Browsing by Author "Daly, Mark"

Now showing items 41-55 of 55

    • Mismatch Repair Genes Mlh1 and Mlh3 Modify CAG Instability in Huntington's Disease Mice: Genome-Wide and Candidate Approaches 

      Pinto, Ricardo Mouro; Dragileva, Ella; Kirby, Andrew; Lloret, Alejandro; Lopez, Edith; St. Claire, Jason; Panigrahi, Gagan B.; Hou, Caixia; Holloway, Kim; Gillis, Tammy; Guide, Jolene R.; Cohen, Paula E.; Li, Guo-Min; Pearson, Christopher E.; Daly, Mark J.; Wheeler, Vanessa C. (Public Library of Science, 2013)
      The Huntington's disease gene (HTT) CAG repeat mutation undergoes somatic expansion that correlates with pathogenesis. Modifiers of somatic expansion may therefore provide routes for therapies targeting the underlying ...

    • Mono- and Biallelic Variant Effects on Disease at Biobank Scale 

      Heyne, Henrike; Karjalainen, Juha; Karczewski, Konrad; Lemmelä, Susanna; Zhou, Wei; Havulinna, Aki S.; Kurki, Mitja; Rehm, Heidi; Palotie, Aarno; Daly, Mark (Springer Science and Business Media LLC, 2023-01-18)
      Identifying causal factors for Mendelian and common diseases is an ongoing challenge in medical genetics 1 . Population bottleneck events, such as in the Finnish population history, enrich some homozygous variants to ...

    • Mutations causing medullary cystic kidney disease type 1 (MCKD1) lie in a large VNTR in MUC1 missed by massively parallel sequencing 

      Kirby, Andrew; Gnirke, Andreas; Jaffe, David B.; Barešová, Veronika; Pochet, Nathalie; Blumenstiel, Brendan; Ye, Chun; Aird, Daniel; Stevens, Christine; Robinson, James T.; Cabili, Moran N.; Gat-Viks, Irit; Kelliher, Edward; Daza, Riza; DeFelice, Matthew; Hůlková, Helena; Sovová, Jana; Vylet’al, Petr; Antignac, Corinne; Guttman, Mitchell; Handsaker, Robert E.; Perrin, Danielle; Steelman, Scott; Sigurdsson, Snaevar; Scheinman, Steven J.; Sougnez, Carrie; Cibulskis, Kristian; Parkin, Melissa; Green, Todd; Rossin, Elizabeth; Zody, Michael C.; Xavier, Ramnik J.; Pollak, Martin R.; Alper, Seth L.; Lindblad-Toh, Kerstin; Gabriel, Stacey; Hart, P. Suzanne; Regev, Aviv; Nusbaum, Chad; Kmoch, Stanislav; Bleyer, Anthony J.; Lander, Eric S.; Daly, Mark J. (2014)
      While genetic lesions responsible for some Mendelian disorders can be rapidly discovered through massively parallel sequencing (MPS) of whole genomes or exomes, not all diseases readily yield to such efforts. We describe ...

    • Network Analysis of Genome-Wide Selective Constraint Reveals a Gene Network Active in Early Fetal Brain Intolerant of Mutation 

      Choi, Jinmyung; Shooshtari, Parisa; Samocha, Kaitlin E.; Daly, Mark J.; Cotsapas, Chris (Public Library of Science, 2016)
      Using robust, integrated analysis of multiple genomic datasets, we show that genes depleted for non-synonymous de novo mutations form a subnetwork of 72 members under strong selective constraint. We further show this ...

    • No Evidence for Association of Autism with Rare Heterozygous Point Mutations in Contactin-Associated Protein-Like 2 (CNTNAP2), or in Other Contactin-Associated Proteins or Contactins 

      Murdoch, John D.; Gupta, Abha R.; Sanders, Stephan J.; Walker, Michael F.; Keaney, John; Fernandez, Thomas V.; Murtha, Michael T.; Anyanwu, Samuel; Ober, Gordon T.; Raubeson, Melanie J.; DiLullo, Nicholas M.; Villa, Natalie; Waqar, Zainabdul; Sullivan, Catherine; Gonzalez, Luis; Willsey, A. Jeremy; Choe, So-Yeon; Neale, Benjamin M.; Daly, Mark J.; State, Matthew W. (Public Library of Science, 2015)
      Contactins and Contactin-Associated Proteins, and Contactin-Associated Protein-Like 2 (CNTNAP2) in particular, have been widely cited as autism risk genes based on findings from homozygosity mapping, molecular cytogenetics, ...

    • Partitioning heritability by functional annotation using genome-wide association summary statistics 

      Finucane, Hilary K.; Bulik-Sullivan, Brendan; Gusev, Alexander; Trynka, Gosia; Reshef, Yakir; Loh, Po-Ru; Anttila, Verneri; Xu, Han; Zang, Chongzhi; Farh, Kyle; Ripke, Stephan; Day, Felix R.; Consortium, ReproGen; Purcell, Shaun; Stahl, Eli; Lindstrom, Sara; Perry, John R. B.; Okada, Yukinori; Raychaudhuri, Soumya; Daly, Mark; Patterson, Nick; Neale, Benjamin M.; Price, Alkes L. (2015)
      Recent work has demonstrated that some functional categories of the genome contribute disproportionately to the heritability of complex diseases. Here, we analyze a broad set of functional elements, including cell-type-specific ...

    • 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 ...

    • A protein-truncating R179X variant in RNF186 confers protection against ulcerative colitis 

      Rivas, Manuel A.; Graham, Daniel; Sulem, Patrick; Stevens, Christine; Desch, A. Nicole; Goyette, Philippe; Gudbjartsson, Daniel; Jonsdottir, Ingileif; Thorsteinsdottir, Unnur; Degenhardt, Frauke; Mucha, Sören; Kurki, Mitja I.; Li, Dalin; D'Amato, Mauro; Annese, Vito; Vermeire, Severine; Weersma, Rinse K.; Halfvarson, Jonas; Paavola-Sakki, Paulina; Lappalainen, Maarit; Lek, Monkol; Cummings, Beryl; Tukiainen, Taru; Haritunians, Talin; Halme, Leena; Koskinen, Lotta L. E.; Ananthakrishnan, Ashwin N.; Luo, Yang; Heap, Graham A.; Visschedijk, Marijn C.; Barrett, J; de Lange, K; Edwards, C; Hart, A; Hawkey, C; Jostins, L; Kennedy, N; Lamb, C; Lee, J; Lees, C; Mansfield, J; Mathew, C; Mowatt, C; Newman, W; Nimmo, E; Parkes, M; Pollard, M; Prescott, N; Randall, J; Rice, D; Satsangi, J; Simmons, A; Tremelling, M; Uhlig, H; Wilson, D; Abraham, C; Achkar, J.P; Bitton, A; Boucher, G; Croitoru, K; Fleshner, P; Glas, J; Kugathasan, S; Limbergen, J.V; Milgrom, R; Proctor, D; Regueiro, M; Schumm, P.L; Sharma, Y; Stempak, J.M; Targan, S.R; Wang, M.H; MacArthur, Daniel G.; Neale, Benjamin M.; Ahmad, Tariq; Anderson, Carl A.; Brant, Steven R.; Duerr, Richard H.; Silverberg, Mark S.; Cho, Judy H; Palotie, Aarno; Saavalainen, Päivi; Kontula, Kimmo; Färkkilä, Martti; McGovern, Dermot P. B.; Franke, Andre; Stefansson, Kari; Rioux, John D.; Xavier, Ramnik J.; Daly, Mark J.; Barrett, J.; de Lane, K.; Edwards, C.; Hart, A.; Hawkey, C.; Jostins, L.; Kennedy, N.; Lamb, C.; Lee, J.; Lees, C.; Mansfield, J.; Mathew, C.; Mowatt, C.; Newman, B.; Nimmo, E.; Parkes, M.; Pollard, M.; Prescott, N.; Randall, J.; Rice, D.; Satsangi, J.; Simmons, A.; Tremelling, M.; Uhlig, H.; Wilson, D.; Abraham, C.; Achkar, J. P.; Bitton, A.; Boucher, G.; Croitoru, K.; Fleshner, P.; Glas, J.; Kugathasan, S.; Limbergen, J. V.; Milgrom, R.; Proctor, D.; Regueiro, M.; Schumm, P. L.; Sharma, Y.; Stempak, J. M.; Targan, S. R.; Wang, M. H. (Nature Publishing Group, 2016)
      Protein-truncating variants protective against human disease provide in vivo validation of therapeutic targets. Here we used targeted sequencing to conduct a search for protein-truncating variants conferring protection ...

    • The Proteomic Landscape of Human Disease: Construction and Evaluation of Networks Associated to Complex Traits 

      Rossin, Elizabeth Jeffries (2012-11-15)
      Genetic mapping of complex traits has been successful over the last decade, with over 2,000 regions in the genome associated to disease. Yet, the translation of these findings into a better understanding of disease biology ...

    • 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 ...

    • Schizophrenia risk from complex variation of complement component 4 

      Sekar, Aswin; Bialas, Allison R.; de Rivera, Heather; Davis, Avery; Hammond, Timothy R.; Kamitaki, Nolan; Tooley, Katherine; Presumey, Jessy; Baum, Matthew; Van Doren, Vanessa; Genovese, Giulio; Rose, Samuel A.; Handsaker, Robert E.; Daly, Mark J.; Carroll, Michael C.; Stevens, Beth; McCarroll, Steven A. (2016)
      Schizophrenia is a heritable brain illness with unknown pathogenic mechanisms. Schizophrenia’s strongest genetic association at a population level involves variation in the Major Histocompatibility Complex (MHC) locus, but ...

    • A Second Major Histocompatibility Complex Susceptibility Locus for Multiple Sclerosis 

      Yeo, Tai Wai; Gregory, Simon G; Barcellos, Lisa F; Walton, Amie; Goris, An; Fenoglio, Chiara; Ban, Maria; Taylor, Craig J; Goodman, Reyna S; Walsh, Emily; Wolfish, Cara S; Horton, Roger; Traherne, James; Beck, Stephan; Trowsdale, John; Caillier, Stacy J; Green, Todd; Pobywajlo, Susan; Pericak-Vance, Margaret A; Haines, Jonathan L; Oksenberg, Jorge R; Hauser, Stephen L; Compston, Alastair; Rioux, John D; Sawcer, Stephen; De Jager, Philip Lawrence; Ivinson, Adrian J.; Lander, Eric Steven; Daly, Mark Joseph; Hafler, David A. (Wiley Subscription Services, Inc., A Wiley Company, 2007)
      Objective: Variation in the major histocompatibility complex (MHC) on chromosome 6p21 is known to influence susceptibility to multiple sclerosis with the strongest effect originating from the HLA-DRB1 gene in the class II ...

    • Structural Forms of the Human Amylase Locus and Their Relationships to SNPs, Haplotypes, and Obesity 

      Usher, Christina Leigh (2015-05-18)
      Hundreds of human genes reside in structurally complex loci that elude molecular analysis and assessment in genome-wide association studies (GWAS). One such locus contains the three different amylase genes (AMY2B, AMY2A, ...

    • 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 ...

    • Testing For An Unusual Distribution Of Rare Variants 

      Neale, Benjamin Michael; Rivas, Manuel A.; Voight, Benjamin F.; Altshuler, David Matthew; Devlin, Bernie; Orho-Melander, Marju; Kathiresan, Sekar; Purcell, Shaun; Roeder, Kathryn; Daly, Mark Joseph (Public Library of Science, 2011)
      Technological advances make it possible to use high-throughput sequencing as a primary discovery tool of medical genetics, specifically for assaying rare variation. Still this approach faces the analytic challenge that the ...