Search

Your search keyword '"Sharpe, Ted"' showing total 6 results
Start Over Author "Sharpe, Ted" Publisher cold spring harbor laboratory
6 results on '"Sharpe, Ted"'

1. Defining protein variant functions using high-complexity mutagenesis libraries and enhanced mutant detection software ASMv1.0

Author

Yang, Xiaoping, primary, Hong, Andrew L., additional, Sharpe, Ted, additional, Giacomelli, Andrew O., additional, Lintner, Robert E., additional, Alan, Douglas, additional, Green, Thomas, additional, Hayes, Tikvah K., additional, Piccioni, Federica, additional, Fritchman, Briana, additional, Kawabe, Hinako, additional, Sawyer, Edith, additional, Sprenkle, Luke, additional, Lee, Benjamin P., additional, Persky, Nicole S., additional, Brown, Adam, additional, Greulich, Heidi, additional, Aguirre, Andrew J., additional, Meyerson, Matthew, additional, Hahn, William C., additional, Johannessen, Cory M., additional, and Root, David E., additional

Published
2021
Full Text
View/download PDF

2. An open resource of structural variation for medical and population genetics

Author

Collins, Ryan L., Brand, Harrison, Karczewski, Konrad J., Zhao, Xuefang, Alföldi, Jessica, Francioli, Laurent C., Khera, Amit V., Lowther, Chelsea, Gauthier, Laura D., Wang, Harold, Watts, Nicholas A., Solomonson, Matthew, O’Donnell-Luria, Anne, Baumann, Alexander, Munshi, Ruchi, Walker, Mark, Whelan, Christopher, Huang, Yongqing, Brookings, Ted, Sharpe, Ted, Stone, Matthew R., Valkanas, Elise, Fu, Jack, Tiao, Grace, Laricchia, Kristen M., Ruano-Rubio, Valentin, Stevens, Christine, Gupta, Namrata, Margolin, Lauren, Taylor, Kent D., Lin, Henry J., Rich, Stephen S., Post, Wendy, Chen, Yii-Der Ida, Rotter, Jerome I., Nusbaum, Chad, Philippakis, Anthony, Lander, Eric, Gabriel, Stacey, Neale, Benjamin M., Kathiresan, Sekar, Daly, Mark J., Banks, Eric, MacArthur, Daniel G., and Talkowski, Michael E.

Subjects
Structural variation, 0303 health sciences, 03 medical and health sciences, 0302 clinical medicine, Resource (biology), business.industry, Environmental resource management, Population genetics, Biology, business, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract

SUMMARYStructural variants (SVs) rearrange large segments of the genome and can have profound consequences for evolution and human diseases. As national biobanks, disease association studies, and clinical genetic testing grow increasingly reliant on genome sequencing, population references such as the Genome Aggregation Database (gnomAD) have become integral for interpreting genetic variation. To date, no large-scale reference maps of SVs exist from high-coverage sequencing comparable to those available for point mutations in protein-coding genes. Here, we constructed a reference atlas of SVs across 14,891 genomes from diverse global populations (54% non-European) as a component of gnomAD. We discovered a rich landscape of 433,371 distinct SVs, including 5,295 multi-breakpoint complex SVs across 11 mutational subclasses, and examples of localized chromosome shattering, as in chromothripsis. The average individual harbored 7,439 SVs, which accounted for 25-29% of all rare protein-truncating events per genome. We found strong correlations between constraint against damaging point mutations and rare SVs that both disrupt and duplicate protein-coding sequence, suggesting intolerance to reciprocal dosage alterations for a subset of tightly regulated genes. We also uncovered modest selection against noncoding SVs in cis-regulatory elements, although selection against protein-truncating SVs was stronger than any effect on noncoding SVs. Finally, we benchmarked carrier rates for medically relevant SVs, finding very large (≥1Mb) rare SVs in 3.8% of genomes (~1:26 individuals) and clinically reportable incidental SVs in 0.18% of genomes (~1:556 individuals). These data have been integrated directly into the gnomAD browser (https://gnomad.broadinstitute.org) and will have broad utility for population genetics, disease association, and diagnostic screening.

Published
2019
Full Text
View/download PDF

3. SvABA: genome-wide detection of structural variants and indels by local assembly

Author

Wala, Jeremiah A., primary, Bandopadhayay, Pratiti, additional, Greenwald, Noah F., additional, O'Rourke, Ryan, additional, Sharpe, Ted, additional, Stewart, Chip, additional, Schumacher, Steve, additional, Li, Yilong, additional, Weischenfeldt, Joachim, additional, Yao, Xiaotong, additional, Nusbaum, Chad, additional, Campbell, Peter, additional, Getz, Gad, additional, Meyerson, Matthew, additional, Zhang, Cheng-Zhong, additional, Imielinski, Marcin, additional, and Beroukhim, Rameen, additional

Published
2018
Full Text
View/download PDF

4. SvABA: Genome-wide detection of structural variants and indels by local assembly

Author

Wala, Jeremiah, primary, Bandopadhayay, Pratiti, additional, Greenwald, Noah, additional, O’Rourke, Ryan, additional, Sharpe, Ted, additional, Stewart, Chip, additional, Schumacher, Steve, additional, Li, Yilong, additional, Weischenfeldt, Joachim, additional, Yao, Xiaotong, additional, Nusbaum, Chad, additional, Campbell, Peter, additional, Meyerson, Matthew, additional, Zhang, Cheng-Zhong, additional, Imielinski, Marcin, additional, and Beroukhim, Rameen, additional

Published
2017
Full Text
View/download PDF

5. Finished bacterial genomes from shotgun sequence data

Author

Ribeiro, Filipe J., primary, Przybylski, Dariusz, additional, Yin, Shuangye, additional, Sharpe, Ted, additional, Gnerre, Sante, additional, Abouelleil, Amr, additional, Berlin, Aaron M., additional, Montmayeur, Anna, additional, Shea, Terrance P., additional, Walker, Bruce J., additional, Young, Sarah K., additional, Russ, Carsten, additional, Nusbaum, Chad, additional, MacCallum, Iain, additional, and Jaffe, David B., additional

Published
2012
Full Text
View/download PDF

6. Assemblathon 1: A competitive assessment of de novo short read assembly methods

Author

Earl, Dent, primary, Bradnam, Keith, additional, St. John, John, additional, Darling, Aaron, additional, Lin, Dawei, additional, Fass, Joseph, additional, Yu, Hung On Ken, additional, Buffalo, Vince, additional, Zerbino, Daniel R., additional, Diekhans, Mark, additional, Nguyen, Ngan, additional, Ariyaratne, Pramila Nuwantha, additional, Sung, Wing-Kin, additional, Ning, Zemin, additional, Haimel, Matthias, additional, Simpson, Jared T., additional, Fonseca, Nuno A., additional, Birol, İnanç, additional, Docking, T. Roderick, additional, Ho, Isaac Y., additional, Rokhsar, Daniel S., additional, Chikhi, Rayan, additional, Lavenier, Dominique, additional, Chapuis, Guillaume, additional, Naquin, Delphine, additional, Maillet, Nicolas, additional, Schatz, Michael C., additional, Kelley, David R., additional, Phillippy, Adam M., additional, Koren, Sergey, additional, Yang, Shiaw-Pyng, additional, Wu, Wei, additional, Chou, Wen-Chi, additional, Srivastava, Anuj, additional, Shaw, Timothy I., additional, Ruby, J. Graham, additional, Skewes-Cox, Peter, additional, Betegon, Miguel, additional, Dimon, Michelle T., additional, Solovyev, Victor, additional, Seledtsov, Igor, additional, Kosarev, Petr, additional, Vorobyev, Denis, additional, Ramirez-Gonzalez, Ricardo, additional, Leggett, Richard, additional, MacLean, Dan, additional, Xia, Fangfang, additional, Luo, Ruibang, additional, Li, Zhenyu, additional, Xie, Yinlong, additional, Liu, Binghang, additional, Gnerre, Sante, additional, MacCallum, Iain, additional, Przybylski, Dariusz, additional, Ribeiro, Filipe J., additional, Yin, Shuangye, additional, Sharpe, Ted, additional, Hall, Giles, additional, Kersey, Paul J., additional, Durbin, Richard, additional, Jackman, Shaun D., additional, Chapman, Jarrod A., additional, Huang, Xiaoqiu, additional, DeRisi, Joseph L., additional, Caccamo, Mario, additional, Li, Yingrui, additional, Jaffe, David B., additional, Green, Richard E., additional, Haussler, David, additional, Korf, Ian, additional, and Paten, Benedict, additional

Published
2011
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results