ROMPrev 0.2.1 beta

ROMPrev 0.2.1 beta estimates overall and locus-specific heritabilities and tests associations between quantitative traits and candidate genetic loci using the revised Regression of Offspring on Mid-Parent (ROMP(rev)) method.

Key Features:

• Revised ROMP(rev) methodology: Implements a refined version of the original ROMP approach to estimate heritability and test locus-specific effects.
• Offspring-only genotyping: Requires genotyping only the offspring while using parental information in the regression framework.
• Locus-specific heritability estimation: Provides estimates of locus-specific heritability that align closely with simulated values in controlled settings.
• Statistical validation and bootstrap recommendation: Uses computer simulations to assess type I error control and power, and recommends a bootstrap approach to address downward bias in standard errors for 95% confidence interval coverage.
• Application example: Detects locus–trait associations such as an association within the fibrinogen gene cluster with plasma fibrinogen levels (p < 0.005) accounting for a notable portion of heritability.

Scientific Applications:

• Locus-specific heritability analysis: Quantifies the contribution of individual genetic loci to variance in quantitative traits.
• Association testing for quantitative traits: Tests associations between candidate genetic loci and continuous phenotypes using offspring genotypes.
• Cardiovascular and multifactorial trait studies: Applied to complex traits such as plasma fibrinogen levels to identify locus-specific effects and estimate their heritable contributions.

Methodology:

Implements the ROMP(rev) method to estimate overall and locus-specific heritabilities; conducts association tests between quantitative traits and candidate loci using offspring genotypes; uses computer simulations to evaluate type I error and power; and applies a bootstrap approach to improve 95% confidence interval coverage when standard errors are biased downward.