Search Results - "Handsaker, Robert"

Pathways Disrupted in Human ALS Motor Neurons Identified through Genetic Correction of Mutant SOD1 by Kiskinis, Evangelos, Sandoe, Jackson, Williams, Luis A., Boulting, Gabriella L., Moccia, Rob, Wainger, Brian J., Han, Steve, Peng, Theodore, Thams, Sebastian, Mikkilineni, Shravani, Mellin, Cassidy, Merkle, Florian T., Davis-Dusenbery, Brandi N., Ziller, Michael, Oakley, Derek, Ichida, Justin, Di Costanzo, Stefania, Atwater, Nick, Maeder, Morgan L., Goodwin, Mathew J., Nemesh, James, Handsaker, Robert E., Paull, Daniel, Noggle, Scott, McCarroll, Steven A., Joung, J. Keith, Woolf, Clifford J., Brown, Robert H., Eggan, Kevin

“…Although many distinct mutations in a variety of genes are known to cause Amyotrophic Lateral Sclerosis (ALS), it remains poorly understood how they…”
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Protein-coding repeat polymorphisms strongly shape diverse human phenotypes by Mukamel, Ronen E, Handsaker, Robert E, Sherman, Maxwell A, Barton, Alison R, Zheng, Yiming, McCarroll, Steven A, Loh, Po-Ru

“…Many human proteins contain domains that vary in size or copy number because of variable numbers of tandem repeats (VNTRs) in protein-coding exons. However,…”
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Schizophrenia risk from complex variation of complement component 4 by 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.

“…Schizophrenia is a heritable brain illness with unknown pathogenic mechanisms. Schizophrenia’s strongest genetic association at a population level involves…”
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Genetic Variation in Human DNA Replication Timing by Koren, Amnon, Handsaker, Robert E., Kamitaki, Nolan, Karlić, Rosa, Ghosh, Sulagna, Polak, Paz, Eggan, Kevin, McCarroll, Steven A.

“…Genomic DNA replicates in a choreographed temporal order that impacts the distribution of mutations along the genome. We show here that DNA replication timing…”
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The variant call format and VCFtools by Danecek, Petr, Auton, Adam, Abecasis, Goncalo, Albers, Cornelis A., Banks, Eric, DePristo, Mark A., Handsaker, Robert E., Lunter, Gerton, Marth, Gabor T., Sherry, Stephen T., McVean, Gilean, Durbin, Richard

“…The variant call format (VCF) is a generic format for storing DNA polymorphism data such as SNPs, insertions, deletions and structural variants, together with…”
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Discovery and Statistical Genotyping of Copy-Number Variation from Whole-Exome Sequencing Depth by FROMER, Menachem, MORAN, Jennifer L, KIROV, George, SULLIVAN, Patrick F, HULTMAN, Christina M, SKLAR, Pamela, PURCELL, Shaun M, CHAMBERT, Kimberly, BANKS, Eric, BERGEN, Sarah E, RUDERFER, DouglasM, HANDSAKER, Robert E, MCCARROLL, Steven A, O'DONOVAN, Michael C, OWEN, Michael J

“…Sequencing of gene-coding regions (the exome) is increasingly used for studying human disease, for which copy-number variants (CNVs) are a critical genetic…”
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Human pluripotent stem cells recurrently acquire and expand dominant negative P53 mutations by Merkle, Florian T., Ghosh, Sulagna, Kamitaki, Nolan, Mitchell, Jana, Avior, Yishai, Mello, Curtis, Kashin, Seva, Mekhoubad, Shila, Ilic, Dusko, Charlton, Maura, Saphier, Genevieve, Handsaker, Robert E., Genovese, Giulio, Bar, Shiran, Benvenisty, Nissim, McCarroll, Steven A., Eggan, Kevin

“…The authors surveyed whole-exome and RNA-sequencing data from 252 unique pluripotent stem cell lines, some of which are in the pipeline for clinical use, and…”
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Large multiallelic copy number variations in humans by Handsaker, Robert E, Van Doren, Vanessa, Berman, Jennifer R, Genovese, Giulio, Kashin, Seva, Boettger, Linda M, McCarroll, Steven A

“…Steven McCarroll and colleagues report an analysis of multiallelic copy number variants (mCNVs). They characterize mCNVs in 849 whole-genome sequences from the…”
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Clonal Hematopoiesis and Blood-Cancer Risk Inferred from Blood DNA Sequence by Genovese, Giulio, Kähler, Anna K, Handsaker, Robert E, Lindberg, Johan, Rose, Samuel A, Bakhoum, Samuel F, Chambert, Kimberly, Mick, Eran, Neale, Benjamin M, Fromer, Menachem, Purcell, Shaun M, Svantesson, Oscar, Landén, Mikael, Höglund, Martin, Lehmann, Sören, Gabriel, Stacey B, Moran, Jennifer L, Lander, Eric S, Sullivan, Patrick F, Sklar, Pamela, Grönberg, Henrik, Hultman, Christina M, McCarroll, Steven A

“…In this study, clonal hematopoiesis with somatic mutations was found in 10% of otherwise healthy people older than 65. The risk of hematologic cancer was…”
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Insights into clonal haematopoiesis from 8,342 mosaic chromosomal alterations by Loh, Po-Ru, Genovese, Giulio, Handsaker, Robert E., Finucane, Hilary K., Reshef, Yakir A., Palamara, Pier Francesco, Birmann, Brenda M., Talkowski, Michael E., Bakhoum, Samuel F., McCarroll, Steven A., Price, Alkes L.

“…The selective pressures that shape clonal evolution in healthy individuals are largely unknown. Here we investigate 8,342 mosaic chromosomal alterations, from…”
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Discovery and genotyping of genome structural polymorphism by sequencing on a population scale by McCarroll, Steven A, Handsaker, Robert E, Korn, Joshua M, Nemesh, James

“…Steven McCarroll and colleagues report an analytical framework for characterizing genome deletion polymorphism in populations, applied here to the low coverage…”
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Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences by Poznik, G David, Xue, Yali, Mendez, Fernando L, Willems, Thomas F, Massaia, Andrea, Wilson Sayres, Melissa A, Ayub, Qasim, McCarthy, Shane A, Narechania, Apurva, Kashin, Seva, Chen, Yuan, Banerjee, Ruby, Rodriguez-Flores, Juan L, Cerezo, Maria, Shao, Haojing, Gymrek, Melissa, Malhotra, Ankit, Louzada, Sandra, Desalle, Rob, Ritchie, Graham R S, Cerveira, Eliza, Fitzgerald, Tomas W, Garrison, Erik, Marcketta, Anthony, Mittelman, David, Romanovitch, Mallory, Zhang, Chengsheng, Zheng-Bradley, Xiangqun, Abecasis, Gonçalo R, McCarroll, Steven A, Flicek, Paul, Underhill, Peter A, Coin, Lachlan, Zerbino, Daniel R, Yang, Fengtang, Lee, Charles, Clarke, Laura, Auton, Adam, Erlich, Yaniv, Handsaker, Robert E, Bustamante, Carlos D, Tyler-Smith, Chris

“…Chris Tyler-Smith, Carlos Bustamante and colleagues report an analysis of 1,244 human Y chromosomes from the 1000 Genomes Project. They find that copy number…”
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SNAP: a web-based tool for identification and annotation of proxy SNPs using HapMap by Johnson, Andrew D., Handsaker, Robert E., Pulit, Sara L., Nizzari, Marcia M., O'Donnell, Christopher J., de Bakker, Paul I. W.

“…The interpretation of genome-wide association results is confounded by linkage disequilibrium between nearby alleles. We have developed a flexible…”
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An integrated map of structural variation in 2,504 human genomes by Sudmant, Peter H., Rausch, Tobias, Gardner, Eugene J., Handsaker, Robert E., Abyzov, Alexej, Huddleston, John, Zhang, Yan, Ye, Kai, Jun, Goo, Hsi-Yang Fritz, Markus, Konkel, Miriam K., Malhotra, Ankit, Stütz, Adrian M., Shi, Xinghua, Paolo Casale, Francesco, Chen, Jieming, Hormozdiari, Fereydoun, Dayama, Gargi, Chen, Ken, Malig, Maika, Chaisson, Mark J. P., Walter, Klaudia, Meiers, Sascha, Kashin, Seva, Garrison, Erik, Auton, Adam, Lam, Hugo Y. K., Jasmine Mu, Xinmeng, Alkan, Can, Antaki, Danny, Bae, Taejeong, Cerveira, Eliza, Chines, Peter, Chong, Zechen, Clarke, Laura, Dal, Elif, Ding, Li, Emery, Sarah, Fan, Xian, Gujral, Madhusudan, Kahveci, Fatma, Kidd, Jeffrey M., Kong, Yu, Lameijer, Eric-Wubbo, McCarthy, Shane, Flicek, Paul, Gibbs, Richard A., Marth, Gabor, Mason, Christopher E., Menelaou, Androniki, Muzny, Donna M., Nelson, Bradley J., Noor, Amina, Parrish, Nicholas F., Pendleton, Matthew, Quitadamo, Andrew, Raeder, Benjamin, Schadt, Eric E., Romanovitch, Mallory, Schlattl, Andreas, Sebra, Robert, Shabalin, Andrey A., Untergasser, Andreas, Walker, Jerilyn A., Wang, Min, Yu, Fuli, Zhang, Chengsheng, Zhang, Jing, Zheng-Bradley, Xiangqun, Zhou, Wanding, Zichner, Thomas, Sebat, Jonathan, Batzer, Mark A., McCarroll, Steven A., Mills, Ryan E., Gerstein, Mark B., Bashir, Ali, Stegle, Oliver, Devine, Scott E., Lee, Charles, Eichler, Evan E., Korbel, Jan O.

“…Structural variants are implicated in numerous diseases and make up the majority of varying nucleotides among human genomes. Here we describe an integrated set…”
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Genetic studies of body mass index yield new insights for obesity biology by Croteau-Chonka, Damien C., Wood, Andrew R., Absher, Devin, Bragg-Gresham, Jennifer L., Buyske, Steven, Feitosa, Mary F., Mangino, Massimo, Mateo Leach, Irene, Palmer, Cameron D., Pasko, Dorota, Ju Sung, Yun, Teumer, Alexander, van der Laan, Sander W., Ärnlöv, Johan, Berne, Christian, Bonnycastle, Lori L., Bruinenberg, Marcel, Ida Chen, Yii-Der, de Craen, Anton J. M., Delgado, Graciela, Fraser, Ross M., Grönberg, Henrik, Gusto, Gaëlle, Hassinen, Maija, Jeff, Janina M., Kinnunen, Leena, Kratzer, Wolfgang, Lee, Nanette R., Lichtner, Peter, Lind, Lars, Sin Lo, Ken, Lorbeer, Roberto, Mahajan, Anubha, Milani, Lili, Monda, Keri L., Nolte, Ilja M., Pilz, Stefan, Rettig, Rainer, Ripke, Stephan, Sanna, Serena, Schumacher, Fredrick R., Scott, William R., Smolonska, Joanna, Stirrups, Kathleen, Stringham, Heather M., Uh, Hae-Won, Vandenput, Liesbeth, Warren, Helen R., Brennan, Eoin P., Drong, Alexander W., Min, Josine L., Okada, Yukinori, Takahashi, Atsushi, Tanaka, Toshihiro, Westra, Harm-Jan, Campbell, Harry, den Ruijter, Hester M., Erbel, Raimund, Farrall, Martin, Franco, Oscar H., Gejman, Pablo V., Gieger, Christian, Gottesman, Omri, Hingorani, Aroon D., Hyppönen, Elina, Jarvelin, Marjo-Riitta, Jöckel, Karl-Heinz, Johansen, Berit, Kooperberg, Charles, Langenberg, Claudia, Postma, Dirkje S., Price, Jackie F., Rao, D. C., Rioux, John D., Schunkert, Heribert, Shuldiner, Alan R., Strauch, Konstantin, Tremblay, Angelo, Adair, Linda S., de Bakker, Paul I. W., Ferrucci, Luigi, Hveem, Kristian, März, Winfried, Munroe, Patricia B., Njølstad, Inger, Palmer, Colin N. A., Pedersen, Nancy L., Pérusse, Louis, Saaristo, Timo E., Saleheen, Danish, Sattar, Naveed, Eline Slagboom, P., Tuomilehto, Jaakko, Deloukas, Panos, Stefansson, Kari, van Duijn, Cornelia M., Willer, Cristen J., Ingelsson, Erik, Hirschhorn, Joel N., Loos, Ruth J. F.

“…Obesity is heritable and predisposes to many diseases. To understand the genetic basis of obesity better, here we conduct a genome-wide association study and…”
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Recurring exon deletions in the HP (haptoglobin) gene contribute to lower blood cholesterol levels by Boettger, Linda M, Salem, Rany M, Handsaker, Robert E, Peloso, Gina M, Kathiresan, Sekar, Hirschhorn, Joel N, McCarroll, Steven A

“…Steven McCarroll and colleagues present a detailed study of copy number variation of exons within the human HP (haptoglobin) gene. They show that HP exons…”
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A whole-genome sequence study identifies genetic risk factors for neuromyelitis optica by Estrada, Karol, Whelan, Christopher W., Zhao, Fengmei, Bronson, Paola, Handsaker, Robert E., Sun, Chao, Carulli, John P., Harris, Tim, Ransohoff, Richard M., McCarroll, Steven A., Day-Williams, Aaron G., Greenberg, Benjamin M., MacArthur, Daniel G.

“…Neuromyelitis optica (NMO) is a rare autoimmune disease that affects the optic nerve and spinal cord. Most NMO patients ( > 70%) are seropositive for…”
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Mutations causing medullary cystic kidney disease type 1 lie in a large VNTR in MUC1 missed by massively parallel sequencing by 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

“…Anthony Bleyer, Eric Lander, Mark Daly and colleagues show that frameshift mutations in a large VNTR of MUC1 cause medullary cystic kidney disease type 1…”
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A concerted neuron–astrocyte program declines in ageing and schizophrenia by Ling, Emi, Nemesh, James, Goldman, Melissa, Kamitaki, Nolan, Reed, Nora, Handsaker, Robert E., Genovese, Giulio, Vogelgsang, Jonathan S., Gerges, Sherif, Kashin, Seva, Ghosh, Sulagna, Esposito, John M., Morris, Kiely, Meyer, Daniel, Lutservitz, Alyssa, Mullally, Christopher D., Wysoker, Alec, Spina, Liv, Neumann, Anna, Hogan, Marina, Ichihara, Kiku, Berretta, Sabina, McCarroll, Steven A.

“…Human brains vary across people and over time; such variation is not yet understood in cellular terms. Here we describe a relationship between people’s…”
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Structural haplotypes and recent evolution of the human 17q21.31 region by Boettger, Linda M, Handsaker, Robert E, Zody, Michael C, McCarroll, Steven A

“…Steven McCarroll and colleagues use a population genetics approach to identify nine different structural forms of the 17q21.31 inversion region. They show that…”
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