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2. Rare X-linked variants carry predominantly male risk in autism, Tourette syndrome, and ADHD.

Author

Drury, Vanessa, Drake, Sam, Sun, Nawei, Alkhairo, Hasan, Arbelaez, Juan, Duhn, Clif, Bal, Vanessa, Langley, Kate, Martin, Joanna, Hoekstra, Pieter, Dietrich, Andrea, Xing, Jinchuan, Heiman, Gary, Tischfield, Jay, Fernandez, Thomas, Owen, Michael, ODonovan, Michael, Thapar, Anita, State, Matthew, Wang, Sheng, Willsey, Arthur, and Wang, Belinda

Subjects
Humans, Male, Female, Attention Deficit Disorder with Hyperactivity, Tourette Syndrome, Autistic Disorder, Autism Spectrum Disorder, Neurodevelopmental Disorders
Abstract

Autism spectrum disorder (ASD), Tourette syndrome (TS), and attention-deficit/hyperactivity disorder (ADHD) display strong male sex bias, due to a combination of genetic and biological factors, as well as selective ascertainment. While the hemizygous nature of chromosome X (Chr X) in males has long been postulated as a key point of male vulnerability, rare genetic variation on this chromosome has not been systematically characterized in large-scale whole exome sequencing studies of idiopathic ASD, TS, and ADHD. Here, we take advantage of informative recombinations in simplex ASD families to pinpoint risk-enriched regions on Chr X, within which rare maternally-inherited damaging variants carry substantial risk in males with ASD. We then apply a modified transmission disequilibrium test to 13,052 ASD probands and identify a novel high confidence ASD risk gene at exome-wide significance (MAGEC3). Finally, we observe that rare damaging variants within these risk regions carry similar effect sizes in males with TS or ADHD, further clarifying genetic mechanisms underlying male vulnerability in multiple neurodevelopmental disorders that can be exploited for systematic gene discovery.

Published
2023

4. Whole-exome sequencing identifies genes associated with Tourette’s disorder in multiplex families

Author

Cao, Xiaolong, Zhang, Yeting, Abdulkadir, Mohamed, Deng, Li, Fernandez, Thomas V, Garcia-Delgar, Blanca, Hagstrøm, Julie, Hoekstra, Pieter J, King, Robert A, Koesterich, Justin, Kuperman, Samuel, Morer, Astrid, Nasello, Cara, Plessen, Kerstin J, Thackray, Joshua K, Zhou, Lisheng, Dietrich, Andrea, Tischfield, Jay A, Heiman, Gary A, and Xing, Jinchuan

Subjects
Human Genome, Brain Disorders, Genetics, Clinical Research, Biotechnology, Neurosciences, Genetic Testing, Aetiology, 2.1 Biological and endogenous factors, Cadherin Related Proteins, Family, Genetic Predisposition to Disease, Humans, Nerve Tissue Proteins, Pedigree, Serine Endopeptidases, Tourette Syndrome, Exome Sequencing, Tourette International Collaborative Genetics Study, Biological Sciences, Medical and Health Sciences, Psychology and Cognitive Sciences, Psychiatry
Abstract

Tourette's Disorder (TD) is a neurodevelopmental disorder (NDD) that affects about 0.7% of the population and is one of the most heritable NDDs. Nevertheless, because of its polygenic nature and genetic heterogeneity, the genetic etiology of TD is not well understood. In this study, we combined the segregation information in 13 TD multiplex families with high-throughput sequencing and genotyping to identify genes associated with TD. Using whole-exome sequencing and genotyping array data, we identified both small and large genetic variants within the individuals. We then combined multiple types of evidence to prioritize candidate genes for TD, including variant segregation pattern, variant function prediction, candidate gene expression, protein-protein interaction network, candidate genes from previous studies, etc. From the 13 families, 71 strong candidate genes were identified, including both known genes for NDDs and novel genes, such as HtrA Serine Peptidase 3 (HTRA3), Cadherin-Related Family Member 1 (CDHR1), and Zinc Finger DHHC-Type Palmitoyltransferase 17 (ZDHHC17). The candidate genes are enriched in several Gene Ontology categories, such as dynein complex and synaptic membrane. Candidate genes and pathways identified in this study provide biological insight into TD etiology and potential targets for future studies.

Published
2021

6. Rare X-linked variants carry predominantly male risk in autism, Tourette syndrome, and ADHD

Author

Wang, Sheng, Wang, Belinda, Drury, Vanessa, Drake, Sam, Sun, Nawei, Alkhairo, Hasan, Arbelaez, Juan, Duhn, Clif, Bal, Vanessa H., Langley, Kate, Martin, Joanna, Hoekstra, Pieter J., Dietrich, Andrea, Xing, Jinchuan, Heiman, Gary A., Tischfield, Jay A., Fernandez, Thomas V., Owen, Michael J., O’Donovan, Michael C., Thapar, Anita, State, Matthew W., and Willsey, A. Jeremy

Published
2023
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10. Centers for Mendelian Genomics: A decade of facilitating gene discovery

Author

Adams, Marcia, Aguet, François, Akay, Gulsen, Anderson, Peter, Antonescu, Corina, Arachchi, Harindra M., Atik, Mehmed M., Austin-Tse, Christina A., Babb, Larry, Bacus, Tamara J., Bahrambeigi, Vahid, Balasubramanian, Suganthi, Bayram, Yavuz, Beaudet, Arthur L., Beck, Christine R., Belmont, John W., Below, Jennifer E., Bilguvar, Kaya, Boehm, Corinne D., Boerwinkle, Eric, Boone, Philip M., Bowne, Sara J., Brand, Harrison, Buckingham, Kati J., Byrne, Alicia B., Calame, Daniel, Campbell, Ian M., Cao, Xiaolong, Carvalho, Claudia, Chander, Varuna, Chang, Jaime, Chao, Katherine R., Chinn, Ivan K., Clarke, Declan, Collins, Ryan L., Cummings, Beryl, Dardas, Zain, Dawood, Moez, Delano, Kayla, DiTroia, Stephanie P., Doddapaneni, Harshavardhan, Du, Haowei, Du, Renqian, Duan, Ruizhi, Eldomery, Mohammad, Eng, Christine M., England, Eleina, Evangelista, Emily, Everett, Selin, Fatih, Jawid, Felsenfeld, Adam, Francioli, Laurent C., Frazar, Christian D., Fu, Jack, Gamarra, Emmanuel, Gambin, Tomasz, Gan, Weiniu, Gandhi, Mira, Ganesh, Vijay S., Garimella, Kiran V., Gauthier, Laura D., Giroux, Danielle, Gonzaga-Jauregui, Claudia, Goodrich, Julia K., Gordon, William W., Griffith, Sean, Grochowski, Christopher M., Gu, Shen, Gudmundsson, Sanna, Hall, Stacey J., Hansen, Adam, Harel, Tamar, Harmanci, Arif O., Herman, Isabella, Hetrick, Kurt, Hijazi, Hadia, Horike-Pyne, Martha, Hsu, Elvin, Hu, Jianhong, Huang, Yongqing, Hurless, Jameson R., Jahl, Steve, Jarvik, Gail P., Jiang, Yunyun, Johanson, Eric, Jolly, Angad, Karaca, Ender, Khayat, Michael, Knight, James, Kolar, J. Thomas, Kumar, Sushant, Lalani, Seema, Laricchia, Kristen M., Larkin, Kathryn E., Leal, Suzanne M., Lemire, Gabrielle, Lewis, Richard A., Li, He, Ling, Hua, Lipson, Rachel B., Liu, Pengfei, Lovgren, Alysia Kern, López-Giráldez, Francesc, MacMillan, Melissa P., Mangilog, Brian E., Mano, Stacy, Marafi, Dana, Marosy, Beth, Marshall, Jamie L., Martin, Renan, Marvin, Colby T., Mawhinney, Michelle, McGee, Sean, McGoldrick, Daniel J., Mehaffey, Michelle, Mekonnen, Betselote, Meng, Xiaolu, Mitani, Tadahiro, Miyake, Christina Y., Mohr, David, Morris, Shaine, Mullen, Thomas E., Murdock, David R., Murugan, Mullai, Muzny, Donna M., Myers, Ben, Neira, Juanita, Nguyen, Kevin K., Nielsen, Patrick M., Nudelman, Natalie, O’Heir, Emily, O’Leary, Melanie C., Ongaco, Chrissie, Orange, Jordan, Osei-Owusu, Ikeoluwa A., Paine, Ingrid S., Pais, Lynn S., Paschall, Justin, Patterson, Karynne, Pehlivan, Davut, Pelle, Benjamin, Penney, Samantha, Perez de Acha Chavez, Jorge, Pierce-Hoffman, Emma, Poli, Cecilia M., Punetha, Jaya, Radhakrishnan, Aparna, Richardson, Matthew A., Rodrigues, Eliete, Roote, Gwendolin T., Rosenfeld, Jill A., Ryke, Erica L., Sabo, Aniko, Sanchez, Alice, Schrauwen, Isabelle, Scott, Daryl A., Sedlazeck, Fritz, Serrano, Jillian, Shaw, Chad A., Shelford, Tameka, Shively, Kathryn M., Singer-Berk, Moriel, Smith, Joshua D., Snow, Hana, Snyder, Grace, Solomonson, Matthew, Son, Rachel G., Song, Xiaofei, Stankiewicz, Pawel, Stephan, Taylorlyn, Sutton, V. Reid, Sveden, Abigail, Sánchez, Diana Cornejo, Tackett, Monica, Talkowski, Michael, Threlkeld, Machiko S., Tiao, Grace, Udler, Miriam S., Vail, Laura, Valivullah, Zaheer, Valkanas, Elise, VanNoy, Grace E., Wang, Qingbo S., Wang, Gao, Wang, Lu, Wangler, Michael F., Watts, Nicholas A., Weisburd, Ben, Weiss, Jeffrey M., Wheeler, Marsha M., White, Janson J., Williamson, Clara E., Wilson, Michael W., Wiszniewski, Wojciech, Withers, Marjorie A., Witmer, Dane, Witzgall, Lauren, Wohler, Elizabeth, Wojcik, Monica H., Wong, Isaac, Wood, Jordan C., Wu, Nan, Xing, Jinchuan, Yang, Yaping, Yi, Qian, Yuan, Bo, Zeiger, Jordan E., Zhang, Chaofan, Zhang, Peng, Zhang, Yan, Zhang, Xiaohong, Zhang, Yeting, Zhang, Shifa, Zoghbi, Huda, van den Veyver, Igna, Baxter, Samantha M., Posey, Jennifer E., Lake, Nicole J., Sobreira, Nara, Chong, Jessica X., Buyske, Steven, Blue, Elizabeth E., Chadwick, Lisa H., Coban-Akdemir, Zeynep H., Doheny, Kimberly F., Davis, Colleen P., Lek, Monkol, Wellington, Christopher, Jhangiani, Shalini N., Gerstein, Mark, Gibbs, Richard A., Lifton, Richard P., MacArthur, Daniel G., Matise, Tara C., Lupski, James R., Valle, David, Bamshad, Michael J., Hamosh, Ada, Mane, Shrikant, Nickerson, Deborah A., Rehm, Heidi L., and O’Donnell-Luria, Anne

Published
2022
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11. De Novo Sequence 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, Tourette International Collaborative Genetics Study (TIC Genetics), Tourette Syndrome Genetics Southern and Eastern Europe Initiative (TSGENESEE), Tourette Association of America International Consortium for Genetics (TAAICG), 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

Subjects
Tourette International Collaborative Genetics Study, Tourette Syndrome Genetics Southern and Eastern Europe Initiative, Tourette Association of America International Consortium for Genetics, Humans, Tourette Syndrome, Cadherins, Receptors, Cell Surface, Pedigree, Cell Polarity, Adult, Child, Female, Male, DNA Copy Number Variations, TIC Genetics, Tourette disorder, cell polarity, copy number variants, de novo variants, gene discovery, microarray genotyping, multiplex, simplex, whole exome sequencing, Clinical Research, Pediatric, Biotechnology, Genetics, Brain Disorders, Human Genome, Intellectual and Developmental Disabilities (IDD), Neurodegenerative, 2.1 Biological and endogenous factors, Aetiology, Biochemistry and Cell Biology, Medical Physiology
Abstract

We previously established the contribution of de novo damaging 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 novo damaging 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 novo copy number variants in TD. Finally, we identify significant overlap of de novo sequence variants between TD and obsessive-compulsive disorder and de novo copy number variants between TD and autism spectrum disorder, consistent with shared genetic risk.

Published
2018

15. De Novo Coding Variants Are Strongly Associated with Tourette Disorder.

Author

Willsey, A Jeremy, Fernandez, Thomas V, Yu, Dongmei, King, Robert A, Dietrich, Andrea, Xing, Jinchuan, Sanders, Stephan J, Mandell, Jeffrey D, Huang, Alden Y, Richer, Petra, Smith, Louw, Dong, Shan, Samocha, Kaitlin E, Tourette International Collaborative Genetics (TIC Genetics), Tourette Syndrome Association International Consortium for Genetics (TSAICG), Neale, Benjamin M, Coppola, Giovanni, Mathews, Carol A, Tischfield, Jay A, Scharf, Jeremiah M, State, Matthew W, and Heiman, Gary A

Subjects
Tourette International Collaborative Genetics, Tourette Syndrome Association International Consortium for Genetics, Humans, Tourette Syndrome, Genetic Predisposition to Disease, Intracellular Signaling Peptides and Proteins, Proteins, Cell Cycle Proteins, Fibronectins, Cadherins, Receptors, Cell Surface, Phosphoproteins, Odds Ratio, Cohort Studies, Sequence Analysis, DNA, Parents, Mutation, Adult, Child, Female, Male, Genetic Variation, TIC Genetics, TSAICG, Tourette disorder, Tourette syndrome, de novo variants, gene discovery, whole-exome sequencing, Biotechnology, Brain Disorders, Human Genome, Neurosciences, Clinical Research, Genetics, 2.1 Biological and endogenous factors, Aetiology, Psychology, Cognitive Sciences, Neurology & Neurosurgery
Abstract

Whole-exome sequencing (WES) and de novo variant detection have proven a powerful approach to gene discovery in complex neurodevelopmental disorders. We have completed WES of 325 Tourette disorder trios from the Tourette International Collaborative Genetics cohort and a replication sample of 186 trios from the Tourette Syndrome Association International Consortium on Genetics (511 total). We observe strong and consistent evidence for the contribution of de novo likely gene-disrupting (LGD) variants (rate ratio [RR] 2.32, p = 0.002). Additionally, de novo damaging variants (LGD and probably damaging missense) are overrepresented in probands (RR 1.37, p = 0.003). We identify four likely risk genes with multiple de novo damaging variants in unrelated probands: WWC1 (WW and C2 domain containing 1), CELSR3 (Cadherin EGF LAG seven-pass G-type receptor 3), NIPBL (Nipped-B-like), and FN1 (fibronectin 1). Overall, we estimate that de novo damaging variants in approximately 400 genes contribute risk in 12% of clinical cases. VIDEO ABSTRACT.

Published
2017

18. Author response: Dysregulation of mTOR signaling mediates common neurite and migration defects in both idiopathic and 16p11.2 deletion autism neural precursor cells

Author

Prem, Smrithi, primary, Dev, Bharati, additional, Peng, Cynthia, additional, Mehta, Monal, additional, Alibutud, Rohan, additional, Connacher, Robert J, additional, St Thomas, Madeline, additional, Zhou, Xiaofeng, additional, Matteson, Paul, additional, Xing, Jinchuan, additional, Millonig, James H, additional, and DiCicco-Bloom, Emanuel, additional

Published
2024
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20. Mutations in ASH1L confer susceptibility to Tourette syndrome

Author

Liu, Shiguo, Tian, Miaomiao, He, Fan, Li, Jiani, Xie, Hong, Liu, Wenmiao, Zhang, Yeting, Zhang, Ru, Yi, Mingji, Che, Fengyuan, Ma, Xu, Zheng, Yi, Deng, Hao, Wang, Guiju, Chen, Lang, Sun, Xue, Xu, Yinglei, Wang, Jingli, Zang, Yucui, Han, Mengmeng, Wang, Xiuhai, Guan, Hongzai, Ge, Yinlin, Wu, Chunmei, Wang, Haiyan, Liang, Hui, Li, Hui, Ran, Ni, Yang, Zhaochuan, Huang, Huanhuan, Wei, Yanzhao, Zheng, Xueping, Sun, Xiangrong, Feng, Xueying, Zheng, Lanlan, Zhu, Tao, Luo, Wenhan, Chen, Qinan, Yan, Yuze, Huang, Zuzhou, Jing, Zhongcui, Guo, Yixia, Zhang, Xuzhan, Schaaf, Christian P., Xing, Jinchuan, Wang, Chuanyue, Yu, Fuli, and Guan, Ji-Song

Published
2020
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22. A unified test of linkage analysis and rare-variant association for analysis of pedigree sequence data

Author

Hu, Hao, Roach, Jared C, Coon, Hilary, Guthery, Stephen L, Voelkerding, Karl V, Margraf, Rebecca L, Durtschi, Jacob D, Tavtigian, Sean V, Shankaracharya, Wu, Wilfred, Scheet, Paul, Wang, Shuoguo, Xing, Jinchuan, Glusman, Gustavo, Hubley, Robert, Li, Hong, Garg, Vidu, Moore, Barry, Hood, Leroy, Galas, David J, Srivastava, Deepak, Reese, Martin G, Jorde, Lynn B, Yandell, Mark, and Huff, Chad D

Subjects
Epidemiology, Biological Sciences, Health Sciences, Genetics, Generic health relevance, Base Sequence, Chromosome Mapping, DNA, DNA Mutational Analysis, Genetic Linkage, Genetic Markers, Genetic Variation, High-Throughput Nucleotide Sequencing, Molecular Sequence Data, Pedigree
Abstract

High-throughput sequencing of related individuals has become an important tool for studying human disease. However, owing to technical complexity and lack of available tools, most pedigree-based sequencing studies rely on an ad hoc combination of suboptimal analyses. Here we present pedigree-VAAST (pVAAST), a disease-gene identification tool designed for high-throughput sequence data in pedigrees. pVAAST uses a sequence-based model to perform variant and gene-based linkage analysis. Linkage information is then combined with functional prediction and rare variant case-control association information in a unified statistical framework. pVAAST outperformed linkage and rare-variant association tests in simulations and identified disease-causing genes from whole-genome sequence data in three human pedigrees with dominant, recessive and de novo inheritance patterns. The approach is robust to incomplete penetrance and locus heterogeneity and is applicable to a wide variety of genetic traits. pVAAST maintains high power across studies of monogenic, high-penetrance phenotypes in a single pedigree to highly polygenic, common phenotypes involving hundreds of pedigrees.

Published
2014

24. De Novo Sequence and Copy Number Variants Are Strongly Associated with Tourette Disorder and Implicate Cell Polarity in Pathogenesis

Author

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, 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, Kumar, Yogesh, Morris, Montana T., Yang, Zhiyu, Padmanabhuni, Shanmukha S., Khalifa, Najah, Dahl, Niklas, Buxbaum, Joseph D., De Rubeis, Silvia, and Willsey, A. Jeremy

Published
2018
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26. Structural Variations Contribute to the Genetic Etiology of Autism Spectrum Disorder and Language Impairments

Author

Alibutud, Rohan, primary, Hansali, Sammy, additional, Cao, Xiaolong, additional, Zhou, Anbo, additional, Mahaganapathy, Vaidhyanathan, additional, Azaro, Marco, additional, Gwin, Christine, additional, Wilson, Sherri, additional, Buyske, Steven, additional, Bartlett, Christopher W., additional, Flax, Judy F., additional, Brzustowicz, Linda M., additional, and Xing, Jinchuan, additional

Published
2023
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27. Alu Elements and Hominid Phylogenetics

Author

Salem, Abdel-Halim, Ray, David A., Xing, Jinchuan, Callinan, Pauline A., Myers, Jeremy S., Hedges, Dale J., Garber, Randall K., Witherspoon, David J., Jorde, Lynn B., and Batzer, Mark A.

Published
2003

29. De Novo Coding Variants Are Strongly Associated with Tourette Disorder

Author

Abdulkadir, Mohamed, Bohnenpoll, Julia, Bromberg, Yana, Brown, Lawrence W., Cheon, Keun-Ah, Coffey, Barbara J., Deng, Li, Dietrich, Andrea, Dong, Shan, Elzerman, Lonneke, Fernandez, Thomas V., Fründt, Odette, Garcia-Delgar, Blanca, Gedvilaite, Erika, Gilbert, Donald L., Grice, Dorothy E., Hagstrøm, Julie, Hedderly, Tammy, Heiman, Gary A., Heyman, Isobel, Hoekstra, Pieter J., Hong, Hyun Ju, Huyser, Chaim, Ibanez-Gomez, Laura, Kim, Young Key, Kim, Young-Shin, King, Robert A., Koh, Yun-Joo, Kook, Sodahm, Kuperman, Samuel, Lamerz, Andreas, Leventhal, Bennett, Ludolph, Andrea G., Lühr da Silva, Claudia, Madruga-Garrido, Marcos, Mandell, Jeffrey D., Maras, Athanasios, Mir, Pablo, Morer, Astrid, Münchau, Alexander, Murphy, Tara L., Nasello, Cara, Openneer, Thaïra J.C., Plessen, Kerstin J., Richer, Petra, Roessner, Veit, Sanders, Stephan, Shin, Eun-Young, Sival, Deborah A., Smith, Louw, Song, Dong-Ho, Song, Jungeun, State, Matthew W., Stolte, Anne Marie, Sun, Nawei, Tischfield, Jay A., Tübing, Jennifer, Visscher, Frank, Walker, Michael F., Wanderer, Sina, Wang, Shuoguo, Willsey, A. Jeremy, Woods, Martin, Xing, Jinchuan, Zhang, Yeting, Zhou, Anbo, Zinner, Samuel H., 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, Kurlan, Roger, Leckman, James F., Lyon, Gholson J., Malaty, Irene A., Mathews, Carol A., MaMahon, 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, Sanders, Stephan J., and Samocha, Kaitlin E.

Published
2017
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32. Whole Transcriptome and Functional Analyses Identify Novel Genes Involved in Meiosis and Fertility in Drosophila melanogaster

Author

Sun, Siqi, primary, Defosse, Tyler, additional, Boyd, Ayla, additional, Sop, Joel, additional, Verderose, Faith, additional, Surray, Diya, additional, Aziz, Mark, additional, Howland, Margaret, additional, Wu, Siwen, additional, Changela, Neha, additional, Jang, Janet, additional, Schindler, Karen, additional, Xing, Jinchuan, additional, and McKim, Kim, additional

Published
2023
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34. Spontaneous hyperactivity in Ash1l mutant mice, a new model for Tourette syndrome

Author

Liu, Shiguo, Tian, Miaomiao, He, Fan, Li, Jiani, Xie, Hong, Liu, Wenmiao, Zhang, Yeting, Zhang, Ru, Yi, Mingji, Che, Fengyuan, Ma, Xu, Zheng, Yi, Deng, Hao, Wang, Guiju, Chen, Lang, Sun, Xue, Xu, Yinglei, Wang, Jingli, Zang, Yucui, Han, Mengmeng, Wang, Xiuhai, Guan, Hongzai, Ge, Yinlin, Wu, Chunmei, Wang, Haiyan, Liang, Hui, Li, Hui, Ran, Ni, Yang, Zhaochuan, Huang, Huanhuan, Wei, Yanzhao, Zheng, Xueping, Sun, Xiangrong, Feng, Xueying, Zheng, Lanlan, Zhu, Tao, Luo, Wenhan, Chen, Qinan, Yan, Yuze, Huang, Zuzhou, Jing, Zhongcui, Guo, Yixia, Zhang, Xuzhan, Schaaf, Christian P., Xing, Jinchuan, Wang, Chuanyue, Yu, Fuli, and Guan, Ji-Song

Published
2020
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36. Rare X-linked variants carry predominantly male risk in autism, Tourette syndrome, and ADHD

Author

National Institute of Mental Health (US), Tourette Association of America, Human Genetics Institute of New Jersey, Tourette Syndrome Association of New Jersey, Wang, Sheng, Wang, Belinda, Drury, Vanessa, Drake, Sam, Sun, Nawei, Alkhairo, Hasan, Arbelaez, Juan, Duhn, Clif, Tourette International Collaborative Genetics (TIC Genetics), Madruga, Marcos, Mir, Pablo, Bal, Vanessa H., Langley, Kate, Martin, Joanna, Hoekstra, Pieter J., Dietrich, Andrea, Xing, Jinchuan, Heiman, Gary A., Tischfield, Jay A., Fernández, Thomas V., Owen, Michael J., O’Donovan, Michael C., Thapar, Anita, State, Matthew W., Willsey, A. Jeremy, National Institute of Mental Health (US), Tourette Association of America, Human Genetics Institute of New Jersey, Tourette Syndrome Association of New Jersey, Wang, Sheng, Wang, Belinda, Drury, Vanessa, Drake, Sam, Sun, Nawei, Alkhairo, Hasan, Arbelaez, Juan, Duhn, Clif, Tourette International Collaborative Genetics (TIC Genetics), Madruga, Marcos, Mir, Pablo, Bal, Vanessa H., Langley, Kate, Martin, Joanna, Hoekstra, Pieter J., Dietrich, Andrea, Xing, Jinchuan, Heiman, Gary A., Tischfield, Jay A., Fernández, Thomas V., Owen, Michael J., O’Donovan, Michael C., Thapar, Anita, State, Matthew W., and Willsey, A. Jeremy

Abstract

Autism spectrum disorder (ASD), Tourette syndrome (TS), and attention-deficit/hyperactivity disorder (ADHD) display strong male sex bias, due to a combination of genetic and biological factors, as well as selective ascertainment. While the hemizygous nature of chromosome X (Chr X) in males has long been postulated as a key point of “male vulnerability”, rare genetic variation on this chromosome has not been systematically characterized in large-scale whole exome sequencing studies of “idiopathic” ASD, TS, and ADHD. Here, we take advantage of informative recombinations in simplex ASD families to pinpoint risk-enriched regions on Chr X, within which rare maternally-inherited damaging variants carry substantial risk in males with ASD. We then apply a modified transmission disequilibrium test to 13,052 ASD probands and identify a novel high confidence ASD risk gene at exome-wide significance (MAGEC3). Finally, we observe that rare damaging variants within these risk regions carry similar effect sizes in males with TS or ADHD, further clarifying genetic mechanisms underlying male vulnerability in multiple neurodevelopmental disorders that can be exploited for systematic gene discovery.

Published
2023

37. Spplementary Table 1 from SMAD4 Suppresses WNT-Driven Dedifferentiation and Oncogenesis in the Differentiated Gut Epithelium

Author

Perekatt, Ansu O., primary, Shah, Pooja P., primary, Cheung, Shannon, primary, Jariwala, Nidhi, primary, Wu, Alex, primary, Gandhi, Vishal, primary, Kumar, Namit, primary, Feng, Qiang, primary, Patel, Neeket, primary, Chen, Lei, primary, Joshi, Shilpy, primary, Zhou, Anbo, primary, Taketo, M. Mark, primary, Xing, Jinchuan, primary, White, Eileen, primary, Gao, Nan, primary, Gatza, Michael L., primary, and Verzi, Michael P., primary

Published
2023
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38. Supplementary Table 3. from SMAD4 Suppresses WNT-Driven Dedifferentiation and Oncogenesis in the Differentiated Gut Epithelium

Author

Perekatt, Ansu O., primary, Shah, Pooja P., primary, Cheung, Shannon, primary, Jariwala, Nidhi, primary, Wu, Alex, primary, Gandhi, Vishal, primary, Kumar, Namit, primary, Feng, Qiang, primary, Patel, Neeket, primary, Chen, Lei, primary, Joshi, Shilpy, primary, Zhou, Anbo, primary, Taketo, M. Mark, primary, Xing, Jinchuan, primary, White, Eileen, primary, Gao, Nan, primary, Gatza, Michael L., primary, and Verzi, Michael P., primary

Published
2023
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39. Supplementary Table 4 from SMAD4 Suppresses WNT-Driven Dedifferentiation and Oncogenesis in the Differentiated Gut Epithelium

Author

Perekatt, Ansu O., primary, Shah, Pooja P., primary, Cheung, Shannon, primary, Jariwala, Nidhi, primary, Wu, Alex, primary, Gandhi, Vishal, primary, Kumar, Namit, primary, Feng, Qiang, primary, Patel, Neeket, primary, Chen, Lei, primary, Joshi, Shilpy, primary, Zhou, Anbo, primary, Taketo, M. Mark, primary, Xing, Jinchuan, primary, White, Eileen, primary, Gao, Nan, primary, Gatza, Michael L., primary, and Verzi, Michael P., primary

Published
2023
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40. Spplementary Table 2 from SMAD4 Suppresses WNT-Driven Dedifferentiation and Oncogenesis in the Differentiated Gut Epithelium

Author

Perekatt, Ansu O., primary, Shah, Pooja P., primary, Cheung, Shannon, primary, Jariwala, Nidhi, primary, Wu, Alex, primary, Gandhi, Vishal, primary, Kumar, Namit, primary, Feng, Qiang, primary, Patel, Neeket, primary, Chen, Lei, primary, Joshi, Shilpy, primary, Zhou, Anbo, primary, Taketo, M. Mark, primary, Xing, Jinchuan, primary, White, Eileen, primary, Gao, Nan, primary, Gatza, Michael L., primary, and Verzi, Michael P., primary

Published
2023
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41. Figure S5 from SMAD4 Suppresses WNT-Driven Dedifferentiation and Oncogenesis in the Differentiated Gut Epithelium

Author

Perekatt, Ansu O., primary, Shah, Pooja P., primary, Cheung, Shannon, primary, Jariwala, Nidhi, primary, Wu, Alex, primary, Gandhi, Vishal, primary, Kumar, Namit, primary, Feng, Qiang, primary, Patel, Neeket, primary, Chen, Lei, primary, Joshi, Shilpy, primary, Zhou, Anbo, primary, Taketo, M. Mark, primary, Xing, Jinchuan, primary, White, Eileen, primary, Gao, Nan, primary, Gatza, Michael L., primary, and Verzi, Michael P., primary

Published
2023
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42. Data from SMAD4 Suppresses WNT-Driven Dedifferentiation and Oncogenesis in the Differentiated Gut Epithelium

Author

Perekatt, Ansu O., primary, Shah, Pooja P., primary, Cheung, Shannon, primary, Jariwala, Nidhi, primary, Wu, Alex, primary, Gandhi, Vishal, primary, Kumar, Namit, primary, Feng, Qiang, primary, Patel, Neeket, primary, Chen, Lei, primary, Joshi, Shilpy, primary, Zhou, Anbo, primary, Taketo, M. Mark, primary, Xing, Jinchuan, primary, White, Eileen, primary, Gao, Nan, primary, Gatza, Michael L., primary, and Verzi, Michael P., primary

Published
2023
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44. Functional equivalence of genome sequencing analysis pipelines enables harmonized variant calling across human genetics projects

Author

Regier, Allison A., Farjoun, Yossi, Larson, David E., Krasheninina, Olga, Kang, Hyun Min, Howrigan, Daniel P., Chen, Bo-Juen, Kher, Manisha, Banks, Eric, Ames, Darren C., English, Adam C., Li, Heng, Xing, Jinchuan, Zhang, Yeting, Matise, Tara, Abecasis, Goncalo R., Salerno, Will, Zody, Michael C., Neale, Benjamin M., and Hall, Ira M.

Published
2018
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45. Whole-exome sequencing identifies genes associated with Tourette’s disorder in multiplex families

Author

Cao, Xiaolong, Zhang, Yeting, Abdulkadir, Mohamed, Deng, Li, Fernandez, Thomas V., Garcia-Delgar, Blanca, Hagstrøm, Julie, Hoekstra, Pieter J., King, Robert A., Koesterich, Justin, Kuperman, Samuel, Morer, Astrid, Nasello, Cara, Plessen, Kerstin J., Thackray, Joshua K., Zhou, Lisheng, Dietrich, Andrea, Tischfield, Jay A., Heiman, Gary A., and Xing, Jinchuan

Abstract

Tourette’s Disorder (TD) is a neurodevelopmental disorder (NDD) that affects about 0.7% of the population and is one of the most heritable NDDs. Nevertheless, because of its polygenic nature and genetic heterogeneity, the genetic etiology of TD is not well understood. In this study, we combined the segregation information in 13 TD multiplex families with high-throughput sequencing and genotyping to identify genes associated with TD. Using whole-exome sequencing and genotyping array data, we identified both small and large genetic variants within the individuals. We then combined multiple types of evidence to prioritize candidate genes for TD, including variant segregation pattern, variant function prediction, candidate gene expression, protein–protein interaction network, candidate genes from previous studies, etc. From the 13 families, 71 strong candidate genes were identified, including both known genes for NDDs and novel genes, such as HtrA Serine Peptidase 3 (HTRA3), Cadherin-Related Family Member 1 (CDHR1), and Zinc Finger DHHC-Type Palmitoyltransferase 17 (ZDHHC17). The candidate genes are enriched in several Gene Ontology categories, such as dynein complex and synaptic membrane. Candidate genes and pathways identified in this study provide biological insight into TD etiology and potential targets for future studies.

Published
2024
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46. Common genetic risk factors in ASD and ADHD co-occurring families

Author

Zhou, Anbo, primary, Cao, Xiaolong, additional, Mahaganapathy, Vaidhyanathan, additional, Azaro, Marco, additional, Gwin, Christine, additional, Wilson, Sherri, additional, Buyske, Steven, additional, Bartlett, Christopher W., additional, Flax, Judy F., additional, Brzustowicz, Linda M., additional, and Xing, Jinchuan, additional

Published
2022
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47. Dysregulation of mTOR Signaling Mediates Common Neurite and Migration Defects in Both Idiopathic and 16p11.2 Deletion Autism Neural Precursor Cells

Author

Prem, Smrithi, primary, Dev, Bharati, additional, Peng, Cynthia, additional, Mehta, Monal, additional, Alibutud, Rohan, additional, Connacher, Robert J., additional, Thomas, Madeline St, additional, Zhou, Xiaofeng, additional, Matteson, Paul, additional, Xing, Jinchuan, additional, Millonig, James H., additional, and DiCicco-Bloom, Emanuel, additional

Published
2022
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50. Transposable Elements Shape the Genome Diversity and the Evolution of Noctuidae Species.

Author

Zhang, Chunhui, Wang, Lei, Dou, Liang, Yue, Bisong, Xing, Jinchuan, and Li, Jing

Subjects
BEET armyworm, GENOME size, SPECIES, SPECIES diversity, TRANSPOSONS
Abstract

Noctuidae is known to have high species diversity, although the genomic diversity of Noctuidae species has yet to be studied extensively. Investigation of transposable elements (TEs) in this family can improve our understanding of the genomic diversity of Noctuidae. In this study, we annotated and characterized genome-wide TEs in ten noctuid species belonging to seven genera. With multiple annotation pipelines, we constructed a consensus sequence library containing 1038–2826 TE consensus. The genome content of TEs showed high variation in the ten Noctuidae genomes, ranging from 11.3% to 45.0%. The relatedness analysis indicated that the TE content, especially the content of LINEs and DNA transposons, is positively correlated with the genome size (r = 0.86, p-value = 0.001). We identified SINE/B2 as a lineage-specific subfamily in Trichoplusia ni, a species-specific expansion of the LTR/Gypsy subfamily in Spodoptera exigua, and a recent expansion of SINE/5S subfamily in Busseola fusca. We further revealed that of the four TE classes, only LINEs showed phylogenetic signals with high confidence. We also examined how the expansion of TEs contributed to the evolution of noctuid genomes. Moreover, we identified 56 horizontal transfer TE (HTT) events among the ten noctuid species and at least three HTT events between the nine Noctuidae species and 11 non-noctuid arthropods. One of the HTT events of a Gypsy transposon might have caused the recent expansion of the Gypsy subfamily in the S. exigua genome. By determining the TE content, dynamics, and HTT events in the Noctuidae genomes, our study emphasized that TE activities and HTT events substantially impacted the Noctuidae genome evolution. [ABSTRACT FROM AUTHOR]

Published
2023
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