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Combining accurate tumour genome simulation with crowd-sourcing to benchmark somatic structural variant detection
Anna Y. Lee, Adam D. Ewing, Kyle Ellrott, Yin Hu, Kathleen E. Houlahan, J. Christopher Bare, G. Espiritu Shadrielle Melijah, Vincent Huang, Kristen Dang, Zechen Chong, Cristian Caloian, Takafumi N. Yamaguchi, ICGC-TCGA DREAM Somatic Mutation Calling Challenge Participants, Michael R. Kellen, Ken Chen, Thea C. Norman, Stephen H. Friend, Justin Guinney, Gustavo Stolovitzky, David Haussler, Adam A. Margolin, Joshua M. Stuart, Paul C. Boutros
doi: https://doi.org/10.1101/224733
Anna Y. Lee
1Ontario Institute for Cancer Research; Toronto, Ontario, Canada
Adam D. Ewing
2Department of Biomolecular Engineering; University of California, Santa Cruz; Santa Cruz, CA, USA
3Mater Research Institute; University of Queensland; Woolloongabba, QLD, Australia
Kyle Ellrott
2Department of Biomolecular Engineering; University of California, Santa Cruz; Santa Cruz, CA, USA
4Computational Biology Program; Oregon Health & Science University; Portland, OR, USA
Yin Hu
5Sage Bionetworks; Seattle, WA, USA
Kathleen E. Houlahan
1Ontario Institute for Cancer Research; Toronto, Ontario, Canada
J. Christopher Bare
5Sage Bionetworks; Seattle, WA, USA
G. Espiritu Shadrielle Melijah
1Ontario Institute for Cancer Research; Toronto, Ontario, Canada
Vincent Huang
1Ontario Institute for Cancer Research; Toronto, Ontario, Canada
Kristen Dang
5Sage Bionetworks; Seattle, WA, USA
Zechen Chong
6Department of Bioinformatics and Computational Biology; University of Texas MD Anderson Cancer Center; Houston, TX, USA
7Department of Genetics; University of Alabama at Birmingham; Birmingham, AL, USA
8Informatics Institute; University of Alabama at Birmingham; Birmingham, AL, USA
Cristian Caloian
1Ontario Institute for Cancer Research; Toronto, Ontario, Canada
Takafumi N. Yamaguchi
1Ontario Institute for Cancer Research; Toronto, Ontario, Canada
Michael R. Kellen
5Sage Bionetworks; Seattle, WA, USA
Ken Chen
6Department of Bioinformatics and Computational Biology; University of Texas MD Anderson Cancer Center; Houston, TX, USA
Thea C. Norman
5Sage Bionetworks; Seattle, WA, USA
Stephen H. Friend
5Sage Bionetworks; Seattle, WA, USA
Justin Guinney
5Sage Bionetworks; Seattle, WA, USA
Gustavo Stolovitzky
9IBM Computational Biology Center; T.J.Watson Research Center; Yorktown Heights, NY, USA
David Haussler
2Department of Biomolecular Engineering; University of California, Santa Cruz; Santa Cruz, CA, USA
Adam A. Margolin
4Computational Biology Program; Oregon Health & Science University; Portland, OR, USA
5Sage Bionetworks; Seattle, WA, USA
Joshua M. Stuart
2Department of Biomolecular Engineering; University of California, Santa Cruz; Santa Cruz, CA, USA
Paul C. Boutros
1Ontario Institute for Cancer Research; Toronto, Ontario, Canada
10Department of Medical Biophysics; University of Toronto; Toronto, Ontario, Canada
11Department of Pharmacology & Toxicology; University of Toronto; Toronto, Ontario, Canada
- Additional file 1: Figures S1-S26
- Additional file 2: Table S1
- Additional file 3: Table S2
- Additional file 4: Descriptions of pipelines used to generate submissions
- Additional file 5: Table S3
- Additional file 6: Table S4
- Additional file 7: BAMSurgeon input files used to generate the three in silico tumour-normal pairs
Posted November 25, 2017.
Combining accurate tumour genome simulation with crowd-sourcing to benchmark somatic structural variant detection
Anna Y. Lee, Adam D. Ewing, Kyle Ellrott, Yin Hu, Kathleen E. Houlahan, J. Christopher Bare, G. Espiritu Shadrielle Melijah, Vincent Huang, Kristen Dang, Zechen Chong, Cristian Caloian, Takafumi N. Yamaguchi, ICGC-TCGA DREAM Somatic Mutation Calling Challenge Participants, Michael R. Kellen, Ken Chen, Thea C. Norman, Stephen H. Friend, Justin Guinney, Gustavo Stolovitzky, David Haussler, Adam A. Margolin, Joshua M. Stuart, Paul C. Boutros
bioRxiv 224733; doi: https://doi.org/10.1101/224733
Combining accurate tumour genome simulation with crowd-sourcing to benchmark somatic structural variant detection
Anna Y. Lee, Adam D. Ewing, Kyle Ellrott, Yin Hu, Kathleen E. Houlahan, J. Christopher Bare, G. Espiritu Shadrielle Melijah, Vincent Huang, Kristen Dang, Zechen Chong, Cristian Caloian, Takafumi N. Yamaguchi, ICGC-TCGA DREAM Somatic Mutation Calling Challenge Participants, Michael R. Kellen, Ken Chen, Thea C. Norman, Stephen H. Friend, Justin Guinney, Gustavo Stolovitzky, David Haussler, Adam A. Margolin, Joshua M. Stuart, Paul C. Boutros
bioRxiv 224733; doi: https://doi.org/10.1101/224733
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