Comprehensive analysis of coding variants highlights genetic complexity in developmental and epileptic encephalopathy View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2019-06-07

AUTHORS

Atsushi Takata, Mitsuko Nakashima, Hirotomo Saitsu, Takeshi Mizuguchi, Satomi Mitsuhashi, Yukitoshi Takahashi, Nobuhiko Okamoto, Hitoshi Osaka, Kazuyuki Nakamura, Jun Tohyama, Kazuhiro Haginoya, Saoko Takeshita, Ichiro Kuki, Tohru Okanishi, Tomohide Goto, Masayuki Sasaki, Yasunari Sakai, Noriko Miyake, Satoko Miyatake, Naomi Tsuchida, Kazuhiro Iwama, Gaku Minase, Futoshi Sekiguchi, Atsushi Fujita, Eri Imagawa, Eriko Koshimizu, Yuri Uchiyama, Kohei Hamanaka, Chihiro Ohba, Toshiyuki Itai, Hiromi Aoi, Ken Saida, Tomohiro Sakaguchi, Kouhei Den, Rina Takahashi, Hiroko Ikeda, Tokito Yamaguchi, Kazuki Tsukamoto, Shinsaku Yoshitomi, Taikan Oboshi, Katsumi Imai, Tomokazu Kimizu, Yu Kobayashi, Masaya Kubota, Hirofumi Kashii, Shimpei Baba, Mizue Iai, Ryutaro Kira, Munetsugu Hara, Masayasu Ohta, Yohane Miyata, Rie Miyata, Jun-ichi Takanashi, Jun Matsui, Kenji Yokochi, Masayuki Shimono, Masano Amamoto, Rumiko Takayama, Shinichi Hirabayashi, Kaori Aiba, Hiroshi Matsumoto, Shin Nabatame, Takashi Shiihara, Mitsuhiro Kato, Naomichi Matsumoto

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. More... »

PAGES

2506

References to SciGraph publications

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  • Journal

    TITLE

    Nature Communications

    ISSUE

    1

    VOLUME

    10

    Author Affiliations

  • Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, 236-0004, Yokohama, Japan
  • Department of Biochemistry, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, 431-3192, Hamamatsu, Japan
  • National Epilepsy Center, NHO Shizuoka Institute of Epilepsy and Neurological Disorders, 886 Urushiyama, Aoi-ku, 420-8688, Shizuoka, Japan
  • Department of Medical Genetics, Osaka Women’s and Children’s Hospital, 840 Murodo-cho, Izumi, 594-1101, Osaka, Japan
  • Department of Pediatrics, Jichi Medical University, 3311-1 Yakushiji, 329-0498, Shimotsuke, Japan
  • Department of Pediatrics, Yamagata University Faculty of Medicine, 2-2-2 Iida-nishi, 990-9585, Yamagata, Japan
  • Department of Child Neurology, NHO Nishiniigata Chuo Hospital, 1-14-1 Masago, Nishi-ku, 950-2085, Niigata, Japan
  • Department of Pediatric Neurology, Miyagi Children’s Hospital, 4-3-17 Ochiai, Aoba-ku, 989-3126, Sendai, Japan
  • Department of Pediatrics, Yokohama City University Medical Center, 4-57 Urafunecho, Minami-ku, 232-0024, Yokohama, Japan
  • Department of Pediatric Neurology, Osaka City General Hospital, 2-13-22 Miyakojimahondori, Miyakojima-ku, 534-0021, Osaka, Japan
  • Department of Child Neurology, Comprehensive Epilepsy Center, Seirei Hamamatsu General Hospital, 2-12-12 Sumiyoshi, Naka-ku, 430-8558, Hamamatsu, Japan
  • Division of Neurology, Kanagawa Children’s Medical Center, 2-138-4 Mutsukawa, Minami-ku, 232-8555, Yokohama, Japan
  • Department of Child Neurology, National Center of Neurology and Psychiatry, 4-1-1 Ogawahigashi, 187-8551, Kodaira, Japan
  • Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, 812-8582, Fukuoka, Japan
  • Department of Pediatric Neurology, Osaka Women’s and Children’s Hospital, 840 Murodo-cho, Izumi, 594-1101, Osaka, Japan
  • Division of Neurology, National Center for Child Health and Development, 2-10-1 Okura, Setagaya-ku, 157-8535, Tokyo, Japan
  • Department of Pediatric Neurology, Fukuoka Children’s Hospital, 5-1-1 Kashiiteriha, Higashi-ku, 813-0017, Fukuoka, Japan
  • Department of Pediatrics and Child Health, Kurume University School of Medicine, 67 Asahi-machi, Kurume, 830-0011, Fukuoka, Japan
  • Department of Neuropediatrics, Aiseikai Memorial Ibaraki Welfare Medical Center, 1872-1 Motoyoshida-cho, 310-0836, Mito, Japan
  • Department of Neuropediatrics, Tokyo Metropolitan Neurological Hospital, 2-6-1 Musashidai, 183-0042, Fuchu, Japan
  • Department of Pediatrics, Tokyo-kita Medical Center, 4-17-56 Akabanedai, Kita-ku, 115-0053, Tokyo, Japan
  • Department of Pediatrics, Tokyo Women’s Medical University Yachiyo Medical Center, 477-96 Owadashinden, 276-8524, Yachiyo, Japan
  • Department of Pediatrics, Shiga University of Medical Science, Setatsukinowacho, 520-2192, Otsu, Japan
  • Department of Pediatric Neurology, Seirei-Mikatahara General Hospital, 3453 Mikatahara-cho, Kita-ku, 431-1304, Hamamatsu, Japan
  • Department of Pediatrics, School of Medicine, University of Occupational and Environmental Health, 1-1 Iseigaoka, Yahatanishi-ku, 807-8555, Kitakyushu, Japan
  • Kutakyushu Municipal Yahata Hospital Pediatric Emergency Center, 4-18-1 Nishihonmachi, Yahatahigashi-ku, 805-8534, Kutakyushu, Japan
  • Hokkaido Medical Center for Child Health and Rehabilitation, 1-240-6 Kanayama 1-jo, Teine-ku, 006-0041, Sapporo, Japan
  • Division of Neurology, Nagano Children’s Hospital, 3100 Toyoshina, 399-8288, Azumino, Japan
  • Department of Pediatrics, Toyohashi Municipal Hospital, 50 Aza Hachiken Nishi, Aotake-Cho, 441-8570, Toyohashi, Japan
  • Department of Pediatrics, National Defense Medical College, 3-2 Namiki, 359-8513, Tokorozawa, Japan
  • Department of Pediatrics, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, 565-0871, Suita, Japan
  • Department of Neurology, Gunma Children’s Medical Center, 779 Shimohakoda, Hokkitsu-machi, 377-8577, Shibukawa, Japan
  • Department of Pediatrics, Showa University School of Medicine, 1-5-8 Hatanodai, Shinagawa-ku, 142-8666, Tokyo, Japan
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/s41467-019-10482-9

    DOI

    http://dx.doi.org/10.1038/s41467-019-10482-9

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1116881156

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/31175295


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