When a case is not a case: Effects of phenotype misclassification on power and sample size requirements for the transmission disequilibrium test with affected child trios

Human Heredity

Volumn 67, Issue 4, 2009, Pages 287-292

  Buyske, Steven ^a   Yang, Guang ^a   Matise, Tara C ^a   Gordon, Derek ^a  

^a RUTGERS UNIVERSITY   (United States)

Author keywords

Diagnosis error; Diagnostic error; Family based association; Genome wide association; Phenotyping error

Indexed keywords

ANALYTIC METHOD; ARTICLE; CALCULATION; COMPUTER PROGRAM; DISEASE CLASSIFICATION; GENE LINKAGE DISEQUILIBRIUM; GENETIC ASSOCIATION; GENOTYPE; GROUPS BY AGE; MARKER GENE; PARENT; PHENOTYPE; POWER ANALYSIS; PREVALENCE; QUANTITATIVE TRAIT LOCUS; SAMPLE SIZE; SIMULATION;

CASE-CONTROL STUDIES; CHILD; DIAGNOSTIC ERRORS; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; HUMANS; LINKAGE DISEQUILIBRIUM; PHENOTYPE; SAMPLE SIZE; SENSITIVITY AND SPECIFICITY; SOFTWARE;

EID: 58549086194     PISSN: 00015652     EISSN: 14230062     Source Type: Journal    
DOI: 10.1159/000194981     Document Type: Article

References (31)

1. Hampe J, Franke A, Rosenstiel P, Till A, Teuber M, Huse K, Albrecht M, Mayr G, De La Vega FM, Briggs J, Gunther S, Prescott NJ, Onnie CM, Hasler R, Sipos B, Folsch UR, Lengauer T, Platzer M, Mathew CG, Krawczak M, Schreiber S: A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1. Nat Genet 2007;39:207-211.
2. Klein RJ, Zeiss C, Chew EY, Tsai JY, Sackler RS, Haynes C, Henning AK, Sangiovanni JP, Mane SM, Mayne ST, Bracken MB, Ferris FL, Ott J, Barnstable C, Hoh J: Complement factor H polymorphism in age-related macular degeneration. Science 2005;308:385-389.
3. Tomlinson IP, Webb E, Carvajal-Carmona L, Broderick P, Howarth K, Pittman AM, Spain S, Lubbe S, Walther A, Sullivan K, Jaeger E, Fielding S, Rowan A, Vijayakrishnan J, Domingo E, Chandler I, Kemp Z, Qureshi M, Farrington SM, Tenesa A, Prendergast JG, Barnetson RA, Penegar S, Barclay E, Wood W, Martin L, Gorman M, Thomas H, Peto J, Bishop DT, Gray R, Maher ER, Lucassen A, Kerr D, Evans DG, Schafmayer C, Buch S, Volzke H, Hampe J, Schreiber S, John U, Koessler T, Pharoah P, van Wezel T, Morreau H, Wijnen JT, Hopper JL, Southey MC, Giles GG, Severi G, Castellvi-Bel S, Ruiz-Ponte C, Carracedo A, Castells A, Forsti A, Hemminki K, Vodicka P, Naccarati A, Lipton L, Ho JW, Cheng KK, Sham PC, Luk J, Agundez JA, Ladero JM, de la Hoya M, Caldes T, Niittymaki I, Tuupanen S, Karhu A, Aaltonen L, Cazier JB, Campbell H, Dunlop MG, Houlston RS: A genome-wide association study identifies colorectal cancer susceptibility loci on chromosomes 10p14 and 8q23.3. Nat Genet 2008;40:623-630.
4. Buch S, Schafmayer C, Volzke H, Becker C, Franke A, von Eller-Eberstein H, Kluck C, Bassmann I, Brosch M, Lammert F, Miquel JF, Nervi F, Wittig M, Rosskopf D, Timm B, Holl C, Seeger M, ElSharawy A, Lu T, Egberts J, Fandrich F, Folsch UR, Krawczak M, Schreiber S, Nurnberg P, Tepel J, Hampe J: A genomewide association scan identifies the hepatic cholesterol transporter ABCG8 as a susceptibility factor for human gallstone disease. Nat Genet 2007;39:995-999.
5. Gordon D: Gene mapping: Balance among quality, quantity and cost of data in the era of whole-genome mapping for complex disease. Eur J Hum Genet 2006;14:1147-1148.
6. Gordon D, Finch SJ: Factors affecting statistical power in the detection of genetic association. J Clin Invest 2005;115:1408-1418.
7. 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.
8. Mote VL, Anderson RL: An investigation of the effect of misclassification on the properties of chisquare-tests in the analysis of categorical data. Biometrika 1965;52:95-109.
9. Kang SJ, Gordon D, Finch SJ: What SNP genotyping errors are most costly for genetic association studies? Genet Epidemiol 2004;26:132- 141.
10. Edwards BJ, Haynes C, Levenstien MA, Finch SJ, Gordon D: Power and sample size calculations in the presence of phenotype errors for case/control genetic association studies. BMC Genet 2005;6:18.
11. Zheng G, Tian X: The impact of diagnostic error on testing genetic association in case-control studies. Stat Med 2005;24:869-882.
12. Silverberg MS, Daly MJ, Moskovitz DN, Rioux JD, McLeod RS, Cohen Z, Greenberg GR, Hudson TJ, Siminovitch KA, Steinhart AH: Diagnostic misclassification reduces the ability to detect linkage in inflammatory bowel disease genetic studies. Gut 2001;49:773-776.
13. Pompanon F, Bonin A, Bellemain E, Taberlet P: Genotyping errors: causes, consequences and solutions. Nat Rev Genet 2005;6:847- 859.
14. Gordon D, Finch SJ: Consequences of error; in Dunn MJ, Jorde LB, Little PFR, Subramaniam S (eds): Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. Hoboken: J Wiley and Sons, 2006.
15. Gordon D, Haynes C, Blumenfeld J, Finch SJ: PAWE-3D: visualizing power for association with error in case-control genetic studies of complex traits. Bioinformatics 2005;21:3935- 3937.
16. Scott L, Rogus JJ: Using unaffected child trios to test for transmission distortion. Genet Epidemiol 2000;19:381-394.
17. Spielman RS, McGinnis RE, Ewens WJ: Transmission test for linkage disequilibrium: the insulin gene region and insulin-dependent diabetes mellitus (IDDM). Am J Hum Genet 1993;52:506-516.
18. Mahoney WJ, Szatmari P, MacLean JE, Bryson SE, Bartolucci G, Walter SD, Jones MB, Zwaigenbaum L: Reliability and accuracy of differentiating pervasive developmental disorder subtypes. J Am Acad Child Adolesc Psychiatry 1998;37:278-285.
19. Lei KJ, Shelly LL, Lin B, Sidbury JB, Chen YT, Nordlie RC, Chou JY: Mutations in the glucose- 6-phosphatase gene are associated with glycogen storage disease types 1a and 1aSP but not 1b and 1c. J Clin Invest 1995;95:234-240.
20. Burgess JA, Walters EH, Byrnes GB, Wharton C, Jenkins MA, Abramson MJ, Hopper JL, Dharmage SC: Who remembers whether they had asthma as children? J Asthma 2006;43:727- 730.
21. Novakovic B, Goldstein AM, Wexler LH, Tucker MA: Increased risk of neuroectodermal tumors and stomach cancer in relatives of patients with Ewing's sarcoma family of tumors. J Natl Cancer Inst 1994;86:1702-1706.
22. Gordon D, Devoto M: Advances in familybased association analysis. Introduction. Hum Hered 2008;66:65-66.
23. Spielman RS, Ewens WJ: The TDT and other family-based tests for linkage disequilibrium and association. Am J Hum Genet 1996;59: 983-989.
24. Deng H, Chen W: The power of the transmission disequilibrium test (TDT) with both case-parent and control-parent trios. Genet Res 2001;78:289-302.
25. Lewontin RC: The interaction of selection and linkage. I. General considerations; heterotic models. Genetics 1964;49:49-67.
26. Schaid DJ, Sommer SS: Genotype relative risks: methods for design and analysis of candidate- gene association studies. Am J Hum Genet 1993;53:1114-1126.
27. Box GEP, Hunter WG, Hunter JS: Statistics for Experimenters. New York, John Wiley and Sons, 1978.
28. Weeks DE, Ott J, M. LG: SLINK: a general simulation program for linkage analysis. Am J Hum Genet 1990;47(suppl):A204.
29. Terwilliger JD, Ott J: Handbook of Human Genetic Linkage. Baltimore, Johns Hopkins, 1994.
30. Purcell S, Cherny SS, Sham PC: Genetic Power Calculator: design of linkage and association genetic mapping studies of complex traits. Bioinformatics 2003;19:149-150.
31. Greenberg DA: There is more than one way to collect data for linkage analysis. What a study of epilepsy can tell us about linkage strategy for psychiatric disease. Arch Gen Psychiatry 1992;49:745-750.