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14 results on '"Najgebauer, Hanna"'

3. Agreement between two large pan-cancer CRISPR-Cas9 gene dependency data sets

Author

Dempster, Joshua M., Pacini, Clare, Pantel, Sasha, Behan, Fiona M., Green, Thomas, Krill-Burger, John, Beaver, Charlotte M., Younger, Scott T., Zhivich, Victor, Najgebauer, Hanna, Allen, Felicity, Gonçalves, Emanuel, Shepherd, Rebecca, Doench, John G., Yusa, Kosuke, Vazquez, Francisca, Parts, Leopold, Boehm, Jesse S., Golub, Todd R., Hahn, William C., Root, David E., Garnett, Mathew J., Tsherniak, Aviad, and Iorio, Francesco

Published
2019
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5. Integrated cross-study datasets of genetic dependencies in cancer

Author

Pacini, Clare, primary, Dempster, Joshua M., additional, Boyle, Isabella, additional, Gonçalves, Emanuel, additional, Najgebauer, Hanna, additional, Karakoc, Emre, additional, van der Meer, Dieudonne, additional, Barthorpe, Andrew, additional, Lightfoot, Howard, additional, Jaaks, Patricia, additional, McFarland, James M., additional, Garnett, Mathew J., additional, Tsherniak, Aviad, additional, and Iorio, Francesco, additional

Published
2020
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7. An integrated landscape of protein expression in human cancer

Author

Jarnuczak, Andrew F., primary, Najgebauer, Hanna, additional, Barzine, Mitra, additional, Kundu, Deepti J., additional, Ghavidel, Fatemeh, additional, Perez-Riverol, Yasset, additional, Papatheodorou, Irene, additional, Brazma, Alvis, additional, and Vizcaíno, Juan Antonio, additional

Published
2019
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8. Agreement between two large pan-cancer CRISPR-Cas9 gene dependency datasets

Author

Dempster, Joshua M., primary, Pacini, Clare, additional, Pantel, Sasha, additional, Behan, Fiona M., additional, Green, Thomas, additional, Krill-Burger, John, additional, Beaver, Charlotte M., additional, Younger, Scott T., additional, Zhivich, Victor, additional, Najgebauer, Hanna, additional, Allen, Felicity, additional, Gonçalves, Emanuel, additional, Shepherd, Rebecca, additional, Doench, John G., additional, Yusa, Kosuke, additional, Vazquez, Francisca, additional, Parts, Leopold, additional, Boehm, Jesse S., additional, Golub, Todd R., additional, Hahn, William C., additional, Root, David E., additional, Garnett, Mathew J., additional, Iorio, Francesco, additional, and Tsherniak, Aviad, additional

Published
2019
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11. CardioClassifier: disease- and gene-specific computational decision support for clinical genome interpretation

Author

Whiffin, Nicola, primary, Walsh, Roddy, additional, Govind, Risha, additional, Edwards, Matthew, additional, Ahmad, Mian, additional, Zhang, Xiaolei, additional, Tayal, Upasana, additional, Buchan, Rachel, additional, Midwinter, William, additional, Wilk, Alicja E., additional, Najgebauer, Hanna, additional, Francis, Catherine, additional, Wilkinson, Sam, additional, Monk, Thomas, additional, Brett, Laura, additional, O’Regan, Declan P., additional, Prasad, Sanjay K., additional, Morris-Rosendahl, Deborah J., additional, Barton, Paul J.R., additional, Edwards, Elizabeth, additional, Ware, James S., additional, and Cook, Stuart A., additional

Published
2018
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13. CardioClassifier – demonstrating the power of disease- and gene-specific computational decision support for clinical genome interpretation

Author

Whiffin, Nicola, primary, Walsh, Roddy, additional, Govind, Risha, additional, Edwards, Matthew, additional, Ahmad, Mian, additional, Zhang, Xiaolei, additional, Tayal, Upasana, additional, Buchan, Rachel, additional, Midwinter, William, additional, Wilk, Alicja E, additional, Najgebauer, Hanna, additional, Francis, Catherine, additional, Wilkinson, Sam, additional, Monk, Thomas, additional, Brett, Laura, additional, O'Regan, Declan P, additional, Prasad, Sanjay K, additional, Morris-Rosendahl, Deborah J, additional, Barton, Paul JR, additional, Edwards, Elizabeth, additional, Ware, James S, additional, and Cook, Stuart A, additional

Published
2017
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14. Agreement between two large pan-cancer CRISPR-Cas9 gene dependency data sets

Author

Dempster, Joshua M, Pacini, Clare, Pantel, Sasha, Behan, Fiona M, Green, Thomas, Krill-Burger, John, Beaver, Charlotte M, Younger, Scott T, Zhivich, Victor, Najgebauer, Hanna, Allen, Felicity, Gonçalves, Emanuel, Shepherd, Rebecca, Doench, John G, Yusa, Kosuke, Vazquez, Francisca, Parts, Leopold, Boehm, Jesse S, Golub, Todd R, Hahn, William C, Root, David E, Garnett, Mathew J, Tsherniak, Aviad, and Iorio, Francesco

Subjects
Genes, Essential, Gene Expression Profiling, Datasets as Topic, Reproducibility of Results, Antineoplastic Agents, Genomics, Oncogenes, 3. Good health, Small Molecule Libraries, Cell Line, Tumor, Neoplasms, Biomarkers, Tumor, Humans, Molecular Targeted Therapy, CRISPR-Cas Systems, Drug Screening Assays, Antitumor, Precision Medicine
Abstract

Genome-scale CRISPR-Cas9 viability screens performed in cancer cell lines provide a systematic approach to identify cancer dependencies and new therapeutic targets. As multiple large-scale screens become available, a formal assessment of the reproducibility of these experiments becomes necessary. We analyze data from recently published pan-cancer CRISPR-Cas9 screens performed at the Broad and Sanger Institutes. Despite significant differences in experimental protocols and reagents, we find that the screen results are highly concordant across multiple metrics with both common and specific dependencies jointly identified across the two studies. Furthermore, robust biomarkers of gene dependency found in one data set are recovered in the other. Through further analysis and replication experiments at each institute, we show that batch effects are driven principally by two key experimental parameters: the reagent library and the assay length. These results indicate that the Broad and Sanger CRISPR-Cas9 viability screens yield robust and reproducible findings.

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