Quantifying bias due to allele misclassification in case-control studies of haplotypes

Genetic Epidemiology

Volumn 30, Issue 7, 2006, Pages 590-601

  Govindarajulu, Usha S ^a   Spiegelman, Donna ^a   Miller, Katie L ^a   Kraft, Peter ^a  

^a HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

Author keywords

Case control; Genotyping error; Haplotype; Misclassification; Odds ratio; SNP

Indexed keywords

ALLELE; ANALYTICAL ERROR; ARTICLE; CASE CONTROL STUDY; DATA ANALYSIS; GENE LOCUS; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOTYPE; HAPLOTYPE; HUMAN; QUANTITATIVE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL ANALYSIS; STATISTICAL MODEL;

ALLELES; BIAS (EPIDEMIOLOGY); CASE-CONTROL STUDIES; GENOTYPE; HAPLOTYPES; HUMANS; MODELS, GENETIC; ODDS RATIO; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 33750286548     PISSN: 07410395     EISSN: 10982272     Source Type: Journal    
DOI: 10.1002/gepi.20170     Document Type: Article

References (33)

1. Akey J, Jin L, Xiong M. 2001. Haplotypes vs. single marker linkage disequilibrium tests: what do we gain? Eur J Hum Genet 9: 291-300.
2. Armstrong BK, White E, Saracci R. 1994. Principles of Exposure Measurement in Epidemiology. USA: Oxford University Press.
3. Carlson CS, Eberle MA, Rieder MJ, Yi Q, Kruglyak L, Nickerson DA. 2004. Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium. Am J Hum Genet 74:106-120.
4. Clark AB. 2004. The role of haplotypes in candidate gene studies. Genet Epidemiol 321-333.
5. Copeland KT, Checkoway H, McMichael AJ, Holbrook R. 1977. Bias due to misclassification in the estimation of relative risk. Am J Epidemiol 105:488-495.
6. Cox DG, Kraft P. 2006. Quantification of the power of Hardy-Weinberg Equilibrium testing to detect genotyping error. Hum Hered 61:10-14.
7. Epstein MP, Satten GA. 2003. Inference on haplotype effects in case-control studies using unphased genotype data. Am J Hum Genet 73:1316-1329.
8. Gabriel SB, Schaffner SF, Nguyen H, Moore JM, 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.
9. Gordon D, Ott J. 2001. Assessment and management of single nucleotide polymorphism genotype errors in genetic association analysis. Pac Symp Biocomput 18-29.
10. Gordon D, Finch SJ, Nothnagel M, Ott J. 2002. Power and sample size calculations for case-control genetic association tests when errors are present: application to single nucleotide polymorphisms. Hum Hered 54:22-33.
11. Gordon D, Yang Y, Haynes C, Finch SJ, Mendell NR, Brown AM, Haroutunian V. 2004. 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 3:26.
12. Gustafson P. 2004. Measurement Error and Misclassification in Statistics and Epidemiology, New York: Chapman & Hall/ CRC press.
13. Hao K, Li C, Rosenow C, Wong WH. 2004. Estimation of genotype error rate using samples with pedigree information-an application on the GeneChip Mapping 10K array. Genomics 84:623-630.
14. Heid I, Lamina C, Fischer G, Gieger C, Huth C, Klopp N, Kolz M, Vollmert C, Wagner S, Paulweber B. 2005. Quantification and characterization of genotyping error in a large epidemiological sample with repeated measurements. Genet Epidemiol 29:255.
15. Johnson VJ, Yucesoy B, Luster MI. 2004. Genotyping of single nucleotide polymorphisms in cytokine genes using real-time PCR allelic discrimination technology. Cytokine 27:135-141.
16. Kang H, Qin ZS, Niu T, Liu JS. 2004. Incorporating genotyping uncertainty in haplotype inference for single-nucleotide polymorphisms. Am J Hum Genet 74:495-510.
17. Kang SJ, Finch SJ, Haynes C, Gordon D. 2004. Quantifying the percent increase in minimum sample size for SNP genotyping errors in genetic model-based association studies. Hum Hered 58:139-144.
18. Kleinbaum DG, Kupper LL, Morgenstern H. 1982. Epidemiologic Research, Belmont, CA. Lifetime Learning Publications.
19. Kraft P, Cox DG, Paynter RA, Hunter D, De Vivo I. 2005. Accounting for haplotype uncertainty in matched association studies: A comparison of simple and flexible techniques. Genet Epidemiol 28:261-272.
20. Kuha G, Skinner C, Palmgren J. 1998. Misclassification error. In: Armitage P, Colton T, editors. Encyclopedia of Biostatistics, Vol. 4, New York: Wiley, p 2615-2621.
21. Lalani SR, Safiullah AA, Fernbach SD, Phillips M, Bacino CA, Molinari LM, Glass NL, Towbin JA, Craigen WJ, Belmont JW. 2005. SNP genotyping to screen for a common deletion in CHARGE Syndrome. BMC Med Genet 6:1-7.
22. Lamina C, Kuchenhoff H, Bongardt F, Paulweber B, Kronenberg F, Wichmann HE, Held I. 2005. On the haplotype uncertainty from genotyping and reconstruction error and its impact on association analysis. Genet Epidemiol 29:260.
23. Olivier M, Chuang LM, Chang MS, Chen YT, Pei D, Ranade K, de Witte A, Allen J, Tran N, Curb D, Pratt R, Neefs H, de Arruda Indig M, Law S, Neri B, Wang L, Cox DR. 2002. High-throughput genotyping of single nucleotide polymorphisms using new biplex invader technology. Nucleic Acids Res 30:e53.
24. Proudnikov D, LaForge KS, Hofflich H, Levenstien M, Gordon D, Barral S, Ott J, Kreek MJ. 2006. Association analysis of polymorphisms in serotonin 1B receptor (HTR1B) gene with heroin addiction: a comparison of molecular and statistically estimated haplotypes. Pharmacogenet Genomics 16:25-36.
25. Ranade K, Chang MS, Ting CT, Pei D, Hsiao CF, Olivier M, Pesich R, Herbert J, Chen UD, Dzau VJ, Curb D, Olshen R, Risch N, Cox DR, Botstein D. 2001. High-throughput genotyping with single nucleotide polymorphisms. Genome Res 11:1262-1268.
26. Rice KM, Holmans P. 2003. Allowing for genotyping error in analysis of unmatched case-control studies. Ann Hum Genet 67:165-174.
27. Schaid DJ. 2004. Evaluating associations of haplotypes with traits. Genet Epidemiol 27:348-364.
28. Sobel E, Papp JC, Lange K. 2002. Detection and integration of genotyping errors in statistical genetics. Am J Hum Genet 70: 496-508.
29. Stram D, Haiman C, Hirschhorn J, Altshuler D, Kolonel L, Henderson B, Pike M. 2003. Choosing haplotype-tagging SNPs based on unphased genotype data using as preliminary sample of unrelated subjects with an example from the multiethnic cohort study. Hum Hered 55:27-36.
30. Wong MY, Day NE, Luan JA, Wareham NJ. 2004. Estimation of magnitude in gene-environment interactions in the presence of measurement error. Stat Med 23:987-998.
31. Zaykin D, Westfall P, Young S, Karnoub M, Wagner M, Ehm M. 2002. Testing association of statistically inferred haplotypes with discrete and continuous traits in samples of unrelated individuals. Hum Hered 53:79-91.
32. Zhao L, Li S, Khalid N. 2003. A method for the assessment of disease associations with single-nucleotide polymorphism haplotypes and environmental variables in case-control studies. Am J Hum Genet 72:1231-1250.
33. Zou G, Zhao H. 2003. Haplotype frequency estimation in the presence of genotyping errors. Hum Hered 56:131-138.