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

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 TsuchidaKazuhiro 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

Research output: Contribution to journalArticle

1 Citation (Scopus)

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.

Original languageEnglish
Article number2506
JournalNature communications
Volume10
Issue number1
DOIs
Publication statusPublished - Dec 1 2019

Fingerprint

Brain Diseases
genes
coding
Genes
Exome
spasms
disorders
mutations
Infantile Spasms
Neurofibromatoses
set theory
Mutation

All Science Journal Classification (ASJC) codes

  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Physics and Astronomy(all)

Cite this

Takata, A., Nakashima, M., Saitsu, H., Mizuguchi, T., Mitsuhashi, S., Takahashi, Y., ... Matsumoto, N. (2019). Comprehensive analysis of coding variants highlights genetic complexity in developmental and epileptic encephalopathy. Nature communications, 10(1), [2506]. https://doi.org/10.1038/s41467-019-10482-9

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

In: Nature communications, Vol. 10, No. 1, 2506, 01.12.2019.

Research output: Contribution to journalArticle

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 2019, 'Comprehensive analysis of coding variants highlights genetic complexity in developmental and epileptic encephalopathy', Nature communications, vol. 10, no. 1, 2506. https://doi.org/10.1038/s41467-019-10482-9
Takata, Atsushi ; Nakashima, Mitsuko ; Saitsu, Hirotomo ; Mizuguchi, Takeshi ; Mitsuhashi, Satomi ; Takahashi, Yukitoshi ; Okamoto, Nobuhiko ; Osaka, Hitoshi ; Nakamura, Kazuyuki ; Tohyama, Jun ; Haginoya, Kazuhiro ; Takeshita, Saoko ; Kuki, Ichiro ; Okanishi, Tohru ; Goto, Tomohide ; Sasaki, Masayuki ; Sakai, Yasunari ; Miyake, Noriko ; Miyatake, Satoko ; Tsuchida, Naomi ; Iwama, Kazuhiro ; Minase, Gaku ; Sekiguchi, Futoshi ; Fujita, Atsushi ; Imagawa, Eri ; Koshimizu, Eriko ; Uchiyama, Yuri ; Hamanaka, Kohei ; Ohba, Chihiro ; Itai, Toshiyuki ; Aoi, Hiromi ; Saida, Ken ; Sakaguchi, Tomohiro ; Den, Kouhei ; Takahashi, Rina ; Ikeda, Hiroko ; Yamaguchi, Tokito ; Tsukamoto, Kazuki ; Yoshitomi, Shinsaku ; Oboshi, Taikan ; Imai, Katsumi ; Kimizu, Tomokazu ; Kobayashi, Yu ; Kubota, Masaya ; Kashii, Hirofumi ; Baba, Shimpei ; Iai, Mizue ; Kira, Ryutaro ; Hara, Munetsugu ; Ohta, Masayasu ; Miyata, Yohane ; Miyata, Rie ; Takanashi, Jun ichi ; Matsui, Jun ; Yokochi, Kenji ; Shimono, Masayuki ; Amamoto, Masano ; Takayama, Rumiko ; Hirabayashi, Shinichi ; Aiba, Kaori ; Matsumoto, Hiroshi ; Nabatame, Shin ; Shiihara, Takashi ; Kato, Mitsuhiro ; Matsumoto, Naomichi. / Comprehensive analysis of coding variants highlights genetic complexity in developmental and epileptic encephalopathy. In: Nature communications. 2019 ; Vol. 10, No. 1.
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