Revised Regression of Offspring on Mid-Parent (ROMP): Suite of R functions

Abstract

Testing for associations between polymorphisms and quantitative traits provides a tool that can help to identify the genetic effects underlying multifactorial disease. In addition to testing for association, the ability to estimate how much of the variation in a quantitative trait is attributable to variation at a given marker locus, i.e. the heritability attributable to the locus (or the locus-specific heritability), can help to assess the importance of a polymorphism found through association testing, and may help to prioritize subsequent studies. Locus-specific heritability can be used in a manner similar to the use of attributable risk in assessing what proportion of the disease in the population is attributable to a risk factor. This can be especially helpful in studying the etiology of multifactorial disease in which several loci and environmental factors are likely to play a role. The Regression of Offspring on Mid-Parent (ROMP) method [Pugh et al. 2001; Roy-Gagnon 2004] is a test of association between a quantitative trait and a candidate locus. ROMP also estimates the trait heritability and the heritability attributable to a locus and requires genotyping offspring only. The revised version of the ROMP method (ROMPrev) [Roy-Gagnon et al. 2008] is implemented in this R suite of functions.