The 64th Annual Meeting of the American Society of Human Genetics
San Diego Convention Center, San Diego, U. S.
October 20, 2014
Poster presentation

Copy number variants identified in Japanese women
Ohsuke Migita1,2, Kayoko Maehara2, Kazuhiko Nakabayashi2, Kohji Okamura3, and Kenichiro Hata2
1Department of Pediatrics, St. Marianna University School of Medicine, Kanagawa, Japan, 2Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan, 3Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo, Japan
Using a high-resolution SNP array, we examined copy number variations (CNVs) found within 411 healthy Japanese women. With increasing public concern about infertility and the frequent involvement of chromosomal anomalies in miscarriage, analyses of CNVs have been used to identify the genomic regions responsible for each process of childbearing. Although associations between CNVs and phenotype have been reported, previous studies accumulated unsusceptible CNVs with insufficient phenotypic information on pregnancies. It will be necessary to collect large number of control data that focused on normal parity. We collected samples from Japanese women who have experienced normal delivery without significant complications and have compiled 1043 copy number variable regions. The copy number differences in these regions may be irrelevant not only to infertility but also to a wide range of diseases. The utility of this resource are assumed to be useful for reducing the number of candidate pathogenetic variants, especially in Japanese subjects. Because our identification strategy was based on a microarray technique, it is inevitable that cross-hybridization would have occurred. We carefully curated output data for each CNVR and validated 9 regions out of 12 homozygous deleted regions by conventional PCRs and 10 copy variable regions by the NanoString analysis system. We found that many implausible calls were situated in regions with high GC contents; for example, in subtelomeric regions. Those were mostly gain-type CNVs rather than loss-type CNVs. Development of more sophisticated methods and algorithm to determine CNV regions are awaited.