  RNA sequencing allows one to study allelic imbalance of gene expression,
which may be due to genetic factors or genomic imprinting. It is desirable to
model both genetic and parent-of-origin effects simultaneously to avoid
confounding and to improve the power to detect either effect. In a study of
experimental cross, separation of genetic and parent-of-origin effects can be
achieved by studying reciprocal cross of two inbred strains. In contrast, this
task is much more challenging for an outbred population such as human
population. To address this challenge, we propose a new framework to combine
experimental strategies and novel statistical methods. Specifically, we propose
to collect genotype data from family trios as well as RNA-seq data from the
children of family trios. We have developed a new statistical method to
estimate both genetic and parent-of-origin effects from such data sets. We
demonstrated this approach by studying 30 trios of HapMap samples. Our results
support some of previous finding of imprinted genes and also recover new
candidate imprinted genes.
