1
|
Smyth LM, Zhou Q, Nguyen B, Yu C, Lepisto EM, Arnedos M, Hasset MJ, Lenoue-Newton ML, Blauvelt N, Dogan S, Micheel CM, Wathoo C, Horlings H, Hudecek J, Gross BE, Kundra R, Sweeney SM, Gao J, Schultz N, Zarski A, Gardos SM, Lee J, Sheffler-Collins S, Park BH, Sawyers CL, André F, Levy M, Meric-Bernstam F, Bedard PL, Iasonos A, Schrag D, Hyman DM. Characteristics and Outcome of AKT1 E17K-Mutant Breast Cancer Defined through AACR Project GENIE, a Clinicogenomic Registry. Cancer Discov 2020; 10:526-535. [PMID: 31924700 DOI: 10.1158/2159-8290.cd-19-1209] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/18/2019] [Accepted: 01/10/2020] [Indexed: 01/10/2023]
Abstract
AKT inhibitors have promising activity in AKT1 E17K-mutant estrogen receptor (ER)-positive metastatic breast cancer, but the natural history of this rare genomic subtype remains unknown. Utilizing AACR Project GENIE, an international clinicogenomic data-sharing consortium, we conducted a comparative analysis of clinical outcomes of patients with matched AKT1 E17K-mutant (n = 153) and AKT1-wild-type (n = 302) metastatic breast cancer. AKT1-mutant cases had similar adjusted overall survival (OS) compared with AKT1-wild-type controls (median OS, 24.1 vs. 29.9, respectively; P = 0.98). AKT1-mutant cases enjoyed longer durations on mTOR inhibitor therapy, an observation previously unrecognized in pivotal clinical trials due to the rarity of this alteration. Other baseline clinicopathologic features, as well as durations on other classes of therapy, were broadly similar. In summary, we demonstrate the feasibility of using a novel and publicly accessible clincogenomic registry to define outcomes in a rare genomically defined cancer subtype, an approach with broad applicability to precision oncology. SIGNIFICANCE: We delineate the natural history of a rare genomically distinct cancer, AKT1 E17K-mutant ER-positive breast cancer, using a publicly accessible registry of real-world patient data, thereby illustrating the potential to inform drug registration through synthetic control data.See related commentary by Castellanos and Baxi, p. 490.
Collapse
Affiliation(s)
| | - Qin Zhou
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Bastien Nguyen
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Celeste Yu
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | | | | | | | | | | | | | | | - Chetna Wathoo
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hugo Horlings
- Netherlands Cancer Institute (NKI), Amsterdam, the Netherlands
| | - Jan Hudecek
- Netherlands Cancer Institute (NKI), Amsterdam, the Netherlands
| | | | - Ritika Kundra
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Shawn M Sweeney
- American Association for Cancer Research, Philadelphia, Pennsylvania
| | - JianJiong Gao
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Andrew Zarski
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Jocelyn Lee
- American Association for Cancer Research, Philadelphia, Pennsylvania
| | | | - Ben H Park
- Vanderbilt Ingram Cancer Center, Nashville, Tennessee
| | | | | | - Mia Levy
- Vanderbilt Ingram Cancer Center, Nashville, Tennessee
| | | | | | - Alexia Iasonos
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | | |
Collapse
|
2
|
Wang Q, Armenia J, Zhang C, Penson AV, Reznik E, Zhang L, Minet T, Ochoa A, Gross BE, Iacobuzio-Donahue CA, Betel D, Taylor BS, Gao J, Schultz N. Unifying cancer and normal RNA sequencing data from different sources. Sci Data 2018; 5:180061. [PMID: 29664468 PMCID: PMC5903355 DOI: 10.1038/sdata.2018.61] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 02/12/2018] [Indexed: 01/21/2023] Open
Abstract
Driven by the recent advances of next generation sequencing (NGS) technologies and an urgent need to decode complex human diseases, a multitude of large-scale studies were conducted recently that have resulted in an unprecedented volume of whole transcriptome sequencing (RNA-seq) data, such as the Genotype Tissue Expression project (GTEx) and The Cancer Genome Atlas (TCGA). While these data offer new opportunities to identify the mechanisms underlying disease, the comparison of data from different sources remains challenging, due to differences in sample and data processing. Here, we developed a pipeline that processes and unifies RNA-seq data from different studies, which includes uniform realignment, gene expression quantification, and batch effect removal. We find that uniform alignment and quantification is not sufficient when combining RNA-seq data from different sources and that the removal of other batch effects is essential to facilitate data comparison. We have processed data from GTEx and TCGA and successfully corrected for study-specific biases, enabling comparative analysis between TCGA and GTEx. The normalized datasets are available for download on figshare.
Collapse
Affiliation(s)
- Qingguo Wang
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,College of Computing & Technology, Lipscomb University, Nashville, Tennessee 37204, USA
| | - Joshua Armenia
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Chao Zhang
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, 10021, USA
| | - Alexander V Penson
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Ed Reznik
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Liguo Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Thais Minet
- College of Computing & Technology, Lipscomb University, Nashville, Tennessee 37204, USA
| | - Angelica Ochoa
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Benjamin E Gross
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | | | - Doron Betel
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, 10021, USA
| | - Barry S Taylor
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Jianjiong Gao
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Nikolaus Schultz
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| |
Collapse
|
3
|
Janjigian YY, Sanchez-Vega F, Jonsson P, Chatila WK, Hechtman JF, Ku GY, Riches JC, Tuvy Y, Kundra R, Bouvier N, Vakiani E, Gao J, Heins ZJ, Gross BE, Kelsen DP, Zhang L, Strong VE, Schattner M, Gerdes H, Coit DG, Bains M, Stadler ZK, Rusch VW, Jones DR, Molena D, Shia J, Robson ME, Capanu M, Middha S, Zehir A, Hyman DM, Scaltriti M, Ladanyi M, Rosen N, Ilson DH, Berger MF, Tang L, Taylor BS, Solit DB, Schultz N. Genetic Predictors of Response to Systemic Therapy in Esophagogastric Cancer. Cancer Discov 2018; 8:49-58. [PMID: 29122777 PMCID: PMC5813492 DOI: 10.1158/2159-8290.cd-17-0787] [Citation(s) in RCA: 258] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 10/20/2017] [Accepted: 11/06/2017] [Indexed: 12/14/2022]
Abstract
The incidence of esophagogastric cancer is rapidly rising, but only a minority of patients derive durable benefit from current therapies. Chemotherapy as well as anti-HER2 and PD-1 antibodies are standard treatments. To identify predictive biomarkers of drug sensitivity and mechanisms of resistance, we implemented prospective tumor sequencing of patients with metastatic esophagogastric cancer. There was no association between homologous recombination deficiency defects and response to platinum-based chemotherapy. Patients with microsatellite instability-high tumors were intrinsically resistant to chemotherapy but more likely to achieve durable responses to immunotherapy. The single Epstein-Barr virus-positive patient achieved a durable, complete response to immunotherapy. The level of ERBB2 amplification as determined by sequencing was predictive of trastuzumab benefit. Selection for a tumor subclone lacking ERBB2 amplification, deletion of ERBB2 exon 16, and comutations in the receptor tyrosine kinase, RAS, and PI3K pathways were associated with intrinsic and/or acquired trastuzumab resistance. Prospective genomic profiling can identify patients most likely to derive durable benefit to immunotherapy and trastuzumab and guide strategies to overcome drug resistance.Significance: Clinical application of multiplex sequencing can identify biomarkers of treatment response to contemporary systemic therapies in metastatic esophagogastric cancer. This large prospective analysis sheds light on the biological complexity and the dynamic nature of therapeutic resistance in metastatic esophagogastric cancers. Cancer Discov; 8(1); 49-58. ©2017 AACR.See related commentary by Sundar and Tan, p. 14See related article by Pectasides et al., p. 37This article is highlighted in the In This Issue feature, p. 1.
Collapse
Affiliation(s)
- Yelena Y Janjigian
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York.
| | - Francisco Sanchez-Vega
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Philip Jonsson
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology-Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Walid K Chatila
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jaclyn F Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Geoffrey Y Ku
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York
| | - Jamie C Riches
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York
| | - Yaelle Tuvy
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York
| | - Ritika Kundra
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nancy Bouvier
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Efsevia Vakiani
- Department of Epidemiology-Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jianjiong Gao
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Zachary J Heins
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Benjamin E Gross
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David P Kelsen
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York
| | - Liying Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Vivian E Strong
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mark Schattner
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York
| | - Hans Gerdes
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York
| | - Daniel G Coit
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Manjit Bains
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Zsofia K Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York
| | - Valerie W Rusch
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David R Jones
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Daniela Molena
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jinru Shia
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mark E Robson
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York
| | - Marinela Capanu
- Department of Epidemiology-Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sumit Middha
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David M Hyman
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York
| | - Maurizio Scaltriti
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc Ladanyi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Neal Rosen
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York
| | - David H Ilson
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York
| | - Michael F Berger
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Laura Tang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Barry S Taylor
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology-Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David B Solit
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nikolaus Schultz
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology-Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| |
Collapse
|
4
|
Zehir A, Benayed R, Shah RH, Syed A, Middha S, Kim HR, Srinivasan P, Gao J, Chakravarty D, Devlin SM, Hellmann MD, Barron DA, Schram AM, Hameed M, Dogan S, Ross DS, Hechtman JF, DeLair DF, Yao J, Mandelker DL, Cheng DT, Chandramohan R, Mohanty AS, Ptashkin RN, Jayakumaran G, Prasad M, Syed MH, Rema AB, Liu ZY, Nafa K, Borsu L, Sadowska J, Casanova J, Bacares R, Kiecka IJ, Razumova A, Son JB, Stewart L, Baldi T, Mullaney KA, Al-Ahmadie H, Vakiani E, Abeshouse AA, Penson AV, Jonsson P, Camacho N, Chang MT, Won HH, Gross BE, Kundra R, Heins ZJ, Chen HW, Phillips S, Zhang H, Wang J, Ochoa A, Wills J, Eubank M, Thomas SB, Gardos SM, Reales DN, Galle J, Durany R, Cambria R, Abida W, Cercek A, Feldman DR, Gounder MM, Hakimi AA, Harding JJ, Iyer G, Janjigian YY, Jordan EJ, Kelly CM, Lowery MA, Morris LGT, Omuro AM, Raj N, Razavi P, Shoushtari AN, Shukla N, Soumerai TE, Varghese AM, Yaeger R, Coleman J, Bochner B, Riely GJ, Saltz LB, Scher HI, Sabbatini PJ, Robson ME, Klimstra DS, Taylor BS, Baselga J, Schultz N, Hyman DM, Arcila ME, Solit DB, Ladanyi M, Berger MF. Erratum: Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients. Nat Med 2017; 23:1004. [PMID: 28777785 DOI: 10.1038/nm0817-1004c] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
|
5
|
Zehir A, Benayed R, Shah RH, Syed A, Middha S, Kim HR, Srinivasan P, Gao J, Chakravarty D, Devlin SM, Hellmann MD, Barron DA, Schram AM, Hameed M, Dogan S, Ross DS, Hechtman JF, DeLair DF, Yao J, Mandelker DL, Cheng DT, Chandramohan R, Mohanty AS, Ptashkin RN, Jayakumaran G, Prasad M, Syed MH, Rema AB, Liu ZY, Nafa K, Borsu L, Sadowska J, Casanova J, Bacares R, Kiecka IJ, Razumova A, Son JB, Stewart L, Baldi T, Mullaney KA, Al-Ahmadie H, Vakiani E, Abeshouse AA, Penson AV, Jonsson P, Camacho N, Chang MT, Won HH, Gross BE, Kundra R, Heins ZJ, Chen HW, Phillips S, Zhang H, Wang J, Ochoa A, Wills J, Eubank M, Thomas SB, Gardos SM, Reales DN, Galle J, Durany R, Cambria R, Abida W, Cercek A, Feldman DR, Gounder MM, Hakimi AA, Harding JJ, Iyer G, Janjigian YY, Jordan EJ, Kelly CM, Lowery MA, Morris LGT, Omuro AM, Raj N, Razavi P, Shoushtari AN, Shukla N, Soumerai TE, Varghese AM, Yaeger R, Coleman J, Bochner B, Riely GJ, Saltz LB, Scher HI, Sabbatini PJ, Robson ME, Klimstra DS, Taylor BS, Baselga J, Schultz N, Hyman DM, Arcila ME, Solit DB, Ladanyi M, Berger MF. Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients. Nat Med 2017; 23:703-713. [PMID: 28481359 PMCID: PMC5461196 DOI: 10.1038/nm.4333] [Citation(s) in RCA: 2144] [Impact Index Per Article: 306.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 04/04/2017] [Indexed: 02/07/2023]
Abstract
Tumor molecular profiling is a fundamental component of precision oncology, enabling the identification of genomic alterations in genes and pathways that can be targeted therapeutically. The existence of recurrent targetable alterations across distinct histologically defined tumor types, coupled with an expanding portfolio of molecularly targeted therapies, demands flexible and comprehensive approaches to profile clinically relevant genes across the full spectrum of cancers. We established a large-scale, prospective clinical sequencing initiative using a comprehensive assay, MSK-IMPACT, through which we have compiled tumor and matched normal sequence data from a unique cohort of more than 10,000 patients with advanced cancer and available pathological and clinical annotations. Using these data, we identified clinically relevant somatic mutations, novel noncoding alterations, and mutational signatures that were shared by common and rare tumor types. Patients were enrolled on genomically matched clinical trials at a rate of 11%. To enable discovery of novel biomarkers and deeper investigation into rare alterations and tumor types, all results are publicly accessible.
Collapse
Affiliation(s)
- Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ronak H Shah
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Aijazuddin Syed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Sumit Middha
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Hyunjae R Kim
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Preethi Srinivasan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jianjiong Gao
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Debyani Chakravarty
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Sean M Devlin
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Matthew D Hellmann
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - David A Barron
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Alison M Schram
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Meera Hameed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Snjezana Dogan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Dara S Ross
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jaclyn F Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Deborah F DeLair
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - JinJuan Yao
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Diana L Mandelker
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Donavan T Cheng
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Raghu Chandramohan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Abhinita S Mohanty
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ryan N Ptashkin
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Gowtham Jayakumaran
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Meera Prasad
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Mustafa H Syed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | | | - Zhen Y Liu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Khedoudja Nafa
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Laetitia Borsu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Justyna Sadowska
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jacklyn Casanova
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ruben Bacares
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Iwona J Kiecka
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Anna Razumova
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Julie B Son
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Lisa Stewart
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Tessara Baldi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Kerry A Mullaney
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Hikmat Al-Ahmadie
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Efsevia Vakiani
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Adam A Abeshouse
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Alexander V Penson
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Philip Jonsson
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Niedzica Camacho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Matthew T Chang
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Helen H Won
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Benjamin E Gross
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ritika Kundra
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Zachary J Heins
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Hsiao-Wei Chen
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Sarah Phillips
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Hongxin Zhang
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jiaojiao Wang
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Angelica Ochoa
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jonathan Wills
- Information Systems, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Michael Eubank
- Information Systems, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Stacy B Thomas
- Information Systems, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Stuart M Gardos
- Information Systems, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Dalicia N Reales
- Clinical Research Administration, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jesse Galle
- Clinical Research Administration, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Robert Durany
- Clinical Research Administration, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Roy Cambria
- Clinical Research Administration, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Wassim Abida
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Andrea Cercek
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Darren R Feldman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Mrinal M Gounder
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - A Ari Hakimi
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - James J Harding
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Gopa Iyer
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Yelena Y Janjigian
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Emmet J Jordan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ciara M Kelly
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Maeve A Lowery
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Luc G T Morris
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Antonio M Omuro
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Nitya Raj
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Pedram Razavi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | | | - Neerav Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Tara E Soumerai
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Anna M Varghese
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Rona Yaeger
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jonathan Coleman
- Clinical Research Administration, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Bernard Bochner
- Clinical Research Administration, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Gregory J Riely
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Leonard B Saltz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Howard I Scher
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Paul J Sabbatini
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Mark E Robson
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - David S Klimstra
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Barry S Taylor
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jose Baselga
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Nikolaus Schultz
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - David M Hyman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Maria E Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - David B Solit
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Michael F Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| |
Collapse
|
6
|
Cerami E, Gao J, Dogrusoz U, Gross BE, Sumer SO, Aksoy BA, Jacobsen A, Byrne CJ, Heuer ML, Larsson E, Antipin Y, Reva B, Goldberg AP, Sander C, Schultz N. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov 2012; 2:401-4. [PMID: 22588877 DOI: 10.1158/2159-8290.cd-12-0095] [Citation(s) in RCA: 11022] [Impact Index Per Article: 918.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The cBio Cancer Genomics Portal (http://cbioportal.org) is an open-access resource for interactive exploration of multidimensional cancer genomics data sets, currently providing access to data from more than 5,000 tumor samples from 20 cancer studies. The cBio Cancer Genomics Portal significantly lowers the barriers between complex genomic data and cancer researchers who want rapid, intuitive, and high-quality access to molecular profiles and clinical attributes from large-scale cancer genomics projects and empowers researchers to translate these rich data sets into biologic insights and clinical applications.
Collapse
Affiliation(s)
- Ethan Cerami
- Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
7
|
Cerami E, Gao J, Dogrusoz U, Gross BE, Sumer SO, Aksoy BA, Jacobsen A, Byrne CJ, Heuer ML, Larsson E, Antipin Y, Reva B, Goldberg AP, Sander C, Schultz N. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov 2012. [PMID: 22588877 DOI: 10.1158/2159‐8290.cd‐12‐0095] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The cBio Cancer Genomics Portal (http://cbioportal.org) is an open-access resource for interactive exploration of multidimensional cancer genomics data sets, currently providing access to data from more than 5,000 tumor samples from 20 cancer studies. The cBio Cancer Genomics Portal significantly lowers the barriers between complex genomic data and cancer researchers who want rapid, intuitive, and high-quality access to molecular profiles and clinical attributes from large-scale cancer genomics projects and empowers researchers to translate these rich data sets into biologic insights and clinical applications.
Collapse
Affiliation(s)
- Ethan Cerami
- Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
8
|
Cerami EG, Gross BE, Demir E, Rodchenkov I, Babur O, Anwar N, Schultz N, Bader GD, Sander C. Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res 2010; 39:D685-90. [PMID: 21071392 PMCID: PMC3013659 DOI: 10.1093/nar/gkq1039] [Citation(s) in RCA: 747] [Impact Index Per Article: 53.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Pathway Commons (http://www.pathwaycommons.org) is a collection of publicly available pathway data from multiple organisms. Pathway Commons provides a web-based interface that enables biologists to browse and search a comprehensive collection of pathways from multiple sources represented in a common language, a download site that provides integrated bulk sets of pathway information in standard or convenient formats and a web service that software developers can use to conveniently query and access all data. Database providers can share their pathway data via a common repository. Pathways include biochemical reactions, complex assembly, transport and catalysis events and physical interactions involving proteins, DNA, RNA, small molecules and complexes. Pathway Commons aims to collect and integrate all public pathway data available in standard formats. Pathway Commons currently contains data from nine databases with over 1400 pathways and 687 000 interactions and will be continually expanded and updated.
Collapse
Affiliation(s)
- Ethan G Cerami
- Computational Biology Center, Memorial Sloan-Kettering Cancer Center 1275 York Avenue, Box 460, New York, NY 10065, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
9
|
Cerami EG, Bader GD, Gross BE, Sander C. cPath: open source software for collecting, storing, and querying biological pathways. BMC Bioinformatics 2006; 7:497. [PMID: 17101041 PMCID: PMC1660554 DOI: 10.1186/1471-2105-7-497] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2006] [Accepted: 11/13/2006] [Indexed: 11/10/2022] Open
Abstract
Background Biological pathways, including metabolic pathways, protein interaction networks, signal transduction pathways, and gene regulatory networks, are currently represented in over 220 diverse databases. These data are crucial for the study of specific biological processes, including human diseases. Standard exchange formats for pathway information, such as BioPAX, CellML, SBML and PSI-MI, enable convenient collection of this data for biological research, but mechanisms for common storage and communication are required. Results We have developed cPath, an open source database and web application for collecting, storing, and querying biological pathway data. cPath makes it easy to aggregate custom pathway data sets available in standard exchange formats from multiple databases, present pathway data to biologists via a customizable web interface, and export pathway data via a web service to third-party software, such as Cytoscape, for visualization and analysis. cPath is software only, and does not include new pathway information. Key features include: a built-in identifier mapping service for linking identical interactors and linking to external resources; built-in support for PSI-MI and BioPAX standard pathway exchange formats; a web service interface for searching and retrieving pathway data sets; and thorough documentation. The cPath software is freely available under the LGPL open source license for academic and commercial use. Conclusion cPath is a robust, scalable, modular, professional-grade software platform for collecting, storing, and querying biological pathways. It can serve as the core data handling component in information systems for pathway visualization, analysis and modeling.
Collapse
Affiliation(s)
- Ethan G Cerami
- Computational Biology Center, Memorial Sloan-Kettering Cancer Center 1275 York Avenue, Box 460, New York, NY 10021, USA
| | - Gary D Bader
- Banting and Best Department of Medical Research, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College St, Toronto, Ontario M5S 3E1, Canada
| | - Benjamin E Gross
- Computational Biology Center, Memorial Sloan-Kettering Cancer Center 1275 York Avenue, Box 460, New York, NY 10021, USA
| | - Chris Sander
- Computational Biology Center, Memorial Sloan-Kettering Cancer Center 1275 York Avenue, Box 460, New York, NY 10021, USA
| |
Collapse
|