FBAT-SNP-PC: an approach for multiple markers and single trait in family-based association tests.

OBJECTIVE

Develop a new test for family-based association studies and continuous traits that incorporates power- enhancing techniques from two existing testing strategies.

METHODS

The new procedure initiates with an extraction of the relevant information from the variability of the genotypes and an assessment of the approximate individual markers effects and their directions. This information is incorporated in the construction of the actual test statistic through a selection of a data-determined number of optimal linear combinations of the offspring genotypes which, in a power enhancing step, are consequently combined into a single degree of freedom test. We conduct a comparison simulation study in which the performance of the new test is contrasted with the test that is currently known to offer the highest overall power, FBAT-LC.

RESULTS

The new test has an overall performance very similar to that of FBAT-LC but attains higher power in candidate genes with lower average pairwise correlations and moderate to high allele frequencies with large gains (up to 80%) for some of the analyzed genes possessing the above-mentioned characteristics.

CONCLUSION

The new test is a promising tool for candidate gene studies with substantial power gains for genes that are characterized by SNPs with low mean pairwise correlation.