Using duplicate genotyped data in genetic analyses: Testing association and estimating error rates

Statistical Applications in Genetics and Molecular Biology

Volumn 6, Issue 1, 2007, Pages

  Tintle, Nathan L ^a   Gordon, Derek ^b   McMahon, Francis J ^c   Finch, Stephen J ^d  

^a HOPE COLLEGE   (United States)

^b RUTGERS UNIVERSITY   (United States)

^c NATIONAL INSTITUTES OF HEALTH   (United States)

^d STONY BROOK UNIVERSITY   (United States)

Author keywords

Case control; Duplicate genotype; Genome wide association; Genotype error; Inconsistency rate; Misclassification; Re genotype; Test of association; Whole genome association

Indexed keywords

ANALYTICAL ERROR; ANALYTICAL RESEARCH; ARTICLE; CASE CONTROL STUDY; COMPUTER PROGRAM; GENETIC ANALYSIS; GENOME ANALYSIS; GENOTYPE; MULTIVARIATE ANALYSIS OF VARIANCE; PHENOTYPE; SIMULATION; ANALYSIS OF VARIANCE; BIOLOGICAL MODEL; HUMAN; STATISTICAL ANALYSIS;

ANALYSIS OF VARIANCE; DATA INTERPRETATION, STATISTICAL; GENOTYPE; HUMANS; MODELS, GENETIC;

EID: 33846897439     PISSN: None     EISSN: 15446115     Source Type: Journal    
DOI: 10.2202/1544-6115.1251     Document Type: Article

References (40)

1. Barral S, Haynes C, Stone M, Gordon D (2006) LRTae: Improving statistical power for genetic association with case/control data when phenotype and/or genotype misclassification errors are present. BMC Genet 7:24
2. Bonin A, Bellemain E, Bronken-Eidesen P, Pompanon F, Brochmann C, Taberlet P (2004) How to track and assess genotyping errors in population genetics studies. Mol Ecol 13:3261-3273.
3. Bross I (1954) Misclassification in 2x2 tables. Biometrics 10:478-486
4. Brzustowicz LM, Merette C, Xie X, Townsend L, Gilliam TC, Ott J (1993) Molecular and statistical approaches to the detection and correction of errors in genotype databases. Am J Hum Genet 53:1137-1145
5. Casella G, Berger RL (2002). Statistical Inference, Second edition, United States: Duxbury Thomson Learning.
6. Clayton DG, Walker NM, Smyth DJ, Pask R, Cooper JD, Maier LM, Smink LJ, Lam AC, Ovington NR, Stevens HE, Nutland S, Howson JM, Faham M, Moorhead M, Jones HB, Falkowski M, Hardenbol P, Willis TD, Todd JA (2005) Population structure, differential bias and genomic control in a large-scale, case-control association study. Nat Genet 37(11):1243-6.
7. Cochran WG (1968) Errors of measurement in statistics. Technometrics 10:637-666
8. Dataplot. Version 4/2006. JJ Filliben and A Heckert. Information Technology Laboratory of the National Institute of Standards and Technology.
9. Edwards B, Haynes C, Levenstien MA, Finch SJ, Gordon D (2005) Power and sample size calculations in the presence of phenotype errors for case/control genetic studies. BMC Genet 6:18
10. Fujisawa J, Izumi S (2000) Inference about misclassification probabilities from repeated binary responses. Biometrics 56:706-711
11. Genetic Analysis Workshop 14 (GAW14) in Noordwijkherout, The Netherlands. (2004) Participant documentation. (http://www.gaworkshop.net)
12. Gordon D and Finch SJ (2005) Factors affecting statistical power in the detection of genetic association. J Clin Invest 115:1408-1418
13. Gordon D, Finch SJ, Nothnagel M, Ott J (2002) Power and sample size calcualtions for case-control genetic association tests when errors are present: application to single nucleotide polymorphisms. Hum Hered 54:22-33
14. Gordon D, Ott J (2001) Assessment and management of single nucleotide polymorphism genotype errosr in genetic association analysis. Pac Symp Biocomput: 18-29
15. 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. (2004) Stat Appl Gen Mol Bio 3(1):26 (http://www.bepress.com/sagmb/vol3/iss1/art26/)
16. Hao K, Wang X (2004) Incorporating individual error rate into association test of unmatched case-control design. Hum Hered 58:154-163
17. Ji F, Yang Y, Haynes C, Finch SJ, Gordon D (2005) Computing asymptotic power and sample size for case-control genetic association studies in the presence of phenotype and/or genotype misclassification errors. Stat Appl Gen Mol Bio 4(1):37 (http://www.bepress.com/sagmb/vol4/iss1/art37/)
18. Johnson RA, Wichern DW (1998). Applied Multivariate Statistical Analysis, Fourth edition, Upper Saddle River, NJ: Prentice Hall.
19. Kang SJ, Gordon D, Brown AM, Ott J, Finch SJ (2004) Tradeoff between no-call reduction in genotyping error rate and loss of sample size for genetic case/control association studies. Pac Symp Biocomput: 116-127
20. Kang SJ, Gordon D, Finch SJ (2004) What SNP genotyping errors are most costly for genetic association studies? Genet Epidemiol 26:132-141
21. Koch G (1969) The effect of non-sampling errors on measures of association in 2x2 contingency tables. J Am Stat Assoc 64:852-863
22. Lai R, Zhang H, Yang Y (in press) Repeated Measurement Sampling in Genetic Association Analysis with Genotyping Errors Genet Epidemiol
23. Lincoln SE, Lander ES (1992) Systematic detection of errors in genetic linkage data. Genomics 14:604-610.
24. McMahon FJ. Unpublished dataset. Personal Communication. 2006.
25. McMahon FJ, Buervenich S, Charney D, Lipsky R, Rush AJ, Wilson AF, Sorant AJ, Papanicolaou GJ, Laje G, Fava M, Trivedi MH, Wisniewski SR, Manji H (2006) Variation in the gene encoding the serotonin 2A receptor is associated with outcome of antidepressant treatment. Am J Hum Genet 78: 804-814.
26. Moskvina V, Craddock N, Holmans P, Owen MJ, O'Donovan MC (2006) Effects of differential genotyping error rate on the type I error probability in case-control studies. Hum Hered 61(1):55-64.
27. Moskvina V, Schmidt KM (In press) Susceptibility of Biallelic Haplotype and Genotype Frequencies to Genotyping Error. Biometrics
28. 2-tests in the analysis of categorical data. Biometrika 52:95-109
29. Muller KE, LaVange LM, Landesman-Ramey S, Ramey CT (1992) Power calculations for general linear multivariate models including repeated measures applications. J Am Stat Assoc 87:1209-1226
30. Pompanon F, Bonin A, Bellemain E and Taberlet P. (2005) Genotyping Errors: Causes, consequences and solutions. Nature Reviews Genetics 6: 847-59
31. Rice KM, Holmans P (2003) Allowing for genotyping error in analysis of unmatched case-control studies. Ann Hum Genet 67:165-174 SAS (2005) Version 9.1.3.
32. Service SK, Sandkuijl LA, Freimer NB (2003) Cost-effective designs for linkage disequilibrium mapping of complex traits. Am J Hum Genet 72:1213-20
33. Sobel E, Papp JC, Lange K (2002) Detection and Integration of Genotyping Errors in Statistical Genetics. Am J Hum Genet 70:496-508
34. Sutcliffe JP (1965) A probability model for errors of classification: general considerations. Psychometrika 30:73-96
35. Sutcliffe JP (1965) A probability model for errors of classification: particular cases. Psychometrika 30:129-155
36. Tenenbein A (1970) A double sampling scheme for estimating from binomial data with misclassifications. J Am Stat Assoc 65:1350-1361
37. Tenenbein A (1972) A double sampling scheme for estimating from misclassified multinomial data with applications to sampling inspection. Technometrics 14:187-202
38. Tintle NL, Ahn K, Mendell NR, Gordon D, Finch SJ (2005) Characteristics of replicated single-nucleotide polymorphism genotypes from COGA: Affymetrix and Center for Inherited Disease Research. BMC Genet 6(Suppl 1):S154
39. Ward KJ, Ellard S, Yajnik CS, Frayling TM, Hattersley AT, Venigalla PNS, Chandak GR (2006) Allelic drop-out may occur with a primer binding site polymorphism for the commonly used RFLP assay for the -1131T>C polymorphism of the Apolipoprotein AV gene. Lipids Health Dis 5:11
40. Zheng G, Tian X (2005) The impact of diagnostic error on testing genetic association in case-control studies. Stat Med 24:869-82