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1. Comprehensive whole-genome sequence analyses provide insights into the genomic architecture of cerebral palsy

Author

Fehlings, Darcy L., Zarrei, Mehdi, Engchuan, Worrawat, Sondheimer, Neal, Thiruvahindrapuram, Bhooma, MacDonald, Jeffrey R., Higginbotham, Edward J., Thapa, Ritesh, Behlim, Tarannum, Aimola, Sabrina, Switzer, Lauren, Ng, Pamela, Wei, John, Danthi, Prakroothi S., Pellecchia, Giovanna, Lamoureux, Sylvia, Ho, Karen, Pereira, Sergio L., de Rijke, Jill, Sung, Wilson W. L., Mowjoodi, Alireza, Howe, Jennifer L., Nalpathamkalam, Thomas, Manshaei, Roozbeh, Ghaffari, Siavash, Whitney, Joseph, Patel, Rohan V., Hamdan, Omar, Shaath, Rulan, Trost, Brett, Knights, Shannon, Samdup, Dawa, McCormick, Anna, Hunt, Carolyn, Kirton, Adam, Kawamura, Anne, Mesterman, Ronit, Gorter, Jan Willem, Dlamini, Nomazulu, Merico, Daniele, Hilali, Murto, Hirschfeld, Kyle, Grover, Kritika, Bautista, Nelson X., Han, Kara, Marshall, Christian R., Yuen, Ryan K. C., Subbarao, Padmaja, Azad, Meghan B., Turvey, Stuart E., Mandhane, Piush, Moraes, Theo J., Simons, Elinor, Maxwell, George, Shevell, Michael, Costain, Gregory, Michaud, Jacques L., Hamdan, Fadi F., Gauthier, Julie, Uguen, Kevin, Stavropoulos, Dimitri J., Wintle, Richard F., Oskoui, Maryam, and Scherer, Stephen W.

Published
2024
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2. Rare copy number variation in posttraumatic stress disorder

Author

Maihofer, Adam X, Engchuan, Worrawat, Huguet, Guillaume, Klein, Marieke, MacDonald, Jeffrey R, Shanta, Omar, Thiruvahindrapuram, Bhooma, Jean-louis, Martineau, Saci, Zohra, Jacquemont, Sebastien, Scherer, Stephen W, Ketema, Elizabeth, Aiello, Allison E, Amstadter, Ananda B, Avdibegović, Esmina, Babic, Dragan, Baker, Dewleen G, Bisson, Jonathan I, Boks, Marco P, Bolger, Elizabeth A, Bryant, Richard A, Bustamante, Angela C, Caldas-de-Almeida, Jose Miguel, Cardoso, Graça, Deckert, Jurgen, Delahanty, Douglas L, Domschke, Katharina, Dunlop, Boadie W, Dzubur-Kulenovic, Alma, Evans, Alexandra, Feeny, Norah C, Franz, Carol E, Gautam, Aarti, Geuze, Elbert, Goci, Aferdita, Hammamieh, Rasha, Jakovljevic, Miro, Jett, Marti, Jones, Ian, Kaufman, Milissa L, Kessler, Ronald C, King, Anthony P, Kremen, William S, Lawford, Bruce R, Lebois, Lauren AM, Lewis, Catrin, Liberzon, Israel, Linnstaedt, Sarah D, Lugonja, Bozo, Luykx, Jurjen J, Lyons, Michael J, Mavissakalian, Matig R, McLaughlin, Katie A, McLean, Samuel A, Mehta, Divya, Mellor, Rebecca, Morris, Charles Phillip, Muhie, Seid, Orcutt, Holly K, Peverill, Matthew, Ratanatharathorn, Andrew, Risbrough, Victoria B, Rizzo, Albert, Roberts, Andrea L, Rothbaum, Alex O, Rothbaum, Barbara O, Roy-Byrne, Peter, Ruggiero, Kenneth J, Rutten, Bart PF, Schijven, Dick, Seng, Julia S, Sheerin, Christina M, Sorenson, Michael A, Teicher, Martin H, Uddin, Monica, Ursano, Robert J, Vinkers, Christiaan H, Voisey, Joanne, Weber, Heike, Winternitz, Sherry, Xavier, Miguel, Yang, Ruoting, McD Young, Ross, Zoellner, Lori A, Salem, Rany M, Shaffer, Richard A, Wu, Tianying, Ressler, Kerry J, Stein, Murray B, Koenen, Karestan C, Sebat, Jonathan, and Nievergelt, Caroline M

Subjects
Post-Traumatic Stress Disorder (PTSD), Mental Health, Human Genome, Genetics, Neurosciences, Brain Disorders, Mental health, Humans, DNA Copy Number Variations, Stress Disorders, Post-Traumatic, Genome, Brain, Genome-Wide Association Study, Polymorphism, Single Nucleotide, Genetic Predisposition to Disease, Psychiatric Genomics Consortium PTSD Working Group, Psychiatric Genomics Consortium CNV Working Group, Biological Sciences, Medical and Health Sciences, Psychology and Cognitive Sciences, Psychiatry
Abstract

Posttraumatic stress disorder (PTSD) is a heritable (h2 = 24-71%) psychiatric illness. Copy number variation (CNV) is a form of rare genetic variation that has been implicated in the etiology of psychiatric disorders, but no large-scale investigation of CNV in PTSD has been performed. We present an association study of CNV burden and PTSD symptoms in a sample of 114,383 participants (13,036 cases and 101,347 controls) of European ancestry. CNVs were called using two calling algorithms and intersected to a consensus set. Quality control was performed to remove strong outlier samples. CNVs were examined for association with PTSD within each cohort using linear or logistic regression analysis adjusted for population structure and CNV quality metrics, then inverse variance weighted meta-analyzed across cohorts. We examined the genome-wide total span of CNVs, enrichment of CNVs within specified gene-sets, and CNVs overlapping individual genes and implicated neurodevelopmental regions. The total distance covered by deletions crossing over known neurodevelopmental CNV regions was significant (beta = 0.029, SE = 0.005, P = 6.3 × 10-8). The genome-wide neurodevelopmental CNV burden identified explains 0.034% of the variation in PTSD symptoms. The 15q11.2 BP1-BP2 microdeletion region was significantly associated with PTSD (beta = 0.0206, SE = 0.0056, P = 0.0002). No individual significant genes interrupted by CNV were identified. 22 gene pathways related to the function of the nervous system and brain were significant in pathway analysis (FDR q

Published
2022

3. Genomic architecture of autism from comprehensive whole-genome sequence annotation

Author

Trost, Brett, Thiruvahindrapuram, Bhooma, Chan, Ada J.S., Engchuan, Worrawat, Higginbotham, Edward J., Howe, Jennifer L., Loureiro, Livia O., Reuter, Miriam S., Roshandel, Delnaz, Whitney, Joe, Zarrei, Mehdi, Bookman, Matthew, Somerville, Cherith, Shaath, Rulan, Abdi, Mona, Aliyev, Elbay, Patel, Rohan V., Nalpathamkalam, Thomas, Pellecchia, Giovanna, Hamdan, Omar, Kaur, Gaganjot, Wang, Zhuozhi, MacDonald, Jeffrey R., Wei, John, Sung, Wilson W.L., Lamoureux, Sylvia, Hoang, Ny, Selvanayagam, Thanuja, Deflaux, Nicole, Geng, Melissa, Ghaffari, Siavash, Bates, John, Young, Edwin J., Ding, Qiliang, Shum, Carole, D'Abate, Lia, Bradley, Clarrisa A., Rutherford, Annabel, Aguda, Vernie, Apresto, Beverly, Chen, Nan, Desai, Sachin, Du, Xiaoyan, Fong, Matthew L.Y., Pullenayegum, Sanjeev, Samler, Kozue, Wang, Ting, Ho, Karen, Paton, Tara, Pereira, Sergio L., Herbrick, Jo-Anne, Wintle, Richard F., Fuerth, Jonathan, Noppornpitak, Juti, Ward, Heather, Magee, Patrick, Al Baz, Ayman, Kajendirarajah, Usanthan, Kapadia, Sharvari, Vlasblom, Jim, Valluri, Monica, Green, Joseph, Seifer, Vicki, Quirbach, Morgan, Rennie, Olivia, Kelley, Elizabeth, Masjedi, Nina, Lord, Catherine, Szego, Michael J., Zawati, Ma'n H., Lang, Michael, Strug, Lisa J., Marshall, Christian R., Costain, Gregory, Calli, Kristina, Iaboni, Alana, Yusuf, Afiqah, Ambrozewicz, Patricia, Gallagher, Louise, Amaral, David G., Brian, Jessica, Elsabbagh, Mayada, Georgiades, Stelios, Messinger, Daniel S., Ozonoff, Sally, Sebat, Jonathan, Sjaarda, Calvin, Smith, Isabel M., Szatmari, Peter, Zwaigenbaum, Lonnie, Kushki, Azadeh, Frazier, Thomas W., Vorstman, Jacob A.S., Fakhro, Khalid A., Fernandez, Bridget A., Lewis, M.E. Suzanne, Weksberg, Rosanna, Fiume, Marc, Yuen, Ryan K.C., Anagnostou, Evdokia, Sondheimer, Neal, Glazer, David, Hartley, Dean M., and Scherer, Stephen W.

Published
2022
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4. Genome-wide rare variant score associates with morphological subtypes of autism spectrum disorder

Author

Chan, Ada J. S., Engchuan, Worrawat, Reuter, Miriam S., Wang, Zhuozhi, Thiruvahindrapuram, Bhooma, Trost, Brett, Nalpathamkalam, Thomas, Negrijn, Carol, Lamoureux, Sylvia, Pellecchia, Giovanna, Patel, Rohan V., Sung, Wilson W. L., MacDonald, Jeffrey R., Howe, Jennifer L., Vorstman, Jacob, Sondheimer, Neal, Takahashi, Nicole, Miles, Judith H., Anagnostou, Evdokia, Tammimies, Kristiina, Zarrei, Mehdi, Merico, Daniele, Stavropoulos, Dimitri J., Yuen, Ryan K. C., Fernandez, Bridget A., and Scherer, Stephen W.

Published
2022
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5. Genetic variants in DDX53 contribute to autism spectrum disorder associated with the Xp22.11 locus

Author

Scala, Marcello, Bradley, Clarrisa A., Howe, Jennifer L., Trost, Brett, Salazar, Nelson Bautista, Shum, Carole, Mendes, Marla, Reuter, Miriam S., Anagnostou, Evdokia, MacDonald, Jeffrey R., Ko, Sangyoon Y., Frankland, Paul W., Charlebois, Jessica, Elsabbagh, Mayada, Granger, Leslie, Anadiotis, George, Pullano, Verdiana, Brusco, Alfredo, Keller, Roberto, Parisotto, Sarah, Pedro, Helio F., Lusk, Laina, McDonnell, Pamela Pojomovsky, Helbig, Ingo, Mullegama, Sureni V., Douine, Emilie D., Corona, Rosario Ivetth, Russell, Bianca E., Nelson, Stanley F., Graziano, Claudio, Schwab, Maria, Simone, Laurie, Zara, Federico, and Scherer, Stephen W.

Published
2025
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6. Disruption of the ASTN2/TRIM32 locus at 9q33.1 is a risk factor in males for autism spectrum disorders, ADHD and other neurodevelopmental phenotypes

Author

Lionel, Anath C, Tammimies, Kristiina, Vaags, Andrea K, Rosenfeld, Jill A, Ahn, Joo Wook, Merico, Daniele, Noor, Abdul, Runke, Cassandra K, Pillalamarri, Vamsee K, Carter, Melissa T, Gazzellone, Matthew J, Thiruvahindrapuram, Bhooma, Fagerberg, Christina, Laulund, Lone W, Pellecchia, Giovanna, Lamoureux, Sylvia, Deshpande, Charu, Clayton-Smith, Jill, White, Ann C, Leather, Susan, Trounce, John, Bedford, H Melanie, Hatchwell, Eli, Eis, Peggy S, Yuen, Ryan KC, Walker, Susan, Uddin, Mohammed, Geraghty, Michael T, Nikkel, Sarah M, Tomiak, Eva M, Fernandez, Bridget A, Soreni, Noam, Crosbie, Jennifer, Arnold, Paul D, Schachar, Russell J, Roberts, Wendy, Paterson, Andrew D, So, Joyce, Szatmari, Peter, Chrysler, Christina, Woodbury-Smith, Marc, Lowry, R Brian, Zwaigenbaum, Lonnie, Mandyam, Divya, Wei, John, MacDonald, Jeffrey R, Howe, Jennifer L, Nalpathamkalam, Thomas, Wang, Zhuozhi, Tolson, Daniel, Cobb, David S, Wilks, Timothy M, Sorensen, Mark J, Bader, Patricia I, An, Yu, Wu, Bai-Lin, Musumeci, Sebastiano Antonino, Romano, Corrado, Postorivo, Diana, Nardone, Anna M, Della Monica, Matteo, Scarano, Gioacchino, Zoccante, Leonardo, Novara, Francesca, Zuffardi, Orsetta, Ciccone, Roberto, Antona, Vincenzo, Carella, Massimo, Zelante, Leopoldo, Cavalli, Pietro, Poggiani, Carlo, Cavallari, Ugo, Argiropoulos, Bob, Chernos, Judy, Brasch-Andersen, Charlotte, Speevak, Marsha, Fichera, Marco, Ogilvie, Caroline Mackie, Shen, Yiping, Hodge, Jennelle C, Talkowski, Michael E, Stavropoulos, Dimitri J, Marshall, Christian R, and Scherer, Stephen W

Subjects
Pediatric Research Initiative, Pediatric, Intellectual and Developmental Disabilities (IDD), Mental Health, Brain Disorders, Human Genome, Neurosciences, Autism, Clinical Research, Behavioral and Social Science, Genetics, 2.1 Biological and endogenous factors, Aetiology, Mental health, Adolescent, Adult, Attention Deficit Disorder with Hyperactivity, Case-Control Studies, Child, Child Development Disorders, Pervasive, Child, Preschool, Chromosomes, Human, Pair 9, DNA Copy Number Variations, Exons, Female, Gene Expression, Genetic Association Studies, Genetic Predisposition to Disease, Glycoproteins, Humans, Infant, Infant, Newborn, Male, Nerve Tissue Proteins, Organ Specificity, Phenotype, Polymorphism, Single Nucleotide, Protein Isoforms, Receptors, Cell Surface, Risk Factors, Sequence Deletion, Transcription Factors, Transcription Initiation Site, Tripartite Motif Proteins, Ubiquitin-Protein Ligases, Young Adult, Biological Sciences, Medical and Health Sciences, Genetics & Heredity
Abstract

Rare copy number variants (CNVs) disrupting ASTN2 or both ASTN2 and TRIM32 have been reported at 9q33.1 by genome-wide studies in a few individuals with neurodevelopmental disorders (NDDs). The vertebrate-specific astrotactins, ASTN2 and its paralog ASTN1, have key roles in glial-guided neuronal migration during brain development. To determine the prevalence of astrotactin mutations and delineate their associated phenotypic spectrum, we screened ASTN2/TRIM32 and ASTN1 (1q25.2) for exonic CNVs in clinical microarray data from 89 985 individuals across 10 sites, including 64 114 NDD subjects. In this clinical dataset, we identified 46 deletions and 12 duplications affecting ASTN2. Deletions of ASTN1 were much rarer. Deletions near the 3' terminus of ASTN2, which would disrupt all transcript isoforms (a subset of these deletions also included TRIM32), were significantly enriched in the NDD subjects (P = 0.002) compared with 44 085 population-based controls. Frequent phenotypes observed in individuals with such deletions include autism spectrum disorder (ASD), attention deficit hyperactivity disorder (ADHD), speech delay, anxiety and obsessive compulsive disorder (OCD). The 3'-terminal ASTN2 deletions were significantly enriched compared with controls in males with NDDs, but not in females. Upon quantifying ASTN2 human brain RNA, we observed shorter isoforms expressed from an alternative transcription start site of recent evolutionary origin near the 3' end. Spatiotemporal expression profiling in the human brain revealed consistently high ASTN1 expression while ASTN2 expression peaked in the early embryonic neocortex and postnatal cerebellar cortex. Our findings shed new light on the role of the astrotactins in psychopathology and their interplay in human neurodevelopment.

Published
2014

7. Genetic variants inDDX53contribute to Autism Spectrum Disorder associated with the Xp22.11 locus

Author

Scala, Marcello, primary, Bradley, Clarrisa A., additional, Howe, Jennifer L., additional, Trost, Brett, additional, Bautista Salazar, Nelson, additional, Shum, Carole, additional, Reuter, Miriam S., additional, MacDonald, Jeffrey R., additional, Ko, Sangyoon Y., additional, Frankland, Paul W., additional, Granger, Leslie, additional, Anadiotis, George, additional, Pullano, Verdiana, additional, Brusco, Alfredo, additional, Keller, Roberto, additional, Parisotto, Sarah, additional, Pedro, Helio F., additional, Lusk, Laina, additional, Pojomovsky McDonnell, Pamela, additional, Helbig, Ingo, additional, Mullegama, Sureni V., additional, Douine, Emilie D., additional, Russell, Bianca E., additional, Nelson, Stanley F., additional, Zara, Federico, additional, and Scherer, Stephen W., additional

Published
2023
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8. De novo and rare inherited copy-number variations in the hemiplegic form of cerebral palsy

Author

Zarrei, Mehdi, Fehlings, Darcy L., Mawjee, Karizma, Switzer, Lauren, Thiruvahindrapuram, Bhooma, Walker, Susan, Merico, Daniele, Casallo, Guillermo, Uddin, Mohammed, MacDonald, Jeffrey R., Gazzellone, Matthew J., Higginbotham, Edward J., Campbell, Craig, deVeber, Gabrielle, Frid, Pam, Gorter, Jan Willem, Hunt, Carolyn, Kawamura, Anne, Kim, Marie, McCormick, Anna, Mesterman, Ronit, Samdup, Dawa, Marshall, Christian R., Stavropoulos, Dimitri J., Wintle, Richard F., and Scherer, Stephen W.

Published
2018
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10. 70. GENE-BASED ANALYSIS OF RARE CNVS ACROSS SIX PSYCHIATRIC DISORDERS IDENTIFIES COMMON BIOLOGICAL COMPONENTS BUT DISTINCTLY DIFFERENT GENETIC EFFECTS IN AUTISM AND SCHIZOPHRENIA

Author

Engchuan, Worrawat, primary, Thiruvahindrapuram, Bhooma, additional, MacDonald, Jeffrey R., additional, Shanta, Omar, additional, Kumar, Kuldeep, additional, Klein, Marieke, additional, Huguet, Guillaume, additional, Wang, Zhuozhi, additional, Pellecchia, Giovanna, additional, Yuen, Ryan KC, additional, Merico, Daniele, additional, Jacquemont, Sebastien, additional, Scherer, Stephen W., additional, and Sebat, Jonathan, additional

Published
2023
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11. Human Chromosome 7: DNA Sequence and Biology

Author

Scherer, Stephen W., Cheung, Joseph, MacDonald, Jeffrey R., Osborne, Lucy R., Nakabayashi, Kazuhiko, Herbrick, Jo-Anne, Carson, Andrew R., Parker-Katiraee, Layla, Skaug, Jennifer, Khaja, Razi, Zhang, Junjun, Hudek, Alexander K., Li, Martin, Haddad, May, Duggan, Gavin E., Fernandez, Bridget A., Kanematsu, Emiko, Gentles, Simone, Christopoulos, Constantine C., Choufani, Sanaa, Kwasnicka, Dorota, Zheng, Xiangqun H., Lai, Zhongwu, Nusskern, Deborah, Zhang, Qing, Gu, Zhiping, Lu, Fu, Zeesman, Susan, Nowaczyk, Malgorzata J., Teshima, Ikuko, Chitayat, David, Shuman, Cheryl, Weksberg, Rosanna, Zackai, Elaine H., Grebe, Theresa A., Cox, Sarah R., Kirkpatrick, Susan J., Rahman, Nazneen, Friedman, Jan M., Pelicci, Pier Giuseppe, Lo-Coco, Francesco, Belloni, Elena, Shaffer, Lisa G., Pober, Barbara, Morton, Cynthia C., Gusella, James F., Korf, Bruce R., Quade, Bradley J., Ligon, Azra H., Ferguson, Heather, Higgins, Anne W., Leach, Natalia T., Herrick, Steven R., Lemyre, Emmanuelle, Farra, Chantal G., Kim, Hyung-Goo, Summers, Anne M., Gripp, Karen W., Roberts, Wendy, Szatmari, Peter, Grzeschik, Karl-Heinz, Teebi, Ahmed, Minassian, Berge A., Kere, Juha, Armengol, Lluis, Pujana, Miguel Angel, Estivill, Xavier, Wilson, Michael D., Koop, Ben F., Tosi, Sabrina, Moore, Gudrun E., Boright, Andrew P., Zlotorynski, Eitan, Kerem, Batsheva, Kroisel, Peter M., Petek, Erwin, Oscier, David G., Mould, Sarah J., Döhner, Hartmut, Döhner, Konstanze, Rommens, Johanna M., Vincent, John B., Venter, J. Craig, Li, Peter W., Mural, Richard J., Adams, Mark D., and Tsui, Lap-Chee

Published
2003

12. Gene copy number variation and pediatric mental health/neurodevelopment in a general population

Author

Zarrei, Mehdi, primary, Burton, Christie L, additional, Engchuan, Worrawat, additional, Higginbotham, Edward J, additional, Wei, John, additional, Shaikh, Sabah, additional, Roslin, Nicole M, additional, MacDonald, Jeffrey R, additional, Pellecchia, Giovanna, additional, Nalpathamkalam, Thomas, additional, Lamoureux, Sylvia, additional, Manshaei, Roozbeh, additional, Howe, Jennifer, additional, Trost, Brett, additional, Thiruvahindrapuram, Bhooma, additional, Marshall, Christian R, additional, Yuen, Ryan K C, additional, Wintle, Richard F, additional, Strug, Lisa J, additional, Stavropoulos, Dimitri J, additional, Vorstman, Jacob A S, additional, Arnold, Paul, additional, Merico, Daniele, additional, Woodbury-Smith, Marc, additional, Crosbie, Jennifer, additional, Schachar, Russell, additional, and Scherer, Stephen W, additional

Published
2023
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13. A large data resource of genomic copy number variation across neurodevelopmental disorders

Author

Zarrei, Mehdi, Burton, Christie L., Engchuan, Worrawat, Young, Edwin J., Higginbotham, Edward J., MacDonald, Jeffrey R., Trost, Brett, Chan, Ada J. S., Walker, Susan, Lamoureux, Sylvia, Heung, Tracy, Mojarad, Bahareh A., Kellam, Barbara, Paton, Tara, Faheem, Muhammad, Miron, Karin, Lu, Chao, Wang, Ting, Samler, Kozue, Wang, Xiaolin, Costain, Gregory, Hoang, Ny, Pellecchia, Giovanna, Wei, John, Patel, Rohan V., Thiruvahindrapuram, Bhooma, Roifman, Maian, Merico, Daniele, Goodale, Tara, Drmic, Irene, Speevak, Marsha, Howe, Jennifer L., Yuen, Ryan K. C., Buchanan, Janet A., Vorstman, Jacob A. S., Marshall, Christian R., Wintle, Richard F., Rosenberg, David R., Hanna, Gregory L., Woodbury-Smith, Marc, Cytrynbaum, Cheryl, Zwaigenbaum, Lonnie, Elsabbagh, Mayada, Flanagan, Janine, Fernandez, Bridget A., Carter, Melissa T., Szatmari, Peter, Roberts, Wendy, Lerch, Jason, Liu, Xudong, Nicolson, Rob, Georgiades, Stelios, Weksberg, Rosanna, Arnold, Paul D., Bassett, Anne S., Crosbie, Jennifer, Schachar, Russell, Stavropoulos, Dimitri J., Anagnostou, Evdokia, and Scherer, Stephen W.

Published
2019
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14. The Personal Genome Project Canada: findings from whole genome sequences of the inaugural 56 participants

Author

Reuter, Miriam S., Walker, Susan, Thiruvahindrapuram, Bhooma, Whitney, Joe, Cohn, Iris, Sondheimer, Neal, Yuen, Ryan K.C., Trost, Brett, Paton, Tara A., Pereira, Sergio L., Herbrick, Jo-Anne, Wintle, Richard F., Merico, Daniele, Howe, Jennifer, MacDonald, Jeffrey R., Lu, Chao, Nalpathamkalam, Thomas, Sung, Wilson W.L., Wang, Zhuozhi, Patel, Rohan V., Pellecchia, Giovanna, Wei, John, Strug, Lisa J., Bell, Sherilyn, Kellam, Barbara, Mahtani, Melanie M., Bassett, Anne S., Bombard, Yvonne, Weksberg, Rosanna, Shuman, Cheryl, Cohn, Ronald D., Stavropoulos, Dimitri J., Bowdin, Sarah, Hildebrandt, Matthew R., Wei, Wei, Romm, Asli, Pasceri, Peter, Ellis, James, Ray, Peter, Meyn, M. Stephen, Monfared, Nasim, Hosseini, S. Mohsen, Joseph-George, Ann M., Keeley, Fred W., Cook, Ryan A., Fiume, Marc, Lee, Hin C., Marshall, Christian R., Davies, Jill, Hazell, Allison, Buchanan, Janet A., Szego, Michael J., and Scherer, Stephen W.

Subjects
Health policy -- Analysis, DNA sequencing -- Analysis, Pharmacogenomics -- Analysis, Health
Abstract

BACKGROUND: The Personal Genome Project Canada is a comprehensive public data resource that integrates whole genome sequencing data and health information. We describe genomic variation identified in the initial recruitment cohort of 56 volunteers. METHODS: Volunteers were screened for eligibility and provided informed consent for open data sharing. Using blood DNA, we performed whole genome sequencing and identified all possible classes of DNA variants. A genetic counsellor explained the implication of the results to each participant. RESULTS: Whole genome sequencing of the first 56 participants identified 207662 805 sequence variants and 27494 copy number variations. We analyzed a prioritized disease-associated data set (n = 1606 variants) according to standardized guidelines, and interpreted 19 variants in 14 participants (25%) as having obvious health implications. Six of these variants (e.g., in BRCA1 or mosaic loss of an X chromosome) were pathogenic or likely pathogenic. Seven were risk factors for cancer, cardiovascular or neurobehavioural conditions. Four other variants--associated with cancer, cardiac or neurodegenerative phenotypes--remained of uncertain significance because of discrepancies among databases. We also identified a large structural chromosome aberration and a likely pathogenic mitochondrial variant. There were 172 recessive disease alleles (e.g., 5 individuals carried mutations for cystic fibrosis). Pharmacogenomics analyses revealed another 3.9 potentially relevant genotypes per individual. INTERPRETATION: Our analyses identified a spectrum of genetic variants with potential health impact in 25% of participants. When also considering recessive alleles and variants with potential pharmacologic relevance, all 56 participants had medically relevant findings. Although access is mostly limited to research, whole genome sequencing can provide specific and novel information with the potential of major impact for health care., Rapid technological advances are enabling a view of human genetic variation in ever-increasing detail and at plummeting costs. (1) Until recently, analysis has been targeted largely to defined genes, but [...]

Published
2018
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16. Gene copy number variation in pediatric mental illness in a general population

Author

Zarrei, Mehdi, primary, Burton, Christie L., additional, Engchuan, Worrawat, additional, Higginbotham, Edward J, additional, Wei, John, additional, Shaikh, Sabah, additional, Roslin, Nicole M., additional, MacDonald, Jeffrey R., additional, Pellecchia, Giovanna, additional, Nalpathamkalam, Thomas, additional, Lamoureux, Sylvia, additional, Manshaei, Roozbeh, additional, Howe, Jennifer, additional, Trost, Brett, additional, Thiruvahindrapuram, Bhooma, additional, Marshall, Christian R., additional, Yuen, Ryan K.C., additional, Wintle, Richard F., additional, Strug, Lisa J, additional, Stavropoulos, Dimitri J., additional, Vorstman, Jacob A.S., additional, Arnold, Paul, additional, Merico, Daniele, additional, Woodbury-Smith, Marc, additional, Crosbie, Jennifer, additional, Schachar, Russell, additional, and Scherer, Stephen W., additional

Published
2022
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20. Genomic architecture of Autism Spectrum Disorder from comprehensive whole-genome sequence annotation

Author

Trost, Brett, primary, Thiruvahindrapuram, Bhooma, additional, Chan, Ada J.S., additional, Engchuan, Worrawat, additional, Higginbotham, Edward J., additional, Howe, Jennifer L., additional, Loureiro, Livia O., additional, Reuter, Miriam S., additional, Roshandel, Delnaz, additional, Whitney, Joe, additional, Zarrei, Mehdi, additional, Bookman, Matthew, additional, Somerville, Cherith, additional, Shaath, Rulan, additional, Abdi, Mona, additional, Aliyev, Elbay, additional, Patel, Rohan V., additional, Nalpathamkalam, Thomas, additional, Pellecchia, Giovanna, additional, Hamdan, Omar, additional, Kaur, Gaganjot, additional, Wang, Zhuozhi, additional, MacDonald, Jeffrey R., additional, Wei, John, additional, Sung, Wilson W.L., additional, Lamoureux, Sylvia, additional, Hoang, Ny, additional, Selvanayagam, Thanuja, additional, Deflaux, Nicole, additional, Geng, Melissa, additional, Ghaffari, Siavash, additional, Bates, John, additional, Young, Edwin J., additional, Ding, Qiliang, additional, Shum, Carole, additional, D’abate, Lia, additional, Bradley, Clarissa A., additional, Rutherford, Annabel, additional, Aguda, Vernie, additional, Apresto, Beverly, additional, Chen, Nan, additional, Desai, Sachin, additional, Du, Xiaoyan, additional, Fong, Matthew L.Y., additional, Pullenayegum, Sanjeev, additional, Samler, Kozue, additional, Wang, Ting, additional, Ho, Karen, additional, Paton, Tara, additional, Pereira, Sergio L., additional, Herbrick, Jo-Anne, additional, Wintle, Richard F., additional, Fuerth, Jonathan, additional, Noppornpitak, Juti, additional, Ward, Heather, additional, Magee, Patrick, additional, Baz, Ayman Al, additional, Kajendirarajah, Usanthan, additional, Kapadia, Sharvari, additional, Vlasblom, Jim, additional, Valluri, Monica, additional, Green, Joseph, additional, Seifer, Vicki, additional, Quirbach, Morgan, additional, Rennie, Olivia, additional, Kelley, Elizabeth, additional, Masjedi, Nina, additional, Lord, Catherine, additional, Szego, Michael J., additional, Zawati, Ma’n H., additional, Lang, Michael, additional, Strug, Lisa J., additional, Marshall, Christian R., additional, Costain, Gregory, additional, Calli, Kristina, additional, Iaboni, Alana, additional, Yusuf, Afiqah, additional, Ambrozewicz, Patricia, additional, Gallagher, Louise, additional, Amaral, David G., additional, Brian, Jessica, additional, Elsabbagh, Mayada, additional, Georgiades, Stelios, additional, Messinger, Daniel S., additional, Ozonoff, Sally, additional, Sebat, Jonathan, additional, Sjaarda, Calvin, additional, Smith, Isabel M., additional, Szatmari, Peter, additional, Zwaigenbaum, Lonnie, additional, Kushki, Azadeh, additional, Frazier, Thomas W., additional, Vorstman, Jacob A.S., additional, Fakhro, Khalid A., additional, Fernandez, Bridget A., additional, Lewis, M.E. Suzanne, additional, Weksberg, Rosanna, additional, Fiume, Marc, additional, Yuen, Ryan K.C., additional, Anagnostou, Evdokia, additional, Sondheimer, Neal, additional, Glazer, David, additional, Hartley, Dean M., additional, and Scherer, Stephen W., additional

Published
2022
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22. Genome-wide rare variant score associates with morphological subtypes of autism spectrum disorder

Author

Chan, Ada J.S, primary, Engchuan, Worrawat, additional, Reuter, Miriam S., additional, Wang, Zhuozhi, additional, Thiruvahindrapuram, Bhooma, additional, Trost, Brett, additional, Nalpathamkalam, Thomas, additional, Negrijn, Carol, additional, Lamoureux, Sylvia, additional, Pellecchia, Giovanna, additional, Patel, Rohan, additional, Sung, Wilson W.L., additional, MacDonald, Jeffrey R., additional, Howe, Jennifer L., additional, Vorstman, Jacob, additional, Sondheimer, Neal, additional, Takahashi, Nicole, additional, Miles, Judith H., additional, Anagnostou, Evdokia, additional, Tammimies, Kristiina, additional, Zarrei, Mehdi, additional, Merico, Daniele, additional, Stavropoulos, Dimitri J., additional, Yuen, Ryan K.C., additional, Fernandez, Bridget A., additional, and Scherer, Stephen W., additional

Published
2021
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23. Origins and functional impact of copy number variation in the human genome

Author

Conrad, Donald F., Pinto, Dalila, Redon, Richard, Feuk, Lars, Gokcumen, Omer, Zhang, Yujun, Aerts, Jan, Andrews, T. Daniel, Barnes, Chris, Campbell, Peter, Fitzgerald, Tomas, Hu, Min, Ihm, Chun Hwa, Kristiansson, Kati, MacArthur, Daniel G., MacDonald, Jeffrey R., Onyiah, Ifejinelo, Pang, Andy Wing Chun, Robson, Sam, Stirrups, Kathy, Valsesia, Armand, Walter, Klaudia, Wei, John, Tyler-Smith, Chris, Carter, Nigel P., Lee, Charles, Scherer, Stephen W., and Hurles, Matthew E.

Subjects
Genetic variation -- Research, Human genome -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Structural variations of DNA greater than 1 kilobase in size account for most bases that vary among human genomes, but are still relatively under-ascertained. Here we use tiling oligonucleotide microarrays, comprising 42 million probes, to generate a comprehensive map of 11,700 copy number variations (CNVs) greater than 443 base pairs, of which most (8,599) have been validated independently. For 4,978 of these CNVs, we generated reference genotypes from 450 individuals of European, African or East Asian ancestry. The predominant mutational mechanisms differ among CNV size classes. Retrotransposition has duplicated and inserted some coding and non-coding DNA segments randomly around the genome. Furthermore, by correlation with known trait-associated single nucleotide polymorphisms (SNPs), we identified 30 loci with CNVs that are candidates for influencing disease susceptibility. Despite this, having assessed the completeness of our map and the patterns of linkage disequilibrium between CNVs and SNPs, we conclude that, for complex traits, the heritability void left by genome-wide association studies will not be accounted for by common CNVs., Genomes vary from one another in multifarious ways, and the totality of this genetic variation underpins the heritability of human traits. Over the past two years, the human reference sequence [...]

Published
2010
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25. Global variation in copy number in the human genome

Author

Redon, Richard, Ishikawa, Shumpei, Fitch, Karen R., Feuk, Lars, Perry, George H., Andrews, T. Daniel, Fiegler, Heike, Shapero, Michael H., Carson, Andrew R., Chen, Wenwei, Cho, Eun Kyung, Dallaire, Stephanie, Freeman, Jennifer L., Gonzalez, Juan R., Gratacos, Monica, Huang, Jing, Kalaitzopoulos, Dimitrios, Komura, Daisuke, MacDonald, Jeffrey R., Marshall, Christian R., Mei, Rui, Montgomery, Lyndal, Nishimura, Kunihiro, Okamura, Kohji, Shen, Fan, Somerville, Martin J., Tchinda, Joelle, Valsesia, Armand, Woodwark, Cara, Yang, Fengtang, Zhang, Junjun, Zerjal, Tatiana, Zhang, Jane, Armengol, Lluis, Conrad, Donald F., Estivill, Xavier, Tyler-Smith, Chris, Carter, Nigel P., Aburatani, Hiroyuki, Lee, Charles, Jones, Keith W., Scherer, Stephen W., and Hurles, Matthew E.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Richard Redon [1]; Shumpei Ishikawa [2, 3]; Karen R. Fitch [4]; Lars Feuk [5, 6]; George H. Perry [7]; T. Daniel Andrews [1]; Heike Fiegler [1]; Michael H. Shapero [...]

Published
2006
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26. The clinical performance of professionally dispensed bleaching gel with added amorphous calcium phosphate

Author

Giniger, Martin, MacDonald, Jeffrey R., Ziemba, Steven, and Felix, Heather

Subjects
Dentifrices -- Evaluation, Oral hygiene products -- Evaluation, Drugs -- Product/Service Evaluations, Health
Abstract

A study on the impact of adding amorphous calcium phosphate to bleaching gel on tooth color and sensitivity is presented. The clinical outcomes are positive, indicating significant reduction of hypersensitivity.

Published
2005

27. Identification of C7orf11 (TTDN1) gene mutations and genetic heterogeneity in nonphotosensitive trichothiodystrophy

Author

Nakabayashi, Kazuhiko, Amann, Daniela, Ren, Yan, Saarialho-Kere, Ulpu, Avidan, Nili, Gentles, Simone, MacDonald, Jeffrey R., Puffenberger, Erik G., Christiano, Angela M., Martinez-Mir, Amalia, Salas-Alanis, Julio C., Rizzo, Renata, Vamos, Esther, Raams, Anja, Les, Clifford, Seboun, Eric, Jaspers, Nicolaas G.J., Beckmann, Jacques S., Jackson, Charles E., and Scherer, Stephen W.

Subjects
Genetic disorders -- Research, Genetics -- Research, Biological sciences
Published
2005

33. Human sterile alpha motif domain 9, a novel gene identified as down-regulated in aggressive fibromatosis, is absent in the mouse

Author

Bell Sherilyn, Koffman Rachel, Kandel Christopher, Lau Kimberly, Ray Jocelyn, Wei Robert Y, MacDonald Jeffrey R, Li Catherine F, Scherer Stephen W, and Alman Benjamin A

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Neoplasia can be driven by mutations resulting in dysregulation of transcription. In the mesenchymal neoplasm, aggressive fibromatosis, subtractive hybridization identified sterile alpha motif domain 9 (SAMD9) as a substantially down regulated gene in neoplasia. SAMD9 was recently found to be mutated in normophosphatemic familial tumoral calcinosis. In this study, we studied the gene structure and function of SAMD9, and its paralogous gene, SAMD9L, and examined these in a variety of species. Results SAMD9 is located on human chromosome 7q21.2 with a paralogous gene sterile alpha motif domain 9 like (SAMD9L) in the head-to-tail orientation. Although both genes are present in a variety of species, the orthologue for SAMD9 is lost in the mouse lineage due to a unique genomic rearrangement. Both SAMD9 and SAMD9L are ubiquitously expressed in human tissues. SAMD9 is expressed at a lower level in a variety of neoplasms associated with β-catenin stabilization, such as aggressive fibromatosis, breast, and colon cancers. SAMD9 and SAMD9L contain an amino-terminal SAM domain, but the remainder of the predicted protein structure does not exhibit substantial homology to other known protein motifs. The putative protein product of SAMD9 localizes to the cytoplasm. In vitro data shows that SAMD9 negatively regulates cell proliferation. Over expression of SAMD9 in the colon cancer cell line, SW480, reduces the volume of tumors formed when transplanted into immune-deficient mice. Conclusion SAMD9 and SAMD9L are a novel family of genes, which play a role regulating cell proliferation and suppressing the neoplastic phenotype. This is the first report as far as we know about a human gene that exists in rat, but is lost in mouse, due to a mouse specific rearrangement, resulting in the loss of the SAMD9 gene.

Published
2007
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34. Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder

Author

Yuen, Ryan K C, Merico, Daniele, Bookman, Matt, Howe, Jennifer L., Thiruvahindrapuram, Bhooma, Patel, Rohan V., Whitney, Joe, Deflaux, Nicole, Bingham, Jonathan, Wang, Zhuozhi, Pellecchia, Giovanna, Buchanan, Janet A., Walker, Susan, Marshall, Christian R., Uddin, Mohammed, Zarrei, Mehdi, Deneault, Eric, D'Abate, Lia, Chan, Ada J S, Koyanagi, Stephanie, Paton, Tara, Pereira, Sergio L., Hoang, Ny, Engchuan, Worrawat, Higginbotham, Edward J., Ho, Karen, Lamoureux, Sylvia, Li, Weili, MacDonald, Jeffrey R., Nalpathamkalam, Thomas, Sung, Wilson W L, Tsoi, Fiona J., Wei, John, Xu, Lizhen, Tasse, Anne Marie, Kirby, Emily, Van Etten, William, Twigger, Simon, Roberts, Wendy, Drmic, Irene, Jilderda, Sanne, Modi, Bonnie Mackinnon, Kellam, Barbara, Szego, Michael, Cytrynbaum, Cheryl, Weksberg, Rosanna, Zwaigenbaum, Lonnie, Woodbury-Smith, Marc, Brian, Jessica, Senman, Lili, Iaboni, Alana, Doyle-Thomas, Krissy, Thompson, Ann, Chrysler, Christina, Leef, Jonathan, Savion-Lemieux, Tal, Smith, Isabel M., Liu, Xudong, Nicolson, Rob, Seifer, Vicki, Fedele, Angie, Cook, Edwin H., Dager, Stephen, Estes, Annette, Gallagher, Louise, Malow, Beth A., Parr, Jeremy R., Spence, Sarah J., Vorstman, Jacob, Frey, Brendan J., Robinson, James T., Strug, Lisa J., Fernandez, Bridget A., Elsabbagh, Mayada, Carter, Melissa T., Hallmayer, Joachim, Knoppers, Bartha M., Anagnostou, Evdokia, Szatmari, Peter, Ring, Robert H., Glazer, David, Pletcher, Mathew T., and Scherer, Stephen W.

Subjects
Neuroscience(all), Next-generation sequencing, Journal Article, Autism spectrum disorders
Abstract

We are performing whole-genome sequencing of families with autism spectrum disorder (ASD) to build a resource (MSSNG) for subcategorizing the phenotypes and underlying genetic factors involved. Here we report sequencing of 5,205 samples from families with ASD, accompanied by clinical information, creating a database accessible on a cloud platform and through a controlled-access internet portal. We found an average of 73.8 de novo single nucleotide variants and 12.6 de novo insertions and deletions or copy number variations per ASD subject. We identified 18 new candidate ASD-risk genes and found that participants bearing mutations in susceptibility genes had significantly lower adaptive ability (P = 6 × 10-4). In 294 of 2,620 (11.2%) of ASD cases, a molecular basis could be determined and 7.2% of these carried copy number variations and/or chromosomal abnormalities, emphasizing the importance of detecting all forms of genetic variation as diagnostic and therapeutic targets in ASD.

Published
2017

35. Nine-year study of the occurrence of culturable viruses in source water for two drinking water treatment plants and the influent and effluent of a wastewater treatment plant in Milwaukee, Wisconsin (August 1194 through July 2003)

Author

Sedmak, Gerald, Bina, David, MacDonald, Jeffrey R., and Couillard, Lon

Subjects
Water treatment plants -- Research, Culture contamination (Biology) -- Research, Sewage -- Purification, Sewage -- Research, Biological sciences
Abstract

The influent and effluent of a local wastewater treatment plant (WWTP) were tested monthly by a modified U.S. Environmental Protection Agency Information Collection Rule (ICR) organic flocculation cell culture procedure for the detection of culturable viruses. Eighteen of 204 samples of source waters for the two drinking water treatment plants were positive for virus and exclusively positive for reoviruses at relatively low titers.

Published
2005

37. Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder

Author

C Yuen, Ryan K, primary, Merico, Daniele, additional, Bookman, Matt, additional, L Howe, Jennifer, additional, Thiruvahindrapuram, Bhooma, additional, Patel, Rohan V, additional, Whitney, Joe, additional, Deflaux, Nicole, additional, Bingham, Jonathan, additional, Wang, Zhuozhi, additional, Pellecchia, Giovanna, additional, Buchanan, Janet A, additional, Walker, Susan, additional, Marshall, Christian R, additional, Uddin, Mohammed, additional, Zarrei, Mehdi, additional, Deneault, Eric, additional, D'Abate, Lia, additional, Chan, Ada J S, additional, Koyanagi, Stephanie, additional, Paton, Tara, additional, Pereira, Sergio L, additional, Hoang, Ny, additional, Engchuan, Worrawat, additional, Higginbotham, Edward J, additional, Ho, Karen, additional, Lamoureux, Sylvia, additional, Li, Weili, additional, MacDonald, Jeffrey R, additional, Nalpathamkalam, Thomas, additional, Sung, Wilson W L, additional, Tsoi, Fiona J, additional, Wei, John, additional, Xu, Lizhen, additional, Tasse, Anne-Marie, additional, Kirby, Emily, additional, Van Etten, William, additional, Twigger, Simon, additional, Roberts, Wendy, additional, Drmic, Irene, additional, Jilderda, Sanne, additional, Modi, Bonnie MacKinnon, additional, Kellam, Barbara, additional, Szego, Michael, additional, Cytrynbaum, Cheryl, additional, Weksberg, Rosanna, additional, Zwaigenbaum, Lonnie, additional, Woodbury-Smith, Marc, additional, Brian, Jessica, additional, Senman, Lili, additional, Iaboni, Alana, additional, Doyle-Thomas, Krissy, additional, Thompson, Ann, additional, Chrysler, Christina, additional, Leef, Jonathan, additional, Savion-Lemieux, Tal, additional, Smith, Isabel M, additional, Liu, Xudong, additional, Nicolson, Rob, additional, Seifer, Vicki, additional, Fedele, Angie, additional, Cook, Edwin H, additional, Dager, Stephen, additional, Estes, Annette, additional, Gallagher, Louise, additional, Malow, Beth A, additional, Parr, Jeremy R, additional, Spence, Sarah J, additional, Vorstman, Jacob, additional, Frey, Brendan J, additional, Robinson, James T, additional, Strug, Lisa J, additional, Fernandez, Bridget A, additional, Elsabbagh, Mayada, additional, Carter, Melissa T, additional, Hallmayer, Joachim, additional, Knoppers, Bartha M, additional, Anagnostou, Evdokia, additional, Szatmari, Peter, additional, Ring, Robert H, additional, Glazer, David, additional, Pletcher, Mathew T, additional, and Scherer, Stephen W, additional

Published
2017
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38. Assessment of an enterovirus sewage surveillance system by comparison of clinical isolates with sewage isolates from Milwaukee, Wisconsin, collected August 1994 to December 2002

Author

Sedmak, Gerald, Bina, David, and MacDonald, Jeffrey R.

Subjects
Enteroviruses -- Research, Microbiological research, Biological sciences
Abstract

The quantity and serotypes of enteroviruses (EVs) in the influent of a local sewage treatment plant were compared to local clinical EV cases to determine if testing of sewage is adequate for an EV surveillance system. Annual peaks of both sewage EV titers and clinical cases occurred in late summer or early fall.

Published
2003

39. Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder

Author

Onderzoek, Brain, Yuen, Ryan K C, Merico, Daniele, Bookman, Matt, Howe, Jennifer L., Thiruvahindrapuram, Bhooma, Patel, Rohan V., Whitney, Joe, Deflaux, Nicole, Bingham, Jonathan, Wang, Zhuozhi, Pellecchia, Giovanna, Buchanan, Janet A., Walker, Susan, Marshall, Christian R., Uddin, Mohammed, Zarrei, Mehdi, Deneault, Eric, D'Abate, Lia, Chan, Ada J S, Koyanagi, Stephanie, Paton, Tara, Pereira, Sergio L., Hoang, Ny, Engchuan, Worrawat, Higginbotham, Edward J., Ho, Karen, Lamoureux, Sylvia, Li, Weili, MacDonald, Jeffrey R., Nalpathamkalam, Thomas, Sung, Wilson W L, Tsoi, Fiona J., Wei, John, Xu, Lizhen, Tasse, Anne Marie, Kirby, Emily, Van Etten, William, Twigger, Simon, Roberts, Wendy, Drmic, Irene, Jilderda, Sanne, Modi, Bonnie Mackinnon, Kellam, Barbara, Szego, Michael, Cytrynbaum, Cheryl, Weksberg, Rosanna, Zwaigenbaum, Lonnie, Woodbury-Smith, Marc, Brian, Jessica, Senman, Lili, Iaboni, Alana, Doyle-Thomas, Krissy, Thompson, Ann, Chrysler, Christina, Leef, Jonathan, Savion-Lemieux, Tal, Smith, Isabel M., Liu, Xudong, Nicolson, Rob, Seifer, Vicki, Fedele, Angie, Cook, Edwin H., Dager, Stephen, Estes, Annette, Gallagher, Louise, Malow, Beth A., Parr, Jeremy R., Spence, Sarah J., Vorstman, Jacob, Frey, Brendan J., Robinson, James T., Strug, Lisa J., Fernandez, Bridget A., Elsabbagh, Mayada, Carter, Melissa T., Hallmayer, Joachim, Knoppers, Bartha M., Anagnostou, Evdokia, Szatmari, Peter, Ring, Robert H., Glazer, David, Pletcher, Mathew T., Scherer, Stephen W., Onderzoek, Brain, Yuen, Ryan K C, Merico, Daniele, Bookman, Matt, Howe, Jennifer L., Thiruvahindrapuram, Bhooma, Patel, Rohan V., Whitney, Joe, Deflaux, Nicole, Bingham, Jonathan, Wang, Zhuozhi, Pellecchia, Giovanna, Buchanan, Janet A., Walker, Susan, Marshall, Christian R., Uddin, Mohammed, Zarrei, Mehdi, Deneault, Eric, D'Abate, Lia, Chan, Ada J S, Koyanagi, Stephanie, Paton, Tara, Pereira, Sergio L., Hoang, Ny, Engchuan, Worrawat, Higginbotham, Edward J., Ho, Karen, Lamoureux, Sylvia, Li, Weili, MacDonald, Jeffrey R., Nalpathamkalam, Thomas, Sung, Wilson W L, Tsoi, Fiona J., Wei, John, Xu, Lizhen, Tasse, Anne Marie, Kirby, Emily, Van Etten, William, Twigger, Simon, Roberts, Wendy, Drmic, Irene, Jilderda, Sanne, Modi, Bonnie Mackinnon, Kellam, Barbara, Szego, Michael, Cytrynbaum, Cheryl, Weksberg, Rosanna, Zwaigenbaum, Lonnie, Woodbury-Smith, Marc, Brian, Jessica, Senman, Lili, Iaboni, Alana, Doyle-Thomas, Krissy, Thompson, Ann, Chrysler, Christina, Leef, Jonathan, Savion-Lemieux, Tal, Smith, Isabel M., Liu, Xudong, Nicolson, Rob, Seifer, Vicki, Fedele, Angie, Cook, Edwin H., Dager, Stephen, Estes, Annette, Gallagher, Louise, Malow, Beth A., Parr, Jeremy R., Spence, Sarah J., Vorstman, Jacob, Frey, Brendan J., Robinson, James T., Strug, Lisa J., Fernandez, Bridget A., Elsabbagh, Mayada, Carter, Melissa T., Hallmayer, Joachim, Knoppers, Bartha M., Anagnostou, Evdokia, Szatmari, Peter, Ring, Robert H., Glazer, David, Pletcher, Mathew T., and Scherer, Stephen W.

Published
2017

40. Genome-wide characteristics of de novo mutations in autism

Author

Yuen, Ryan KC, primary, Merico, Daniele, additional, Cao, Hongzhi, additional, Pellecchia, Giovanna, additional, Alipanahi, Babak, additional, Thiruvahindrapuram, Bhooma, additional, Tong, Xin, additional, Sun, Yuhui, additional, Cao, Dandan, additional, Zhang, Tao, additional, Wu, Xueli, additional, Jin, Xin, additional, Zhou, Ze, additional, Liu, Xiaomin, additional, Nalpathamkalam, Thomas, additional, Walker, Susan, additional, Howe, Jennifer L, additional, Wang, Zhuozhi, additional, MacDonald, Jeffrey R, additional, Chan, Ada JS, additional, D’Abate, Lia, additional, Deneault, Eric, additional, Siu, Michelle T, additional, Tammimies, Kristiina, additional, Uddin, Mohammed, additional, Zarrei, Mehdi, additional, Wang, Mingbang, additional, Li, Yingrui, additional, Wang, Jun, additional, Wang, Jian, additional, Yang, Huanming, additional, Bookman, Matt, additional, Bingham, Jonathan, additional, Gross, Samuel S, additional, Loy, Dion, additional, Pletcher, Mathew, additional, Marshall, Christian R, additional, Anagnostou, Evdokia, additional, Zwaigenbaum, Lonnie, additional, Weksberg, Rosanna, additional, Fernandez, Bridget A, additional, Roberts, Wendy, additional, Szatmari, Peter, additional, Glazer, David, additional, Frey, Brendan J, additional, Ring, Robert H, additional, Xu, Xun, additional, and Scherer, Stephen W, additional

Published
2016
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41. New England Evangelicals Innovate and Grow

Author

MacDonald, Jeffrey R.

Subjects
Vision New England -- Management, Evangelicalism -- New England, Philosophy and religion, Company business management, Management
Abstract

After many years of frustration with New England's rocky spiritual soil, evangelicals in the region have launched more than 100 new churches in the past five years. They have had [...]

Published
2001

42. A high-resolution copy-number variation resource for clinical and population genetics

Author

Uddin, Mohammed, primary, Thiruvahindrapuram, Bhooma, additional, Walker, Susan, additional, Wang, Zhuozhi, additional, Hu, Pingzhao, additional, Lamoureux, Sylvia, additional, Wei, John, additional, MacDonald, Jeffrey R., additional, Pellecchia, Giovanna, additional, Lu, Chao, additional, Lionel, Anath C., additional, Gazzellone, Matthew J., additional, McLaughlin, John R., additional, Brown, Catherine, additional, Andrulis, Irene L., additional, Knight, Julia A., additional, Herbrick, Jo-Anne, additional, Wintle, Richard F., additional, Ray, Peter, additional, Stavropoulos, Dimitri J., additional, Marshall, Christian R., additional, and Scherer, Stephen W., additional

Published
2015
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44. Comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants

Author

Pinto, Dalila, Darvishi, Katayoon, Shi, Xinghua, Rajan, Diana, Rigler, Diane, Fitzgerald, Tom, Lionel, Anath C., Thiruvahindrapuram, Bhooma, MacDonald, Jeffrey R., Mills, Ryan, Prasad, Aparna, Noonan, Kristin, Gribble, Susan, Prigmore, Elena, Donahoe, Patricia K., Smith, Richard S., Park, Ji Hyeon, Hurles, Matthew E., Carter, Nigel P., Lee, Charles, Scherer, Stephen W., Feuk, Lars, Pinto, Dalila, Darvishi, Katayoon, Shi, Xinghua, Rajan, Diana, Rigler, Diane, Fitzgerald, Tom, Lionel, Anath C., Thiruvahindrapuram, Bhooma, MacDonald, Jeffrey R., Mills, Ryan, Prasad, Aparna, Noonan, Kristin, Gribble, Susan, Prigmore, Elena, Donahoe, Patricia K., Smith, Richard S., Park, Ji Hyeon, Hurles, Matthew E., Carter, Nigel P., Lee, Charles, Scherer, Stephen W., and Feuk, Lars

Abstract

We have systematically compared copy number variant (CNV) detection on eleven microarrays to evaluate data quality and CNV calling, reproducibility, concordance across array platforms and laboratory sites, breakpoint accuracy and analysis tool variability. Different analytic tools applied to the same raw data typically yield CNV calls with <50% concordance. Moreover, reproducibility in replicate experiments is <70% for most platforms. Nevertheless, these findings should not preclude detection of large CNVs for clinical diagnostic purposes because large CNVs with poor reproducibility are found primarily in complex genomic regions and would typically be removed by standard clinical data curation. The striking differences between CNV calls from different platforms and analytic tools highlight the importance of careful assessment of experimental design in discovery and association studies and of strict data curation and filtering in diagnostics. The CNV resource presented here allows independent data evaluation and provides a means to benchmark new algorithms.

Published
2011
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45. Towards a comprehensive structural variation map of an individual human genome

Author

Pang, Andy W., MacDonald, Jeffrey R., Pinto, Dalila, Wei, John, Rafiq, Muhammad A., Conrad, Donald F., Park, Hansoo, Hurles, Matthew E., Lee, Charles, Venter, J. Craig, Kirkness, Ewen F., Levy, Samuel, Feuk, Lars, Scherer, Stephen W., Pang, Andy W., MacDonald, Jeffrey R., Pinto, Dalila, Wei, John, Rafiq, Muhammad A., Conrad, Donald F., Park, Hansoo, Hurles, Matthew E., Lee, Charles, Venter, J. Craig, Kirkness, Ewen F., Levy, Samuel, Feuk, Lars, and Scherer, Stephen W.

Abstract

Background: Several genomes have now been sequenced, with millions of genetic variants annotated. While significant progress has been made in mapping single nucleotide polymorphisms (SNPs) and small (< 10 bp) insertion/deletions (indels), the annotation of larger structural variants has been less comprehensive. It is still unclear to what extent a typical genome differs from the reference assembly, and the analysis of the genomes sequenced to date have shown varying results for copy number variation (CNV) and inversions. Results: We have combined computational re-analysis of existing whole genome sequence data with novel microarray-based analysis, and detect 12,178 structural variants covering 40.6 Mb that were not reported in the initial sequencing of the first published personal genome. We estimate a total non-SNP variation content of 48.8 Mb in a single genome. Our results indicate that this genome differs from the consensus reference sequence by approximately 1.2% when considering indels/CNVs, 0.1% by SNPs and approximately 0.3% by inversions. The structural variants impact 4,867 genes, and >24% of structural variants would not be imputed by SNP-association. Conclusions: Our results indicate that a large number of structural variants have been unreported in the individual genomes published to date. This significant extent and complexity of structural variants, as well as the growing recognition of their medical relevance, necessitate they be actively studied in health-related analyses of personal genomes. The new catalogue of structural variants generated for this genome provides a crucial resource for future comparison studies., Delat sista-författarskap.

Published
2010
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49. Association of IMMP2Ldeletions with autism spectrum disorder: A trio family study and meta‐analysis

Author

Zhang, Yanqing, Liu, Yi, Zarrei, Mehdi, Tong, Winnie, Dong, Rui, Wang, Ying, Zhang, Haiyan, Yang, Xiaomeng, MacDonald, Jeffrey R., Uddin, Mohammed, Scherer, Stephen W., and Gai, Zhongtao

Abstract

IMMP2L, the gene encoding the inner mitochondrial membrane peptidase subunit 2‐like protein, has been reported as a candidate gene for Tourette syndrome, autism spectrum disorder (ASD) and additional neurodevelopmental disorders. Here we genotyped 100 trio families with an index proband with autism spectrum disorder in Han Chinese population and found three cases with rare exonic IMMP2Ldeletions. We have conducted a comprehensive meta‐analysis to quantify the association of IMMP2Ldeletions with ASD using 5,568 cases and 10,279 controls. While the IMMP2Ldeletions carried non‐recurrent breakpoints, in contrast to previous reports, our meta‐analysis found no evidence of association (P > 0.05) between IMMP2Ldeletions and ASD. We also observed common exonic deletions impacting IMMP2Lin a separate control (5,971 samples) cohort where subjects were screened for psychiatric conditions. This is the first systematic review and meta‐analysis regarding the effect of IMMP2Ldeletions on ASD, but further investigations in different populations, especially Chinese population may be still needed to confirm our results.

Published
2018
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50. Comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants

Author

Pinto, Dalila, primary, Darvishi, Katayoon, additional, Shi, Xinghua, additional, Rajan, Diana, additional, Rigler, Diane, additional, Fitzgerald, Tom, additional, Lionel, Anath C, additional, Thiruvahindrapuram, Bhooma, additional, MacDonald, Jeffrey R, additional, Mills, Ryan, additional, Prasad, Aparna, additional, Noonan, Kristin, additional, Gribble, Susan, additional, Prigmore, Elena, additional, Donahoe, Patricia K, additional, Smith, Richard S, additional, Park, Ji Hyeon, additional, Hurles, Matthew E, additional, Carter, Nigel P, additional, Lee, Charles, additional, Scherer, Stephen W, additional, and Feuk, Lars, additional

Published
2011
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