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

Publication ,  Journal Article
McFarland, JM; Ho, ZV; Kugener, G; Dempster, JM; Montgomery, PG; Bryan, JG; Krill-Burger, JM; Green, TM; Vazquez, F; Boehm, JS; Golub, TR ...
Published in: Nature communications
November 2018

The availability of multiple datasets comprising genome-scale RNAi viability screens in hundreds of diverse cancer cell lines presents new opportunities for understanding cancer vulnerabilities. Integrated analyses of these data to assess differential dependency across genes and cell lines are challenging due to confounding factors such as batch effects and variable screen quality, as well as difficulty assessing gene dependency on an absolute scale. To address these issues, we incorporated cell line screen-quality parameters and hierarchical Bayesian inference into DEMETER2, an analytical framework for analyzing RNAi screens ( https://depmap.org/R2-D2 ). This model substantially improves estimates of gene dependency across a range of performance measures, including identification of gold-standard essential genes and agreement with CRISPR/Cas9-based viability screens. It also allows us to integrate information across three large RNAi screening datasets, providing a unified resource representing the most extensive compilation of cancer cell line genetic dependencies to date.

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Published In

Nature communications

DOI

EISSN

2041-1723

ISSN

2041-1723

Publication Date

November 2018

Volume

9

Issue

1

Start / End Page

4610

Related Subject Headings

  • Software
  • RNA Interference
  • Neoplasms
  • Models, Genetic
  • Humans
  • Genetic Testing
  • Genes, Essential
 

Citation

APA
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McFarland, J. M., Ho, Z. V., Kugener, G., Dempster, J. M., Montgomery, P. G., Bryan, J. G., … Tsherniak, A. (2018). Improved estimation of cancer dependencies from large-scale RNAi screens using model-based normalization and data integration. Nature Communications, 9(1), 4610. https://doi.org/10.1038/s41467-018-06916-5
McFarland, James M., Zandra V. Ho, Guillaume Kugener, Joshua M. Dempster, Phillip G. Montgomery, Jordan G. Bryan, John M. Krill-Burger, et al. “Improved estimation of cancer dependencies from large-scale RNAi screens using model-based normalization and data integration.Nature Communications 9, no. 1 (November 2018): 4610. https://doi.org/10.1038/s41467-018-06916-5.
McFarland JM, Ho ZV, Kugener G, Dempster JM, Montgomery PG, Bryan JG, et al. Improved estimation of cancer dependencies from large-scale RNAi screens using model-based normalization and data integration. Nature communications. 2018 Nov;9(1):4610.
McFarland, James M., et al. “Improved estimation of cancer dependencies from large-scale RNAi screens using model-based normalization and data integration.Nature Communications, vol. 9, no. 1, Nov. 2018, p. 4610. Epmc, doi:10.1038/s41467-018-06916-5.
McFarland JM, Ho ZV, Kugener G, Dempster JM, Montgomery PG, Bryan JG, Krill-Burger JM, Green TM, Vazquez F, Boehm JS, Golub TR, Hahn WC, Root DE, Tsherniak A. Improved estimation of cancer dependencies from large-scale RNAi screens using model-based normalization and data integration. Nature communications. 2018 Nov;9(1):4610.

Published In

Nature communications

DOI

EISSN

2041-1723

ISSN

2041-1723

Publication Date

November 2018

Volume

9

Issue

1

Start / End Page

4610

Related Subject Headings

  • Software
  • RNA Interference
  • Neoplasms
  • Models, Genetic
  • Humans
  • Genetic Testing
  • Genes, Essential