Abstract: Methods for identifying imprinted genes. In some embodiments, the methods comprise (a) providing a first data set comprising a plurality of nucleic acid sequences, wherein the nucleic acid sequences comprise genomic DNA sequences corresponding to a plurality of genes known to be imprinted in the subject; (b) providing a second data set comprising a plurality of nucleic acid sequences, wherein the nucleic acid sequences comprise genomic DNA sequences corresponding to a plurality of genes known not to be imprinted in the subject; (c) identifying one or more features that by themselves or in combination are differentially present or absent from the first data set as compared to the second data set; and (d) applying the one or more features to a test data set comprising a plurality of genomic DNA sequences which correspond to one or more genes for which the imprinting status is unknown to thereby identify an imprinted gene in a subject.