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RNA sequencing allows one to study allelic imbalance of gene expression,which may be due to genetic factors or genomic imprinting. It is desirable tomodel both genetic and parent-of-origin effects simultaneously to avoidconfounding and to improve the power to detect either effect. In a study ofexperimental cross, separation of genetic and parent-of-origin effects can beachieved by studying reciprocal cross of two inbred strains. In contrast, thistask is much more challenging for an outbred population such as humanpopulation. To address this challenge, we propose a new framework to combineexperimental strategies and novel statistical methods. Specifically, we proposeto collect genotype data from family trios as well as RNA-seq data from thechildren of family trios. We have developed a new statistical method toestimate both genetic and parent-of-origin effects from such data sets. Wedemonstrated this approach by studying 30 trios of HapMap samples. Our resultssupport some of previous finding of imprinted genes and also recover newcandidate imprinted genes.

Joint estimation of genetic and parent-of-origin effects using RNA-seq data from human