Flexible designs for genomewide association studies

Biometrics

Volumn 65, Issue 3, 2009, Pages 815-821

  Scherag, André ^a   Hebebrand, Johannes ^b   Schäfer, Helmut ^a   Müller, Hans Helge ^a  

^a PHILIPPS UNIVERSITY MARBURG   (Germany)

^b UNIVERSITY OF DUISBURG ESSEN   (Germany)

Author keywords

Adaptive design; Conditional rejection probability; Design adaptation; Family wise error rate; Flexible design; Genomewide association study; Interim analysis; Multiple testing; Two stage design

Indexed keywords

STATISTICAL TESTS;

ADAPTIVE DESIGNS; CONDITIONAL REJECTION PROBABILITY; DESIGN ADAPTATIONS; ERROR RATE; FAMILY-WISE ERROR RATE; FLEXIBLE DESIGNS; GENOME-WIDE ASSOCIATION STUDIES; INTERIM ANALYSIS; MULTIPLE TESTING; REJECTION PROBABILITY; TWO STAGE DESIGNS;

GENES;

BIOLOGICAL MARKER;

DESIGN; ETIOLOGY; GENETIC MARKER; GENOME;

ANALYTICAL ERROR; ARTICLE; GENE CONTROL; GENE LINKAGE DISEQUILIBRIUM; GENETIC ALGORITHM; GENETIC ASSOCIATION; GENETIC DISORDER; GENETIC MARKER; GENOME ANALYSIS; GENOTYPE; SAMPLE SIZE; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM;

ALGORITHMS; CHROMOSOME MAPPING; DATA INTERPRETATION, STATISTICAL; GENETIC MARKERS; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; HUMANS; RESEARCH DESIGN;

EID: 70349234337     PISSN: 0006341X     EISSN: 15410420     Source Type: Journal    
DOI: 10.1111/j.1541-0420.2008.01174.x     Document Type: Article

References (26)

1. Arking, D. E., Pfeufer, A., Post, W., Kao, W. H., Newton-Cheh, C., Ikeda, M., West, K., Kashuk, C., Akyol, M., Perz, S., Jalilzadeh, S., Illig, T., Gieger, C., Guo, C. Y., Larson, M. G., Wichmann, H. E., Marban, E., O'donnell, C. J., Hirschhorn, J. N., Kaab, S., Spooner, P. M., Meitinger, T., and Chakravarti, A. (2006). A common genetic variant in the nos1 regulator nos1ap modulates cardiac repolarization. Nature Genetics 38, 644 651.
2. Barrett, J. C. and Cardon, L. R. (2006). Evaluating coverage of genome-wide association studies. Nature Genetics 38, 659 662.
3. Boehringer, S., Epplen, J. T., and Krawczak, M. (2000). Genetic association studies of bronchial asthma - a need for Bonferroni correction Human Genetics 107, 197.
4. Dupuy, A. and Simon, R. M. (2007). Critical review of published microarray studies for cancer outcome and guidelines on statistical analysis and reporting. Journal of the National Cancer Institute 99, 147 157.
5. Goll, A. and Bauer, P. (2007). Two-stage designs applying methods differing in costs. Bioinformatics 23, 1519 1526.
6. Hartl, D. L. and Clark, A. G. (2007). Principles of Population Genetics, 4th edition. Sunderland, Massachusetts : Sinauer Associates.
7. Hinney, A., Nguyen, T. T., Scherag, A., Friedel, S., Brönner, G., Müller, T. D., Grallert, H., Illig, T., Wichmann, H.-E., Rief, W., Schäfer, H., and Hebebrand, J. (2007). Genome wide association (GWA) study for early onset extreme obesity supports the role of fat mass and obesity associated gene (FTO) variants. Public Library of Science ONE 2, 1 5.
8. Ioannidis, J. P. A., Trikalinos, T. A., and Khoury, M. J. (2006). Implications of small effect sizes of individual genetic variants on the design and interpretation of genetic association studies of complex diseases. American Journal of Epidemiolgy 164, 609 614.
9. Jennison, C. and Turnbull, B. W. (2006). Adaptive and nonadaptive group sequential tests. Biometrika 93, 1 21.
10. Marcus, R., Peritz, E., and Gabriel, K. R. (1976). On closed testing procedures with special reference to ordered analysis of variance. Biometrika 63, 655 660.
11. Müller, H.-H. and Schäfer, H. (2004). A general statistical principle for changing a design any time during the course of a trial. Statistics in Medicine 23, 2497 2508.
12. Müller, H.-H., Pahl, R., and Schäfer, H. (2007). Including sampling and phenotyping costs into the optimization of two stage designs for genome wide association studies. Genetic Epidemiolgy 31, 844 852.
13. Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D., Maller, J., Sklar, P., de Bakker, P. I. W., Daly, M. J., and Sham, P. C. (2007). PLINK: A tool set for whole-genome association and population-based linkage analyses. American Journal of Human Genetics 81, 559 575.
14. Sasieni, P. D. (1997). From genotypes to genes: Doubling the sample size. Biometrics 53, 1253 1261.
15. Satagopan, J. M., Venkatraman, E. S., and Begg, C. B. (2004). Two-stage designs for gene-disease association studies with sample size constraints. Biometrics 60, 589 597.
16. Scherag, A., Müller, H.-H., Dempfle, A., Hebebrand, J., and Schäfer, H. (2003). Data adaptive interim modification of sample sizes for candidate-gene association studies. Human Heredity 56, 56 62.
17. Scuteri, A., Sanna, S., Chen, W.-M., Uda, M., Albai, G., Strait, J., Najjar, S., Nagaraja, R., Orrú, M., Usala, G., Dei, M., Lai, S., Maschio, A., Busonero, F., Mulas, A., Ehret, G. B., Fink, A. A., Weder, A. B., Cooper, R. S., Galan, P., Chakravarti, A., Schlessinger, D., Cao, A., Lakatta, E., and Abecasis, G. R. (2007). Genome-wide association scan shows genetic variants in the fto gene are associated with obesity-related traits. Public Library of Science Genetics 3, 1200 1210.
18. Skol, A. D., Scott, L. J., Abecasis, G. R., and Boehnke, M. (2006). Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies. Nature Genetics 38, 209 213.
19. Skol, A. D., Scott, L. J., Abecasis, G. R., and Boehnke, M. (2007). Optimal designs for two-stage genome-wide association studies. Genetic Epidemiolgy 31, 776 788.
20. Terwilliger, J. D. and Hiekkalinna, T. (2006). An utter refutation of the "fundamental theorem of the hapmap European Journal of Human Genetics 14, 426 437.
21. Tsiatis, A. A. and Mehta, C. (2003). On the inefficiency of the adaptive design for monitoring clinical trials. Biometrika 90, 367 378.
22. Wang, H., Thomas, D. C., Pe'er, I., and Stram, D. O. (2006). Optimal two-stage genotyping designs for genome-wide association scans. Genetic Epidemiolgy 30, 356 368.
23. Weinberg, C. R. and Umbach, D. M. (2005). A hybrid design for studying genetic influences on risk of diseases with onset early in life. American Journal of Human Genetics 77, 627 636.
24. Wellcome Trust Case Control Consortium 2007). Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447, 661 678.
25. Witte, J. S., Elston, R. C., and Cardon, L. R. (2000). On the relative sample size required for multiple comparisons. Statistics in Medicine 19, 369 372.
26. Yu, K., Chatterjee, N., Wheeler, W., Li, Q., Wang, S., Rothman, N., and Wacholder, S. (2007). Flexible design for following up positive findings. American Journal of Human Genetics 81, 540 551.