Sequentially testing for a gene-drug interaction in a genomewide analysis

Statistics in Medicine

Volumn 27, Issue 11, 2008, Pages 2022-2034

  Kelly, Patrick ^a   Zhou, Yinghui ^b   Whitehead, John ^c   Stallard, Nigel ^d   Bowman, Clive ^e  

^a UNIVERSITY OF SYDNEY   (Australia)

^b UNIVERSITY OF READING   (United Kingdom)

^c LANCASTER UNIVERSITY   (United Kingdom)

^d UNIVERSITY OF WARWICK   (United Kingdom)

^e GLAXOSMITHKLINE   (United Kingdom)

Author keywords

Adaptive designs; Clinical trials; Drug development; Group sequential designs; Pharmacogenetics

Indexed keywords

ANTIOBESITY AGENT; PLACEBO;

ALLELE; ANALYTICAL ERROR; ARTICLE; CALCULATION; CHROMOSOME 17; CLINICAL TRIAL; CONTROLLED CLINICAL TRIAL; CORRELATION ANALYSIS; DRUG EFFICACY; FEASIBILITY STUDY; GENE FREQUENCY; GENETIC MARKER; HUMAN; INDIVIDUALIZATION; INHERITANCE; MATHEMATICAL COMPUTING; MEDICAL DECISION MAKING; NULL HYPOTHESIS; PHARMACOGENETICS; SAMPLE SIZE; SEQUENTIAL ANALYSIS; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM; TREATMENT PLANNING;

ALGORITHMS; CLINICAL TRIALS AS TOPIC; DATA INTERPRETATION, STATISTICAL; DRUG DESIGN; GENE FREQUENCY; HUMANS; MODELS, STATISTICAL; PHARMACOGENETICS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 42949087971     PISSN: 02776715     EISSN: 10970258     Source Type: Journal    
DOI: 10.1002/sim.3059     Document Type: Article

References (34)

1. Roses AD. Pharmacogenetics and drug development: the path to safer and more effective drugs. Nature Reviews Genetics 2004; 5:645-656.
2. Penny MA, McHale D. Pharmacogenomics and the drug discovery pipeline: when should it be implemented? American Journal of Pharmacogenomics 2005; 5:153-162.
3. Risner ME, Saunders AM, Altman JFB, Ormandy GC, Craft S, Foley IM, Zvartau-Hind ME, Hosford DA, Roses AD. Efficacy of rosiglitazone in a genetically defined population with mild-to-moderate Alzheimer's disease. Pharmacogenomics Journal 2006; 6:246-254.
4. Roses AD, Burns DK, Chissoe S, Middleton LT, St Jean P. Disease specific target selection: a critical first step down the right road. Drug Discovery Today 2005; 10:177-189.
5. Hoh J, Witte A, Ott J. Trimming, weighting, and grouping SNPs in human case-control association studies. Genome Research 2001; 11:2115-2119.
6. 2 test for genome association studies. American Journal of Human Genetics 2002; 70:1257-1268.
7. Zaykin DV, Zhivotovsky LA, Westfall PH, Weir BS. Truncated product method for combining p-values. Genetic Epidemiology 2002; 22:170-185.
8. Wille A, Hoh J, Ott J. Sum statistics for the joint detection of multiple disease loci in case-control association studies with SNP markers. Genetic Epidemiology 2003; 25:350-359.
9. Dudbridge F, Koeleman BPC. Rank truncated product of p-values, with application to genomewide association scans. Genetic Epidemiology 2003; 25:360-366.
10. Potter DM. Omnibus permutation tests of the association of an ensemble of genetic markers with disease in case-control studies. Genetic Epidemiology 2006; 30:438-446.
11. Kelly P, Stallard N, Zhou Y, Whitehead J, Bowman C. Sequential genomewide association studies for monitoring adverse events in clinical evaluation of new drugs. Statistics in Medicine 2006; 25:3081-3092.
12. Elston RC, Idury RM, Cardon LR, Lichter JB. The study of candidate genes in drug trials: sample size considerations. Statistics in Medicine 1999; 18:741-751.
13. Kelly PJ, Stallard N, Whittaker JC. Statistical design and analysis of pharmacogenetic trials. Statistics in Medicine 2005; 24:1495-1508.
14. Fisher RA. The Design of Experiments. Oliver and Boyd: Edinburgh, 1935.
15. Manly BFJ. Randomization, Bootstrap and Monte Carlo Methods in Biology (2nd edn). Chapman & Hall: London, 1998.
16. Westfall PH, Young SS. Resampling-based Multiple Testing: Examples and Methods for P-value Adjustment. Wiley: New York, 1993.
17. Whitehead J. The Design and Analysis of Sequential Clinical Trials. Wiley: Chichester, 1997.
18. Jennison C, Turnbull BW. Group Sequential Methods with Applications to Clinical Trials. Chapman & Hall/CRC: Boca Raton, FL, 2000.
19. Armitage P, McPherson CK, Rowe BC. Repeated significance tests on accumulating data. Journal of the Royal Statistical Society, Series A 1969; 132:235-244.
20. Kim K, DeMets DL. Design and analysis of group sequential tests based on the type I error spending function. Biometrika 1987; 74:149-154.
21. Lan KKG, DeMets DL. Discrete sequential boundaries for clinical trials. Biometrika 1983; 70:659-663.
22. Fairbanks K, Madsen R. P-values for tests using a repeated significance test design. Biometrika 1982; 69:69-74.
23. Tsiatis AA, Rosner GL, Mehta CR. Exact confidence intervals following a group sequential test. Biometrics 1984; 40:797-803.
24. Bauer P, Köhne K. Evaluation of experiments with adaptive interim analyses. Biometrics 1994; 51:1315-1324.
25. Gallo P, Chuang-Stein C, Dragalin V, Gaydos B, Krams M, Pinheiro J. Adaptive designs in clinical drug development - an executive summary of the PhRMA Working Group. Journal of Biopharmaceutical Statistics 2006; 16:275-383.
26. Lehmacher W, Wassmer G. Adaptive sample size calculations in group sequential trials. Biometrics 1999; 5:1286-1290.
27. Müller HH, Schäfer H. Adaptive group sequential designs for clinical trials: combining the advantages of adaptive and of classical group sequential approaches. Biometrics 2001; 57:886-891.
28. Šidák Z. Rectangular confidence regions for the means of multivariate normal distributions. Journal of the American Statistical Association 1967; 62:626-633.
29. Bowman C, Delrieu O, Roger J. Filtering pharmacogenetic signals. In Interdisciplinary Statistics and Bioinformatics, Barber S, Baxter P, Mardia K, Walls R (eds). University of Leeds: Leeds, 2006; 41-47.
30. Mehta CR, Patel N, Senchaudhuri P, Tsiatis A. Exact permutational tests for group sequential clinical trials. Biometrics 1994; 50:1042-1053.
31. Costello TJ, Falk CT, Ye KQ. Data mining and computationally intensive methods: summary of group 7 contributions to Genetic Analysis Workshop 13. Genetic Epidemiology 2003; 25:S57-S63.
32. Evans DM, Cardon LR. Genomewide association: a promising start to a long race. Trends in Genetics 2006; 22:350-354.
33. Verzilli CJ, Stallard N, Whittaker JC. Bayesian graphical models for genomewide association studies. American Journal of Human Genetics 2006; 79:100-113.
34. Delrieu O, Bowman C. Visualising gene determinants of disease in drug discovery. Pharmacogenomics 2006; 7:311-329.