Protocol for obtaining cancer type and subtype predictions using subSCOPE
Summary: We present a protocol for obtaining cancer type and subtype predictions using a machine learning method (subSCOPE). We describe steps for data preparation, subSCOPE setup, and running subSCOPE inference on prepared data. The protocol supports five -omics data types as input (DNA methylation...
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| Format: | Article |
| Language: | English |
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Elsevier
2025-06-01
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| Series: | STAR Protocols |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S266616672500111X |
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| author | Jasleen K. Grewal A. Gordon Robertson Kyle Ellrott Christopher K. Wong Jordan A. Lee Christina Yau Bahar Tercan Mauro A.A. Castro Christopher C. Benz Jean C. Zenklusen Andrew D. Cherniack Peter W. Laird Steven J.M. Jones Theo A. Knijnenburg Mauro A.A. Castro Vinicius S. Chagas Victor H. Apolonio Verena Friedl Joshua M. Stuart Vladislav Uzunangelov Christopher K. Wong Jesper B. Andersen Andrew D. Cherniack Galen F. Gao Gad Getz Stephanie H. Hoyt Whijae Roh Lindsay Westlake Christopher C. Benz Jasleen K. Grewal Steven J.M. Jones A. Gordon Robertson Samantha J. Caesar-Johnson John A. Demchok Ina Felau Anab Kemal Roy Tarnuzzer Zhining Wang Liming Yang Jean C. Zenklusen Rehan Akbani Bradley M. Broom Zhenlin Ju Andre Schultz Akinyemi I. Ojesina Katherine A. Hoadley Avantika Lal Daniele Ramazzotti Chen Wang Alexander J. Lazar Lewis R. Roberts Taek-Kyun Kim Ilya Shmulevich Bahar Tercan Paulos Charonyktakis Vincenzo Lagani Ioannis Tsamardinos Esther Drill Ronglai Shen Martin L. Ferguson Kami E. Chiotti Kyle Ellrott Brian J. Karlberg Jordan A. Lee Eve Lowenstein Adam Struck Paul T. Spellman Christina Yau Toshinori Hinoue Peter W. Laird |
| author_facet | Jasleen K. Grewal A. Gordon Robertson Kyle Ellrott Christopher K. Wong Jordan A. Lee Christina Yau Bahar Tercan Mauro A.A. Castro Christopher C. Benz Jean C. Zenklusen Andrew D. Cherniack Peter W. Laird Steven J.M. Jones Theo A. Knijnenburg Mauro A.A. Castro Vinicius S. Chagas Victor H. Apolonio Verena Friedl Joshua M. Stuart Vladislav Uzunangelov Christopher K. Wong Jesper B. Andersen Andrew D. Cherniack Galen F. Gao Gad Getz Stephanie H. Hoyt Whijae Roh Lindsay Westlake Christopher C. Benz Jasleen K. Grewal Steven J.M. Jones A. Gordon Robertson Samantha J. Caesar-Johnson John A. Demchok Ina Felau Anab Kemal Roy Tarnuzzer Zhining Wang Liming Yang Jean C. Zenklusen Rehan Akbani Bradley M. Broom Zhenlin Ju Andre Schultz Akinyemi I. Ojesina Katherine A. Hoadley Avantika Lal Daniele Ramazzotti Chen Wang Alexander J. Lazar Lewis R. Roberts Taek-Kyun Kim Ilya Shmulevich Bahar Tercan Paulos Charonyktakis Vincenzo Lagani Ioannis Tsamardinos Esther Drill Ronglai Shen Martin L. Ferguson Kami E. Chiotti Kyle Ellrott Brian J. Karlberg Jordan A. Lee Eve Lowenstein Adam Struck Paul T. Spellman Christina Yau Toshinori Hinoue Peter W. Laird |
| author_sort | Jasleen K. Grewal |
| collection | DOAJ |
| description | Summary: We present a protocol for obtaining cancer type and subtype predictions using a machine learning method (subSCOPE). We describe steps for data preparation, subSCOPE setup, and running subSCOPE inference on prepared data. The protocol supports five -omics data types as input (DNA methylation, gene expression, microRNA [miRNA] expression, point mutations, and copy-number variants) and allows individual cancer type and data type selection. For non-The Cancer Genome Atlas (TCGA) cancer samples, it provides subtype-level classification across 26 different TCGA cancer cohorts and 106 subtypes.For complete details on the use and execution of this protocol, please refer to Ellrott et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics. |
| format | Article |
| id | doaj-art-467b2f5af5744591a89c30de2dc1ccb0 |
| institution | OA Journals |
| issn | 2666-1667 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | STAR Protocols |
| spelling | doaj-art-467b2f5af5744591a89c30de2dc1ccb02025-08-20T02:11:36ZengElsevierSTAR Protocols2666-16672025-06-016210370510.1016/j.xpro.2025.103705Protocol for obtaining cancer type and subtype predictions using subSCOPEJasleen K. Grewal0A. Gordon Robertson1Kyle Ellrott2Christopher K. Wong3Jordan A. Lee4Christina Yau5Bahar Tercan6Mauro A.A. Castro7Christopher C. Benz8Jean C. Zenklusen9Andrew D. Cherniack10Peter W. Laird11Steven J.M. Jones12Theo A. KnijnenburgMauro A.A. CastroVinicius S. ChagasVictor H. ApolonioVerena FriedlJoshua M. StuartVladislav UzunangelovChristopher K. WongJesper B. AndersenAndrew D. CherniackGalen F. GaoGad GetzStephanie H. HoytWhijae RohLindsay WestlakeChristopher C. BenzJasleen K. GrewalSteven J.M. JonesA. Gordon RobertsonSamantha J. Caesar-JohnsonJohn A. DemchokIna FelauAnab KemalRoy TarnuzzerZhining WangLiming YangJean C. ZenklusenRehan AkbaniBradley M. BroomZhenlin JuAndre SchultzAkinyemi I. OjesinaKatherine A. HoadleyAvantika LalDaniele RamazzottiChen WangAlexander J. LazarLewis R. RobertsTaek-Kyun KimIlya ShmulevichBahar TercanPaulos CharonyktakisVincenzo LaganiIoannis TsamardinosEsther DrillRonglai ShenMartin L. FergusonKami E. ChiottiKyle EllrottBrian J. KarlbergJordan A. LeeEve LowensteinAdam StruckPaul T. SpellmanChristina YauToshinori HinouePeter W. LairdCanada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada; Corresponding authorCanada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, CanadaOregon Health and Science University, Portland, OR 97239, USAUC Santa Cruz Genomics Institute and Department of Biomolecular Engineering, Santa Cruz, CA 95060, USAOregon Health and Science University, Portland, OR 97239, USAUniversity of California, San Francisco, Department of Surgery, San Francisco, CA 94158, USA; Buck Institute for Research on Aging, Novato, CA 94945, USAInstitute of Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USABioinformatics and Systems Biology Laboratory, Federal University of Paraná, Curitiba, Paraná 81520-260, BrazilBuck Institute for Research on Aging, Novato, CA 94945, USACenter for Cancer Genomics, National Cancer Institute, Bethesda, MD 20892, USAThe Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02115, USA; Corresponding authorDepartment of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA; Corresponding authorCanada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada; Corresponding authorSummary: We present a protocol for obtaining cancer type and subtype predictions using a machine learning method (subSCOPE). We describe steps for data preparation, subSCOPE setup, and running subSCOPE inference on prepared data. The protocol supports five -omics data types as input (DNA methylation, gene expression, microRNA [miRNA] expression, point mutations, and copy-number variants) and allows individual cancer type and data type selection. For non-The Cancer Genome Atlas (TCGA) cancer samples, it provides subtype-level classification across 26 different TCGA cancer cohorts and 106 subtypes.For complete details on the use and execution of this protocol, please refer to Ellrott et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.http://www.sciencedirect.com/science/article/pii/S266616672500111XBioinformaticsCancerGenomicsComputer sciences |
| spellingShingle | Jasleen K. Grewal A. Gordon Robertson Kyle Ellrott Christopher K. Wong Jordan A. Lee Christina Yau Bahar Tercan Mauro A.A. Castro Christopher C. Benz Jean C. Zenklusen Andrew D. Cherniack Peter W. Laird Steven J.M. Jones Theo A. Knijnenburg Mauro A.A. Castro Vinicius S. Chagas Victor H. Apolonio Verena Friedl Joshua M. Stuart Vladislav Uzunangelov Christopher K. Wong Jesper B. Andersen Andrew D. Cherniack Galen F. Gao Gad Getz Stephanie H. Hoyt Whijae Roh Lindsay Westlake Christopher C. Benz Jasleen K. Grewal Steven J.M. Jones A. Gordon Robertson Samantha J. Caesar-Johnson John A. Demchok Ina Felau Anab Kemal Roy Tarnuzzer Zhining Wang Liming Yang Jean C. Zenklusen Rehan Akbani Bradley M. Broom Zhenlin Ju Andre Schultz Akinyemi I. Ojesina Katherine A. Hoadley Avantika Lal Daniele Ramazzotti Chen Wang Alexander J. Lazar Lewis R. Roberts Taek-Kyun Kim Ilya Shmulevich Bahar Tercan Paulos Charonyktakis Vincenzo Lagani Ioannis Tsamardinos Esther Drill Ronglai Shen Martin L. Ferguson Kami E. Chiotti Kyle Ellrott Brian J. Karlberg Jordan A. Lee Eve Lowenstein Adam Struck Paul T. Spellman Christina Yau Toshinori Hinoue Peter W. Laird Protocol for obtaining cancer type and subtype predictions using subSCOPE STAR Protocols Bioinformatics Cancer Genomics Computer sciences |
| title | Protocol for obtaining cancer type and subtype predictions using subSCOPE |
| title_full | Protocol for obtaining cancer type and subtype predictions using subSCOPE |
| title_fullStr | Protocol for obtaining cancer type and subtype predictions using subSCOPE |
| title_full_unstemmed | Protocol for obtaining cancer type and subtype predictions using subSCOPE |
| title_short | Protocol for obtaining cancer type and subtype predictions using subSCOPE |
| title_sort | protocol for obtaining cancer type and subtype predictions using subscope |
| topic | Bioinformatics Cancer Genomics Computer sciences |
| url | http://www.sciencedirect.com/science/article/pii/S266616672500111X |
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