1. Comprehensive analysis of coding variants highlights genetic complexity in developmental and epileptic encephalopathy
- Author
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Satomi Mitsuhashi, Kohei Hamanaka, Rie Miyata, Kazuki Tsukamoto, Tokito Yamaguchi, Satoko Miyatake, Taikan Oboshi, Toshiyuki Itai, Gaku Minase, Tomokazu Kimizu, Masayuki Shimono, Eriko Koshimizu, Takashi Shiihara, Kazuyuki Nakamura, Yasunari Sakai, Jun Tohyama, Masano Amamoto, Shinsaku Yoshitomi, Kazuhiro Iwama, Masayasu Ohta, Futoshi Sekiguchi, Rina Takahashi, Hirotomo Saitsu, Tohru Okanishi, Noriko Miyake, Shin Nabatame, Atsushi Takata, Masaya Kubota, Yohane Miyata, Rumiko Takayama, Naomi Tsuchida, Tomohiro Sakaguchi, Kouhei Den, Mizue Iai, Takeshi Mizuguchi, Tomohide Goto, Yukitoshi Takahashi, Shinichi Hirabayashi, Ken Saida, Yuri Uchiyama, Eri Imagawa, Hiroshi Matsumoto, Hirofumi Kashii, Katsumi Imai, Nobuhiko Okamoto, Kaori Aiba, Hitoshi Osaka, Mitsuhiro Kato, Hiromi Aoi, Saoko Takeshita, Yu Kobayashi, Ryutaro Kira, Naomichi Matsumoto, Ichiro Kuki, Mitsuko Nakashima, Munetsugu Hara, Kazuhiro Haginoya, Chihiro Ohba, Jun Matsui, Jun-ichi Takanashi, Atsushi Fujita, Kenji Yokochi, Masayuki Sasaki, Shimpei Baba, and Hiroko Ikeda
- Subjects
0301 basic medicine ,Genetics of the nervous system ,General Physics and Astronomy ,Epilepsies, Myoclonic ,02 engineering and technology ,medicine.disease_cause ,Japan ,Polymorphism (computer science) ,Guanine Nucleotide Exchange Factors ,DNA (Cytosine-5-)-Methyltransferases ,lcsh:Science ,Exome sequencing ,Genetics ,Principal Component Analysis ,Mutation ,Neurofibromin 1 ,Multidisciplinary ,Disease genetics ,021001 nanoscience & nanotechnology ,symbols ,0210 nano-technology ,Spasms, Infantile ,Science ,TRPM Cation Channels ,Biology ,Polymorphism, Single Nucleotide ,Article ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,symbols.namesake ,Asian People ,Exome Sequencing ,Genetic variation ,medicine ,Humans ,Gene ,Epilepsy ,Lennox Gastaut Syndrome ,Case-control study ,Genetic Variation ,Infant ,General Chemistry ,Genetic architecture ,Adaptor Proteins, Vesicular Transport ,Logistic Models ,030104 developmental biology ,Case-Control Studies ,Next-generation sequencing ,Mendelian inheritance ,lcsh:Q - Abstract
Although there are many known Mendelian genes linked to epileptic or developmental and epileptic encephalopathy (EE/DEE), its genetic architecture is not fully explained. Here, we address this incompleteness by analyzing exomes of 743 EE/DEE cases and 2366 controls. We observe that damaging ultra-rare variants (dURVs) unique to an individual are significantly overrepresented in EE/DEE, both in known EE/DEE genes and the other non-EE/DEE genes. Importantly, enrichment of dURVs in non-EE/DEE genes is significant, even in the subset of cases with diagnostic dURVs (P = 0.000215), suggesting oligogenic contribution of non-EE/DEE gene dURVs. Gene-based analysis identifies exome-wide significant (P = 2.04 × 10−6) enrichment of damaging de novo mutations in NF1, a gene primarily linked to neurofibromatosis, in infantile spasm. Together with accumulating evidence for roles of oligogenic or modifier variants in severe neurodevelopmental disorders, our results highlight genetic complexity in EE/DEE, and indicate that EE/DEE is not an aggregate of simple Mendelian disorders., Many causative genes are known for epileptic or developmental and epileptic encephalopathies (EE/DEE) yet a genetic diagnosis cannot be made for many patients. Here, the authors analyse whole exome sequencing data from a Japanese case−control cohort to identify common, rare and ultra-rare coding variants associated with EE/DEE.
- Published
- 2019