A
Amy Goodale
Researcher at Broad Institute
Publications - 42
Citations - 5340
Amy Goodale is an academic researcher from Broad Institute. The author has contributed to research in topics: Biology & Gene. The author has an hindex of 15, co-authored 25 publications receiving 3055 citations.
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Journal ArticleDOI
Defining a Cancer Dependency Map
Aviad Tsherniak,Francisca Vazquez,Francisca Vazquez,Phil Montgomery,Barbara A. Weir,Barbara A. Weir,Gregory Kryukov,Gregory Kryukov,Glenn S. Cowley,Stanley Gill,Stanley Gill,William F. Harrington,Sasha Pantel,John M. Krill-Burger,Robin M. Meyers,Levi D. Ali,Amy Goodale,Yenarae Lee,Guozhi Jiang,Jessica Hsiao,William F.J Gerath,Sara Howell,Erin Merkel,Mahmoud Ghandi,Levi A. Garraway,David E. Root,Todd R. Golub,Jesse S. Boehm,William C. Hahn +28 more
TL;DR: DEMETER, an analytical framework that segregates on- from off-target effects of RNAi, demonstrates the basis behind one such predictive model linking hypermethylation of the UBB ubiquitin gene to a dependency on UBC and provides a foundation for a cancer dependency map that facilitates the prioritization of therapeutic targets.
Journal ArticleDOI
Computational correction of copy number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells.
Robin M. Meyers,Jordan Bryan,James M. McFarland,Barbara A. Weir,Ann E. Sizemore,Han Xu,Neekesh V. Dharia,Phillip G. Montgomery,Glenn S. Cowley,Sasha Pantel,Amy Goodale,Yenarae Lee,Levi D. Ali,Guozhi Jiang,Rakela Lubonja,William F. Harrington,Matthew Strickland,Ting Wu,Derek C. Hawes,Victor A. Zhivich,Meghan R. Wyatt,Zohra Kalani,Jaime J. Chang,Michael Okamoto,Kimberly Stegmaier,Todd R. Golub,Jesse S. Boehm,Francisca Vazquez,Francisca Vazquez,David E. Root,William C. Hahn,Aviad Tsherniak +31 more
TL;DR: CERES, a computational method to estimate gene-dependency levels from CRISPR–Cas9 essentiality screens while accounting for the copy number–specific effect, is developed and found that CERES decreased false-positive results and estimated sgRNA activity for both this data set and previously published screens performed with different sg RNA libraries.
Journal ArticleDOI
Genomic Copy Number Dictates a Gene-Independent Cell Response to CRISPR/Cas9 Targeting
Andrew J. Aguirre,Robin M. Meyers,Barbara A. Weir,Francisca Vazquez,Cheng-Zhong Zhang,Uri Ben-David,April Cook,Gavin Ha,William F. Harrington,Mihir B. Doshi,Maria Kost-Alimova,Stanley Gill,Han Xu,Levi D. Ali,Guozhi Jiang,Sasha Pantel,Yenarae Lee,Amy Goodale,Andrew D. Cherniack,Coyin Oh,Gregory V. Kryukov,Glenn S. Cowley,Levi A. Garraway,Kimberly Stegmaier,Charles W. M. Roberts,Todd R. Golub,Matthew Meyerson,David E. Root,Aviad Tsherniak,William C. Hahn +29 more
TL;DR: It is found that the number of CRISPR/Cas9-induced DNA breaks dictates a gene-independent antiproliferative response in cells, which has practical implications for using CRISpr/cas9 to interrogate cancer gene function and illustrate that cancer cells are highly sensitive to site-specific DNA damage, which may provide a path to novel therapeutic strategies.
Posted ContentDOI
Computational correction of copy-number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells
Robin M. Meyers,Jordan Bryan,James M. McFarland,Barbara A. Weir,Ann E. Sizemore,Han Xu,Neekesh V. Dharia,Phillip G. Montgomery,Glenn S. Cowley,Sasha Pantel,Amy Goodale,Yenarae Lee,Levi D. Ali,Guozhi Jiang,Rakela Lubonja,William F. Harrington,Matthew Strickland,Ting Wu,Derek C. Hawes,Victor A. Zhivich,Meghan R. Wyatt,Zohra Kalani,Jaime J. Chang,Michael Okamoto,Todd R. Golub,Jesse S. Boehm,Francisca Vazquez,David E. Root,William C. Hahn,Aviad Tsherniak +29 more
TL;DR: CERES, a computational method to estimate gene dependency levels from CRISPR-Cas9 essentiality screens while accounting for the copy-number-specific effect, as well as variable sgRNA activity, is developed and applied to sets of screens performed with different sgRNAs and found that it reduces false positive results and provides meaningful estimates of sg RNA activity.
Journal ArticleDOI
Optimized libraries for CRISPR-Cas9 genetic screens with multiple modalities
Kendall R Sanson,Ruth E Hanna,Mudra Hegde,Katherine F Donovan,Christine Strand,Meagan E Sullender,Emma W Vaimberg,Amy Goodale,David E. Root,Federica Piccioni,John G. Doench +10 more
TL;DR: The recently-described CRISPRko library (Brunello) is more effective than previously published libraries at distinguishing essential and non-essential genes, providing approximately the same perturbation-level performance improvement over GeC KO libraries as GeCKO provided over RNAi.