Figure 1.

Examples of allelic expression patters. In panels A and B, each dot represents RNA-seq haplotype counts of an individual, summed up over phased heterozygous sites across the gene, and in C–E, each dot is a SNP in an individual. (A) The strong monoallelic expression of DLK1 supports its previously known status as an imprinted gene. (B) MEST is almost fully imprinted in lung but biallelic in testis. (C) In PAX8, some individuals show (nearly) monoallelic expression, while others are biallelic. It is an example of a gene that has been excluded from our list of imprinted genes due to the high heterogeneity of allelic expression, which could be due to variable imprinting, cis-regulatory variants, or other effects. (D) MAP2K3 in Geuvadis LCLs has substantial monoallelic expression without additional genotype quality filters on 1000 Genomes data. In fact, many of the SNPs are likely to be truly homozygous, since they fail the HWE test, and are removed from the final analysis. (E) UQCRFS1 in Geuvadis LCLs shows a pattern where all monoallelic sites have only the alternative allele present. This pattern is not consistent with imprinting, and the gene will be filtered out by the “flip test” requiring observation of monoallelic expression of both alleles.