Improved estimation of cancer dependencies from large-scale RNAi screens using model-based normalization and data integration

James M. McFarland; Zandra V. Ho; Guillaume Kugener; Joshua M. Dempster; Phillip G. Montgomery; Jordan G. Bryan; John M. Krill-Burger; Thomas M. Green; Francisca Vazquez; Jesse S. Boehm; Todd R. Golub; William C. Hahn; David E. Root; Aviad Tsherniak

doi:10.1038/s41467-018-06916-5

Nature Communications (Nov 2018)

Improved estimation of cancer dependencies from large-scale RNAi screens using model-based normalization and data integration

James M. McFarland,
Zandra V. Ho,
Guillaume Kugener,
Joshua M. Dempster,
Phillip G. Montgomery,
Jordan G. Bryan,
John M. Krill-Burger,
Thomas M. Green,
Francisca Vazquez,
Jesse S. Boehm,
Todd R. Golub,
William C. Hahn,
David E. Root,
Aviad Tsherniak

Affiliations

James M. McFarland: Broad Institute of MIT and Harvard
Zandra V. Ho: Broad Institute of MIT and Harvard
Guillaume Kugener: Broad Institute of MIT and Harvard
Joshua M. Dempster: Broad Institute of MIT and Harvard
Phillip G. Montgomery: Broad Institute of MIT and Harvard
Jordan G. Bryan: Broad Institute of MIT and Harvard
John M. Krill-Burger: Broad Institute of MIT and Harvard
Thomas M. Green: Broad Institute of MIT and Harvard
Francisca Vazquez: Broad Institute of MIT and Harvard
Jesse S. Boehm: Broad Institute of MIT and Harvard
Todd R. Golub: Broad Institute of MIT and Harvard
William C. Hahn: Broad Institute of MIT and Harvard
David E. Root: Broad Institute of MIT and Harvard
Aviad Tsherniak: Broad Institute of MIT and Harvard

DOI: https://doi.org/10.1038/s41467-018-06916-5
Journal volume & issue: Vol. 9, no. 1
pp. 1 – 13

Abstract

Read online

Integrated analyses of multiple large-scale screenings can be complicated by batch effects and technical artefacts. McFarland et al. introduce DEMETER2, a hierarchical model coupled with model-based normalization, which allows the assessment of differential dependencies across genes and cell lines.

Published in Nature Communications

ISSN: 2041-1723 (Online)
Publisher: Nature Portfolio
Country of publisher: United Kingdom
LCC subjects: Science
Website: https://www.nature.com/ncomms/

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