The imprinted gene and parent-of-origin effect database now includes parental origin of de novo mutations

Abstract

The imprinted gene and parent-of-origin effect database () consists of two sections. One section catalogues the current literature on imprinted genes in humans and animals. The second, and new, section catalogues current reports of parental origin of de novo mutations in humans alone. The addition of a catalogue of de novo mutations that show a parent-of-origin effect expands the scope of the database and provides a useful tool for examining parental origin trends for different types of spontaneous mutations. This new section includes >1700 mutations, found in 59 different disorders. The 85 imprinted genes are described in 152 entries from several mammalian species. In addition, >300 other entries describe a range of reported parent-of-origin effects in animals.

De novo SCN1A mutations in Dravet syndrome and related epileptic encephalopathies are largely of paternal origin

“…A bias towards paternal origin of de novo mutations is often, but not always, observed in the genetic disorders for which parent-of-origin has been studied 20. The proportion ranges from exclusively paternal to an approximately equal frequency of paternal and maternal origin.…”

“…Data from many of these studies has been collated in the imprinted gene and parent-of-origin effect database (http://www.otago.ac.nz/IGC) 20. In almost all of the diseases studied, there is a bias towards paternal origin of the de novo mutations, with between 65–100% of mutations arising on the paternal chromosome.…”

Review and Evaluation of Methods Correcting for Population Stratification with a Focus on Underlying Statistical Principles

“…A natural way to identify parent-of-origin effects is to stratify transmission/nontransmission allele counts of parental origin and test for their symmetry. To date, there are more than 1700 mutations with parent-of-origin effects catalogued in the University of Otago database [114] (http://igc.otago.ac.nz/ home.html). Wilcox et al [115] proposed a simple method to analyze case-parent trios in effort to detect maternal genetic risk and estimate relative risks associated with both the mother's and the offspring's genotype.…”

Lack of genomic imprinting of DNA primase, polypeptide 2 (PRIM2) in human term placenta and white blood cells

“…[1][2][3] Over 100 genes have been conclusively demonstrated to be imprinted in mammals; [4][5][6][7] however, both in silico prediction studies and massive parallel sequencing suggest that there may be as many as 1,000 imprinted genes. [8][9][10] PRIM2, encoding a subunit of primase, is involved in purine and pyrimidine metabolism, and processes such as DNA replication and transcription, crucial for normal growth and development.…”