The structure of haplotype blocks in the human genome. Science 2002;296:2225-2229.
18. Mailund T, Schierup MH, Pedersen CN, Mechlenborg PJ, Madsen JN, Schauser L: CoaSim: a flexible environment for simulating genetic data under coalescent models. BMC Bioinformatics 2005;6:252.
19. Sobel E, Papp JC, Lange K: Detection and integration of genotyping errors in statistical genetics. Am J Hum Genet 2002;70:496-508.
20. Schaid DJ, Rowland CM, Tines DE, Jacobson RM, Poland GA: Score tests for association between traits and haplotypes when linkage phase is ambiguous. Am J Hum Genet 2002;70:425-434.
21. Zaykin DV, Westfall PH, Young SS, Karnoub MA, Wagner MJ, Ehm MG: Testing association of statistically inferred haplotypes with discrete and continuous traits in samples of unrelated individuals. Hum Hered 2002;53:79-91.
22. The International HapMap Project. Nature 2003;426:789-796.
23. Douglas JA, Boehnke M, Lange K: A multi-point method for detecting genotyping errors and mutations in sibling-pair linkage data. Am J Hum Genet 2000;66:1287-1297.
24. Abecasis GR, Cherny SS, Cardon LR: The impact of genotyping error on family-based analysis of quantitative traits. Eur J Hum Genet 2001;9:130-134.
25. Akey JM, Zhang K, Xiong M, Doris P, Jin L: The effect that genotyping errors have on the robustness of common linkage-disequilibrium measures. Am J Hum Genet 2001;68:1447-1456.
26. Gordon D, Finch SJ, Nothnagel M, Ott J: Power and sample size calculations for case-control genetic association tests when errors are present: application to single nucleotide polymorphisms. Hum Hered 2002;54:22-33.
27. Altshuler D, Brooks LD, Chakravarti A, Collins FS, Daly MJ, Donnelly P: A haplotype map of the human genome. Nature 2005;437:1299-1320.
28. Kang H, Qin ZS, Niu T, Liu JS: Incorporating genotyping uncertainty in haplotype inference for single-nucleotide polymorphisms. Am J Hum Genet 2004;74:495-510.
29. Zou G, Zhao H: Haplotype frequency estimation in the presence of genotyping errors. Hum Hered 2003;56:131-138.
30. Gordon D YY, Haynes C, Finch SJ, Mendell NR, Brown AM, and Haroutunian V: Increasing power for tests of genetic association in the presence of phenotype and/or genotype error by use of double-sampling. Stat Appl Genet Mol Biol 2004;3:Article 26.
31. Hao K, Wang X: Incorporating individual error rate into association test of unmatched case-control design. Hum Hered 2004;58:154-163.