Partitioning Phenotypic Variance Due to Parent-of-Origin Effects Using Genomic Relatedness Matrices.

Behavior Genetics
Charles LaurinDavid M Evans

Abstract

We propose a new method, G-REMLadp, to estimate the phenotypic variance explained by parent-of-origin effects (POEs) across the genome. Our method uses restricted maximum likelihood analysis of genome-wide genetic relatedness matrices based on individuals' phased genotypes. Genome-wide SNP data from parent child duos or trios is required to obtain relatedness matrices indexing the parental origin of offspring alleles, as well as offspring phenotype data to partition the trait variation into variance components. To calibrate the power of G-REMLadp to detect non-null POEs when they are present, we provide an analytic approximation derived from Haseman-Elston regression. We also used simulated data to quantify the power and Type I Error rates of G-REMLadp, as well as the sensitivity of its variance component estimates to violations of underlying assumptions. We subsequently applied G-REMLadp to 36 phenotypes in a sample of individuals from the Avon Longitudinal Study of Parents and Children (ALSPAC). We found that the method does not seem to be inherently biased in estimating variance due to POEs, and that substantial correlation between parental genotypes is necessary to generate biased estimates. Our empirical results, power cal...Continue Reading

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Citations

Oct 21, 2020·Plant Cell Reports·Magalí Diana GimenezGustavo Rubén Rodríguez
Jan 3, 2021·Behavior Genetics·Espen Moen EilertsenEivind Ystrom

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Methods Mentioned

BETA
chips

Software Mentioned

REML
REMLadp
OpenMx
MACH
GCTA
GREML
LDAK
Perl script
mathop

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