Sample-size properties of a case-control association analysis of multistage SNP studies for identifying disease susceptibility genes

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• 作者：Nobutaka Kitamura ; Kouhei Akazawa ; Shin-ichi Toyabe ; Akinori Miyashita ; Ryozo Kuwano and Junichiro Nakamura
• 关键词：Case ; control association analysis ; Multistage design ; Joint analysis ; Replication ; based analysis
• 刊名：Journal of Human Genetics
• 出版年：2008
• 出版时间：May, 2008
• 年：2008
• 卷：53
• 期：5
• 页码：390-400
• 全文大小：357.4 KB
• 刊物类别：Biomedical and Life Sciences
• 刊物主题：Biomedicine
  Human Genetics
  Molecular Medicine
  Cancer Research
  Cell Biology
  Immunology
  Neurosciences
  
• 出版者：Springer Japan
• ISSN：1435-232X

文摘

A two-stage association study is the most commonly used method to efficiently identify disease susceptibility genes. However, some recent single nucleotide polymorphism (SNP) studies recently utilized three-stage designs. The purpose of this study was to investigate the practical properties of statistical powers and positive predictive values (PPVs) of replication-based analysis (RBA) and the joint analysis (JA) in multistage designs. For this purpose, a program for multistage designs was developed to calculate these performance indicators under various conditions of the number of samples, alleles of candidates, alleles remaining in the final stage, and genotypings. The results showed that the powers and PPVs of RBA and JA in three-stage designs were higher than those in two-stage designs in the range of a smaller proportion of sample size than 0.5 at the first stage. This tendency was more remarkable in JA. In conclusion, researchers who perform SNP studies for identifying disease susceptibility genes need to take account of three-stage case-control association studies, corresponding to study conditions such as the total numbers of samples, alleles, and genotypings. Furthermore, the program developed in this study is useful for estimating powers and PPVs in planning multistage association studies.