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Takata A, Nakashima M, Saitsu H, Mizuguchi T, Mitsuhashi S, Takahashi Y, Okamoto N, Osaka H, Nakamura K, Tohyama J, Haginoya K, Takeshita S, Kuki I, Okanishi T, Goto T, Sasaki M, Sakai Y, Miyake N, Miyatake S, Tsuchida N, Iwama K, Minase G, Sekiguchi F, Fujita A, Imagawa E, Koshimizu E, Uchiyama Y, Hamanaka K, Ohba C, Itai T, Aoi H, Saida K, Sakaguchi T, Den K, Takahashi R, Ikeda H, Yamaguchi T, Tsukamoto K, Yoshitomi S, Oboshi T, Imai K, Kimizu T, Kobayashi Y, Kubota M, Kashii H, Baba S, Iai M, Kira R, Hara M, Ohta M, Miyata Y, Miyata R, Takanashi JI, Matsui J, Yokochi K, Shimono M, Amamoto M, Takayama R, Hirabayashi S, Aiba K, Matsumoto H, Nabatame S, Shiihara T, Kato M, Matsumoto N. Comprehensive analysis of coding variants highlights genetic complexity in developmental and epileptic encephalopathy. Nat Commun 2019; 10:2506. [PMID: 31175295 PMCID: PMC6555845 DOI: 10.1038/s41467-019-10482-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 05/13/2019] [Indexed: 12/30/2022] Open
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.
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Affiliation(s)
- Atsushi Takata
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan.
| | - Mitsuko Nakashima
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan.,Department of Biochemistry, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan
| | - Hirotomo Saitsu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan.,Department of Biochemistry, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Satomi Mitsuhashi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Yukitoshi Takahashi
- National Epilepsy Center, NHO Shizuoka Institute of Epilepsy and Neurological Disorders, 886 Urushiyama, Aoi-ku, Shizuoka, 420-8688, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, 840 Murodo-cho, Izumi, Osaka, 594-1101, Japan
| | - Hitoshi Osaka
- Department of Pediatrics, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, 329-0498, Japan
| | - Kazuyuki Nakamura
- Department of Pediatrics, Yamagata University Faculty of Medicine, 2-2-2 Iida-nishi, Yamagata, 990-9585, Japan
| | - Jun Tohyama
- Department of Child Neurology, NHO Nishiniigata Chuo Hospital, 1-14-1 Masago, Nishi-ku, Niigata, 950-2085, Japan
| | - Kazuhiro Haginoya
- Department of Pediatric Neurology, Miyagi Children's Hospital, 4-3-17 Ochiai, Aoba-ku, Sendai, 989-3126, Japan
| | - Saoko Takeshita
- Department of Pediatrics, Yokohama City University Medical Center, 4-57 Urafunecho, Minami-ku, Yokohama, 232-0024, Japan
| | - Ichiro Kuki
- Department of Pediatric Neurology, Osaka City General Hospital, 2-13-22 Miyakojimahondori, Miyakojima-ku, Osaka, 534-0021, Japan
| | - Tohru Okanishi
- Department of Child Neurology, Comprehensive Epilepsy Center, Seirei Hamamatsu General Hospital, 2-12-12 Sumiyoshi, Naka-ku, Hamamatsu, 430-8558, Japan
| | - Tomohide Goto
- Division of Neurology, Kanagawa Children's Medical Center, 2-138-4 Mutsukawa, Minami-ku, Yokohama, 232-8555, Japan
| | - Masayuki Sasaki
- Department of Child Neurology, National Center of Neurology and Psychiatry, 4-1-1 Ogawahigashi, Kodaira, 187-8551, Japan
| | - Yasunari Sakai
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Kazuhiro Iwama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Gaku Minase
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Futoshi Sekiguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Eri Imagawa
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Kohei Hamanaka
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Chihiro Ohba
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Toshiyuki Itai
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Hiromi Aoi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Ken Saida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Tomohiro Sakaguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Kouhei Den
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Rina Takahashi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Hiroko Ikeda
- National Epilepsy Center, NHO Shizuoka Institute of Epilepsy and Neurological Disorders, 886 Urushiyama, Aoi-ku, Shizuoka, 420-8688, Japan
| | - Tokito Yamaguchi
- National Epilepsy Center, NHO Shizuoka Institute of Epilepsy and Neurological Disorders, 886 Urushiyama, Aoi-ku, Shizuoka, 420-8688, Japan
| | - Kazuki Tsukamoto
- National Epilepsy Center, NHO Shizuoka Institute of Epilepsy and Neurological Disorders, 886 Urushiyama, Aoi-ku, Shizuoka, 420-8688, Japan
| | - Shinsaku Yoshitomi
- National Epilepsy Center, NHO Shizuoka Institute of Epilepsy and Neurological Disorders, 886 Urushiyama, Aoi-ku, Shizuoka, 420-8688, Japan
| | - Taikan Oboshi
- National Epilepsy Center, NHO Shizuoka Institute of Epilepsy and Neurological Disorders, 886 Urushiyama, Aoi-ku, Shizuoka, 420-8688, Japan
| | - Katsumi Imai
- National Epilepsy Center, NHO Shizuoka Institute of Epilepsy and Neurological Disorders, 886 Urushiyama, Aoi-ku, Shizuoka, 420-8688, Japan
| | - Tomokazu Kimizu
- Department of Pediatric Neurology, Osaka Women's and Children's Hospital, 840 Murodo-cho, Izumi, Osaka, 594-1101, Japan
| | - Yu Kobayashi
- Department of Child Neurology, NHO Nishiniigata Chuo Hospital, 1-14-1 Masago, Nishi-ku, Niigata, 950-2085, Japan
| | - Masaya Kubota
- Division of Neurology, National Center for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Hirofumi Kashii
- Division of Neurology, National Center for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Shimpei Baba
- Department of Child Neurology, Comprehensive Epilepsy Center, Seirei Hamamatsu General Hospital, 2-12-12 Sumiyoshi, Naka-ku, Hamamatsu, 430-8558, Japan
| | - Mizue Iai
- Division of Neurology, Kanagawa Children's Medical Center, 2-138-4 Mutsukawa, Minami-ku, Yokohama, 232-8555, Japan
| | - Ryutaro Kira
- Department of Pediatric Neurology, Fukuoka Children's Hospital, 5-1-1 Kashiiteriha, Higashi-ku, Fukuoka, 813-0017, Japan
| | - Munetsugu Hara
- Department of Pediatrics and Child Health, Kurume University School of Medicine, 67 Asahi-machi, Kurume, Fukuoka, 830-0011, Japan
| | - Masayasu Ohta
- Department of Neuropediatrics, Aiseikai Memorial Ibaraki Welfare Medical Center, 1872-1 Motoyoshida-cho, Mito, 310-0836, Japan
| | - Yohane Miyata
- Department of Neuropediatrics, Tokyo Metropolitan Neurological Hospital, 2-6-1 Musashidai, Fuchu, 183-0042, Japan
| | - Rie Miyata
- Department of Pediatrics, Tokyo-kita Medical Center, 4-17-56 Akabanedai, Kita-ku, Tokyo, 115-0053, Japan
| | - Jun-Ichi Takanashi
- Department of Pediatrics, Tokyo Women's Medical University Yachiyo Medical Center, 477-96 Owadashinden, Yachiyo, 276-8524, Japan
| | - Jun Matsui
- Department of Pediatrics, Shiga University of Medical Science, Setatsukinowacho, Otsu, 520-2192, Japan
| | - Kenji Yokochi
- Department of Pediatric Neurology, Seirei-Mikatahara General Hospital, 3453 Mikatahara-cho, Kita-ku, Hamamatsu, 431-1304, Japan
| | - Masayuki Shimono
- Department of Pediatrics, School of Medicine, University of Occupational and Environmental Health, 1-1 Iseigaoka, Yahatanishi-ku, Kitakyushu, 807-8555, Japan
| | - Masano Amamoto
- Kutakyushu Municipal Yahata Hospital Pediatric Emergency Center, 4-18-1 Nishihonmachi, Yahatahigashi-ku, Kutakyushu, 805-8534, Japan
| | - Rumiko Takayama
- Hokkaido Medical Center for Child Health and Rehabilitation, 1-240-6 Kanayama 1-jo, Teine-ku, Sapporo, 006-0041, Japan
| | - Shinichi Hirabayashi
- Division of Neurology, Nagano Children's Hospital, 3100 Toyoshina, Azumino, 399-8288, Japan
| | - Kaori Aiba
- Department of Pediatrics, Toyohashi Municipal Hospital, 50 Aza Hachiken Nishi, Aotake-Cho, Toyohashi, 441-8570, Japan
| | - Hiroshi Matsumoto
- Department of Pediatrics, National Defense Medical College, 3-2 Namiki, Tokorozawa, 359-8513, Japan
| | - Shin Nabatame
- Department of Pediatrics, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, 565-0871, Japan
| | - Takashi Shiihara
- Department of Neurology, Gunma Children's Medical Center, 779 Shimohakoda, Hokkitsu-machi, Shibukawa, 377-8577, Japan
| | - Mitsuhiro Kato
- Department of Pediatrics, Yamagata University Faculty of Medicine, 2-2-2 Iida-nishi, Yamagata, 990-9585, Japan.,Department of Pediatrics, Showa University School of Medicine, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo, 142-8666, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan.
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