Composite statistics for QTL mapping with moderately discordant sibling pairs

Extreme discordant sibling-pair (EDSP) designs have been shown in theory to be very powerful for mapping quantitative-trait loci (QTLs) in humans. However, their practical applicability has been somewhat limited by the need to phenotype very large populations to find enough pairs that are extremely discordant. In this paper, we demonstrate that there is also substantial power in pairs that are only moderately discordant, and that designs using moderately discordant pairs can yield a more practical balance between phenotyping and genotyping efforts. The power we demonstrate for moderately discordant pairs stems from a new statistical result. Statistical analysis in discordant-pair studies is generally done by testing for reduced identity by descent (IBD) sharing in the pairs. By contrast, the most commonly-used statistical methods for more standard QTL mapping are Haseman-Elston regression and variance-components analysis. Both of these use statistics that are functions of the trait values given IBD information for the pedigree. We show that IBD sharing statistics and "trait value given IBD" statistics contribute complementary rather than redundant information, and thus that statistics of the two types can be combined to form more powerful tests of linkage. We propose a simple composite statistic, and test it with simulation studies. The simulation results show that our composite statistic increases power only minimally for extremely discordant pairs. However, it boosts the power of moderately discordant pairs substantially and makes them a very practical alternative. Our composite statistic is straightforward to calculate with existing software; we give a practical example of its use by applying it to a Genetic Analysis Workshop (GAW) data set.