Originally published as Genetics Published Articles Ahead of Print on September 15, 2006.

Genetics, Vol. 174, 1505-1516, November 2006, Copyright © 2006
doi:10.1534/genetics.105.054452

Test of Association Between Haplotypes and Phenotypes in Case–Control Studies: Examination of Validity of the Application of an Algorithm for Samples From Cohort or Clinical Trials to Case–Control Samples Using Simulated and Real Data

Shiori Furihata^*,,1, Toshikazu Ito and Naoyuki Kamatani^*,,2

^* Algorithm Team, Japan Biological Information Research Center (JBIRC), Japan Biological Informatics Consortium (JBIC), Tokyo 135-0064, Japan, Mitsubishi Research Institute, Tokyo 100-8141, Japan and Division of Genomic Medicine, Department of Advanced Biomedical Engineering and Science and Institute of Rheumatology, Tokyo Women's Medical University, Tokyo 162-0054, Japan

² Corresponding author: Division of Genomic Medicine, Department of Advanced Biomedical Engineering and Science and Institute of Rheumatology, Tokyo Women's Medical University, 10-22 Kawada-cho, Shinjuku-ku, Shinjuku, Tokyo 162-0054, Japan.
E-mail: kamatani{at}ior.twmu.ac.jp

The use of haplotype information in case–control studies is an area of focus for the research on the association between phenotypes and genetic polymorphisms. We examined the validity of the application of the likelihood-based algorithm, which was originally developed to analyze the data from cohort studies or clinical trials, to the data from case–control studies. This algorithm was implemented in a computer program called PENHAPLO. In this program, haplotype frequencies and penetrances are estimated using the expectation-maximization algorithm, and the haplotype–phenotype association is tested using the generalized likelihood ratio. We show that this algorithm was useful not only for cohort studies but also for case–control studies. Simulations under the null hypothesis (no association between haplotypes and phenotypes) have shown that the type I error rates were accurately estimated. The simulations under alternative hypotheses showed that PENHAPLO is a robust method for the analysis of the data from case–control studies even when the haplotypes were not in HWE, although real penetrances cannot be estimated. The power of PENHAPLO was higher than that of other methods using the likelihood-ratio test for the comparison of haplotype frequencies. Results of the analysis of real data indicated that a significant association between haplotypes in the SAA1 gene and AA-amyloidosis phenotype was observed in patients with rheumatoid arthritis, thereby suggesting the validity of the application of PENHAPLO for case–control data.

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