Improving the power of association tests for quantitative traits in family studies

Association mapping based on family studies can identify genes that influence complex human traits while providing protection against population stratification. Because no gene is likely to have a very large effect on a complex trait, most family studies have limited power. Among the commonly used family‐based tests of association for quantitative traits, the quantitative transmission‐disequilibrium tests (QTDT) based on the variance‐components model is the most flexible and most powerful. This method assumes that the trait values are normally distributed. Departures from normality can inflate the type I error and reduce the power. Although the family‐based association tests (FBAT) and pedigree disequilibrium tests (PDT) do not require normal traits, nonnormality can also result in loss of power. In many cases, approximate normality can be achieved by transforming the trait values. However, the true transformation is unknown, and incorrect transformations may compromise the type I error and power. We propose a novel class of association tests for arbitrarily distributed quantitative traits by allowing the true transformation function to be completely unspecified and empirically estimated from the data. Extensive simulation studies showed that the new methods provide accurate control of the type I error and can be substantially more powerful than the existing methods. We applied the new methods to the Collaborative Study on the Genetics of Alcoholism and discovered significant association of single nucleotide polymorphisms (SNP) tsc0022400 on chromosome 7 with the quantitative electrophysiological phenotype TTTH1, which was not detected by any existing methods. We have implemented the new methods in a freely available computer program. Genet. Epidemiol. 2006. © 2006 Wiley‐Liss, Inc.