1. ¹Department of Public Health, College of Medicine, Tzu-Chi University, Hua-Lien, 97004, Taiwan
2. ²Department of Statistics and Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27606, USA
3. ³Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, 100, Taiwan
4. ⁴Division of Biostatistics, Institute of Epidemiology, National Taiwan University, Taipei, 100, Taiwan

Correspondence: Chuhsing Kate Hsiao, Division of Biostatistics, Institute of Epidemiology, National Taiwan University, Taipei, 100, Taiwan. Fax: +886-2-23418562. E-mail: ckhsiao@ha.mc.ntu.edu.tw

Received 9 November 2005; Accepted 14 February 2006; Published online 12 May 2006.

Abstract

Modern association studies often involve a large number of markers and hence may encounter the problem of testing multiple hypotheses. Traditional procedures are usually over-conservative and with low power to detect mild genetic effects. From the design perspective, we propose a two-stage selection procedure to address this concern. Our main principle is to reduce the total number of tests by removing clearly unassociated markers in the first-stage test. Next, conditional on the findings of the first stage, which uses a less stringent nominal level, a more conservative test is conducted in the second stage using the augmented data and the data from the first stage. Previous studies have suggested using independent samples to avoid inflated errors. However, we found that, after accounting for the dependence between these two samples, the true discovery rate increases substantially. In addition, the cost of genotyping can be greatly reduced via this approach. Results from a study of hypertriglyceridemia and simulations suggest the two-stage method has a higher overall true positive rate (TPR) with a controlled overall false positive rate (FPR) when compared with single-stage approaches. We also report the analytical form of its overall FPR, which may be useful in guiding study design to achieve a high TPR while retaining the desired FPR.