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3. De Novo Insertions and Deletions of Predominantly Paternal Origin Are Associated with Autism Spectrum Disorder

Author

Dong, Shan, Walker, Michael F., Carriero, Nicholas J., DiCola, Michael, Willsey, A. Jeremy, Ye, Adam Y., Waqar, Zainulabedin, Gonzalez, Luis E., Overton, John D., Frahm, Stephanie, Keaney, John F., Teran, Nicole A., Dea, Jeanselle, Mandell, Jeffrey D., Hus Bal, Vanessa, Sullivan, Catherine A., DiLullo, Nicholas M., Khalil, Rehab O., Gockley, Jake, Yuksel, Zafer, Sertel, Sinem M., Ercan-Sencicek, A. Gulhan, Gupta, Abha R., Mane, Shrikant M., Sheldon, Michael, Brooks, Andrew I., Roeder, Kathryn, Devlin, Bernie, State, Matthew W., Wei, Liping, and Sanders, Stephan J.

Abstract

Whole-exome sequencing (WES) studies have demonstrated the contribution of de novo loss-of-function single-nucleotide variants (SNVs) to autism spectrum disorder (ASD). However, challenges in the reliable detection of de novo insertions and deletions (indels) have limited inclusion of these variants in prior analyses. By applying a robust indel detection method to WES data from 787 ASD families (2,963 individuals), we demonstrate that de novo frameshift indels contribute to ASD risk (OR = 1.6; 95% CI = 1.0–2.7; p = 0.03), are more common in female probands (p = 0.02), are enriched among genes encoding FMRP targets (p = 6 × 10−9), and arise predominantly on the paternal chromosome (p < 0.001). On the basis of mutation rates in probands versus unaffected siblings, we conclude that de novo frameshift indels contribute to risk in approximately 3% of individuals with ASD. Finally, by observing clustering of mutations in unrelated probands, we uncover two ASD-associated genes: KMT2E(MLL5), a chromatin regulator, and RIMS1, a regulator of synaptic vesicle release.

Published
2014
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4. De NovoSequence and Copy Number Variants Are Strongly Associated with Tourette Disorder and Implicate Cell Polarity in Pathogenesis

Author

Wang, Sheng, Mandell, Jeffrey D., Kumar, Yogesh, Sun, Nawei, Morris, Montana T., Arbelaez, Juan, Nasello, Cara, Dong, Shan, Duhn, Clif, Zhao, Xin, Yang, Zhiyu, Padmanabhuni, Shanmukha S., Yu, Dongmei, King, Robert A., Dietrich, Andrea, Khalifa, Najah, Dahl, Niklas, Huang, Alden Y., Neale, Benjamin M., Coppola, Giovanni, Mathews, Carol A., Scharf, Jeremiah M., Abdulkadir, Mohamed, Arbelaez, Juan, Bodmer, Benjamin, Bromberg, Yana, Brown, Lawrence W., Cheon, Keun-Ah, Coffey, Barbara J., Deng, Li, Dietrich, Andrea, Dong, Shan, Duhn, Clif, Elzerman, Lonneke, Fernandez, Thomas V., Fremer, Carolin, Garcia-Delgar, Blanca, Gilbert, Donald L., Grice, Dorothy E., Hagstrøm, Julie, Hedderly, Tammy, Heiman, Gary A., Heyman, Isobel, Hoekstra, Pieter J., Hong, Hyun Ju, Huyser, Chaim, Kim, Eun-Joo, Kim, Young Key, Kim, Young-Shin, King, Robert A., Koh, Yun-Joo, Kook, Sodahm, Kuperman, Samuel, Leventhal, Bennett L, Ludolph, Andrea G., Madruga-Garrido, Marcos, Mandell, Jeffrey D., Maras, Athanasios, Mir, Pablo, Morer, Astrid, Morris, Montana T, Müller-Vahl, Kirsten, Münchau, Alexander, Murphy, Tara L., Nasello, Cara, Plessen, Kerstin J., Poisner, Hannah, Roessner, Veit, Sanders, Stephan J., Shin, Eun-Young, Song, Dong-Ho, Song, Jungeun, State, Matthew W., Sun, Nawei, Thackray, Joshua K., Tischfield, Jay A., Tübing, Jennifer, Visscher, Frank, Wanderer, Sina, Wang, Sheng, Willsey, A Jeremy, Woods, Martin, Xing, Jinchuan, Zhang, Yeting, Zhao, Xin, Zinner, Samuel H., Androutsos, Christos, Barta, Csaba, Farkas, Luca, Fichna, Jakub, Georgitsi, Marianthi, Janik, Piotr, Karagiannidis, Iordanis, Koumoula, Anastasia, Nagy, Peter, Paschou, Peristera, Puchala, Joanna, Rizzo, Renata, Szejko, Natalia, Szymanska, Urszula, Tarnok, Zsanett, Tsironi, Vaia, Wolanczyk, Tomasz, Zekanowski, Cezary, Barr, Cathy L., Batterson, James R., Berlin, Cheston, Bruun, Ruth D., Budman, Cathy L., Cath, Danielle C., Chouinard, Sylvain, Coppola, Giovanni, Cox, Nancy J., Darrow, Sabrina, Davis, Lea K., Dion, Yves, Freimer, Nelson B., Grados, Marco A., Hirschtritt, Matthew E., Huang, Alden Y., Illmann, Cornelia, King, Robert A., Kurlan, Roger, Leckman, James F., Lyon, Gholson J., Malaty, Irene A., Mathews, Carol A., MacMahon, William M., Neale, Benjamin M., Okun, Michael S., Osiecki, Lisa, Pauls, David L., Posthuma, Danielle, Ramensky, Vasily, Robertson, Mary M., Rouleau, Guy A., Sandor, Paul, Scharf, Jeremiah M., Singer, Harvey S., Smit, Jan, Sul, Jae-Hoon, Yu, Dongmei, Fernandez, Thomas V., Buxbaum, Joseph D., De Rubeis, Silvia, Grice, Dorothy E., Xing, Jinchuan, Heiman, Gary A., Tischfield, Jay A., Paschou, Peristera, Willsey, A. Jeremy, and State, Matthew W.

Abstract

We previously established the contribution of de novodamaging sequence variants to Tourette disorder (TD) through whole-exome sequencing of 511 trios. Here, we sequence an additional 291 TD trios and analyze the combined set of 802 trios. We observe an overrepresentation of de novodamaging variants in simplex, but not multiplex, families; we identify a high-confidence TD risk gene, CELSR3(cadherin EGF LAG seven-pass G-type receptor 3); we find that the genes mutated in TD patients are enriched for those related to cell polarity, suggesting a common pathway underlying pathobiology; and we confirm a statistically significant excess of de novocopy number variants in TD. Finally, we identify significant overlap of de novosequence variants between TD and obsessive-compulsive disorder and de novocopy number variants between TD and autism spectrum disorder, consistent with shared genetic risk.

Published
2018
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5. De NovoSequence and Copy Number Variants Are Strongly Associated with Tourette Disorder and Implicate Cell Polarity in Pathogenesis

Author

Wang, Sheng, Mandell, Jeffrey D., Kumar, Yogesh, Sun, Nawei, Morris, Montana T., Arbelaez, Juan, Nasello, Cara, Dong, Shan, Duhn, Clif, Zhao, Xin, Yang, Zhiyu, Padmanabhuni, Shanmukha S., Yu, Dongmei, King, Robert A., Dietrich, Andrea, Khalifa, Najah, Dahl, Niklas, Huang, Alden Y., Neale, Benjamin M., Coppola, Giovanni, Mathews, Carol A., Scharf, Jeremiah M., Fernandez, Thomas V., Buxbaum, Joseph D., De Rubeis, Silvia, Grice, Dorothy E., Xing, Jinchuan, Heiman, Gary A., Tischfield, Jay A., Paschou, Peristera, Willsey, A. Jeremy, and State, Matthew W.

Published
2018
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