Browsing by Author "Samocha, Kaitlin E."
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Analysis of Rare, Exonic Variation amongst Subjects with Autism Spectrum Disorders and Population Controls
Liu, Li; Sabo, Aniko; Neale, Benjamin Michael; Nagaswamy, Uma; Stevens, Christine; Lim, Elaine; Bodea, Corneliu A.; Muzny, Donna; Reid, Jeffrey G.; Banks, Eric; Coon, Hillary; DePristo, Mark; Dinh, Huyen; Fennel, Tim; Flannick, Jason A.; Gabriel, Stacey; Garimella, Kiran; Gross, Shannon; Hawes, Alicia; Lewis, Lora; Makarov, Vladimir; Maguire, Jared; Newsham, Irene; Poplin, Ryan; Ripke, Stephan; Shakir, Khalid; Samocha, Kaitlin Elisabeth; Wu, Yuanqing; Boerwinkle, Eric; Buxbaum, Joseph D.; Cook, Edwin H., Jr.; Devlin, Bernie; Schellenberg, Gerard D.; Sutcliffe, James S.; Daly, Mark Joseph; Gibbs, Richard A.; Roeder, Kathryn (Public Library of Science, 2013)We report on results from whole-exome sequencing (WES) of 1,039 subjects diagnosed with autism spectrum disorders (ASD) and 870 controls selected from the NIMH repository to be of similar ancestry to cases. The WES data ... -
The ExAC browser: displaying reference data information from over 60 000 exomes
Karczewski, Konrad J.; Weisburd, Ben; Thomas, Brett; Solomonson, Matthew; Ruderfer, Douglas M.; Kavanagh, David; Hamamsy, Tymor; Lek, Monkol; Samocha, Kaitlin E.; Cummings, Beryl B.; Birnbaum, Daniel; Daly, Mark J.; MacArthur, Daniel G. (Oxford University Press, 2017)Worldwide, hundreds of thousands of humans have had their genomes or exomes sequenced, and access to the resulting data sets can provide valuable information for variant interpretation and understanding gene function. Here, ... -
Exome Sequencing in Schizophrenia-Affected Parent–offspring Trios Reveals Risk Conferred by Protein-Coding De Novo Mutations
Howrigan, Daniel; Rose, Samuel A.; Samocha, Kaitlin E.; Fromer, Menachem; Cerrato, Felecia; Chen, Wei J.; Churchhouse, Claire; Chambert, Kimberly; Chandler, Sharon D.; Daly, Mark; Dumont, Ashley; Genovese, Giulio; Hwu, Hai-Gwo; Laird, Nan; Kosmicki, Jack; Moran, Jennifer L.; Singh, Tarjinder; McCarroll, Steven; Faraone, Stephen V.; Glatt, Stephen J.; McCarroll, Steven; Tsuang, Ming; Neale, Benjamin (Springer Science and Business Media LLC, 2020-01-13)Protein-coding de novo mutations (DNMs) are significant risk factors in many neurodevelopmental disorders, whereas association with schizophrenia (SCZ) risk thus far has been modest. We analyze whole-exome sequence from ... -
A framework for the interpretation of de novo mutation in human disease
Samocha, Kaitlin E.; Robinson, Elise B.; Sanders, Stephan J.; Stevens, Christine; Sabo, Aniko; McGrath, Lauren M.; Kosmicki, Jack A.; Rehnström, Karola; Mallick, Swapan; Kirby, Andrew; Wall, Dennis P.; MacArthur, Daniel G.; Gabriel, Stacey B.; dePristo, Mark; Purcell, Shaun M.; Palotie, Aarno; Boerwinkle, Eric; Buxbaum, Joseph D.; Cook, Edwin H.; Gibbs, Richard A.; Schellenberg, Gerard D.; Sutcliffe, James S.; Devlin, Bernie; Roeder, Kathryn; Neale, Benjamin M.; Daly, Mark J. (2014)Spontaneously arising (‘de novo’) mutations play an important role in medical genetics. For diseases with extensive locus heterogeneity – such as autism spectrum disorders (ASDs) – the signal from de novo mutations (DNMs) ... -
Genetic risk for autism spectrum disorders and neuropsychiatric variation in the general population
Robinson, Elise B.; St. Pourcain, Beate; Anttila, Verneri; Kosmicki, Jack A.; Bulik-Sullivan, Brendan; Grove, Jakob; Maller, Julian; Samocha, Kaitlin E.; Sanders, Stephan J.; Ripke, Stephan; Martin, Joanna; Hollegaard, Mads V.; Werge, Thomas; Hougaard, David M.; Neale, Benjamin M.; Evans, David M.; Skuse, David; Mortensen, Preben Bo; Børglum, Anders D.; Ronald, Angelica; Smith, George Davey; Daly, Mark J. (2016)Almost all genetic risk factors for autism spectrum disorders (ASDs) can be found in the general population, but the effects of that risk are unclear in people not ascertained for neuropsychiatric symptoms. Using several ... -
Modeling Rare Protein-Coding Variation to Identify Mutation-Intolerant Genes With Application to Disease
Samocha, Kaitlin E. (2016-05-06)Sequencing exomes—the 1% of the genome that codes for proteins—has increased the rate at which the genetic basis of a patient’s disease is determined. Unfortunately, when a patient does not carry a well-established pathogenic ... -
Patterns and rates of exonic de novo mutations in autism spectrum disorders
Neale, Benjamin Michael; Kou, Yan; Liu, Li; Ma'ayan, Avi; Samocha, Kaitlin Elisabeth; Sabo, Aniko; Lin, Chiao-Feng; Stevens, Christine; Wang, Li-San; Makarov, Vladimir; Polak, Pazi Penchas; Yoon, Seungtai; Maguire, Jared; Crawford, Emily L.; Campbell, Nicholas G.; Geller, Evan T.; Valladares, Otto; Shafer, Chad; Liu, Han; Zhao, Tuo; Cai, Guiqing; Lihm, Jayon; Dannenfelser, Ruth; Jabado, Omar; Peralta, Zuleyma; Nagaswamy, Uma; Muzny, Donna; Reid, Jeffrey G.; Newsham, Irene; Wu, Yuanqing; Lewis, Lora; Han, Yi; Voight, Benjamin F.; Lim, Elaine; Rossin, Elizabeth Jeffries; Kirby, Andrew; Flannick, Jason A.; Fromer, Menachem; Shakir, Khalid; Fennell, Tim; Garimella, Kiran; Banks, Eric; Poplin, Ryan; Gabriel, Stacey; DePristo, Mark; Wimbish, Jack R.; Boone, Braden E.; Levy, Shawn E.; Betancur, Catalina; Sunyaev, Shamil R.; Boerwinkle, Eric; Buxbaum, Joseph D.; Cook, Edwin H.; Devlin, Bernie; Gibbs, Richard A.; Roeder, Kathryn; Schellenberg, Gerard D.; Sutcliffe, James S.; Daly, Mark Joseph (2013)Autism spectrum disorders (ASD) are believed to have genetic and environmental origins, yet in only a modest fraction of individuals can specific causes be identified1,2. To identify further genetic risk factors, we assess ... -
Quantifying unobserved protein-coding variants in human populations provides a roadmap for large-scale sequencing projects
Zou, James; Valiant, Gregory; Valiant, Paul; Karczewski, Konrad; Chan, Siu On; Samocha, Kaitlin; Lek, Monkol; Sunyaev, Shamil; Daly, Mark; MacArthur, Daniel G. (Nature Publishing Group, 2016)As new proposals aim to sequence ever larger collection of humans, it is critical to have a quantitative framework to evaluate the statistical power of these projects. We developed a new algorithm, UnseenEst, and applied ... -
Synaptic, transcriptional, and chromatin genes disrupted in autism
De Rubeis, Silvia; He, Xin; Goldberg, Arthur P.; Poultney, Christopher S.; Samocha, Kaitlin; Cicek, A Ercument; Kou, Yan; Liu, Li; Fromer, Menachem; Walker, Susan; Singh, Tarjinder; Klei, Lambertus; Kosmicki, Jack; Fu, Shih-Chen; Aleksic, Branko; Biscaldi, Monica; Bolton, Patrick F.; Brownfeld, Jessica M.; Cai, Jinlu; Campbell, Nicholas J.; Carracedo, Angel; Chahrour, Maria H.; Chiocchetti, Andreas G.; Coon, Hilary; Crawford, Emily L.; Crooks, Lucy; Curran, Sarah R.; Dawson, Geraldine; Duketis, Eftichia; Fernandez, Bridget A.; Gallagher, Louise; Geller, Evan; Guter, Stephen J.; Hill, R. Sean; Ionita-Laza, Iuliana; Gonzalez, Patricia Jimenez; Kilpinen, Helena; Klauck, Sabine M.; Kolevzon, Alexander; Lee, Irene; Lei, Jing; Lehtimäki, Terho; Lin, Chiao-Feng; Ma'ayan, Avi; Marshall, Christian R.; McInnes, Alison L.; Neale, Benjamin; Owen, Michael J.; Ozaki, Norio; Parellada, Mara; Parr, Jeremy R.; Purcell, Shaun; Puura, Kaija; Rajagopalan, Deepthi; Rehnström, Karola; Reichenberg, Abraham; Sabo, Aniko; Sachse, Michael; Sanders, Stephan J.; Schafer, Chad; Schulte-Rüther, Martin; Skuse, David; Stevens, Christine; Szatmari, Peter; Tammimies, Kristiina; Valladares, Otto; Voran, Annette; Wang, Li-San; Weiss, Lauren A.; Willsey, A. Jeremy; Yu, Timothy W.; Yuen, Ryan K.C.; Cook, Edwin H.; Freitag, Christine M.; Gill, Michael; Hultman, Christina M.; Lehner, Thomas; Palotie, Aarno; Schellenberg, Gerard D.; Sklar, Pamela; State, Matthew W.; Sutcliffe, James S.; Walsh, Christopher A.; Scherer, Stephen W.; Zwick, Michael E.; Barrett, Jeffrey C.; Cutler, David J.; Roeder, Kathryn; Devlin, Bernie; Daly, Mark J.; Buxbaum, Joseph D. (2014)Summary The genetic architecture of autism spectrum disorder involves the interplay of common and rare variation and their impact on hundreds of genes. Using exome sequencing, analysis of rare coding variation in 3,871 ...