1
|
Suehnholz SP, Nissan MH, Zhang H, Kundra R, Nandakumar S, Lu C, Carrero S, Dhaneshwar A, Fernandez N, Xu BW, Arcila ME, Zehir A, Syed A, Brannon AR, Rudolph JE, Paraiso E, Sabbatini PJ, Levine RL, Dogan A, Gao J, Ladanyi M, Drilon A, Berger MF, Solit DB, Schultz N, Chakravarty D. Quantifying the Expanding Landscape of Clinical Actionability for Patients with Cancer. Cancer Discov 2024; 14:49-65. [PMID: 37849038 PMCID: PMC10784742 DOI: 10.1158/2159-8290.cd-23-0467] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [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: 05/11/2023] [Revised: 08/18/2023] [Accepted: 10/02/2023] [Indexed: 10/19/2023]
Abstract
There is a continuing debate about the proportion of cancer patients that benefit from precision oncology, attributable in part to conflicting views as to which molecular alterations are clinically actionable. To quantify the expansion of clinical actionability since 2017, we annotated 47,271 solid tumors sequenced with the MSK-IMPACT clinical assay using two temporally distinct versions of the OncoKB knowledge base deployed 5 years apart. Between 2017 and 2022, we observed an increase from 8.9% to 31.6% in the fraction of tumors harboring a standard care (level 1 or 2) predictive biomarker of therapy response and an almost halving of tumors carrying nonactionable drivers (44.2% to 22.8%). In tumors with limited or no clinical actionability, TP53 (43.2%), KRAS (19.2%), and CDKN2A (12.2%) were the most frequently altered genes. SIGNIFICANCE Although clear progress has been made in expanding the availability of precision oncology-based treatment paradigms, our results suggest a continued unmet need for innovative therapeutic strategies, particularly for cancers with currently undruggable oncogenic drivers. See related commentary by Horak and Fröhling, p. 18. This article is featured in Selected Articles from This Issue, p. 5.
Collapse
Affiliation(s)
- Sarah P. Suehnholz
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Moriah H. Nissan
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Hongxin Zhang
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ritika Kundra
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Subhiksha Nandakumar
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Calvin Lu
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Stephanie Carrero
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Amanda Dhaneshwar
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nicole Fernandez
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Benjamin W. Xu
- Department of Computer Science, Yale University, New Haven, Connecticut
| | - Maria E. Arcila
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ahmet Zehir
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Aijazuddin Syed
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - A. Rose Brannon
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Julia E. Rudolph
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Eder Paraiso
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Paul J. Sabbatini
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ross L. Levine
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ahmet Dogan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jianjiong Gao
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc Ladanyi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alexander Drilon
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael F. Berger
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David B. Solit
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, 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 and 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 and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Debyani Chakravarty
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| |
Collapse
|
2
|
Casolino R, Beer PA, Chakravarty D, Davis MB, Malapelle U, Mazzarella L, Normanno N, Pauli C, Subbiah V, Turnbull C, Westphalen CB, Biankin AV. Interpreting and integrating genomic tests results in clinical cancer care: Overview and practical guidance. CA Cancer J Clin 2024. [PMID: 38174605 DOI: 10.3322/caac.21825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/07/2023] [Accepted: 11/27/2023] [Indexed: 01/05/2024] Open
Abstract
The last decade has seen rapid progress in the use of genomic tests, including gene panels, whole-exome sequencing, and whole-genome sequencing, in research and clinical cancer care. These advances have created expansive opportunities to characterize the molecular attributes of cancer, revealing a subset of cancer-associated aberrations called driver mutations. The identification of these driver mutations can unearth vulnerabilities of cancer cells to targeted therapeutics, which has led to the development and approval of novel diagnostics and personalized interventions in various malignancies. The applications of this modern approach, often referred to as precision oncology or precision cancer medicine, are already becoming a staple in cancer care and will expand exponentially over the coming years. Although genomic tests can lead to better outcomes by informing cancer risk, prognosis, and therapeutic selection, they remain underutilized in routine cancer care. A contributing factor is a lack of understanding of their clinical utility and the difficulty of results interpretation by the broad oncology community. Practical guidelines on how to interpret and integrate genomic information in the clinical setting, addressed to clinicians without expertise in cancer genomics, are currently limited. Building upon the genomic foundations of cancer and the concept of precision oncology, the authors have developed practical guidance to aid the interpretation of genomic test results that help inform clinical decision making for patients with cancer. They also discuss the challenges that prevent the wider implementation of precision oncology.
Collapse
Affiliation(s)
- Raffaella Casolino
- Wolfson Wohl Cancer Research Center, School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Philip A Beer
- Wolfson Wohl Cancer Research Center, School of Cancer Sciences, University of Glasgow, Glasgow, UK
- Hull York Medical School, York, UK
| | | | - Melissa B Davis
- Department of Surgery, Weill Cornell Medicine, New York City, New York, USA
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Luca Mazzarella
- Laboratory of Translational Oncology and Division of Gastrointestinal Medical Oncology and Neuroendocrine Tumors IEO European Institute of Oncology, IRCCS, Milan, Italy
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori, IRCCS "Fondazione G. Pascale", Naples, Italy
| | - Chantal Pauli
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Vivek Subbiah
- Sarah Cannon Research Institute, Nashville, Tennessee, USA
| | - Clare Turnbull
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- National Cancer Registration and Analysis Service, National Health Service (NHS) England, London, UK
- Cancer Genetics Unit, The Royal Marsden NHS Foundation Trust, London, UK
| | - C Benedikt Westphalen
- Department of Medicine III, Ludwig Maximilians University (LMU) Hospital Munich, Munich, Germany
- Comprehensive Cancer Center, LMU Hospital Munich, Munich, Germany
- German Cancer Consortium, LMU Hospital Munich, Munich, Germany
| | - Andrew V Biankin
- Wolfson Wohl Cancer Research Center, School of Cancer Sciences, University of Glasgow, Glasgow, UK
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, UK
- South Western Sydney Clinical School, Liverpool, New South Wales, Australia
| |
Collapse
|
3
|
Murciano-Goroff YR, Suehnholz SP, Drilon A, Chakravarty D. Precision Oncology: 2023 in Review. Cancer Discov 2023; 13:2525-2531. [PMID: 38084089 PMCID: PMC10715685 DOI: 10.1158/2159-8290.cd-23-1194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 10/20/2023] [Indexed: 12/18/2023]
Abstract
SUMMARY This article presents a review of recent major advances in precision oncology and the future implications of these advances, specifying the iterative progress achieved from the end of 2022 through 2023. We discuss the different classes of precision oncology drugs and associated biomarkers as well as the improvements in clinical trial design that have enabled the efficient testing of these drugs.
Collapse
Affiliation(s)
| | - Sarah P. Suehnholz
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alexander Drilon
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medical College, New York, New York
| | - Debyani Chakravarty
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| |
Collapse
|
4
|
Jiagge E, Jin DX, Newberg JY, Perea-Chamblee T, Pekala KR, Fong C, Waters M, Ma D, Dei-Adomakoh Y, Erb G, Arora KS, Maund SL, Njiraini N, Ntekim A, Kim S, Bai X, Thomas M, van Eeden R, Hegde P, Jee J, Chakravarty D, Schultz N, Berger MF, Frampton GM, Sokol ES, Carrot-Zhang J. Tumor sequencing of African ancestry reveals differences in clinically relevant alterations across common cancers. Cancer Cell 2023; 41:1963-1971.e3. [PMID: 37890492 DOI: 10.1016/j.ccell.2023.10.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 08/02/2023] [Accepted: 10/04/2023] [Indexed: 10/29/2023]
Abstract
Cancer genomes from patients with African (AFR) ancestry have been poorly studied in clinical research. We leverage two large genomic cohorts to investigate the relationship between genomic alterations and AFR ancestry in six common cancers. Cross-cancer type associations, such as an enrichment of MYC amplification with AFR ancestry in lung, breast, and prostate cancers, and depletion of BRAF alterations are observed in colorectal and pancreatic cancers. There are differences in actionable alterations, such as depletion of KRAS G12C and EGFR L858R, and enrichment of ROS1 fusion with AFR ancestry in lung cancers. Interestingly, in lung cancer, KRAS mutations are less common in both smokers and non-smokers with AFR ancestry, whereas the association of TP53 mutations with AFR ancestry is only seen in smokers, suggesting an ancestry-environment interaction that modifies driver rates. Our study highlights the need to increase representation of patients with AFR ancestry in drug development and biomarker discovery.
Collapse
Affiliation(s)
- Evelyn Jiagge
- Hematology/Oncology Division, Department of Medicine, Henry Ford Health System, Detroit, MI, USA.
| | - Dexter X Jin
- Computational Discovery, Foundation Medicine, Inc., Cambridge, MA, USA.
| | - Justin Y Newberg
- Computational Discovery, Foundation Medicine, Inc., Cambridge, MA, USA
| | - Tomin Perea-Chamblee
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kelly R Pekala
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Surgery, Urology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christopher Fong
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michele Waters
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David Ma
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Gilles Erb
- Global Product Development Medical Affairs - Oncology, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Kanika S Arora
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer, New York, NY, USA
| | - Sophia L Maund
- Computational Sciences, Genentech, Inc., South San Francisco, CA, USA
| | - Njoki Njiraini
- Department of Oncology, Kenyatta University Teaching Research and Referral Hospital, Nairobi, Kenya
| | - Atara Ntekim
- Department of Radiation Oncology, University of Ibadan, Ibadan, Nigeria
| | - Susie Kim
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Xuechun Bai
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marlene Thomas
- Global Product Development Medical Affairs - Oncology, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Ronwyn van Eeden
- Department of Medical Oncology, Chris Hani Academic Baragwanath Hospital, Johannesburg, South Africa
| | - Priti Hegde
- Computational Discovery, Foundation Medicine, Inc., Cambridge, MA, USA
| | - Justin Jee
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Debyani Chakravarty
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer, New York, NY, USA; Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nikolaus Schultz
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael F Berger
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer, New York, NY, USA; Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Ethan S Sokol
- Computational Discovery, Foundation Medicine, Inc., Cambridge, MA, USA
| | - Jian Carrot-Zhang
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Clinial Genetics, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| |
Collapse
|
5
|
Weigelt B, Marra A, Selenica P, Rios-Doria E, Momeni-Boroujeni A, Berger MF, Arora K, Nemirovsky D, Iasonos A, Chakravarty D, Abu-Rustum NR, Da Cruz Paula A, Dessources K, Ellenson LH, Liu YL, Aghajanian C, Brown CL. Molecular Characterization of Endometrial Carcinomas in Black and White Patients Reveals Disparate Drivers with Therapeutic Implications. Cancer Discov 2023; 13:2356-2369. [PMID: 37651310 DOI: 10.1158/2159-8290.cd-23-0546] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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: 05/09/2023] [Revised: 08/09/2023] [Accepted: 08/29/2023] [Indexed: 09/02/2023]
Abstract
Although the incidence of endometrial carcinoma (EC) is similar in Black and White women, racial disparities are stark, with the highest mortality rates observed among Black patients. Here, analysis of 1,882 prospectively sequenced ECs using a clinical FDA-authorized tumor-normal panel revealed a significantly higher prevalence of high-risk histologic and molecular EC subtypes in self-identified Black (n = 259) compared with White (n = 1,623) patients. Clinically actionable alterations, including high tumor mutational burden/microsatellite instability, which confer benefit from immunotherapy, were less frequent in ECs from Black than from White patients. Ultramutated POLE molecular subtype ECs associated with favorable outcomes were rare in Black patients. Results were confirmed by genetic ancestry analysis. CCNE1 gene amplification, which is associated with aggressive clinical behavior, was more prevalent in carcinosarcomas occurring in Black than in White patients. ECs from Black and White patients display important differences in their histologic types, molecular subtypes, driver genetic alterations, and therapeutic targets. SIGNIFICANCE Our comprehensive analysis of prospectively clinically sequenced ECs revealed significant differences in their histologic and molecular composition and in the presence of therapeutic targets in Black versus White patients. These findings emphasize the importance of incorporating diverse populations into molecular studies and clinical trials to address EC disparities. This article is featured in Selected Articles from This Issue, p. 2293.
Collapse
Affiliation(s)
- Britta Weigelt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Antonio Marra
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Pier Selenica
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Eric Rios-Doria
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Amir Momeni-Boroujeni
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael F Berger
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kanika Arora
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David Nemirovsky
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alexia Iasonos
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Debyani Chakravarty
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nadeem R Abu-Rustum
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Obstetrics and Gynecology, Weill Cornell Medical College, New York, New York
| | - Arnaud Da Cruz Paula
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kimberly Dessources
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Lora H Ellenson
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ying L Liu
- Gynecologic Medical Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Carol Aghajanian
- Gynecologic Medical Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Carol L Brown
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Obstetrics and Gynecology, Weill Cornell Medical College, New York, New York
- Office of Health Equity, Memorial Sloan Kettering Cancer Center, New York, New York
| |
Collapse
|
6
|
Ptashkin RN, Ewalt MD, Jayakumaran G, Kiecka I, Bowman AS, Yao J, Casanova J, Lin YTD, Petrova-Drus K, Mohanty AS, Bacares R, Benhamida J, Rana S, Razumova A, Vanderbilt C, Balakrishnan Rema A, Rijo I, Son-Garcia J, de Bruijn I, Zhu M, Lachhander S, Wang W, Haque MS, Seshan VE, Wang J, Liu Y, Nafa K, Borsu L, Zhang Y, Aypar U, Suehnholz SP, Chakravarty D, Park JH, Abdel-Wahab O, Mato AR, Xiao W, Roshal M, Yabe M, Batlevi CL, Giralt S, Salles G, Rampal R, Tallman M, Stein EM, Younes A, Levine RL, Perales MA, van den Brink MRM, Dogan A, Ladanyi M, Berger MF, Brannon AR, Benayed R, Zehir A, Arcila ME. Enhanced clinical assessment of hematologic malignancies through routine paired tumor and normal sequencing. Nat Commun 2023; 14:6895. [PMID: 37898613 PMCID: PMC10613284 DOI: 10.1038/s41467-023-42585-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 10/16/2023] [Indexed: 10/30/2023] Open
Abstract
Genomic profiling of hematologic malignancies has augmented our understanding of variants that contribute to disease pathogenesis and supported development of prognostic models that inform disease management in the clinic. Tumor only sequencing assays are limited in their ability to identify definitive somatic variants, which can lead to ambiguity in clinical reporting and patient management. Here, we describe the MSK-IMPACT Heme cohort, a comprehensive data set of somatic alterations from paired tumor and normal DNA using a hybridization capture-based next generation sequencing platform. We highlight patterns of mutations, copy number alterations, and mutation signatures in a broad set of myeloid and lymphoid neoplasms. We also demonstrate the power of appropriate matching to make definitive somatic calls, including in patients who have undergone allogeneic stem cell transplant. We expect that this resource will further spur research into the pathobiology and clinical utility of clinical sequencing for patients with hematologic neoplasms.
Collapse
Affiliation(s)
- Ryan N Ptashkin
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- C2i Genomics, New York, NY, USA
| | - Mark D Ewalt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Gowtham Jayakumaran
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Guardant Health, Palo Alto, CA, USA
| | - Iwona Kiecka
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anita S Bowman
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - JinJuan Yao
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jacklyn Casanova
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yun-Te David Lin
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kseniya Petrova-Drus
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Abhinita S Mohanty
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ruben Bacares
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jamal Benhamida
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Satshil Rana
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anna Razumova
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chad Vanderbilt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anoop Balakrishnan Rema
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ivelise Rijo
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Julie Son-Garcia
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ino de Bruijn
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Menglei Zhu
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sean Lachhander
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wei Wang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mohammad S Haque
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Venkatraman E Seshan
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jiajing Wang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ying Liu
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Khedoudja Nafa
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Laetitia Borsu
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yanming Zhang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Umut Aypar
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sarah P Suehnholz
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Debyani Chakravarty
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jae H Park
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Omar Abdel-Wahab
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anthony R Mato
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wenbin Xiao
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mikhail Roshal
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mariko Yabe
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Connie Lee Batlevi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sergio Giralt
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gilles Salles
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Raajit Rampal
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Martin Tallman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA
| | - Eytan M Stein
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anas Younes
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Oncology R&D, AstraZeneca, New York, NY, USA
| | - Ross L Levine
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Miguel-Angel Perales
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Marcel R M van den Brink
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ahmet Dogan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marc Ladanyi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael F Berger
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - A Rose Brannon
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ryma Benayed
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Oncology R&D, AstraZeneca, New York, NY, USA
| | - Ahmet Zehir
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Oncology R&D, AstraZeneca, New York, NY, USA.
| | - Maria E Arcila
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| |
Collapse
|
7
|
Suehnholz SP, Nissan M, Zhang H, Kundra R, Lu C, Dhaneshwar A, Fernandez N, Carrero S, Arcila ME, Ladanyi M, Berger MF, Syed A, Brannon R, Levine R, Dogan A, Rosen E, Drilon A, Solit DB, Schultz N, Chakravarty D. Abstract 6585: OncoKB, MSK’s precision oncology knowledge base. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-6585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
OncoKB, Memorial Sloan Kettering Cancer Center’s (MSK) precision oncology knowledge base (www.oncokb.org), is an FDA-recognized* somatic variant database that contains information about the oncogenic effect and clinical implications of genomic alterations in cancer. Since its 2016 public release, OncoKB has grown to include annotation for >5,770 alterations in ~700 cancer-associated genes. OncoKB data is integrated into the cBioPortal for Cancer Genomics and used to annotate >12,000 MSK patient sequencing reports annually, encompassing both solid tumor and hematological malignancies. Users in academic, commercial and hospital settings outside MSK can programmatically access OncoKB data via its web API with an OncoKB license, which is free for academic research. To date, users from ~ 1400 institutions across >70 countries have licensed access to OncoKB annotations. The OncoKB Therapeutic (Tx) Levels of Evidence assign tumor-type specific clinical actionability to individual mutational events based on data supporting whether an alteration is predictive of response to matched targeted therapies. To date, OncoKB includes 44 Level 1 genes (included in the FDA drug label), 23 Level 2 genes (included in professional guidelines), 33 Level 3A genes (predictive of drug response in well-powered clinical studies), 27 Level 4 genes (predictive of drug response based on compelling biological evidence), and 11 R1/R2 resistance genes. In 2022, several major content additions were made to OncoKB based on key shifts in the precision oncology landscape. For example, OncoKB included 2 new tumor-agnostic FDA drug approvals, dabrafenib + trametinib and selpercatinib for BRAF V600E and RET fusion-positive solid tumors respectively (Level 1), capturing 5 tumor-agnostic FDA drug approvals to date. OncoKB promoted ERBB2 oncogenic mutations and FGFR1 fusions to Level 1 following their inclusion as patient eligibility criteria in FDA drug labels for trastuzumab deruxtecan (NSCLC) and pemigatinib (myeloid/lymphoid neoplasms) respectively. NCCN guidelines for uterine sarcoma and pancreatic cancer listed PARP-inhibition for BRCA-mutant disease, making them Level 2 in these indications. Lastly, previously considered undruggable targets, TP53 Y220C and KRAS G12D, were included in OncoKB based on compelling evidence demonstrating response to allele-targeting drugs, PC14586 and RMC-6263, respectively. In sum, 7 novel clinically actionable biomarkers (Levels 1-4) and 11 follow-on precision oncology therapies for existing leveled biomarkers were added to OncoKB in 2022. Current OncoKB efforts are focused on prioritized high-volume cancer gene curation for annotation of whole exome/genome data, annotation of germline alterations and development of a clinical trials matching system. *FDA recognition of OncoKB is partial and limited to the information clearly marked on www.oncokb.org.
Citation Format: Sarah P. Suehnholz, Moriah Nissan, Hongxin Zhang, Ritika Kundra, Calvin Lu, Amanda Dhaneshwar, Nicole Fernandez, Stephanie Carrero, Maria E. Arcila, Marc Ladanyi, Michael F. Berger, Aijazuddin Syed, Rose Brannon, Ross Levine, Ahmet Dogan, Ezra Rosen, Alexander Drilon, David B. Solit, Nikolaus Schultz, Debyani Chakravarty. OncoKB, MSK’s precision oncology knowledge base. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6585.
Collapse
Affiliation(s)
| | - Moriah Nissan
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Hongxin Zhang
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ritika Kundra
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Calvin Lu
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | - Marc Ladanyi
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Rose Brannon
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ross Levine
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Dogan
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ezra Rosen
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | |
Collapse
|
8
|
Giraldo NA, Drill E, Satravada BA, Dika IE, Brannon AR, Dermawan J, Mohanty A, Ozcan K, Chakravarty D, Benayed R, Vakiani E, Abou-Alfa GK, Kundra R, Schultz N, Li BT, Berger MF, Harding JJ, Ladanyi M, O’Reilly EM, Jarnagin W, Vanderbilt C, Basturk O, Arcila ME. Comprehensive Molecular Characterization of Gallbladder Carcinoma and Potential Targets for Intervention. Clin Cancer Res 2022; 28:5359-5367. [PMID: 36228155 PMCID: PMC9772093 DOI: 10.1158/1078-0432.ccr-22-1954] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 06/29/2022] [Revised: 08/04/2022] [Accepted: 10/11/2022] [Indexed: 01/24/2023]
Abstract
PURPOSE Gallbladder carcinoma (GBC) is an uncommon and aggressive disease, which remains poorly defined at a molecular level. Here, we aimed to characterize the molecular landscape of GBC and identify markers with potential prognostic and therapeutic implications. EXPERIMENTAL DESIGN GBC samples were analyzed using the MSK-IMPACT (Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets) platform (targeted NGS assay that analyzes 505 cancer-associated genes). Variants with therapeutic implications were identified using OncoKB database. The associations between recurrent genetic alterations and clinicopathologic characteristics (Fisher exact tests) or overall survival (univariate Cox regression) were evaluated. P values were adjusted for multiple testing. RESULTS Overall, 244 samples (57% primary tumors and 43% metastases) from 233 patients were studied (85% adenocarcinomas, 10% carcinomas with squamous differentiation, and 5% neuroendocrine carcinomas). The most common oncogenic molecular alterations appeared in the cell cycle (TP53 63% and CDKN2A 21%) and RTK_RAS pathways (ERBB2 15% and KRAS 11%). No recurrent structural variants were identified. There were no differences in the molecular landscape of primary and metastasis samples. Variants in SMAD4 and STK11 independently associated with reduced survival in patients with metastatic disease. Alterations considered clinically actionable in GBC or other solid tumor types (e.g., NTRK1 fusions or oncogenic variants in ERBB2, PIK3CA, or BRCA1/2) were identified in 35% of patients; 18% of patients with metastatic disease were treated off-label or enrolled in a clinical trial based on molecular findings. CONCLUSIONS GBC is a genetically diverse malignancy. This large-scale genomic analysis revealed alterations with potential prognostic and therapeutic implications and provides guidance for the development of targeted therapies.
Collapse
Affiliation(s)
- Nicolas A. Giraldo
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Esther Drill
- Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Baby A Satravada
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Imane El Dika
- Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Weill Medical College at Cornell University, 1275 York Avenue, New York, NY, 10065, USA
| | - A. Rose Brannon
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Josephine Dermawan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Abhinita Mohanty
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Kerem Ozcan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Debyani Chakravarty
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Efsevia Vakiani
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Ghassan K. Abou-Alfa
- Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Weill Medical College at Cornell University, 1275 York Avenue, New York, NY, 10065, USA
| | - Ritika Kundra
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Nikolaus Schultz
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Bob T. Li
- Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Weill Medical College at Cornell University, 1275 York Avenue, New York, NY, 10065, USA
| | - Michael F. Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - James J. Harding
- Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Weill Medical College at Cornell University, 1275 York Avenue, New York, NY, 10065, USA
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Eileen M. O’Reilly
- Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Weill Medical College at Cornell University, 1275 York Avenue, New York, NY, 10065, USA
| | - William Jarnagin
- Surgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Weill Medical College at Cornell University, 1275 York Avenue, New York, NY, 10065, USA
| | - Chad Vanderbilt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Olca Basturk
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Weill Medical College at Cornell University, 1275 York Avenue, New York, NY, 10065, USA
| | - Maria E. Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Weill Medical College at Cornell University, 1275 York Avenue, New York, NY, 10065, USA
| |
Collapse
|
9
|
Abstract
This article presents a review of the major advances and future implications in precision oncology accomplished in 2022 and centers on three primary pillars: advances in (i) rational drug design, (ii) study design, and (iii) novel biomarkers.
Collapse
Affiliation(s)
- Ezra Rosen
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | | |
Collapse
|
10
|
Van Egeren D, Kohli K, Warner JL, Bedard PL, Riely G, Lepisto E, Schrag D, LeNoue-Newton M, Catalano P, Kehl KL, Michor F, Fiandalo M, Foti M, Khotskaya Y, Lee J, Peters N, Sweeney S, Abraham J, Brenton JD, Caldas C, Doherty G, Nimmervoll B, Pinilla K, Martin JE, Rueda OM, Sammut SJ, Silva D, Cao K, Heath AP, Li M, Lilly J, MacFarland S, Maris JM, Mason JL, Morgan AM, Resnick A, Welsh M, Zhu Y, Johnson B, Li Y, Sholl L, Beaudoin R, Biswas R, Cerami E, Cushing O, Dand D, Ducar M, Gusev A, Hahn WC, Haigis K, Hassett M, Janeway KA, Jänne P, Jawale A, Johnson J, Kehl KL, Kumari P, Laucks V, Lepisto E, Lindeman N, Lindsay J, Lueders A, Macconaill L, Manam M, Mazor T, Miller D, Newcomb A, Orechia J, Ovalle A, Postle A, Quinn D, Reardon B, Rollins B, Shivdasani P, Tramontano A, Van Allen E, Van Nostrand SC, Bell J, Datto MB, Green M, Hubbard C, McCall SJ, Mettu NB, Strickler JH, Andre F, Besse B, Deloger M, Dogan S, Italiano A, Loriot Y, Ludovic L, Michels S, Scoazec J, Tran-Dien A, Vassal G, Freeman CE, Hsiao SJ, Ingham M, Pang J, Rabadan R, Roman LC, Carvajal R, DuBois R, Arcila ME, Benayed R, Berger MF, Bhuiya M, Brannon AR, Brown S, Chakravarty D, Chu C, de Bruijn I, Galle J, Gao J, Gardos S, Gross B, Kundra R, Kung AL, Ladanyi M, Lavery JA, Li X, Lisman A, Mastrogiacomo B, McCarthy C, Nichols C, Ochoa A, Panageas KS, Philip J, Pillai S, Riely GJ, Rizvi H, Rudolph J, Sawyers CL, Schrag D, Schultz N, Schwartz J, Sheridan R, Solit D, Wang A, Wilson M, Zehir A, Zhang H, Zhao G, Ahmed L, Bedard PL, Bruce JP, Chow H, Cooke S, Del Rossi S, Felicen S, Hakgor S, Jagannathan P, Kamel-Reid S, Krishna G, Leighl N, Lu Z, Nguyen A, Oldfield L, Plagianakos D, Pugh TJ, Rizvi A, Sabatini P, Shah E, Singaravelan N, Siu L, Srivastava G, Stickle N, Stockley T, Tang M, Virtaenen C, Watt S, Yu C, Bernard B, Bifulco C, Cramer JL, Lee S, Piening B, Reynolds S, Slagel J, Tittel P, Urba W, VanCampen J, Weerasinghe R, Acebedo A, Guinney J, Guo X, Hunter-Zinck H, Yu T, Dang K, Anagnostou V, Baras A, Brahmer J, Gocke C, Scharpf RB, Tao J, Velculescu VE, Alexander S, Bailey N, Gold P, Bierkens M, de Graaf J, Hudeček J, Meijer GA, Monkhorst K, Samsom KG, Sanders J, Sonke G, ten Hoeve J, van de Velde T, van den Berg J, Voest E, Steinhardt G, Kadri S, Pankhuri W, Wang P, Segal J, Moung C, Espinosa-Mendez C, Martell HJ, Onodera C, Quintanar Alfaro A, Sweet-Cordero EA, Talevich E, Turski M, Van’t Veer L, Wren A, Aguilar S, Dienstmann R, Mancuso F, Nuciforo P, Tabernero J, Viaplana C, Vivancos A, Anderson I, Chaugai S, Coco J, Fabbri D, Johnson D, Jones L, Li X, Lovly C, Mishra S, Mittendorf K, Wen L, Yang YJ, Ye C, Holt M, LeNoue-Newton ML, Micheel CM, Park BH, Rubinstein SM, Stricker T, Wang L, Warner J, Guan M, Jin G, Liu L, Topaloglu U, Urtis C, Zhang W, D’Eletto M, Hutchison S, Longtine J, Walther Z. Genomic analysis of early-stage lung cancer reveals a role for TP53 mutations in distant metastasis. Sci Rep 2022; 12:19055. [PMID: 36351964 PMCID: PMC9646734 DOI: 10.1038/s41598-022-21448-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 09/27/2022] [Indexed: 11/10/2022] Open
Abstract
Patients with non-small cell lung cancer (NSCLC) who have distant metastases have a poor prognosis. To determine which genomic factors of the primary tumor are associated with metastasis, we analyzed data from 759 patients originally diagnosed with stage I-III NSCLC as part of the AACR Project GENIE Biopharma Collaborative consortium. We found that TP53 mutations were significantly associated with the development of new distant metastases. TP53 mutations were also more prevalent in patients with a history of smoking, suggesting that these patients may be at increased risk for distant metastasis. Our results suggest that additional investigation of the optimal management of patients with early-stage NSCLC harboring TP53 mutations at diagnosis is warranted in light of their higher likelihood of developing new distant metastases.
Collapse
Affiliation(s)
- Debra Van Egeren
- grid.65499.370000 0001 2106 9910Department of Data Science, Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Systems Biology, Harvard Medical School, Boston, MA USA ,grid.2515.30000 0004 0378 8438Stem Cell Program, Boston Children’s Hospital, Boston, MA USA ,grid.5386.8000000041936877XDepartment of Medicine, Weill Cornell Medicine, New York, NY USA
| | - Khushi Kohli
- grid.65499.370000 0001 2106 9910Department of Data Science, Dana-Farber Cancer Institute, Boston, MA USA
| | - Jeremy L. Warner
- grid.152326.10000 0001 2264 7217Department of Medicine, Vanderbilt University, Nashville, TN USA ,grid.152326.10000 0001 2264 7217Department of Biomedical Informatics, Vanderbilt University, Nashville, TN USA
| | - Philippe L. Bedard
- grid.17063.330000 0001 2157 2938Department of Medicine, University of Toronto, Toronto, ON Canada
| | - Gregory Riely
- grid.51462.340000 0001 2171 9952Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Eva Lepisto
- grid.65499.370000 0001 2106 9910Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.429426.f0000 0000 9350 5788Present Address: Multiple Myeloma Research Foundation, Norwalk, CT USA
| | - Deborah Schrag
- grid.51462.340000 0001 2171 9952Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Michele LeNoue-Newton
- grid.412807.80000 0004 1936 9916Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN USA
| | - Paul Catalano
- grid.65499.370000 0001 2106 9910Department of Data Science, Dana-Farber Cancer Institute, Boston, MA USA
| | - Kenneth L. Kehl
- grid.65499.370000 0001 2106 9910Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA USA
| | - Franziska Michor
- grid.65499.370000 0001 2106 9910Department of Data Science, Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA USA ,grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.38142.3c000000041936754XDepartment of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA USA ,grid.65499.370000 0001 2106 9910The Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA USA ,grid.38142.3c000000041936754XThe Ludwig Center at Harvard, Boston, MA USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
11
|
Arora K, Tran TN, Kemel Y, Mehine M, Liu YL, Nandakumar S, Smith SA, Brannon AR, Ostrovnaya I, Stopsack KH, Razavi P, Safonov A, Rizvi HA, Hellmann MD, Vijai J, Reynolds TC, Fagin JA, Carrot-Zhang J, Offit K, Solit DB, Ladanyi M, Schultz N, Zehir A, Brown CL, Stadler ZK, Chakravarty D, Bandlamudi C, Berger MF. Genetic Ancestry Correlates with Somatic Differences in a Real-World Clinical Cancer Sequencing Cohort. Cancer Discov 2022; 12:2552-2565. [PMID: 36048199 PMCID: PMC9633436 DOI: 10.1158/2159-8290.cd-22-0312] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 07/12/2022] [Accepted: 08/29/2022] [Indexed: 01/12/2023]
Abstract
Accurate ancestry inference is critical for identifying genetic contributors of cancer disparities among populations. Although methods to infer genetic ancestry have historically relied upon genome-wide markers, the adaptation to targeted clinical sequencing panels presents an opportunity to incorporate ancestry inference into routine diagnostic workflows. We show that global ancestral contributions and admixture of continental populations can be quantitatively inferred using markers captured by the MSK-IMPACT clinical panel. In a pan-cancer cohort of 45,157 patients, we observed differences by ancestry in the frequency of somatic alterations, recapitulating known associations and revealing novel associations. Despite the comparable overall prevalence of driver alterations by ancestry group, the proportion of patients with clinically actionable alterations was lower for African (30%) compared with European (33%) ancestry. Although this result is largely explained by population-specific cancer subtype differences, it reveals an inequity in the degree to which different populations are served by existing precision oncology interventions. SIGNIFICANCE We performed a comprehensive analysis of ancestral associations with somatic mutations in a real-world pan-cancer cohort, including >5,000 non-European individuals. Using an FDA-authorized tumor sequencing panel and an FDA-recognized oncology knowledge base, we detected differences in the prevalence of clinically actionable alterations, potentially contributing to health care disparities affecting underrepresented populations. This article is highlighted in the In This Issue feature, p. 2483.
Collapse
Affiliation(s)
- Kanika Arora
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Thinh Ngoc. Tran
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yelena Kemel
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Robert and Kate Niehaus Center for Inherited Cancer Genomics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Miika Mehine
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ying L. Liu
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Subhiksha Nandakumar
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shaleigh A Smith
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - A. Rose Brannon
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Irina Ostrovnaya
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Konrad H. Stopsack
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pedram Razavi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anton Safonov
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hira A. Rizvi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matthew D. Hellmann
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joseph Vijai
- Robert and Kate Niehaus Center for Inherited Cancer Genomics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Thomas C. Reynolds
- Office of Health Equity, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - James A. Fagin
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jian Carrot-Zhang
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kenneth Offit
- Robert and Kate Niehaus Center for Inherited Cancer Genomics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David B. Solit
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marc Ladanyi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nikolaus Schultz
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ahmet Zehir
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Carol L. Brown
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Office of Health Equity, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zsofia K. Stadler
- Robert and Kate Niehaus Center for Inherited Cancer Genomics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Debyani Chakravarty
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chaitanya Bandlamudi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael F. Berger
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| |
Collapse
|
12
|
Pitel B, Benary M, Rao S, Campregher P, King I, Raca G, Rajagopal PS, Saliba J, Sonkin D, Vlachos I, Griffith M, Griffith OL, Chakravarty D, Wagner A. 44. An international landscape of cancer NGS reporting practices. Cancer Genet 2022. [DOI: 10.1016/j.cancergen.2022.10.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
13
|
Jee J, Lebow ES, Yeh R, Das JP, Namakydoust A, Paik PK, Chaft JE, Jayakumaran G, Rose Brannon A, Benayed R, Zehir A, Donoghue M, Schultz N, Chakravarty D, Kundra R, Madupuri R, Murciano-Goroff YR, Tu HY, Xu CR, Martinez A, Wilhelm C, Galle J, Daly B, Yu HA, Offin M, Hellmann MD, Lito P, Arbour KC, Zauderer MG, Kris MG, Ng KK, Eng J, Preeshagul I, Victoria Lai W, Fiore JJ, Iqbal A, Molena D, Rocco G, Park BJ, Lim LP, Li M, Tong-Li C, De Silva M, Chan DL, Diakos CI, Itchins M, Clarke S, Pavlakis N, Lee A, Rekhtman N, Chang J, Travis WD, Riely GJ, Solit DB, Gonen M, Rusch VW, Rimner A, Gomez D, Drilon A, Scher HI, Shah SP, Berger MF, Arcila ME, Ladanyi M, Levine RL, Shen R, Razavi P, Reis-Filho JS, Jones DR, Rudin CM, Isbell JM, Li BT. Overall survival with circulating tumor DNA-guided therapy in advanced non-small-cell lung cancer. Nat Med 2022; 28:2353-2363. [PMID: 36357680 PMCID: PMC10338177 DOI: 10.1038/s41591-022-02047-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [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: 02/15/2022] [Accepted: 09/16/2022] [Indexed: 11/12/2022]
Abstract
Circulating tumor DNA (ctDNA) sequencing guides therapy decisions but has been studied mostly in small cohorts without sufficient follow-up to determine its influence on overall survival. We prospectively followed an international cohort of 1,127 patients with non-small-cell lung cancer and ctDNA-guided therapy. ctDNA detection was associated with shorter survival (hazard ratio (HR), 2.05; 95% confidence interval (CI), 1.74-2.42; P < 0.001) independently of clinicopathologic features and metabolic tumor volume. Among the 722 (64%) patients with detectable ctDNA, 255 (23%) matched to targeted therapy by ctDNA sequencing had longer survival than those not treated with targeted therapy (HR, 0.63; 95% CI, 0.52-0.76; P < 0.001). Genomic alterations in ctDNA not detected by time-matched tissue sequencing were found in 25% of the patients. These ctDNA-only alterations disproportionately featured subclonal drivers of resistance, including RICTOR and PIK3CA alterations, and were associated with short survival. Minimally invasive ctDNA profiling can identify heterogeneous drivers not captured in tissue sequencing and expand community access to life-prolonging therapy.
Collapse
Affiliation(s)
- Justin Jee
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Emily S Lebow
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Randy Yeh
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jeeban P Das
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Paul K Paik
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Jamie E Chaft
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | | | - A Rose Brannon
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ryma Benayed
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ahmet Zehir
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mark Donoghue
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | - Ritika Kundra
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | - Hai-Yan Tu
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Chong-Rui Xu
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | | | - Clare Wilhelm
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jesse Galle
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bobby Daly
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Helena A Yu
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Michael Offin
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Matthew D Hellmann
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Piro Lito
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Kathryn C Arbour
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Marjorie G Zauderer
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Mark G Kris
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Kenneth K Ng
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Juliana Eng
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Isabel Preeshagul
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - W Victoria Lai
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - John J Fiore
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Afsheen Iqbal
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Daniela Molena
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Gaetano Rocco
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Bernard J Park
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Lee P Lim
- Resolution Bioscience, Agilent Technologies, Kirkland, WA, USA
| | - Mark Li
- Resolution Bioscience, Agilent Technologies, Kirkland, WA, USA
| | - Candace Tong-Li
- GenesisCare, University of Sydney, Sydney, Australia
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - David L Chan
- GenesisCare, University of Sydney, Sydney, Australia
| | | | | | | | - Nick Pavlakis
- GenesisCare, University of Sydney, Sydney, Australia
| | - Adrian Lee
- GenesisCare, University of Sydney, Sydney, Australia
| | - Natasha Rekhtman
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Jason Chang
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - William D Travis
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Gregory J Riely
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - David B Solit
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Mithat Gonen
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Valerie W Rusch
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Andreas Rimner
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Daniel Gomez
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Alexander Drilon
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Howard I Scher
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Sohrab P Shah
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Maria E Arcila
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Marc Ladanyi
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Ross L Levine
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Ronglai Shen
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pedram Razavi
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Jorge S Reis-Filho
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - David R Jones
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Charles M Rudin
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - James M Isbell
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Bob T Li
- Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Weill Cornell Medicine, Cornell University, New York, NY, USA.
| |
Collapse
|
14
|
Horak P, Chakravarty D, Sonkin D. Response to Mehta et al. Genet Med 2022; 24:1989-1990. [PMID: 35796744 DOI: 10.1016/j.gim.2022.05.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 05/05/2022] [Indexed: 10/17/2022] Open
Affiliation(s)
- Peter Horak
- National Center for Tumor Diseases (NCT), Heidelberg, Germany.
| | | | | |
Collapse
|
15
|
Suehnholz SP, Nissan M, Zhang H, Kundra R, Lu C, Xu B, Arcila ME, Ladanyi M, Berger MF, Zehir A, Syed A, Rudolph JE, Levine RL, Dogan A, Gao J, Solit DB, Schultz N, Chakravarty D. Abstract 1189: OncoKB, MSK’s precision oncology knowledge base. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-1189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
OncoKB, Memorial Sloan Kettering Cancer Center’s (MSK) precision oncology knowledge base (www.oncokb.org), is a comprehensive database that annotates the oncogenic effects and clinical actionability of somatic alterations in cancer. OncoKB supports variant interpretation by the cBioPortal for Cancer Genomics and is used to annotate >12,000 MSK patient sequencing reports annually. Since its introduction in 2016, OncoKB has expanded to include 5685 alterations in 682 genes, and in October 2021, it became the first somatic knowledge base to be partially recognized by the FDA. The scope of the OncoKB FDA recognition includes clinically actionable variants that map to an FDA level of evidence, the processes of variant curation, and policies regarding database oversight, personnel training and transparency of data sources and operations. This recognition credentials OncoKB as providing accurate, reliable and clinically meaningful information to the medical and scientific communities.
The OncoKB Therapeutic (Tx) Levels of Evidence categorize variants based on their tumor type-specific predictive value of sensitivity or resistance to matched standard care or investigational targeted therapies. To date, OncoKB includes 43 Level 1 genes (included in the FDA drug label), 23 Level 2 genes (included in professional guidelines), 25 Level 3A genes (predictive of drug response in well-powered clinical studies), 23 Level 4 genes (predictive of drug response based on compelling biological evidence), and 11 R1 or R2 resistance genes. Initially focused on solid tumors, OncoKB was expanded to include hematologic disease annotation in 2019 and introduced Diagnostic (Dx) and Prognostic (Px) levels of evidence. All three level of evidence systems (Tx, Dx and Px) are consistent with the guidelines for evidence-based categorization of somatic variants published as a joint consensus recommendation by AMP/ASCO/CAP.
OncoKB is governed by a Clinical Genomics Annotation Committee, composed of MSK physicians and scientists who ensure that the information captured is accurate and current, and an external advisory board composed of leaders in the clinical oncology and genomics communities who oversee OncoKB updates and progress. OncoKB curation rules and processes are transparent and documented in the OncoKB Curation Standard Operating Procedure, which is publicly available via the website. User feedback to OncoKB content is encouraged via the website and through cBioPortal. Queries or suggestions by OncoKB users are addressed by the OncoKB team within 72 hours.
OncoKB offers licenses for academic, commercial and hospital use, with which users can programmatically access the web API. Future work includes coverage of additional cancer-associated genes, annotation of germline alterations that are predictive of drug response and/or associated with increased heritable cancer risk and the development of a clinical trial matching system.
Citation Format: Sarah P. Suehnholz, Moriah Nissan, Hongxin Zhang, Ritika Kundra, Calvin Lu, Benjamin Xu, Maria E. Arcila, Marc Ladanyi, Michael F. Berger, Ahmet Zehir, Aijaz Syed, Julia E. Rudolph, Ross L. Levine, Ahmet Dogan, Jianjiong Gao, David B. Solit, Nikolaus Schultz, Debyani Chakravarty. OncoKB, MSK’s precision oncology knowledge base [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1189.
Collapse
Affiliation(s)
| | | | | | | | - Calvin Lu
- 1Memorial Sloan Kettering, New York, NY
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Bandlamudi C, Chatila WK, Smith SA, Nandakumar S, Bielski C, Nguyen B, Walch HS, Kreitzer CK, Arora KS, Ngoc TT, Mehine M, Ostrovnaya I, de Bruijn I, Woo HJ, Kundra R, Fong CJ, Rana S, Zhao G, Zhang M, Zucker MR, Zhang H, Ptashkin R, Brannon R, Reznik E, Gao J, Arcila ME, Benayed R, Chakravarty D, Solit D, Donoghue MT, Ladanyi M, Schultz ND, Berger MF, Zehir A. Abstract 3628: Comprehensive identification of lineage associated cancer genes in 122 histologies. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-3628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Although the majority of cancer genes show a high degree of specificity for certain lineages, genomic profiling of cancer patients routinely identify alterations in genes that are atypical to the presented cancer type but are canonical drivers in a different lineage. It is often unclear if these atypical drivers arose early in tumorigenesis or were acquired during progression. A complete understanding of lineage associated genes (LAGs) will enable better interpretation of the molecular etiology of each diagnosed tumor.
Here, we used a cohort of 38,912 patients across 122 cancer histologies (each with 50 or more patients) profiled for somatic alterations (mutations, copy number alterations and gene fusions) using the MSK-IMPACT assay. Tumors with TMB > 15 were already excluded. All alterations were classified as drivers using OncoKB. Allele-specific copy number calls were assessed using FACETS.
Overall, 95% of patients harbored at least one oncogenic alteration, with a median of 4 drivers per tumor. We observed widespread prevalence of drivers across lineages with each gene mutated in a median of 36 different lineages. Conversely, a median of 103 genes were mutated at least once in each lineage. Hypothesizing that cancer genes are influenced by cell of origin, we sought to identify lineages harboring significantly higher rates of drivers in a given gene compared to its pancancer driver rate. We identified 1781 significant (adjusted P < 0.05) gene and lineage associations, and an additional 109 involving genes mutated at >10% in the respective lineages but which did not reach significance were also included. Lineage-agnostic genes such as TP53 and CDKN2A were associated with a broad spectrum of lineages (90 and 55, respectively). However, overall, each gene we profiled was found to be associated with a median of 3 distinct lineages. For example, while BRAF drivers are found in nearly all histologies (n=91), it is enriched for drivers in only 8 lineages: melanoma (acral and cutaneous), thyroid (poorly differentiated, anaplastic and papillary) and bowel (mucinous adenocarc. of colon/rectum, colon adenocarc. and neuroendocrine carc. of colon/rectum). In all, nearly a third of all drivers were observed in non-associated lineages.
We next compared the somatic properties of drivers among genes in associated lineages vs. the same genes in non-associated lineages. We observed that mutations in LAGs were more often clonal (83% vs. 73%, associated vs. non-associated, P = 0) and showed enrichment for mutant allele imbalance in oncogenes (40% vs. 23%, P = 2e-111) and biallelic inactivation in tumor suppressor LAGs (71% vs. 58%, P = 4e-130). Furthermore, 93% of all OncoKB Level 1/2/3A actionable alterations, which are classified based on their histology, were in LAGs. In conclusion, our findings enable classification of drivers that are relevant for lineage-specific malignant transformation and advance our understanding of tumor biology.
Citation Format: Chaitanya Bandlamudi, Walid K. Chatila, Shaleigh A. Smith, Subhiksha Nandakumar, Craig Bielski, Bastien Nguyen, Henry S. Walch, Christoph K. Kreitzer, Kanika S. Arora, Tran Thinh Ngoc, Miika Mehine, Irina Ostrovnaya, Ino de Bruijn, Hyung Jun Woo, Ritika Kundra, Christopher J. Fong, Satshil Rana, Gaofei Zhao, Mingxuan Zhang, Mark R. Zucker, Hongxin Zhang, Ryan Ptashkin, Rose Brannon, Eduard Reznik, JianJiong Gao, Maria E. Arcila, Ryma Benayed, Debyani Chakravarty, David Solit, Mark T. Donoghue, Marc Ladanyi, Nikolaus D. Schultz, Michael F. Berger, Ahmet Zehir. Comprehensive identification of lineage associated cancer genes in 122 histologies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3628.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Miika Mehine
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Ino de Bruijn
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Hyung Jun Woo
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ritika Kundra
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Satshil Rana
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Gaofei Zhao
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Hongxin Zhang
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ryan Ptashkin
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Rose Brannon
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Eduard Reznik
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - JianJiong Gao
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Ryma Benayed
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - David Solit
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Marc Ladanyi
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Ahmet Zehir
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| |
Collapse
|
17
|
Walch H, Luthra A, Chatila WK, Wu F, Chakravarty D, Chen CT, Sood R, Omer DM, Smith JJ, Schultz N, Ganesh K, Garcia-Aguilar J, Yaeger R, Sanchez-Vega F. Abstract 3634: Integrative analysis of the contribution of genomic and clinical factors to worse clinical outcomes in non-Hispanic Black patients with colorectal cancer. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-3634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Non-Hispanic Black (NHB) patients have higher incidence and higher mortality from colorectal cancer (CRC) than non-Hispanic white (NHW) patients. The extent to which this aggressive behavior in NHB patients is driven by differences in cancer genomics is presently unknown.
We analyzed clinical and genomic data from 3,963 CRC patients treated at Memorial Sloan Kettering, including 336 (8%) NHB and 3,627 (92%) NHW patients. Tumors were sequenced using the clinical MSK-IMPACT test, a targeted next-generation DNA sequencing assay that identifies mutations, copy number changes and structural rearrangements in 341-505 genes using solid tissue and matched blood.
No significant differences by race were observed for stage at diagnosis or sex. While the difference in median age at diagnosis was small (53.4 for NHB vs. 55 years for NHW patients, p=0.012), significantly fewer NHB patients were diagnosed after 65 years of age (17% vs. 27%, p=0.001). Right-sided colon tumors were more common among NHB patients (37% vs. 25%, p=0.02); the proportion of rectal tumors was similar in both racial groups (31% in NHB vs. 34% in NHW patients, n.s.). Hypermutated tumors, including tumors with microsatellite instability (MSI) and POLE hypermutants, were more frequent among NHW patients (12% vs. 8%, p=0.02). Right-sided tumors were more frequently MSI/hypermutated in the NHW patients (27% vs. 13%, p=0.008), whereas no differences by race were observed for left-sided colon (5% vs. 1%, n.s.) or rectal primaries (4% vs. 5%, n.s.).
Genomic analysis of the non-hypermutated tumors revealed no significant differences in tumor mutational burden or fraction of genome altered between racial groups. Tumors in NHB patients were enriched in KRAS mutations (60% vs. 45%, p<0.001), but G12C mutations accounted only for 3% of all driver KRAS mutations in NHB patients vs. 8% of all driver mutations in NHW patients (p=0.01). BRAF mutations were more frequent in non-hypermutated NHW patients (7% vs. 3%, p=0.006), but the overall frequency of RTK/RAS pathway alterations was higher in the NHB group (74% vs. 66%, p=0.004).
Even though all patients were treated at the same single institution during the study, NHB patients had shorter overall survival (OS) from the time of sequencing (median 28 months [95% CI 25-38] vs. 50 months [95% CI 47-53], p<0.001). NHB patients also had worse OS [HR 1.64, CI 1.3 - 2.1, p<0.001] in a multivariate analysis using Cox Proportional-Hazards and accounting for age at diagnosis, stage at diagnosis, body mass index, primary tumor location, MSI status and oncogenic alterations in APC, TP53, KRAS, SMAD4, and BRAF.
Our data confirms that NHB patients with CRC have worse clinical outcomes than NHW patients. Clinically relevant differences in the frequency of alterations in cancer driver genes are observed based on racial origin, but they do not fully explain the difference in survival.
Citation Format: Henry Walch, Anisha Luthra, Walid K. Chatila, Fan Wu, Debyani Chakravarty, Chin-Tung Chen, Rupa Sood, Dana M. Omer, Jesse J. Smith, Nikolaus Schultz, Karuna Ganesh, Julio Garcia-Aguilar, Rona Yaeger, Francisco Sanchez-Vega. Integrative analysis of the contribution of genomic and clinical factors to worse clinical outcomes in non-Hispanic Black patients with colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3634.
Collapse
Affiliation(s)
| | | | | | - Fan Wu
- 1Memorial Sloan Kettering, New York, NY
| | | | | | - Rupa Sood
- 1Memorial Sloan Kettering, New York, NY
| | | | | | | | | | | | | | | |
Collapse
|
18
|
Arora K, Tran TN, Kemel YM, Mehine M, Liu Y, Smith SA, Nandakumar S, Ostrovnaya I, Reynolds TC, Offit K, Solit D, Ladanyi M, Schultz N, Zehir A, Brown CL, Chakravarty D, Stadler ZK, Bandlamudi C, Berger MF. Abstract 2182: Ancestry inference and population-specific disparities in a real-world clinical sequencing cohort. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-2182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Accurate ancestry inference is crucial for identifying genetic determinants of cancer disparities among specific populations. While methods to infer genetic ancestry and admixture have historically relied upon genome-wide markers from broad-scale next-generation sequencing (NGS), the adaptation to targeted NGS panels presents an opportunity to prospectively incorporate ancestry inference as part of routine clinical diagnosis. Here we show that global ancestral contributions and admixture of African (AFR), European (EUR), East Asian (EAS), Native American (NAM) and South Asian (SAS) populations can be reliably inferred using markers from genomic regions covered by the FDA-authorized clinical NGS panel, MSK-IMPACT. We also show that individuals with Ashkenazi Jewish (ASJ) ancestry can be inferred with 97% accuracy using a set of ASJ ancestry-informative markers. We apply these methods to infer genetic ancestry for over 45,000 patients from the AACR GENIE v10.0-public cohort who were profiled using MSK-IMPACT. We observed 98% concordance between self-reported race and genetic ancestry for non-admixed individuals and were able to quantitatively infer ancestral contributions for individuals from recently admixed populations such as African American and Latin American. Of the discordant cases, manual review of clinical and family histories revealed the vast majority to represent clinical encoding errors where the inferred ancestry was confirmed correct. As self-reported race is not available for 17% of patients in the GENIE cohort, the ability to accurately infer genetic ancestry enables broader analysis of population-specific genomic and clinical features. We systematically evaluated the frequency of somatic and germline alterations in up to 468 genes for each cancer type and recapitulated known differences among ancestral populations. For example, we observed significantly higher frequency of EGFR somatic alterations in EAS (65%) and SAS (66%) compared to non-ASJ EUR (21%) with lung adenocarcinoma, a difference that remained significant even when limiting to never-smokers. Additionally, we found that the frequency of harboring at least one known BRCA founder mutation (BRCA1 68_69delAG, BRCA1 5266dupC, or BRCA2 5946delT) was 26x higher in genetically determined ASJ (5.1%) compared to non-ASJ (0.2%). Strikingly, while the overall rate of driver alterations in solid tumors was similar across different populations, we found that the proportion of patients with clinically actionable somatic alterations (OncoKB Level 1, 2, 3A, or 3B) was lowest in AFR (47%) patients compared to EUR, EAS and SAS (50% each). While this result is partially explained by different cancer type and subtype distributions in different populations in this real-world cohort, it highlights the urgency for greater equity in drug development programs to target alterations represented across all diverse populations.
Citation Format: Kanika Arora, Thinh N. Tran, Yelena M. Kemel, Miika Mehine, Ying Liu, Shaleigh A. Smith, Subhiksha Nandakumar, Irina Ostrovnaya, Thomas C. Reynolds, Kenneth Offit, David Solit, Marc Ladanyi, Nikolaus Schultz, Ahmet Zehir, Carol L. Brown, Debyani Chakravarty, Zsofia K. Stadler, Chaitanya Bandlamudi, Michael F. Berger. Ancestry inference and population-specific disparities in a real-world clinical sequencing cohort [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2182.
Collapse
Affiliation(s)
- Kanika Arora
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Thinh N. Tran
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Miika Mehine
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ying Liu
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | - Kenneth Offit
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - David Solit
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Marc Ladanyi
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Ahmet Zehir
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | | |
Collapse
|
19
|
Liu D, Murciano-Goroff YR, Jee J, Arcila ME, Buonocore DJ, Gao J, Chakravarty D, Schram AM, Callahan MK, Friedman CF, Jhaveri KL, Harding JJ, Gounder MM, Rosen E, Rosen N, Misale S, Lito P, Yaeger R, Drilon AE, Li BT. Clinicopathologic characterization of ERK2 E322K mutation in solid tumors: Implications for treatment and drug development. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.3135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
3135 Background: MAPK1 encodes ERK2, a kinase component of the mitogen activated signaling (MAPK) pathway. ERK2 E322K is a known activating mutation that leads to increased phosphorylation and ERK signaling. In vitro studies found this mutation to be associated with resistance to dabrafenib, trametinib, but potential sensitivity to ERK inhibitors. Despite its potential as a drug target, little is known about the clinicopathologic characteristics of this hotspot mutation across solid tumors. Methods: Patients with solid tumors underwent tumor next-generation sequencing at Memorial Sloan Kettering Cancer Center between Jan 2015 and Sep 2020 using the MSK-IMPACT assay. Using the cBioPortal database and clinical charts, we analyzed tumors harboring MAPK1/ERK2 E322K mutations, assessed their clinicopathologic characteristics, co-mutational status and overall survival (OS). OS was measured from time of tumor sequencing to date of death or last follow-up. Results: A total of 37 tumor samples from 35 patients were identified in 59,822 tumors sequenced (0.06%) to harbor an ERK2 E322K mutation. The distribution across tumor types was as follows: head and neck squamous cell carcinoma (29%), bladder cancer (20%), lymphomas (9%), colorectal cancers (9%), gastric cancers (9%), cholangiocarcinoma (6%), cervical cancers (6%), lung cancers (6%), germ cell tumor (3%), Merkel cell carcinoma (3%), and breast cancers (3%). The OS in patients with metastatic disease and ERK2 E322K was 22.29 months (95%CI: 7.56-NA) months. Other mutations in RAS pathway frequently co-occurred with ERK2 E322K mutation (17/37, 46%). Concurrent mutations are also involved in pathways of cell cycle (71%), PI3K (71%), TP53 (66%), NOTCH (57%), RTK (51%), HIPPO (29%), TGF-beta (29%), WNT (26%), NRF2 (20%), MYC (14%). The median TMB score of samples from solid malignancies was 12.3 (range:0-101, quartiles: 6.9-33.0) mutation/Mb. Two patients (2/35, 6%) had microsatellite-instability high (MSI-H) tumors. The most frequent concurrent activating mutations include ARID1A (29%), FBXW7 (26%), PI3KCA (22%), PI3KR1/2/3 (20%), CDKN2A (11%), PTEN (8%), BRCA1/2(8%), FGFR3 (8%), BRAF (6%), Only one of these 35 patients received treatment targeting BRAF/MEK/ERK pathway and achieved partial response. One patient with NSCLC harboring a concurrent EGFR L858R mutation did not respond to erlotinib. One patient with PI3KCA mutated head and neck cancer did not respond to PI3K inhibitor. Two patients had TMB score of 100.9 and 12.9 mutation/Mb had partial response to pembrolizumab. Conclusions: ERK2 E322K mutation is a rare oncogenic mutation across diverse solid tumor types, associated with a high co-occurrence of other activating mutations and a high TMB. The lack of response to other targeted therapies suggests ERK2 E322K is a potential driver mutation. These findings may inform treatment and further development of ERK inhibitors.
Collapse
Affiliation(s)
- Dazhi Liu
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Justin Jee
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - JianJiong Gao
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | - Claire Frances Friedman
- Memorial Sloan Kettering Cancer Center and Weill Medical College at Cornell University, New York, NY
| | | | - James J. Harding
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mrinal M. Gounder
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY
| | - Ezra Rosen
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Neal Rosen
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Sandra Misale
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Piro Lito
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Rona Yaeger
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Bob T. Li
- Memorial Sloan Kettering Cancer Center, New York, NY
| |
Collapse
|
20
|
Luthra A, Mastrogiacomo B, Smith SA, Chakravarty D, Schultz N, Sanchez-Vega F. Computational methods and translational applications for targeted next-generation sequencing platforms. Genes Chromosomes Cancer 2022; 61:322-331. [PMID: 35066956 PMCID: PMC10129038 DOI: 10.1002/gcc.23023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 01/10/2022] [Indexed: 11/09/2022] Open
Abstract
During the past decade, next-generation sequencing (NGS) technologies have become widely adopted in cancer research and clinical care. Common applications within the clinical setting include patient stratification into relevant molecular subtypes, identification of biomarkers of response and resistance to targeted and systemic therapies, assessment of heritable cancer risk based on known pathogenic variants, and longitudinal monitoring of treatment response. The need for efficient downstream processing and reliable interpretation of sequencing data has led to the development of novel algorithms and computational pipelines, as well as structured knowledge bases that link genomic alterations to currently available drugs and ongoing clinical trials. Cancer centers around the world use different types of targeted solid-tissue and blood based NGS assays to analyze the genomic and transcriptomic profile of patients as part of their routine clinical care. Recently, cross-institutional collaborations have led to the creation of large pooled datasets that can offer valuable insights into the genomics of rare cancers.
Collapse
Affiliation(s)
- Anisha Luthra
- 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
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Brooke Mastrogiacomo
- 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
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Shaleigh A Smith
- 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
| | - Debyani Chakravarty
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Pathology, 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
- Human Oncology and Pathogenesis Program, 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
| | - Francisco Sanchez-Vega
- 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
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| |
Collapse
|
21
|
Sánchez-Rivera FJ, Diaz BJ, Kastenhuber ER, Schmidt H, Katti A, Kennedy M, Tem V, Ho YJ, Leibold J, Paffenholz SV, Barriga FM, Chu K, Goswami S, Wuest AN, Simon JM, Tsanov KM, Chakravarty D, Zhang H, Leslie CS, Lowe SW, Dow LE. Base editing sensor libraries for high-throughput engineering and functional analysis of cancer-associated single nucleotide variants. Nat Biotechnol 2022; 40:862-873. [PMID: 35165384 PMCID: PMC9232935 DOI: 10.1038/s41587-021-01172-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/29/2021] [Indexed: 12/20/2022]
Abstract
Base editing can be applied to characterize single nucleotide variants of unknown function, yet defining effective combinations of single guide RNAs (sgRNAs) and base editors remains challenging. Here, we describe modular base-editing-activity 'sensors' that link sgRNAs and cognate target sites in cis and use them to systematically measure the editing efficiency and precision of thousands of sgRNAs paired with functionally distinct base editors. By quantifying sensor editing across >200,000 editor-sgRNA combinations, we provide a comprehensive resource of sgRNAs for introducing and interrogating cancer-associated single nucleotide variants in multiple model systems. We demonstrate that sensor-validated tools streamline production of in vivo cancer models and that integrating sensor modules in pooled sgRNA libraries can aid interpretation of high-throughput base editing screens. Using this approach, we identify several previously uncharacterized mutant TP53 alleles as drivers of cancer cell proliferation and in vivo tumor development. We anticipate that the framework described here will facilitate the functional interrogation of cancer variants in cell and animal models.
Collapse
Affiliation(s)
- Francisco J Sánchez-Rivera
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Bianca J Diaz
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Edward R Kastenhuber
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Henri Schmidt
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alyna Katti
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Margaret Kennedy
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, New York, NY, USA
| | - Vincent Tem
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yu-Jui Ho
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Josef Leibold
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medical Oncology and Pneumology, University Hospital Tuebingen, Tuebingen, Germany
- iFIT Cluster of Excellence EXC 2180 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tuebingen, Tuebingen, Germany
| | - Stella V Paffenholz
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, New York, NY, USA
| | - Francisco M Barriga
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kevan Chu
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Sukanya Goswami
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Alexandra N Wuest
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Janelle M Simon
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kaloyan M Tsanov
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Debyani Chakravarty
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hongxin Zhang
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christina S Leslie
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Scott W Lowe
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lukas E Dow
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA.
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
| |
Collapse
|
22
|
Horak P, Griffith M, Danos AM, Pitel BA, Madhavan S, Liu X, Chow C, Williams H, Carmody L, Barrow-Laing L, Rieke D, Kreutzfeldt S, Stenzinger A, Tamborero D, Benary M, Rajagopal PS, Ida CM, Lesmana H, Satgunaseelan L, Merker JD, Tolstorukov MY, Campregher PV, Warner JL, Rao S, Natesan M, Shen H, Venstrom J, Roy S, Tao K, Kanagal-Shamanna R, Xu X, Ritter DI, Pagel K, Krysiak K, Dubuc A, Akkari YM, Li XS, Lee J, King I, Raca G, Wagner AH, Li MM, Plon SE, Kulkarni S, Griffith OL, Chakravarty D, Sonkin D. Standards for the classification of pathogenicity of somatic variants in cancer (oncogenicity): Joint recommendations of Clinical Genome Resource (ClinGen), Cancer Genomics Consortium (CGC), and Variant Interpretation for Cancer Consortium (VICC). Genet Med 2022; 24:986-998. [PMID: 35101336 PMCID: PMC9081216 DOI: 10.1016/j.gim.2022.01.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 12/22/2021] [Accepted: 01/03/2022] [Indexed: 01/21/2023] Open
Abstract
PURPOSE Several professional societies have published guidelines for the clinical interpretation of somatic variants, which specifically address diagnostic, prognostic, and therapeutic implications. Although these guidelines for the clinical interpretation of variants include data types that may be used to determine the oncogenicity of a variant (eg, population frequency, functional, and in silico data or somatic frequency), they do not provide a direct, systematic, and comprehensive set of standards and rules to classify the oncogenicity of a somatic variant. This insufficient guidance leads to inconsistent classification of rare somatic variants in cancer, generates variability in their clinical interpretation, and, importantly, affects patient care. Therefore, it is essential to address this unmet need. METHODS Clinical Genome Resource (ClinGen) Somatic Cancer Clinical Domain Working Group and ClinGen Germline/Somatic Variant Subcommittee, the Cancer Genomics Consortium, and the Variant Interpretation for Cancer Consortium used a consensus approach to develop a standard operating procedure (SOP) for the classification of oncogenicity of somatic variants. RESULTS This comprehensive SOP has been developed to improve consistency in somatic variant classification and has been validated on 94 somatic variants in 10 common cancer-related genes. CONCLUSION The comprehensive SOP is now available for classification of oncogenicity of somatic variants.
Collapse
Affiliation(s)
- Peter Horak
- National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Malachi Griffith
- Washington University School of Medicine in St. Louis, St. Louis, MO
| | - Arpad M Danos
- Washington University School of Medicine in St. Louis, St. Louis, MO
| | | | | | - Xuelu Liu
- Dana-Farber Cancer Institute, Boston, MA
| | - Cynthia Chow
- BC Cancer Agency, Vancouver, British Columbia, Canada
| | | | - Leigh Carmody
- The Jackson Laboratory for Genomic Medicine, Farmington, CT
| | | | - Damian Rieke
- Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Simon Kreutzfeldt
- National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | | | | | - Padma Sheila Rajagopal
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | | | - Harry Lesmana
- Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute, Cleveland, OH
| | | | - Jason D Merker
- UNC School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | | | | | - Shruti Rao
- Georgetown University Medical Center, Washington, DC
| | - Maya Natesan
- Washington University School of Medicine in St. Louis, St. Louis, MO
| | - Haolin Shen
- Washington University School of Medicine in St. Louis, St. Louis, MO
| | | | - Somak Roy
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Kayoko Tao
- National Cancer Center Hospital, Tokyo, Japan
| | | | | | | | - Kym Pagel
- Johns Hopkins University, Baltimore, MD
| | - Kilannin Krysiak
- Washington University School of Medicine in St. Louis, St. Louis, MO
| | - Adrian Dubuc
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | | | | | - Jennifer Lee
- Frederick National Laboratory for Cancer Research, National Cancer Institute, Rockville, MD
| | - Ian King
- University Health Network, Toronto, Ontario, Canada
| | - Gordana Raca
- University of Southern California, Los Angeles, CA
| | - Alex H Wagner
- Nationwide Children's Hospital, Columbus, OH; The Ohio State University College of Medicine, Columbus, OH
| | - Marylin M Li
- Children's Hospital of Philadelphia, Philadelphia, PA
| | | | | | - Obi L Griffith
- Washington University School of Medicine in St. Louis, St. Louis, MO
| | | | | |
Collapse
|
23
|
Shrestha Bhattarai T, Shamu T, Gorelick AN, Chang MT, Chakravarty D, Gavrila EI, Donoghue MTA, Gao J, Patel S, Gao SP, Reynolds MH, Phillips SM, Soumerai T, Abida W, Hyman DM, Schram AM, Solit DB, Smyth LM, Taylor BS. AKT mutant allele-specific activation dictates pharmacologic sensitivities. Nat Commun 2022; 13:2111. [PMID: 35440569 PMCID: PMC9018718 DOI: 10.1038/s41467-022-29638-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 03/25/2022] [Indexed: 12/13/2022] Open
Abstract
AKT- a key molecular regulator of PI-3K signaling pathway, is somatically mutated in diverse solid cancer types, and aberrant AKT activation promotes altered cancer cell growth, survival, and metabolism1-8. The most common of AKT mutations (AKT1 E17K) sensitizes affected solid tumors to AKT inhibitor therapy7,8. However, the pathway dependence and inhibitor sensitivity of the long tail of potentially activating mutations in AKT is poorly understood, limiting our ability to act clinically in prospectively characterized cancer patients. Here we show, through population-scale driver mutation discovery combined with functional, biological, and therapeutic studies that some but not all missense mutations activate downstream AKT effector pathways in a growth factor-independent manner and sensitize tumor cells to diverse AKT inhibitors. A distinct class of small in-frame duplications paralogous across AKT isoforms induce structural changes different than those of activating missense mutations, leading to a greater degree of membrane affinity, AKT activation, and cell proliferation as well as pathway dependence and hyper-sensitivity to ATP-competitive, but not allosteric AKT inhibitors. Assessing these mutations clinically, we conducted a phase II clinical trial testing the AKT inhibitor capivasertib (AZD5363) in patients with solid tumors harboring AKT alterations (NCT03310541). Twelve patients were enrolled, out of which six harbored AKT1-3 non-E17K mutations. The median progression free survival (PFS) of capivasertib therapy was 84 days (95% CI 50-not reached) with an objective response rate of 25% (n = 3 of 12) and clinical benefit rate of 42% (n = 5 of 12). Collectively, our data indicate that the degree and mechanism of activation of oncogenic AKT mutants vary, thereby dictating allele-specific pharmacological sensitivities to AKT inhibition.
Collapse
Affiliation(s)
- Tripti Shrestha Bhattarai
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tambudzai Shamu
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexander N Gorelick
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matthew T Chang
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Loxo Oncology at Lilly, Stamford, CT, USA
| | - Debyani Chakravarty
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elena I Gavrila
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mark T A Donoghue
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - JianJong Gao
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Swati Patel
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sizhi Paul Gao
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Margaret H Reynolds
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sarah M Phillips
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tara Soumerai
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Massachusetts General Hospital, Boston, MA, USA
| | - Wassim Abida
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David M Hyman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
- Loxo Oncology at Lilly, Stamford, CT, USA
| | - Alison M Schram
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David B Solit
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
| | - Lillian M Smyth
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Loxo Oncology at Lilly, Stamford, CT, USA
| | - Barry S Taylor
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Weill Cornell Medical College, New York, NY, USA.
- Loxo Oncology at Lilly, Stamford, CT, USA.
| |
Collapse
|
24
|
Chakravarty D, Johnson A, Sklar J, Lindeman NI, Moore K, Ganesan S, Lovly CM, Perlmutter J, Gray SW, Hwang J, Lieu C, André F, Azad N, Borad M, Tafe L, Messersmith H, Robson M, Meric-Bernstam F. Somatic Genomic Testing in Patients With Metastatic or Advanced Cancer: ASCO Provisional Clinical Opinion. J Clin Oncol 2022; 40:1231-1258. [PMID: 35175857 DOI: 10.1200/jco.21.02767] [Citation(s) in RCA: 76] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
PURPOSE An ASCO provisional clinical opinion offers timely clinical direction to ASCO's membership following publication or presentation of potentially practice-changing data from major studies. This provisional clinical opinion addresses the appropriate use of tumor genomic testing in patients with metastatic or advanced solid tumors. CLINICAL CONTEXT An increasing number of therapies are approved to treat cancers harboring specific genomic biomarkers. However, there is a lack of clarity as to when tumor genomic sequencing should be ordered, what type of assays should be performed, and how to interpret the results for treatment selection. PROVISIONAL CLINICAL OPINION Patients with metastatic or advanced cancer should undergo genomic sequencing in a certified laboratory if the presence of one or more specific genomic alterations has regulatory approval as biomarkers to guide the use of or exclusion from certain treatments for their disease. Multigene panel-based assays should be used if more than one biomarker-linked therapy is approved for the patient's disease. Site-agnostic approvals for any cancer with a high tumor mutation burden, mismatch repair deficiency, or neurotrophic tyrosine receptor kinase (NTRK) fusions provide a rationale for genomic testing for all solid tumors. Multigene testing may also assist in treatment selection by identifying additional targets when there are few or no genotype-based therapy approvals for the patient's disease. For treatment planning, the clinician should consider the functional impact of the targeted alteration and expected efficacy of genomic biomarker-linked options relative to other approved or investigational treatments.Additional information is available at www.asco.org/assays-and-predictive-markers-guidelines.
Collapse
Affiliation(s)
| | | | | | - Neal I Lindeman
- Brigham and Womens' Hospital, Harvard Medical School, Boston, MA
| | | | | | | | | | | | | | | | - Fabrice André
- PRISM, Precision Medicine Center, Institut Gustave Roussy, Villejuif, France
| | | | | | - Laura Tafe
- Dartmouth-Hitchcock Medical Center and The Geisel School of Medicine at Dartmouth, Darmouth, NH
| | | | - Mark Robson
- Memorial Sloan Kettering Cancer Center, New York City, NY
| | | |
Collapse
|
25
|
Nguyen B, Fong C, Luthra A, Smith SA, DiNatale RG, Nandakumar S, Walch H, Chatila WK, Madupuri R, Kundra R, Bielski CM, Mastrogiacomo B, Donoghue MTA, Boire A, Chandarlapaty S, Ganesh K, Harding JJ, Iacobuzio-Donahue CA, Razavi P, Reznik E, Rudin CM, Zamarin D, Abida W, Abou-Alfa GK, Aghajanian C, Cercek A, Chi P, Feldman D, Ho AL, Iyer G, Janjigian YY, Morris M, Motzer RJ, O'Reilly EM, Postow MA, Raj NP, Riely GJ, Robson ME, Rosenberg JE, Safonov A, Shoushtari AN, Tap W, Teo MY, Varghese AM, Voss M, Yaeger R, Zauderer MG, Abu-Rustum N, Garcia-Aguilar J, Bochner B, Hakimi A, Jarnagin WR, Jones DR, Molena D, Morris L, Rios-Doria E, Russo P, Singer S, Strong VE, Chakravarty D, Ellenson LH, Gopalan A, Reis-Filho JS, Weigelt B, Ladanyi M, Gonen M, Shah SP, Massague J, Gao J, Zehir A, Berger MF, Solit DB, Bakhoum SF, Sanchez-Vega F, Schultz N. Genomic characterization of metastatic patterns from prospective clinical sequencing of 25,000 patients. Cell 2022; 185:563-575.e11. [PMID: 35120664 PMCID: PMC9147702 DOI: 10.1016/j.cell.2022.01.003] [Citation(s) in RCA: 190] [Impact Index Per Article: 95.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 10/21/2021] [Accepted: 01/05/2022] [Indexed: 02/06/2023]
Abstract
Metastatic progression is the main cause of death in cancer patients, whereas the underlying genomic mechanisms driving metastasis remain largely unknown. Here, we assembled MSK-MET, a pan-cancer cohort of over 25,000 patients with metastatic diseases. By analyzing genomic and clinical data from this cohort, we identified associations between genomic alterations and patterns of metastatic dissemination across 50 tumor types. We found that chromosomal instability is strongly correlated with metastatic burden in some tumor types, including prostate adenocarcinoma, lung adenocarcinoma, and HR+/HER2+ breast ductal carcinoma, but not in others, including colorectal cancer and high-grade serous ovarian cancer, where copy-number alteration patterns may be established early in tumor development. We also identified somatic alterations associated with metastatic burden and specific target organs. Our data offer a valuable resource for the investigation of the biological basis for metastatic spread and highlight the complex role of chromosomal instability in cancer progression.
Collapse
Affiliation(s)
- Bastien Nguyen
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christopher Fong
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anisha Luthra
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shaleigh A Smith
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Renzo G DiNatale
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA; Urology and Renal Transplantation Service, Virginia Mason Medical Center, Seattle, WA, USA
| | - Subhiksha Nandakumar
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Henry Walch
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Walid K Chatila
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ramyasree Madupuri
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ritika Kundra
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Craig M Bielski
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Medical College at Cornell University, New York, NY, USA
| | - Brooke Mastrogiacomo
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mark T A Donoghue
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Adrienne Boire
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Neurology and Brain Tumor Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sarat Chandarlapaty
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Karuna Ganesh
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - James J Harding
- Weill Medical College at Cornell University, New York, NY, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christine A Iacobuzio-Donahue
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pedram Razavi
- Weill Medical College at Cornell University, New York, NY, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ed Reznik
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Charles M Rudin
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dmitriy Zamarin
- Weill Medical College at Cornell University, New York, NY, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wassim Abida
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ghassan K Abou-Alfa
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Carol Aghajanian
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrea Cercek
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ping Chi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Darren Feldman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alan L Ho
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gopakumar Iyer
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yelena Y Janjigian
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael Morris
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Robert J Motzer
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eileen M O'Reilly
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael A Postow
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nitya P Raj
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gregory J Riely
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mark E Robson
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jonathan E Rosenberg
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anton Safonov
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - William Tap
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Min Yuen Teo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anna M Varghese
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Martin Voss
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rona Yaeger
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marjorie G Zauderer
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nadeem Abu-Rustum
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Julio Garcia-Aguilar
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bernard Bochner
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Abraham Hakimi
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - William R Jarnagin
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David R Jones
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniela Molena
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Luc Morris
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eric Rios-Doria
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Paul Russo
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Samuel Singer
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Vivian E Strong
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Debyani Chakravarty
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lora H Ellenson
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anuradha Gopalan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mithat Gonen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sohrab P Shah
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joan Massague
- Cancer Biology and Genetics Program, Sloan Kettering Institute, New York, NY, USA
| | - Jianjiong Gao
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael F Berger
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David B Solit
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Medical College at Cornell University, New York, NY, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Samuel F Bakhoum
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Francisco Sanchez-Vega
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Nikolaus Schultz
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| |
Collapse
|
26
|
Rehm HL, Page AJ, Smith L, Adams JB, Alterovitz G, Babb LJ, Barkley MP, Baudis M, Beauvais MJ, Beck T, Beckmann JS, Beltran S, Bernick D, Bernier A, Bonfield JK, Boughtwood TF, Bourque G, Bowers SR, Brookes AJ, Brudno M, Brush MH, Bujold D, Burdett T, Buske OJ, Cabili MN, Cameron DL, Carroll RJ, Casas-Silva E, Chakravarty D, Chaudhari BP, Chen SH, Cherry JM, Chung J, Cline M, Clissold HL, Cook-Deegan RM, Courtot M, Cunningham F, Cupak M, Davies RM, Denisko D, Doerr MJ, Dolman LI, Dove ES, Dursi LJ, Dyke SO, Eddy JA, Eilbeck K, Ellrott KP, Fairley S, Fakhro KA, Firth HV, Fitzsimons MS, Fiume M, Flicek P, Fore IM, Freeberg MA, Freimuth RR, Fromont LA, Fuerth J, Gaff CL, Gan W, Ghanaim EM, Glazer D, Green RC, Griffith M, Griffith OL, Grossman RL, Groza T, Guidry Auvil JM, Guigó R, Gupta D, Haendel MA, Hamosh A, Hansen DP, Hart RK, Hartley DM, Haussler D, Hendricks-Sturrup RM, Ho CW, Hobb AE, Hoffman MM, Hofmann OM, Holub P, Hsu JS, Hubaux JP, Hunt SE, Husami A, Jacobsen JO, Jamuar SS, Janes EL, Jeanson F, Jené A, Johns AL, Joly Y, Jones SJ, Kanitz A, Kato K, Keane TM, Kekesi-Lafrance K, Kelleher J, Kerry G, Khor SS, Knoppers BM, Konopko MA, Kosaki K, Kuba M, Lawson J, Leinonen R, Li S, Lin MF, Linden M, Liu X, Liyanage IU, Lopez J, Lucassen AM, Lukowski M, Mann AL, Marshall J, Mattioni M, Metke-Jimenez A, Middleton A, Milne RJ, Molnár-Gábor F, Mulder N, Munoz-Torres MC, Nag R, Nakagawa H, Nasir J, Navarro A, Nelson TH, Niewielska A, Nisselle A, Niu J, Nyrönen TH, O’Connor BD, Oesterle S, Ogishima S, Ota Wang V, Paglione LA, Palumbo E, Parkinson HE, Philippakis AA, Pizarro AD, Prlic A, Rambla J, Rendon A, Rider RA, Robinson PN, Rodarmer KW, Rodriguez LL, Rubin AF, Rueda M, Rushton GA, Ryan RS, Saunders GI, Schuilenburg H, Schwede T, Scollen S, Senf A, Sheffield NC, Skantharajah N, Smith AV, Sofia HJ, Spalding D, Spurdle AB, Stark Z, Stein LD, Suematsu M, Tan P, Tedds JA, Thomson AA, Thorogood A, Tickle TL, Tokunaga K, Törnroos J, Torrents D, Upchurch S, Valencia A, Guimera RV, Vamathevan J, Varma S, Vears DF, Viner C, Voisin C, Wagner AH, Wallace SE, Walsh BP, Williams MS, Winkler EC, Wold BJ, Wood GM, Woolley JP, Yamasaki C, Yates AD, Yung CK, Zass LJ, Zaytseva K, Zhang J, Goodhand P, North K, Birney E. GA4GH: International policies and standards for data sharing across genomic research and healthcare. Cell Genom 2021; 1:100029. [PMID: 35072136 PMCID: PMC8774288 DOI: 10.1016/j.xgen.2021.100029] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular assays) and increasing evidence of its clinical utility will soon drive the generation of sequence data from tens of millions of humans, with increasing levels of diversity. In this perspective, we present the GA4GH strategies for addressing the major challenges of this data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders. We present the GA4GH suite of secure, interoperable technical standards and policy frameworks and review the current status of standards, their relevance to key domains of research and clinical care, and future plans of GA4GH. Broad international participation in building, adopting, and deploying GA4GH standards and frameworks will catalyze an unprecedented effort in data sharing that will be critical to advancing genomic medicine and ensuring that all populations can access its benefits.
Collapse
Affiliation(s)
- Heidi L. Rehm
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Angela J.H. Page
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Global Alliance for Genomics and Health, Toronto, ON, Canada
| | - Lindsay Smith
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Jeremy B. Adams
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Gil Alterovitz
- Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | | | | | - Michael Baudis
- University of Zurich, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Michael J.S. Beauvais
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- McGill University, Montreal, QC, Canada
| | - Tim Beck
- University of Leicester, Leicester, UK
| | | | - Sergi Beltran
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Universitat de Barcelona, Barcelona, Spain
| | - David Bernick
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Tiffany F. Boughtwood
- Australian Genomics, Parkville, VIC, Australia
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
| | - Guillaume Bourque
- McGill University, Montreal, QC, Canada
- Canadian Center for Computational Genomics, Montreal, QC, Canada
| | | | | | - Michael Brudno
- Canadian Center for Computational Genomics, Montreal, QC, Canada
- University of Toronto, Toronto, ON, Canada
- University Health Network, Toronto, ON, Canada
- Vector Institute, Toronto, ON, Canada
- Canadian Distributed Infrastructure for Genomics (CanDIG), Toronto, ON, Canada
| | | | - David Bujold
- McGill University, Montreal, QC, Canada
- Canadian Center for Computational Genomics, Montreal, QC, Canada
- Canadian Distributed Infrastructure for Genomics (CanDIG), Toronto, ON, Canada
| | - Tony Burdett
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | | | - Daniel L. Cameron
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | | | | | | | - Bimal P. Chaudhari
- Nationwide Children’s Hospital, Columbus, OH, USA
- The Ohio State University, Columbus, OH, USA
| | - Shu Hui Chen
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Justina Chung
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Melissa Cline
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | | | | | - Mélanie Courtot
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | | | | | | | | | | | - L. Jonathan Dursi
- University Health Network, Toronto, ON, Canada
- Canadian Distributed Infrastructure for Genomics (CanDIG), Toronto, ON, Canada
| | | | | | | | | | - Susan Fairley
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Khalid A. Fakhro
- Sidra Medicine, Doha, Qatar
- Weill Cornell Medicine - Qatar, Doha, Qatar
| | - Helen V. Firth
- Wellcome Sanger Institute, Hinxton, UK
- Addenbrooke’s Hospital, Cambridge, UK
| | | | | | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Ian M. Fore
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mallory A. Freeberg
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | - Lauren A. Fromont
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | - Clara L. Gaff
- Australian Genomics, Parkville, VIC, Australia
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | - Weiniu Gan
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Elena M. Ghanaim
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - David Glazer
- Verily Life Sciences, South San Francisco, CA, USA
| | - Robert C. Green
- Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Malachi Griffith
- Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Obi L. Griffith
- Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | | | | | | | - Roderic Guigó
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Dipayan Gupta
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | - Ada Hamosh
- Johns Hopkins University, Baltimore, MD, USA
| | - David P. Hansen
- Australian Genomics, Parkville, VIC, Australia
- The Australian e-Health Research Centre, CSIRO, Herston, QLD, Australia
| | - Reece K. Hart
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Invitae, San Francisco, CA, USA
- MyOme, Inc, San Bruno, CA, USA
| | | | - David Haussler
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, University of California, Santa Cruz, CA, USA
| | | | | | | | - Michael M. Hoffman
- University of Toronto, Toronto, ON, Canada
- University Health Network, Toronto, ON, Canada
- Vector Institute, Toronto, ON, Canada
| | - Oliver M. Hofmann
- University of Toronto, Toronto, ON, Canada
- University of Melbourne, Melbourne, VIC, Australia
| | - Petr Holub
- BBMRI-ERIC, Graz, Austria
- Masaryk University, Brno, Czech Republic
| | | | | | - Sarah E. Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Ammar Husami
- Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | | | - Saumya S. Jamuar
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Republic of Singapore
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore, Republic of Singapore
| | - Elizabeth L. Janes
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- University of Waterloo, Waterloo, ON, Canada
| | | | - Aina Jené
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Amber L. Johns
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Yann Joly
- McGill University, Montreal, QC, Canada
| | - Steven J.M. Jones
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Alexander Kanitz
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- University of Basel, Basel, Switzerland
| | | | - Thomas M. Keane
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- University of Nottingham, Nottingham, UK
| | - Kristina Kekesi-Lafrance
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- McGill University, Montreal, QC, Canada
| | | | - Giselle Kerry
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Seik-Soon Khor
- National Center for Global Health and Medicine Hospital, Tokyo, Japan
- University of Tokyo, Tokyo, Japan
| | | | | | | | | | | | - Rasko Leinonen
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Stephanie Li
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Global Alliance for Genomics and Health, Toronto, ON, Canada
| | | | - Mikael Linden
- CSC–IT Center for Science, Espoo, Finland
- ELIXIR Finland, Espoo, Finland
| | | | - Isuru Udara Liyanage
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | | | | | - Alice L. Mann
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Wellcome Sanger Institute, Hinxton, UK
| | | | | | | | - Anna Middleton
- Wellcome Connecting Science, Hinxton, UK
- University of Cambridge, Cambridge, UK
| | - Richard J. Milne
- Wellcome Connecting Science, Hinxton, UK
- University of Cambridge, Cambridge, UK
| | | | - Nicola Mulder
- H3ABioNet, Computational Biology Division, IDM, Faculty of Health Sciences, Cape Town, South Africa
| | | | - Rishi Nag
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Hidewaki Nakagawa
- Japan Agency for Medical Research & Development (AMED), Tokyo, Japan
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Arcadi Navarro
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
- Barcelonaβeta Brain Research Center (BBRC), Pasqual Maragall Foundation, Barcelona, Spain
| | | | - Ania Niewielska
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Amy Nisselle
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
- Human Genetics Society of Australasia Education, Ethics & Social Issues Committee, Alexandria, NSW, Australia
| | - Jeffrey Niu
- University Health Network, Toronto, ON, Canada
| | - Tommi H. Nyrönen
- CSC–IT Center for Science, Espoo, Finland
- ELIXIR Finland, Espoo, Finland
| | | | - Sabine Oesterle
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Vivian Ota Wang
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Emilio Palumbo
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Helen E. Parkinson
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | | | | | | | - Jordi Rambla
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | - Renee A. Rider
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Peter N. Robinson
- The Jackson Laboratory, Farmington, CT, USA
- University of Connecticut, Farmington, CT, USA
| | - Kurt W. Rodarmer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | | | - Alan F. Rubin
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | - Manuel Rueda
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | | | | | - Helen Schuilenburg
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Torsten Schwede
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- University of Basel, Basel, Switzerland
| | | | | | | | - Neerjah Skantharajah
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | - Heidi J. Sofia
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dylan Spalding
- CSC–IT Center for Science, Espoo, Finland
- ELIXIR Finland, Espoo, Finland
| | | | - Zornitza Stark
- Australian Genomics, Parkville, VIC, Australia
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | - Lincoln D. Stein
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- University of Toronto, Toronto, ON, Canada
| | | | - Patrick Tan
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore, Republic of Singapore
- Precision Health Research Singapore, Singapore, Republic of Singapore
- Genome Institute of Singapore, Singapore, Republic of Singapore
| | | | - Alastair A. Thomson
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Adrian Thorogood
- McGill University, Montreal, QC, Canada
- University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | | | - Katsushi Tokunaga
- University of Tokyo, Tokyo, Japan
- National Center for Global Health and Medicine, Tokyo, Japan
| | - Juha Törnroos
- CSC–IT Center for Science, Espoo, Finland
- ELIXIR Finland, Espoo, Finland
| | - David Torrents
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
- Barcelona Supercomputing Center, Barcelona, Spain
| | - Sean Upchurch
- California Institute of Technology, Pasadena, CA, USA
| | - Alfonso Valencia
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
- Barcelona Supercomputing Center, Barcelona, Spain
| | | | - Jessica Vamathevan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Susheel Varma
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- Health Data Research UK, London, UK
| | - Danya F. Vears
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
- Human Genetics Society of Australasia Education, Ethics & Social Issues Committee, Alexandria, NSW, Australia
- Melbourne Law School, University of Melbourne, Parkville, VIC, Australia
| | - Coby Viner
- University of Toronto, Toronto, ON, Canada
- University Health Network, Toronto, ON, Canada
| | | | - Alex H. Wagner
- Nationwide Children’s Hospital, Columbus, OH, USA
- The Ohio State University, Columbus, OH, USA
| | | | | | | | - Eva C. Winkler
- Section of Translational Medical Ethics, University Hospital Heidelberg, Heidelberg, Germany
| | | | | | | | | | - Andrew D. Yates
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Christina K. Yung
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Indoc Research, Toronto, ON, Canada
| | - Lyndon J. Zass
- H3ABioNet, Computational Biology Division, IDM, Faculty of Health Sciences, Cape Town, South Africa
| | - Ksenia Zaytseva
- McGill University, Montreal, QC, Canada
- Canadian Centre for Computational Genomics, Montreal, QC, Canada
| | - Junjun Zhang
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Peter Goodhand
- Global Alliance for Genomics and Health, Toronto, ON, Canada
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Kathryn North
- Murdoch Children’s Research Institute, Parkville, VIC, Australia
- University of Toronto, Toronto, ON, Canada
- University of Melbourne, Melbourne, VIC, Australia
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
- European Molecular Biology Laboratory, Heidelberg, Germany
| |
Collapse
|
27
|
Stadler ZK, Maio A, Chakravarty D, Kemel Y, Sheehan M, Salo-Mullen E, Tkachuk K, Fong CJ, Nguyen B, Erakky A, Cadoo K, Liu Y, Carlo MI, Latham A, Zhang H, Kundra R, Smith S, Galle J, Aghajanian C, Abu-Rustum N, Varghese A, O'Reilly EM, Morris M, Abida W, Walsh M, Drilon A, Jayakumaran G, Zehir A, Ladanyi M, Ceyhan-Birsoy O, Solit DB, Schultz N, Berger MF, Mandelker D, Diaz LA, Offit K, Robson ME. Therapeutic Implications of Germline Testing in Patients With Advanced Cancers. J Clin Oncol 2021; 39:2698-2709. [PMID: 34133209 PMCID: PMC8376329 DOI: 10.1200/jco.20.03661] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [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: 12/18/2020] [Revised: 04/30/2021] [Accepted: 05/06/2021] [Indexed: 12/27/2022] Open
Abstract
PURPOSE Tumor mutational profiling is increasingly performed in patients with advanced cancer. We determined the extent to which germline mutation profiling guides therapy selection in patients with advanced cancer. METHODS Patients with cancer undergoing tumor genomic profiling were prospectively consented for germline cancer predisposition gene analysis (2015-2019). In patients harboring germline likely pathogenic or pathogenic (LP/P) alterations, therapeutic actionability was classified using a precision oncology knowledge base. Patients with metastatic or recurrent cancer receiving germline genotype-directed therapy were determined. RESULTS Among 11,947 patients across > 50 malignancies, 17% (n = 2,037) harbored a germline LP/P variant. By oncology knowledge base classification, 9% (n = 1042) had an LP/P variant in a gene with therapeutic implications (4% level 1; 4% level 3B; < 1% level 4). BRCA1/2 variants accounted for 42% of therapeutically actionable findings, followed by CHEK2 (13%), ATM (12%), mismatch repair genes (11%), and PALB2 (5%). When limited to the 9,079 patients with metastatic or recurrent cancer, 8% (n = 710) harbored level 1 or 3B genetic findings and 3.2% (n = 289) received germline genotype-directed therapy. Germline genotype-directed therapy was received by 61% and 18% of metastatic cancer patients with level 1 and level 3B findings, respectively, and by 54% of BRCA1/2, 75% of mismatch repair, 43% of PALB2, 35% of RAD51C/D, 24% of BRIP1, and 19% of ATM carriers. Of BRCA1/2 patients receiving a poly(ADP-ribose) polymerase inhibitor, 45% (84 of 188) had tumors other than breast or ovarian cancer, wherein the drug, at time of delivery, was delivered in an investigational setting. CONCLUSION In a pan-cancer analysis, 8% of patients with advanced cancer harbored a germline variant with therapeutic actionability with 40% of these patients receiving germline genotype-directed treatment. Germline sequence analysis is additive to tumor sequence analysis for therapy selection and should be considered for all patients with advanced cancer.
Collapse
Affiliation(s)
- Zsofia K. Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Anna Maio
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Debyani Chakravarty
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yelena Kemel
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Margaret Sheehan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Erin Salo-Mullen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kaitlyn Tkachuk
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Christopher J. Fong
- Computational Oncology, Department of Epidemiology and Statistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Bastien Nguyen
- Computational Oncology, Department of Epidemiology and Statistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Amanda Erakky
- David M. Rubinstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Karen Cadoo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ying Liu
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Maria I. Carlo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Alicia Latham
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Hongxin Zhang
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ritika Kundra
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Shaleigh Smith
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jesse Galle
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Carol Aghajanian
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nadeem Abu-Rustum
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Anna Varghese
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Eileen M. O'Reilly
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- David M. Rubinstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael Morris
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Wassim Abida
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael Walsh
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Alexander Drilon
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Gowtham Jayakumaran
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ozge Ceyhan-Birsoy
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - David B. Solit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nikolaus Schultz
- Computational Oncology, Department of Epidemiology and Statistics, Memorial Sloan Kettering Cancer Center, New York, NY
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael F. Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Diana Mandelker
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Luis A. Diaz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mark E. Robson
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| |
Collapse
|
28
|
Momtaz P, O'Connor CA, Chou JF, Capanu M, Park W, Bandlamudi C, Berger MF, Kelsen DP, Suehnholz SP, Chakravarty D, Yu KH, Varghese AM, Zervoudakis A, Li J, Ku GY, Park JS, Shcherba M, Harding JJ, Goldberg Z, Abou-Alfa GK, Salo-Mullen EE, Stadler ZK, Iacobuzio-Donahue CA, O'Reilly EM. Pancreas cancer and BRCA: A critical subset of patients with improving therapeutic outcomes. Cancer 2021; 127:4393-4402. [PMID: 34351646 DOI: 10.1002/cncr.33812] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 06/10/2021] [Accepted: 06/14/2021] [Indexed: 12/24/2022]
Abstract
BACKGROUND Patients with germline/somatic BRCA1/BRCA2 mutations (g/sBRCA1/2) comprise a distinct biologic subgroup of pancreas ductal adenocarcinoma (PDAC). METHODS Institutional databases were queried to identify patients who had PDAC with g/sBRCA1/2. Demographics, clinicopathologic details, genomic data (annotation sBRCA1/2 according to a precision oncology knowledge base for somatic mutations), zygosity, and outcomes were abstracted. Overall survival (OS) was estimated using the Kaplan-Meier method. RESULTS In total, 136 patients with g/sBRCA1/2 were identified between January 2011 and June 2020. Germline BRCA1/2 (gBRCA1/2) mutation was identified in 116 patients (85%). Oncogenic somatic BRCA1/2 (sBRCA1/2) mutation was present in 20 patients (15%). Seventy-seven patients had biallelic BRCA1/2 mutations (83%), and 16 (17%) had heterozygous mutations. Sixty-five patients with stage IV disease received frontline platinum therapy, and 52 (80%) had a partial response. The median OS for entire cohort was 27.6 months (95% CI, 24.9-34.5 months), and the median OS for patients who had stage IV disease was 23 months (95% CI, 19-26 months). Seventy-one patients received a poly(adenosine diphosphate ribose) polymerase (PARP) inhibitor (PARPi), and 52 received PARPi monotherapy. For maintenance PARPi, 10 patients (36%) had a partial response, 12 (43%) had stable disease, and 6 (21%) had progression of disease as their best response. Six patients (21%) received maintenance PARPi for >2 years. For those with stage IV disease who received frontline platinum, the median OS was 26 months (95% CI, 20-52 months) for biallelic patients (n = 39) and 8.66 months (95% CI, 6.2 months to not reached) for heterozygous patients (n = 4). The median OS for those who received PARPi therapy was 26.5 months (95% CI, 24-53 months) for biallelic patients (n = 25) and 8.66 months (95% CI, 7.23 months to not reached) for heterozygous patients (n = 2). CONCLUSIONS g/sBRCA1/2 mutations did not appear to have different actionable utility. Platinum and PARPi therapies offer therapeutic benefit, and very durable outcomes are observed in a subset of patients who have g/sBRCA1/2 mutations with biallelic status.
Collapse
Affiliation(s)
- Parisa Momtaz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Catherine A O'Connor
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Joanne F Chou
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marinela Capanu
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Wungki Park
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York.,David M. Rubenstein Center for Pancreas Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Chaitanya Bandlamudi
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael F Berger
- 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, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York.,David M. Rubenstein Center for Pancreas Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sarah P Suehnholz
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Debyani Chakravarty
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kenneth H Yu
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York.,David M. Rubenstein Center for Pancreas Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Anna M Varghese
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York.,David M. Rubenstein Center for Pancreas Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alice Zervoudakis
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Jia Li
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Geoffrey Y Ku
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Jennifer S Park
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marina Shcherba
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
| | - James J Harding
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Zoe Goldberg
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Ghassan K Abou-Alfa
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Erin E Salo-Mullen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Zsofia K Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York.,David M. Rubenstein Center for Pancreas Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Christine A Iacobuzio-Donahue
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.,Human Oncology Pathogenesis Program, Sloan Kettering Institute, New York, New York
| | - Eileen M O'Reilly
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York.,David M. Rubenstein Center for Pancreas Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| |
Collapse
|
29
|
Kanthasamy S, Guhan B, Chakravarty D, Parker MJ. The efficacy of intravenous tranexamic acid administration at induction in definitive hip fracture surgery: Is there a role? Injury 2021; 52:2361-2366. [PMID: 33568279 DOI: 10.1016/j.injury.2021.01.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 01/19/2021] [Accepted: 01/23/2021] [Indexed: 02/02/2023]
Abstract
UNLABELLED Tranexamic acid (TXA) is a cheap and powerful drug that has several uses in surgery and is well established in elective orthopaedic surgery. At present, limited small studies have looked into its role in the acute hip fracture. Transfusion in the geriatric population presents risks and increased costs to healthcare systems around the world. Our retrospective study looks at the role of TXA administration at induction for both intracapsular fracture requiring hemiarthroplasty and our preferred method of fixation of extracapsular fracture by intramedullary nail (IM nail). We show a statistically significant reduction in the number of patients requiring transfusion as well as mean haemoglobin (Hb) drop in those undergoing hemiarthroplasty. This was not replicated in those undergoing IM nail fixation. Both groups showed no increase in 1-year mortality or thromboembolic events following TXA administration. These results support the use of TXA for hemiarthroplasty for intracapsular hip fractures over the age of 60. OBJECTIVES The aim of this pre and post interventional study looks at the effects of intravenous administration of tranexamic acid on induction for elderly patients undergoing hemiarthroplasty or intramedullary nail fixation for hip fractures. DESIGN Pre and post interventional, randomised observational study SETTING: Large hip fracture unit, Level 2 Trauma Centre, single centre PATIENTS: Two arms of the study looking at those aged above the age of 60 undergoing hemiarthroplasty and intramedullary nail fixation without and with tranexamic acid on induction. RESULTS 12.1% of hemiarthroplasties required post-operative transfusion without tranexamic acid compared to 2.6% of those with tranexamic acid (n=15 vs n=3 respectively, p=0.006). Equally, the mean Hb drop in g/L is reduced in those with tranexamic acid compared to those without (mean Hb = 14.6 vs 17.7 respectively, p=0.034). This was not replicated in the IM nail group between those without and those with tranexamic acid (n=31 vs n=20 respectively, p= 0.16). The mean Hb drop in g/L was not statistically significant in the tranexamic acid arm compared to without (mean Hb = 19.2 vs mean Hb = 21.9, p=0.11). Gross reporting of thromboembolic events did not demonstrate an increase in the number of those with DVT, PE, MI or stroke. 1-year mortality was not statistically significant in either hemiarthroplasty or IM nail fixation following tranexamic acid administration. CONCLUSIONS Tranexamic acid both statistically significantly reduces the number of patients requiring transfusion post hemiarthroplasty and also the value of mean Hb drop without appearing to increase in thromboembolic events or 1 year mortality rates. This does not appear to be emulated in the IM nail fixation although both thrombotic events and 1-year mortality rates are also not affected by administration of TXA. We propose that TXA has a role in hemiarthroplasty surgery in reducing post-operative transfusions. LEVEL OF EVIDENCE Level 3 - retrospective cohort study.
Collapse
Affiliation(s)
- S Kanthasamy
- Surgical Teaching Fellow, Peterborough City Hospital, United Kingdom.
| | - B Guhan
- Specialty Doctor-Trauma and Orthopaedics, Peterborough City Hospital, United Kingdom.
| | - D Chakravarty
- Consultant Orthopaedic Surgeon, Fortis Hospitals, Kolkata, India
| | - Martyn J Parker
- Consultant Orthopaedic Surgeon, Peterborough City Hospital, United Kingdom.
| |
Collapse
|
30
|
Abstract
Technological innovation and rapid reduction in sequencing costs have enabled the genomic profiling of hundreds of cancer-associated genes as a component of routine cancer care. Tumour genomic profiling can refine cancer subtype classification, identify which patients are most likely to benefit from systemic therapies and screen for germline variants that influence heritable cancer risk. Here, we discuss ongoing efforts to enhance the clinical utility of tumour genomic profiling by integrating tumour and germline analyses, characterizing allelic context and identifying mutational signatures that influence therapy response. We also discuss the potential clinical utility of more comprehensive whole-genome and whole-transcriptome sequencing and ultra-sensitive cell-free DNA profiling platforms, which allow for minimally invasive, serial analyses of tumour-derived DNA in blood.
Collapse
Affiliation(s)
- Debyani Chakravarty
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David B Solit
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| |
Collapse
|
31
|
Suehnholz SP, Kundra R, Zhang H, Smith S, Nissan M, Yao Y, LaFave L, Gala K, Miles L, Arcila ME, Ladanyi M, Berger MF, Zehir A, Syed A, Rudolph J, Sabbatini P, Levine R, Dogan A, Gao J, Solit D, Schultz N, Chakravarty D. Abstract 99: Evolution of OncoKB, a precision oncology knowledgebase. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-99] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Genomic sequencing of tumors is a routine part of cancer patient care. To address the need for a comprehensive resource that annotates the oncogenic effects and clinical actionability of somatic alterations in cancer, we developed OncoKB, a precision oncology knowledgebase. Since its introduction in 2016, OncoKB has grown to include annotations for >500 alterations in 682 genes. This includes 42 Level 1 genes (included in the FDA drug label), 12 Level 2 genes (included in the NCCN guidelines), and 29 Level 3A genes (predictive of drug response in well-powered clinical studies).
We evaluated changes in the clinical actionability landscape and evolution of the OncoKB annotation rules and processes by comparing the AACR Project GENIE cohort (v8.1) annotated with the OncoKB version from February 2018 to that from November 2020. Even within a short window of time, this comparison reveals a significant shift of the proportion of samples that harbor a standard care alteration (Level 1 and 2), increasing from ~9% in 2018 to ~24% in 2020, and a Level 3A alteration, decreasing from ~11% to ~5%. This shift is partially attributable to the FDA approval of a PI3K inhibitor in PIK3CA-mutant ER+/HER2- breast cancer, approval of RAF inhibitors in BRAF V600E mutant anaplastic thyroid cancer and colorectal cancer, approval of NTRK-inhibitors in NTRK fusion-positive solid tumors, FGFR-inhibitor approval in FGFR2 fusion-positive bladder cancer and cholangiocarcinoma, RET-inhibitor approval in RET fusion-positive thyroid cancer and non-small cell lung cancer and expansion of indications for PARP inhibitors to include prostate cancer. The tumor agnostic approval of the checkpoint blockade inhibitor, pembrolizumab, in TMB-H solid tumors additionally gave rise to a ~4% increase in Level 1 samples.
Analysis of the AACR Project GENIE cohort also revealed significant changes to the OncoKB process, including those reflected in the updated OncoKB Levels of Evidence v2.0. The refined levels system deprioritized the significance of standard care biomarkers when present in indications outside of the FDA-approved/NCCN listed indication. This change was based on clinical data demonstrating that patients with investigational predictive biomarkers for a specific tumor type based on compelling clinical evidence from phase 3 trials (currently Level 3A) are more likely to experience clinical benefit compared to patients with predictive biomarkers that are considered standard care in a different tumor type (previously Level 2B, currently Level 3B), and is consistent with guidelines published by ASCO/AMP/CAP and ESMO.
Knowledgebases such as OncoKB have emerged as key informational resources that the clinical oncology and scientific communities have used to rapidly connect sequencing results to clinical actionability. Their utility depends on their ability to stay abreast of clinical data and seamlessly adapt their rules and processes to the evolving field of precision medicine.
Citation Format: Sarah P. Suehnholz, Ritika Kundra, Hongxin Zhang, Shaleigh Smith, Moriah Nissan, Yifu Yao, Lindsay LaFave, Kinisha Gala, Linde Miles, Maria E. Arcila, Marc Ladanyi, Michael F. Berger, Ahmet Zehir, Aijaz Syed, Julia Rudolph, Paul Sabbatini, Ross Levine, Ahmet Dogan, Jianjiong Gao, David Solit, Nikolaus Schultz, Debyani Chakravarty. Evolution of OncoKB, a precision oncology knowledgebase [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 99.
Collapse
Affiliation(s)
| | | | | | | | | | - Yifu Yao
- 1Memorial Sloan Kettering, New York, NY
| | - Lindsay LaFave
- 2Koch Institute for Integrative Cancer Research at MIT, Boston, MA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
32
|
Tsui DWY, Cheng ML, Shady M, Yang JL, Stephens D, Won H, Srinivasan P, Huberman K, Meng F, Jing X, Patel J, Hasan M, Johnson I, Gedvilaite E, Houck-Loomis B, Socci ND, Selcuklu SD, Seshan VE, Zhang H, Chakravarty D, Zehir A, Benayed R, Arcila M, Ladanyi M, Funt SA, Feldman DR, Li BT, Razavi P, Rosenberg J, Bajorin D, Iyer G, Abida W, Scher HI, Rathkopf D, Viale A, Berger MF, Solit DB. Tumor fraction-guided cell-free DNA profiling in metastatic solid tumor patients. Genome Med 2021; 13:96. [PMID: 34059130 PMCID: PMC8165771 DOI: 10.1186/s13073-021-00898-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 04/27/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Cell-free DNA (cfDNA) profiling is increasingly used to guide cancer care, yet mutations are not always identified. The ability to detect somatic mutations in plasma depends on both assay sensitivity and the fraction of circulating DNA in plasma that is tumor-derived (i.e., cfDNA tumor fraction). We hypothesized that cfDNA tumor fraction could inform the interpretation of negative cfDNA results and guide the choice of subsequent assays of greater genomic breadth or depth. METHODS Plasma samples collected from 118 metastatic cancer patients were analyzed with cf-IMPACT, a modified version of the FDA-authorized MSK-IMPACT tumor test that can detect genomic alterations in 410 cancer-associated genes. Shallow whole genome sequencing (sWGS) was also performed in the same samples to estimate cfDNA tumor fraction based on genome-wide copy number alterations using z-score statistics. Plasma samples with no somatic alterations detected by cf-IMPACT were triaged based on sWGS-estimated tumor fraction for analysis with either a less comprehensive but more sensitive assay (MSK-ACCESS) or broader whole exome sequencing (WES). RESULTS cfDNA profiling using cf-IMPACT identified somatic mutations in 55/76 (72%) patients for whom MSK-IMPACT tumor profiling data were available. A significantly higher concordance of mutational profiles and tumor mutational burden (TMB) was observed between plasma and tumor profiling for plasma samples with a high tumor fraction (z-score≥5). In the 42 patients from whom tumor data was not available, cf-IMPACT identified mutations in 16/42 (38%). In total, cf-IMPACT analysis of plasma revealed mutations in 71/118 (60%) patients, with clinically actionable alterations identified in 30 (25%), including therapeutic targets of FDA-approved drugs. Of the 47 samples without alterations detected and low tumor fraction (z-score<5), 29 had sufficient material to be re-analyzed using a less comprehensive but more sensitive assay, MSK-ACCESS, which revealed somatic mutations in 14/29 (48%). Conversely, 5 patients without alterations detected by cf-IMPACT and with high tumor fraction (z-score≥5) were analyzed by WES, which identified mutational signatures and alterations in potential oncogenic drivers not covered by the cf-IMPACT panel. Overall, we identified mutations in 90/118 (76%) patients in the entire cohort using the three complementary plasma profiling approaches. CONCLUSIONS cfDNA tumor fraction can inform the interpretation of negative cfDNA results and guide the selection of subsequent sequencing platforms that are most likely to identify clinically-relevant genomic alterations.
Collapse
Affiliation(s)
- Dana W Y Tsui
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.
- Weill Cornell Medical College, Weill Cornell University, New York, USA.
- Present Address: PetDx, Inc., La Jolla, USA.
| | - Michael L Cheng
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
- Present Address: Dana-Farber Cancer Institute, Harvard Medical School, Boston, USA
| | - Maha Shady
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Present Address: Graduate School of Arts and Sciences, Harvard University, Cambridge, USA
| | - Julie L Yang
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Dennis Stephens
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Helen Won
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Preethi Srinivasan
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Kety Huberman
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Fanli Meng
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Xiaohong Jing
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Present Address: NYU Langone Health, New York, USA
| | - Juber Patel
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Maysun Hasan
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Ian Johnson
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Erika Gedvilaite
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Brian Houck-Loomis
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Nicholas D Socci
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - S Duygu Selcuklu
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Venkatraman E Seshan
- Department of Epidemiology-Biostatistics, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Hongxin Zhang
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Debyani Chakravarty
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Maria Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Samuel A Funt
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Darren R Feldman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Bob T Li
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Pedram Razavi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Jonathan Rosenberg
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Dean Bajorin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Gopa Iyer
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Wassim Abida
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Howard I Scher
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Dana Rathkopf
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Agnes Viale
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Michael F Berger
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
- Weill Cornell Medical College, Weill Cornell University, New York, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, USA
| | - David B Solit
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA.
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, USA.
| |
Collapse
|
33
|
Kundra R, Zhang H, Sheridan R, Sirintrapun SJ, Wang A, Ochoa A, Wilson M, Gross B, Sun Y, Madupuri R, Satravada BA, Reales D, Vakiani E, Al-Ahmadie HA, Dogan A, Arcila M, Zehir A, Maron S, Berger MF, Viaplana C, Janeway K, Ducar M, Sholl L, Dogan S, Bedard P, Surrey LF, Sanchez IH, Syed A, Rema AB, Chakravarty D, Suehnholz S, Nissan M, Iyer GV, Murali R, Bouvier N, Soslow RA, Hyman D, Younes A, Intlekofer A, Harding JJ, Carvajal RD, Sabbatini PJ, Abou-Alfa GK, Morris L, Janjigian YY, Gallagher MM, Soumerai TA, Mellinghoff IK, Hakimi AA, Fury M, Huse JT, Bagrodia A, Hameed M, Thomas S, Gardos S, Cerami E, Mazor T, Kumari P, Raman P, Shivdasani P, MacFarland S, Newman S, Waanders A, Gao J, Solit D, Schultz N. OncoTree: A Cancer Classification System for Precision Oncology. JCO Clin Cancer Inform 2021; 5:221-230. [PMID: 33625877 PMCID: PMC8240791 DOI: 10.1200/cci.20.00108] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [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: 08/07/2020] [Revised: 10/26/2020] [Accepted: 12/21/2020] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Cancer classification is foundational for patient care and oncology research. Systems such as International Classification of Diseases for Oncology (ICD-O), Systematized Nomenclature of Medicine Clinical Terms (SNOMED-CT), and National Cancer Institute Thesaurus (NCIt) provide large sets of cancer classification terminologies but they lack a dynamic modernized cancer classification platform that addresses the fast-evolving needs in clinical reporting of genomic sequencing results and associated oncology research. METHODS To meet these needs, we have developed OncoTree, an open-source cancer classification system. It is maintained by a cross-institutional committee of oncologists, pathologists, scientists, and engineers, accessible via an open-source Web user interface and an application programming interface. RESULTS OncoTree currently includes 868 tumor types across 32 organ sites. OncoTree has been adopted as the tumor classification system for American Association for Cancer Research (AACR) Project Genomics Evidence Neoplasia Information Exchange (GENIE), a large genomic and clinical data-sharing consortium, and for clinical molecular testing efforts at Memorial Sloan Kettering Cancer Center and Dana-Farber Cancer Institute. It is also used by precision oncology tools such as OncoKB and cBioPortal for Cancer Genomics. CONCLUSION OncoTree is a dynamic and flexible community-driven cancer classification platform encompassing rare and common cancers that provides clinically relevant and appropriately granular cancer classification for clinical decision support systems and oncology research.
Collapse
Affiliation(s)
- Ritika Kundra
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Hongxin Zhang
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Robert Sheridan
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Avery Wang
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Angelica Ochoa
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Manda Wilson
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Benjamin Gross
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yichao Sun
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ramyasree Madupuri
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Baby A. Satravada
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Dalicia Reales
- Clinical Research Administration, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Efsevia Vakiani
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Ahmet Dogan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Maria Arcila
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Steven Maron
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael F. Berger
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering, New York, NY
| | - Cristina Viaplana
- Oncology Data Science (ODysSey Group), Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Katherine Janeway
- Pediatrics, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA
| | | | - Lynette Sholl
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
- Department of Pathology, Harvard Medical School, Boston, MA
| | - Snjezana Dogan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Philippe Bedard
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Lea F. Surrey
- Cancer Genomics Program, Princess Margaret Cancer Centre, Toronto, ON, Canada
- Department of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA
| | | | - Aijaz Syed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Debyani Chakravarty
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sarah Suehnholz
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Moriah Nissan
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Gopakumar V. Iyer
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Rajmohan Murali
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nancy Bouvier
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Robert A. Soslow
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Andrew Intlekofer
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering, New York, NY
| | - James J. Harding
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Weill Cornell Medical College, New York, NY
| | | | - Paul J. Sabbatini
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Weill Cornell Medical College, New York, NY
| | | | - Luc Morris
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering, New York, NY
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering, New York, NY
- Department of Surgery, Memorial Sloan Kettering, New York, NY
| | - Yelena Y. Janjigian
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Tara A. Soumerai
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Ingo K. Mellinghoff
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering, New York, NY
| | - Abraham A. Hakimi
- Department of Urology, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Jason T. Huse
- Departments of Pathology and Translational Molecular Pathology, University of Texas, MD Anderson Cancer Center, Houston, TX
| | - Aditya Bagrodia
- Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Meera Hameed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Stacy Thomas
- Information Systems, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Stuart Gardos
- Information Systems, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ethan Cerami
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA
| | - Tali Mazor
- Knowledge Systems Group, Dana-Farber Cancer Institute, Boston, MA
| | - Priti Kumari
- Knowledge Systems Group, Dana-Farber Cancer Institute, Boston, MA
| | | | | | - Suzanne MacFarland
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA
- University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Scott Newman
- Department of Computational Biology, St Jude Children's Research Hospital, Memphis, TN
| | | | - Jianjiong Gao
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - David Solit
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering, New York, NY
- Department of Medicine, Columbia University Medical Center, New York, NY
| | - Nikolaus Schultz
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering, New York, NY
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering, New York, NY
| |
Collapse
|
34
|
Spandana D, Desai H, Chakravarty D, Vijay R, Hembram K. Fabrication of a biodegradable Fe-Mn-Si alloy by field assisted sintering. ADV POWDER TECHNOL 2020. [DOI: 10.1016/j.apt.2020.10.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
35
|
Suehnholz S, Zhang H, Nissan M, Kundra R, Su J, LaFave L, Gala K, Vanderbilt C, Arcila M, Ladanyi M, Berger M, Zehir A, Rudolph JE, Sabbatini P, Levine R, Dogan A, Gao J, Solit DB, Schultz N, Chakravarty D. Abstract 3208: OncoKB, a precision oncology knowledgebase. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-3208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
OncoKB is a precision oncology knowledge base that annotates the oncogenic effects and clinical actionability of somatic alterations in cancer. Initially focused on solid tumors, OncoKB was introduced in 2016 with >200 genes and almost 3000 somatic alterations via a public website (oncokb.org) and through the cBioPortal for Cancer Genomics. OncoKB now contains annotations for >5000 alterations in 642 genes. This includes 30 Level 1 alterations (included in the FDA drug label; a growth of 114% since 2016), 15 Level 2 alterations (included in the NCCN guidelines; 50% growth), and 38 Level 3A alterations (predictive of drug response in well-powered clinical studies; 65% growth). OncoKB now also supports hematologic malignancies with two new levels of evidence systems that encompass diagnostic and prognostic implications (in addition to therapeutic implications) and 288 heme-specific alterations in 156 newly curated cancer-associated genes. At MSK, OncoKB is used for the annotation of 1000 molecular patient reports per month. To assess the clinical utility of OncoKB and changes in the frequency of actionable alterations, we performed a comparison between the AACR Project GENIE cohort from 2017 and the most recent one (Table 1). With an increased number of tumor types and greater inclusion of hematologic malignancies, the overall potential actionability rate increased by 3.6 percentage points. A shift in access to targeted cancer therapies is also observed, where Level 1 or 2 alterations increased over 5 percentage points and Level 3 alterations decreased by ~3 percentage points, perhaps reaping the benefits of recent successful phase III trials.
August 2017 (v1.1)December 2019 (v7.2)AACR Project GENIE cohort size18,80480,248Tumor types with >100 samples3151Hematologic malignancies included29Level 1 or 2 annotation7.3%12.9%Level 3A annotation6.4%4.7%Level 3B annotation17.8%17.5%Total potential actionability31.5%35.1%
While only a subset of patients with targetable alterations will benefit from treatments, there is ample evidence that targeted cancer therapies can have profound and durable clinical activity. Knowledgebases such as OncoKB have become a key component to support clinical decision making, and there is a continued need to expand their capabilities while maintaining a nuanced approach to annotation.
Citation Format: Sarah Suehnholz, Hongxin Zhang, Moriah Nissan, Ritika Kundra, Jing Su, Lindsay LaFave, Kinisha Gala, Chad Vanderbilt, Maria Arcila, Marc Ladanyi, Michael Berger, Ahmet Zehir, Julia E. Rudolph, Paul Sabbatini, Ross Levine, Ahmet Dogan, Jianjiong Gao, David B. Solit, Nikolaus Schultz, Debyani Chakravarty. OncoKB, a precision oncology knowledgebase [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3208.
Collapse
Affiliation(s)
| | - Hongxin Zhang
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Moriah Nissan
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ritika Kundra
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jing Su
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Kinisha Gala
- 3University of California, Los Angeles, Los Angeles, CA
| | | | - Maria Arcila
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Marc Ladanyi
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Ahmet Zehir
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Ross Levine
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Dogan
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jianjiong Gao
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | |
Collapse
|
36
|
Pitel BA, Rao S, Fitz CDV, Madhavan S, Dientsmann R, Horak P, King I, Mockus SM, Raca G, Rieke DT, Rogan P, Sonkin D, Tamborero D, Vlachos IS, Walsh B, Warner JL, Griffith M, Griffith OL, Chakravarty D, Wagner AH. Abstract 3222: The Virtual Molecular Tumor Board of the Variant Interpretation for Cancer Consortium: A systematic gateway connecting cancer genome interpretation and progress in genomic knowledgebases in cancer. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-3222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Comprehensive interpretation of a patient's cancer genome is a cross-disciplinary process requiring the expertise of oncologists, molecular pathologists, genetic counselors, genomic scientists, and bioinformaticians. The Variant Interpretation for Cancer Consortium (VICC) has created a non-clinical forum for the variant interpretation process by connecting experts from multiple academic institutions and industry to create a Virtual Molecular Tumor Board (VMTB). During VICC-VMTB sessions, experts retrospectively discuss de-identified, challenging patient cases in the context of genomic interpretation guidelines to evaluate a patient's profile across several distinct components: genomic variants; disease context; therapeutic history; family history; demographic information; genomic assay information; and variant allele frequency. These components are processed through the prism of publically available knowledge and expertise of VMTB members, resulting in a broad spectrum of clinically relevant assertions about the patient's disease that may be of prognostic, diagnostic, or predictive relevance. Through these evaluations, the VICC-VMTB primarily works as a means of illuminating challenges in genomic interpretation and advancing the objectives of domain-specific VICC working groups. Examples of challenges that have been highlighted by the VICC-VMTB forum include: 1) inconsistent disease and therapy ontologies across resources are being addressed by Disease Harmonization & Drug Harmonization working groups, respectively; 2) use of machine-learning and natural language processing into clinical-grade variant interpretation are being addressed by the AI-Assisted Curation working group; 3) aggregation and harmonization of knowledgebase data into a centralized resource is being addressed by the Data Licensing and Variant Harmonization working groups; 4) inefficiencies in knowledgebase search functions are being addressed by the Search working group; 5) determination of accurate prediction of biological consequences of rare variants is being addressed by the In Silico Interpretation working group; and 6) standardization of genomic variant curation is being addressed by the Knowledge Curation and Interpretation Standards working group. These VICC working groups provide dedicated expert assemblies intended to specifically tackle these challenges, further increasing the breadth for which genomic information can be made useful in cancer variant interpretation. The VICC-VMTB has been a pertinent link between cancer genomes and clinical interpretation. We are confident VICC-VMTB will continue to be a gateway of acceleration and progress needed in the field of cancer interpretation to provide accurate and efficient answers for our patients in the future.
Citation Format: Beth A. Pitel, Shruti Rao, Catherine Del Vecchio Fitz, Subha Madhavan, Rodrigo Dientsmann, Peter Horak, Ian King, Susan M. Mockus, Gordana Raca, Damian T. Rieke, Peter Rogan, Dmitriy Sonkin, David Tamborero, Ioannis S. Vlachos, Brian Walsh, Jeremy L. Warner, Malachi Griffith, Obi L. Griffith, Debyani Chakravarty, Alex H. Wagner. The Virtual Molecular Tumor Board of the Variant Interpretation for Cancer Consortium: A systematic gateway connecting cancer genome interpretation and progress in genomic knowledgebases in cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3222.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Ian King
- 6University of Toronto, Toronto, Ontario, Canada
| | - Susan M. Mockus
- 7The Jackson Laboratory for Genomic Medicine, Farmington, CT
| | - Gordana Raca
- 8Children's Hospital Los Angeles, Los Angeles, CA
| | | | - Peter Rogan
- 10University of Western Ontario, London, Ontario, Canada
| | | | | | | | - Brian Walsh
- 14Oregon Health & Science University, Portland, OR
| | | | | | | | | | - Alex H. Wagner
- 16Washington University School of Medicine, St. Louis, MO
| |
Collapse
|
37
|
Horak P, Griffith M, Danos A, Pitel BA, Madhavan S, Liu X, Lee J, Raca G, Li S, Wagner AH, Kulkarni S, Griffith OL, Chakravarty D, Sonkin D. Abstract 5707: A standard operating procedure for the interpretation of oncogenicity/pathogenicity of somatic mutations. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-5707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Somatic variants in cancer-relevant genes are interpreted from multiple partially overlapping perspectives. When considered in discovery and translational research endeavors, it is important to determine if a particular variant observed in a gene of interest is oncogenic/pathogenic or not, as such knowledge provides the foundation on which targeted cancer treatment research is based. In contrast, clinical applications are dominated by diagnostic, prognostic, or therapeutic interpretations which in part also depends on underlying variant oncogenicity/pathogenicity. The Association for Molecular Pathology, the American Society of Clinical Oncology, and the College of American Pathologists (AMP/ASCO/CAP) have published structured somatic variant clinical interpretation guidelines which specifically address diagnostic, prognostic, and therapeutic implications. These guidelines have been well-received by the oncology community. Many variant knowledgebases, clinical laboratories/centers have adopted or are in the process of adopting these guidelines. The AMP/ASCO/CAP guidelines also describe different data types which are used to determine oncogenicity/pathogenicity of a variant, such as: population frequency, functional data, computational predictions, segregation, and somatic frequency. A second collaborative effort created the European Society for Medical Oncology (ESMO) Scale for Clinical Actionability of molecular Targets to provide a harmonized vocabulary that provides an evidence-based ranking system of molecular targets that supports their value as clinical targets. However, neither of these clinical guideline systems provide systematic and comprehensive procedures for aggregating population frequency, functional data, computational predictions, segregation, and somatic frequency to consistently interpret variant oncogenicity/pathogenicity, as has been published in the ACMG/AMP guidelines for interpretation of pathogenicity of germline variants. In order to address this unmet need for somatic variant oncogenicity/pathogenicity interpretation procedures, the Variant Interpretation for Cancer Consortium (VICC, a GA4GH driver project) Knowledge Curation and Interpretation Standards (KCIS) working group (WG) has developed a Standard Operating Procedure (SOP) with contributions from members of ClinGen Somatic Clinical Domain WG, and ClinGen Somatic/Germline variant curation WG using an approach similar to the ACMG/AMP germline pathogenicity guidelines to categorize evidence of oncogenicity/pathogenicity as very strong, strong, moderate or supporting. This SOP enables consistent and comprehensive assessment of oncogenicity/pathogenicity of somatic variants and latest version of an SOP can be found at https://cancervariants.org/wg/kcis/.
Citation Format: Peter Horak, Malachi Griffith, Arpad Danos, Beth A. Pitel, Subha Madhavan, Xuelu Liu, Jennifer Lee, Gordana Raca, Shirley Li, Alex H. Wagner, Shashikant Kulkarni, Obi L. Griffith, Debyani Chakravarty, Dmitriy Sonkin. A standard operating procedure for the interpretation of oncogenicity/pathogenicity of somatic mutations [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5707.
Collapse
Affiliation(s)
- Peter Horak
- 1National Center for Tumor Diseases, Heidelberg, Germany
| | | | - Arpad Danos
- 2Washington University School of Medicine, St. Louis, MO
| | | | | | - Xuelu Liu
- 5Dana-Farber Cancer Institute, Boston, MA
| | - Jennifer Lee
- 6Frederick National Laboratory for Cancer Research, Rockville, MD
| | - Gordana Raca
- 7University of Southern California, Los Angeles, CA
| | | | - Alex H. Wagner
- 2Washington University School of Medicine, St. Louis, MO
| | | | | | | | | |
Collapse
|
38
|
Wagner AH, Hart RK, Babb L, Freimuth RR, Coffman A, Liang Y, Pitel B, Roy A, Brush M, Lee J, Lu A, Coard T, Rao S, Ritter D, Walsh B, Mockus S, Horak P, King I, Sonkin D, Madhavan S, Raca G, Chakravarty D, Griffith M, Griffith OL. Abstract 1096: Harmonization standards from the Variant Interpretation for Cancer Consortium. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-1096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The use of clinical gene sequencing is now commonplace, and genome analysts and molecular pathologists are often tasked with the labor-intensive process of interpreting the clinical significance of large numbers of tumor variants. Numerous independent knowledgebases have been constructed to alleviate this manual burden, however these knowledgebases are non-interoperable. As a result, the analyst is left with a difficult tradeoff: for each knowledgebase used the analyst must understand the nuances particular to that resource and integrate its evidence accordingly when generating the clinical report, but for each knowledgebase omitted there is increased potential for missed findings of clinical significance.The Variant Interpretation for Cancer Consortium (VICC; cancervariants.org) was formed as a driver project of the Global Alliance for Genomics and Health (GA4GH; ga4gh.org) to address this concern. VICC members include representatives from several major somatic interpretation knowledgebases including CIViC, OncoKB, Jax-CKB, the Weill Cornell PMKB, the IRB-Barcelona Cancer Biomarkers Database, and others. Previously, the VICC built and reported on a harmonized meta-knowledgebase of 19,551 biomarker associations of harmonized variants, diseases, drugs, and evidence across the constituent resources.In that study, we analyzed the frequency with which the tumor samples from the AACR Project GENIE cohort would match to harmonized associations. Variant matches increased dramatically from 57% to 86% when broader matching to regions describing categorical variants were allowed. Unlike precise sequence variants with specified alternate alleles, categorical variants describe a collection of potential variants with a common feature, such as “V600” (non-valine alleles at the 600 residue), “Exon 20 mutations” (all non-silent mutations in exon 20), or “Gain-of-function” (hypermorphic alterations that activate or amplify gene activity). However, matching observed sequence variants to categorical variants is challenging, as the latter are typically only described as unstructured text. Here we describe the expressive and computational GA4GH Variation Representation specification (vr-spec.readthedocs.io), which we co-developed as members of the GA4GH Genomic Knowledge Standards work stream. This specification provides a schema for common, precise forms of variation (e.g. SNVs and Indels) and the method for computing identifiers from these objects. We highlight key aspects of the specification and our work to apply it to the characterization of categorical variation, showcasing the variant terminology and classification tools developed by the VICC to support this effort. These standards and tools are free, open-source, and extensible, overcoming barriers to standardized variant knowledge sharing and search.
Citation Format: Alex H. Wagner, Reece K. Hart, Larry Babb, Robert R. Freimuth, Adam Coffman, Yonghao Liang, Beth Pitel, Angshumoy Roy, Matthew Brush, Jennifer Lee, Anna Lu, Thomas Coard, Shruti Rao, Deborah Ritter, Brian Walsh, Susan Mockus, Peter Horak, Ian King, Dmitriy Sonkin, Subha Madhavan, Gordana Raca, Debyani Chakravarty, Malachi Griffith, Obi L. Griffith. Harmonization standards from the Variant Interpretation for Cancer Consortium [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1096.
Collapse
Affiliation(s)
- Alex H. Wagner
- 1Washington University School of Medicine, Saint Louis, MO
| | | | | | | | - Adam Coffman
- 1Washington University School of Medicine, Saint Louis, MO
| | - Yonghao Liang
- 1Washington University School of Medicine, Saint Louis, MO
| | | | | | | | | | - Anna Lu
- 7National Cancer Institute, Bethesda, MD
| | | | | | | | - Brian Walsh
- 6Oregon Health and Science University, Portland, OR
| | - Susan Mockus
- 9The Jackson Laboratory for Genomic Medicine, Farmington, CT
| | - Peter Horak
- 10National Center for Tumor Diseases, Heidelberg, Germany
| | - Ian King
- 11University of Toronto, Toronto, Ontario, Canada
| | | | | | - Gordana Raca
- 12University of Southern California, Los Angeles, CA
| | | | | | | |
Collapse
|
39
|
Mata DA, Yang SR, Ferguson DC, Liu Y, Sharma R, Benhamida JK, Al-Ahmadie HA, Chakravarty D, Solit DB, Tickoo SK, Gupta S, Arcila ME, Ladanyi M, Feldman DR, Reuter VE, Vanderbilt CM. RAS/MAPK Pathway Driver Alterations Are Significantly Associated With Oncogenic KIT Mutations in Germ-cell Tumors. Urology 2020; 144:111-116. [PMID: 32721511 DOI: 10.1016/j.urology.2020.07.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/14/2020] [Accepted: 07/16/2020] [Indexed: 01/09/2023]
Abstract
OBJECTIVE To report the mutational profile and clinical outcomes of a cohort of patients with KIT-mutant seminomas and nonseminomatous germ-cell tumors (SGCT/NSGCTs). PATIENTS AND METHODS Retrospective cohort study of all patients with KIT-mutant GCTs sequenced at Memorial Sloan Kettering between March 2014 and March 2020. Tumors were assessed with MSK-IMPACT, a DNA next-generation sequencing assay for targeted sequencing of up to 468 key cancer genes. RESULTS Among 568 patients with GCTs, 8.1% had somatic KIT mutations, including 28 seminomas and 18 mixed/NSGCTs. Exons 17 (67.3%), 11 (22.4%), and 13 (6.1%) were most commonly affected. KIT-mutant cases were enriched for oncogenic RAS/MAPK pathway alterations compared to KIT-wildtype cases (34.8% vs 19.2%, P = .02). Among KIT-mutant cases, concurrent mutations were noted in KRAS (21.7%), RRAS2 (11.8%), CBL (6.5%), NRAS (4.3%), MAP2K1 (2.2%), and RAC1 (2.2%). Mutations in KRAS, RRAS2, and NRAS were mutually exclusive. In all, 73.9% of patients developed metastases and 95.7% received chemotherapy. No patients received KIT-directed tyrosine kinase inhibitors (TKIs). Classification as a NSGCT rather than a SGCT was associated with an increased risk of death (hazard ratio 9.1, 95% confidence interval 1.1-78.4, P = .04) while the presence of a concurrent RAS/MAPK pathway alteration was not (hazard ratio 0.8, 95% confidence interval 0.1-4.3, P = .76). CONCLUSION Mitogenic driver alterations can co-occur with activating KIT mutations, which may explain the lack of efficacy of KIT-directed TKIs in prior trials. Novel KIT-directed TKIs that target exon 17 mutations may benefit chemotherapy-refractory patients with KIT-mutant GCTs without RAS/MAPK alterations. Dual MEK/KIT inhibitor therapy in KIT-mutant GCTs with concurrent RAS/MAPK alterations could also be a plausible therapeutic strategy.
Collapse
Affiliation(s)
- Douglas A Mata
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY.
| | - Soo-Ryum Yang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Donna C Ferguson
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ying Liu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Rohit Sharma
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jamal K Benhamida
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Hikmat A Al-Ahmadie
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Debyani Chakravarty
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - David B Solit
- Department of Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Satish K Tickoo
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sounak Gupta
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Maria E Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Darren R Feldman
- Department of Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Victor E Reuter
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Chad M Vanderbilt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY.
| |
Collapse
|
40
|
Rao S, Pitel B, Wagner AH, Boca SM, McCoy M, King I, Gupta S, Park BH, Warner JL, Chen J, Rogan PK, Chakravarty D, Griffith M, Griffith OL, Madhavan S. Collaborative, Multidisciplinary Evaluation of Cancer Variants Through Virtual Molecular Tumor Boards Informs Local Clinical Practices. JCO Clin Cancer Inform 2020; 4:602-613. [PMID: 32644817 PMCID: PMC7397775 DOI: 10.1200/cci.19.00169] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2020] [Indexed: 12/17/2022] Open
Abstract
PURPOSE The cancer research community is constantly evolving to better understand tumor biology, disease etiology, risk stratification, and pathways to novel treatments. Yet the clinical cancer genomics field has been hindered by redundant efforts to meaningfully collect and interpret disparate data types from multiple high-throughput modalities and integrate into clinical care processes. Bespoke data models, knowledgebases, and one-off customized resources for data analysis often lack adequate governance and quality control needed for these resources to be clinical grade. Many informatics efforts focused on genomic interpretation resources for neoplasms are underway to support data collection, deposition, curation, harmonization, integration, and analytics to support case review and treatment planning. METHODS In this review, we evaluate and summarize the landscape of available tools, resources, and evidence used in the evaluation of somatic and germline tumor variants within the context of molecular tumor boards. RESULTS Molecular tumor boards (MTBs) are collaborative efforts of multidisciplinary cancer experts equipped with genomic interpretation resources to aid in the delivery of accurate and timely clinical interpretations of complex genomic results for each patient, within an institution or hospital network. Virtual MTBs (VMTBs) provide an online forum for collaborative governance, provenance, and information sharing between experts outside a given hospital network with the potential to enhance MTB discussions. Knowledge sharing in VMTBs and communication with guideline-developing organizations can lead to progress evidenced by data harmonization across resources, crowd-sourced and expert-curated genomic assertions, and a more informed and explainable usage of artificial intelligence. CONCLUSION Advances in cancer genomics interpretation aid in better patient and disease classification, more streamlined identification of relevant literature, and a more thorough review of available treatments and predicted patient outcomes.
Collapse
Affiliation(s)
- Shruti Rao
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC
| | - Beth Pitel
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Alex H. Wagner
- McDonnell Genome Institute and Department of Medicine, Washington University School of Medicine, St Louis, MO
| | - Simina M. Boca
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC
| | - Matthew McCoy
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC
| | - Ian King
- Laboratory Medicine Program, University Health Network and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Samir Gupta
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC
| | - Ben Ho Park
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | - Jeremy L. Warner
- Departments of Medicine and Biomedical Informatics, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | - James Chen
- Division of Medical Oncology, Department of Biomedical Informatics, The Ohio State University, Columbus, OH
| | - Peter K. Rogan
- Departments of Biochemistry and Oncology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Debyani Chakravarty
- Kravis Center of Molecular Oncology, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Malachi Griffith
- McDonnell Genome Institute and Department of Medicine, Washington University School of Medicine, St Louis, MO
| | - Obi L. Griffith
- McDonnell Genome Institute and Department of Medicine, Washington University School of Medicine, St Louis, MO
| | - Subha Madhavan
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC
| |
Collapse
|
41
|
Sakamoto H, Attiyeh MA, Gerold JM, Makohon-Moore AP, Hayashi A, Hong J, Kappagantula R, Zhang L, Melchor JP, Reiter JG, Heyde A, Bielski CM, Penson AV, Gönen M, Chakravarty D, O'Reilly EM, Wood LD, Hruban RH, Nowak MA, Socci ND, Taylor BS, Iacobuzio-Donahue CA. The Evolutionary Origins of Recurrent Pancreatic Cancer. Cancer Discov 2020; 10:792-805. [PMID: 32193223 PMCID: PMC7323937 DOI: 10.1158/2159-8290.cd-19-1508] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/06/2020] [Accepted: 03/16/2020] [Indexed: 11/16/2022]
Abstract
Surgery is the only curative option for stage I/II pancreatic cancer; nonetheless, most patients will experience a recurrence after surgery and die of their disease. To identify novel opportunities for management of recurrent pancreatic cancer, we performed whole-exome or targeted sequencing of 10 resected primary cancers and matched intrapancreatic recurrences or distant metastases. We identified that recurrent disease after adjuvant or first-line platinum therapy corresponds to an increased mutational burden. Recurrent disease is enriched for genetic alterations predicted to activate MAPK/ERK and PI3K-AKT signaling and develops from a monophyletic or polyphyletic origin. Treatment-induced genetic bottlenecks lead to a modified genetic landscape and subclonal heterogeneity for driver gene alterations in part due to intermetastatic seeding. In 1 patient what was believed to be recurrent disease was an independent (second) primary tumor. These findings suggest routine post-treatment sampling may have value in the management of recurrent pancreatic cancer. SIGNIFICANCE: The biological features or clinical vulnerabilities of recurrent pancreatic cancer after pancreaticoduodenectomy are unknown. Using whole-exome sequencing we find that recurrent disease has a distinct genomic landscape, intermetastatic genetic heterogeneity, diverse clonal origins, and higher mutational burden than found for treatment-naïve disease.See related commentary by Bednar and Pasca di Magliano, p. 762.This article is highlighted in the In This Issue feature, p. 747.
Collapse
Affiliation(s)
- Hitomi Sakamoto
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc A Attiyeh
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jeffrey M Gerold
- Program for Evolutionary Dynamics, Harvard University, Cambridge, Massachusetts
- Department of Mathematics and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts
| | - Alvin P Makohon-Moore
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Akimasa Hayashi
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jungeui Hong
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Rajya Kappagantula
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Lance Zhang
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jerry P Melchor
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Johannes G Reiter
- Canary Center for Cancer Early Detection, Department of Radiology, Stanford University, Palo Alto, California
| | - Alexander Heyde
- Program for Evolutionary Dynamics, Harvard University, Cambridge, Massachusetts
- Department of Mathematics and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts
| | - Craig M Bielski
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alexander V Penson
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mithat Gönen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Debyani Chakravarty
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Eileen M O'Reilly
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Laura D Wood
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland
- Sol Goldman Pancreatic Cancer Research Center, Baltimore, Maryland
| | - Ralph H Hruban
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland
- Sol Goldman Pancreatic Cancer Research Center, Baltimore, Maryland
| | - Martin A Nowak
- Program for Evolutionary Dynamics, Harvard University, Cambridge, Massachusetts
- Department of Mathematics and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts
| | - Nicholas D Socci
- Bioinformatics Core, Memorial Sloan Kettering Cancer Center, New York, New York
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Barry S Taylor
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Christine A Iacobuzio-Donahue
- 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
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| |
Collapse
|
42
|
Wagner AH, Walsh B, Mayfield G, Tamborero D, Sonkin D, Krysiak K, Deu-Pons J, Duren RP, Gao J, McMurry J, Patterson S, Del Vecchio Fitz C, Pitel BA, Sezerman OU, Ellrott K, Warner JL, Rieke DT, Aittokallio T, Cerami E, Ritter DI, Schriml LM, Freimuth RR, Haendel M, Raca G, Madhavan S, Baudis M, Beckmann JS, Dienstmann R, Chakravarty D, Li XS, Mockus S, Elemento O, Schultz N, Lopez-Bigas N, Lawler M, Goecks J, Griffith M, Griffith OL, Margolin AA. A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer. Nat Genet 2020; 52:448-457. [PMID: 32246132 PMCID: PMC7127986 DOI: 10.1038/s41588-020-0603-8] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 02/26/2020] [Indexed: 12/19/2022]
Abstract
Precision oncology relies on accurate discovery and interpretation of genomic variants, enabling individualized diagnosis, prognosis and therapy selection. We found that six prominent somatic cancer variant knowledgebases were highly disparate in content, structure and supporting primary literature, impeding consensus when evaluating variants and their relevance in a clinical setting. We developed a framework for harmonizing variant interpretations to produce a meta-knowledgebase of 12,856 aggregate interpretations. We demonstrated large gains in overlap between resources across variants, diseases and drugs as a result of this harmonization. We subsequently demonstrated improved matching between a patient cohort and harmonized interpretations of potential clinical significance, observing an increase from an average of 33% per individual knowledgebase to 57% in aggregate. Our analyses illuminate the need for open, interoperable sharing of variant interpretation data. We also provide a freely available web interface (search.cancervariants.org) for exploring the harmonized interpretations from these six knowledgebases.
Collapse
Affiliation(s)
- Alex H Wagner
- Washington University School of Medicine, St. Louis, MO, USA
| | - Brian Walsh
- Oregon Health and Science University, Portland, OR, USA
| | | | - David Tamborero
- Pompeu Fabra University, Barcelona, Spain
- Karolinska Institute, Solna, Sweden
| | | | | | - Jordi Deu-Pons
- Institute for Research in Biomedicine, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies, Barcelona, Spain
| | | | - Jianjiong Gao
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Julie McMurry
- Oregon Health and Science University, Portland, OR, USA
| | - Sara Patterson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | | | | | - Kyle Ellrott
- Oregon Health and Science University, Portland, OR, USA
| | | | | | - Tero Aittokallio
- Institute for Molecular Medicine Finland, Helsinki, Finland
- University of Turku, Turku, Finland
| | | | - Deborah I Ritter
- Baylor College of Medicine, Houston, TX, USA
- Texas Children's Hospital, Houston, TX, USA
| | - Lynn M Schriml
- University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Melissa Haendel
- Oregon Health and Science University, Portland, OR, USA
- Linus Pauling Institute at Oregon State University, Corvallis, OR, USA
| | - Gordana Raca
- Children's Hospital Los Angeles, Los Angeles, CA, USA
- Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Subha Madhavan
- Georgetown University Medical Center, Washington, DC, USA
| | | | | | | | | | | | - Susan Mockus
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | | | - Nuria Lopez-Bigas
- Pompeu Fabra University, Barcelona, Spain
- Institute for Research in Biomedicine, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies, Barcelona, Spain
| | | | - Jeremy Goecks
- Oregon Health and Science University, Portland, OR, USA
| | | | - Obi L Griffith
- Washington University School of Medicine, St. Louis, MO, USA.
| | | |
Collapse
|
43
|
Mateo J, Chakravarty D, Dienstmann R, Jezdic S, Gonzalez-Perez A, Lopez-Bigas N, Ng CKY, Bedard PL, Tortora G, Douillard JY, Van Allen EM, Schultz N, Swanton C, André F, Pusztai L. A framework to rank genomic alterations as targets for cancer precision medicine: the ESMO Scale for Clinical Actionability of molecular Targets (ESCAT). Ann Oncol 2019; 29:1895-1902. [PMID: 30137196 DOI: 10.1093/annonc/mdy263] [Citation(s) in RCA: 382] [Impact Index Per Article: 76.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Background In order to facilitate implementation of precision medicine in clinical management of cancer, there is a need to harmonise and standardise the reporting and interpretation of clinically relevant genomics data. Methods The European Society for Medical Oncology (ESMO) Translational Research and Precision Medicine Working Group (TR and PM WG) launched a collaborative project to propose a classification system for molecular aberrations based on the evidence available supporting their value as clinical targets. A group of experts from several institutions was assembled to review available evidence, reach a consensus on grading criteria and present a classification system. This was then reviewed, amended and finally approved by the ESMO TR and PM WG and the ESMO leadership. Results This first version of the ESMO Scale of Clinical Actionability for molecular Targets (ESCAT) defines six levels of clinical evidence for molecular targets according to the implications for patient management: tier I, targets ready for implementation in routine clinical decisions; tier II, investigational targets that likely define a patient population that benefits from a targeted drug but additional data are needed; tier III, clinical benefit previously demonstrated in other tumour types or for similar molecular targets; tier IV, preclinical evidence of actionability; tier V, evidence supporting co-targeting approaches; and tier X, lack of evidence for actionability. Conclusions The ESCAT defines clinical evidence-based criteria to prioritise genomic alterations as markers to select patients for targeted therapies. This classification system aims to offer a common language for all the relevant stakeholders in cancer medicine and drug development.
Collapse
Affiliation(s)
- J Mateo
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - D Chakravarty
- Memorial Sloan Kettering Cancer Center, New York, USA
| | - R Dienstmann
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - S Jezdic
- European Society for Medical Oncology, Lugano, Switzerland
| | | | - N Lopez-Bigas
- Institute for Research in Biomedicine (IRB), Barcelona; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - C K Y Ng
- University Hospital Basel, Basel, Switzerland
| | - P L Bedard
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - G Tortora
- University of Verona, Verona; Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - J-Y Douillard
- European Society for Medical Oncology, Lugano, Switzerland
| | - E M Van Allen
- Harvard Medical School Dana-Farber Cancer Center and Broad Institute, Boston, USA
| | - N Schultz
- Memorial Sloan Kettering Cancer Center, New York, USA
| | - C Swanton
- The Francis Crick Institute, London, UK
| | - F André
- Institut Gustave Roussy, Villejuif, France.
| | | |
Collapse
|
44
|
Suehara Y, Alex D, Bowman A, Middha S, Zehir A, Chakravarty D, Wang L, Jour G, Nafa K, Hayashi T, Jungbluth AA, Frosina D, Slotkin E, Shukla N, Meyers P, Healey JH, Hameed M, Ladanyi M. Clinical Genomic Sequencing of Pediatric and Adult Osteosarcoma Reveals Distinct Molecular Subsets with Potentially Targetable Alterations. Clin Cancer Res 2019. [PMID: 31175097 DOI: 10.1158/1078‐0432.ccr‐18‐4032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
PURPOSE Although multimodal chemotherapy has improved outcomes for patients with osteosarcoma, the prognosis for patients who present with metastatic and/or recurrent disease remains poor. In this study, we sought to define how often clinical genomic sequencing of osteosarcoma samples could identify potentially actionable alterations.Experimental Design: We analyzed genomic data from 71 osteosarcoma samples from 66 pediatric and adult patients sequenced using MSK-IMPACT, a hybridization capture-based large panel next-generation sequencing assay. Potentially actionable genetic events were categorized according to the OncoKB precision oncology knowledge base, of which levels 1 to 3 were considered clinically actionable. RESULTS We found at least one potentially actionable alteration in 14 of 66 patients (21%), including amplification of CDK4 (n = 9, 14%: level 2B) and/or MDM2 (n = 9, 14%: level 3B), and somatic truncating mutations/deletions in BRCA2 (n = 3, 5%: level 2B) and PTCH1 (n = 1, level 3B). In addition, we observed mutually exclusive patterns of alterations suggesting distinct biological subsets defined by gains at 4q12 and 6p12-21. Specifically, potentially targetable gene amplifications at 4q12 involving KIT, KDR, and PDGFRA were identified in 13 of 66 patients (20%), which showed strong PDGFRA expression by IHC. In another largely nonoverlapping subset of 14 patients (24%) with gains at 6p12-21, VEGFA amplification was identified. CONCLUSIONS We found potentially clinically actionable alterations in approximately 21% of patients with osteosarcoma. In addition, at least 40% of patients have tumors harboring PDGFRA or VEGFA amplification, representing candidate subsets for clinical evaluation of additional therapeutic options. We propose a new genomically based algorithm for directing patients with osteosarcoma to clinical trial options.
Collapse
Affiliation(s)
- Yoshiyuki Suehara
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Orthopedic Surgery, Juntendo University School of Medicine, Tokyo, Japan
| | - Deepu Alex
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Anita Bowman
- Department of Pathology, 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
| | - Debyani Chakravarty
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Lu Wang
- Department of Pathology, St Jude Children's Research Hospital, Memphis, Tennessee
| | - George Jour
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Khedoudja Nafa
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Takuo Hayashi
- Department of Human Pathology, Juntendo University School of Medicine, Tokyo, Japan
| | - Achim A Jungbluth
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Denise Frosina
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Emily Slotkin
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Neerav Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Paul Meyers
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - John H Healey
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Meera Hameed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York. .,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| |
Collapse
|
45
|
Tao JJ, Eubank MH, Schram AM, Cangemi N, Pamer E, Rosen EY, Schultz N, Chakravarty D, Philip J, Hechtman JF, Harding JJ, Smyth LM, Jhaveri KL, Drilon A, Ladanyi M, Solit DB, Zehir A, Berger MF, Stetson PD, Gardos SM, Hyman DM. Real-World Outcomes of an Automated Physician Support System for Genome-Driven Oncology. JCO Precis Oncol 2019; 3:1900066. [PMID: 32914018 PMCID: PMC7446398 DOI: 10.1200/po.19.00066] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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] [Accepted: 06/13/2019] [Indexed: 01/19/2023] Open
Abstract
PURPOSE Matching patients to investigational therapies requires new tools to support physician decision making. We designed and implemented Precision Insight Support Engine (PRECISE), an automated, just-in-time, clinical-grade informatics platform to identify and dynamically track patients on the basis of molecular and clinical criteria. Real-world use of this tool was analyzed to determine whether PRECISE facilitated enrollment to early-phase, genome-driven trials. MATERIALS AND METHODS We analyzed patients who were enrolled in genome-driven, early-phase trials using PRECISE at Memorial Sloan Kettering Cancer Center between April 2014 and January 2018. Primary end point was the proportion of enrolled patients who were successfully identified using PRECISE before enrollment. Secondary end points included time from sequencing and PRECISE identification to enrollment. Reasons for a failure to identify genomically matched patients were also explored. RESULTS Data were analyzed from 41 therapeutic trials led by 19 principal investigators. In total, 755 patients were accrued to these studies during the period that PRECISE was used. PRECISE successfully identified 327 patients (43%) before enrollment. Patients were diagnosed with 29 tumor types and harbored alterations in 43 oncogenes, most commonly ERBB2 (21.3%), PIK3CA (14.1%), and BRAF (8.7%). Median time from sequencing to enrollment was 163 days (interquartile range, 66 to 357 days), and from PRECISE identification to enrollment 87 days (interquartile range, 37 to 180 days). Common reasons for failing to identify patients before enrollment included accrual on the basis of molecular alterations that did not match pre-established PRECISE genomic eligibility (140 [33%] of 428) and external sequencing not available for parsing (127 [30%] of 428). CONCLUSION PRECISE identified 43% of all patients accrued to a diverse cohort of early-phase, genome-matched studies. Purpose-built informatics platforms represent a novel and potentially effective method for matching patients to molecularly selected studies.
Collapse
Affiliation(s)
- Jessica J Tao
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Alison M Schram
- Memorial Sloan Kettering Cancer Center, New York, NY.,Weill Cornell Medical College, New York, NY
| | | | - Erika Pamer
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ezra Y Rosen
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - John Philip
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - James J Harding
- Memorial Sloan Kettering Cancer Center, New York, NY.,Weill Cornell Medical College, New York, NY
| | - Lillian M Smyth
- Memorial Sloan Kettering Cancer Center, New York, NY.,Weill Cornell Medical College, New York, NY
| | - Komal L Jhaveri
- Memorial Sloan Kettering Cancer Center, New York, NY.,Weill Cornell Medical College, New York, NY
| | - Alexander Drilon
- Memorial Sloan Kettering Cancer Center, New York, NY.,Weill Cornell Medical College, New York, NY
| | - Marc Ladanyi
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - David B Solit
- Memorial Sloan Kettering Cancer Center, New York, NY.,Weill Cornell Medical College, New York, NY
| | - Ahmet Zehir
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael F Berger
- Memorial Sloan Kettering Cancer Center, New York, NY.,Weill Cornell Medical College, New York, NY
| | | | | | - David M Hyman
- Memorial Sloan Kettering Cancer Center, New York, NY.,Weill Cornell Medical College, New York, NY
| |
Collapse
|
46
|
Suehara Y, Alex D, Bowman A, Middha S, Zehir A, Chakravarty D, Wang L, Jour G, Nafa K, Hayashi T, Jungbluth AA, Frosina D, Slotkin E, Shukla N, Meyers P, Healey JH, Hameed M, Ladanyi M. Clinical Genomic Sequencing of Pediatric and Adult Osteosarcoma Reveals Distinct Molecular Subsets with Potentially Targetable Alterations. Clin Cancer Res 2019; 25:6346-6356. [PMID: 31175097 DOI: 10.1158/1078-0432.ccr-18-4032] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 04/25/2019] [Accepted: 06/04/2019] [Indexed: 12/12/2022]
Abstract
PURPOSE Although multimodal chemotherapy has improved outcomes for patients with osteosarcoma, the prognosis for patients who present with metastatic and/or recurrent disease remains poor. In this study, we sought to define how often clinical genomic sequencing of osteosarcoma samples could identify potentially actionable alterations.Experimental Design: We analyzed genomic data from 71 osteosarcoma samples from 66 pediatric and adult patients sequenced using MSK-IMPACT, a hybridization capture-based large panel next-generation sequencing assay. Potentially actionable genetic events were categorized according to the OncoKB precision oncology knowledge base, of which levels 1 to 3 were considered clinically actionable. RESULTS We found at least one potentially actionable alteration in 14 of 66 patients (21%), including amplification of CDK4 (n = 9, 14%: level 2B) and/or MDM2 (n = 9, 14%: level 3B), and somatic truncating mutations/deletions in BRCA2 (n = 3, 5%: level 2B) and PTCH1 (n = 1, level 3B). In addition, we observed mutually exclusive patterns of alterations suggesting distinct biological subsets defined by gains at 4q12 and 6p12-21. Specifically, potentially targetable gene amplifications at 4q12 involving KIT, KDR, and PDGFRA were identified in 13 of 66 patients (20%), which showed strong PDGFRA expression by IHC. In another largely nonoverlapping subset of 14 patients (24%) with gains at 6p12-21, VEGFA amplification was identified. CONCLUSIONS We found potentially clinically actionable alterations in approximately 21% of patients with osteosarcoma. In addition, at least 40% of patients have tumors harboring PDGFRA or VEGFA amplification, representing candidate subsets for clinical evaluation of additional therapeutic options. We propose a new genomically based algorithm for directing patients with osteosarcoma to clinical trial options.
Collapse
Affiliation(s)
- Yoshiyuki Suehara
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Orthopedic Surgery, Juntendo University School of Medicine, Tokyo, Japan
| | - Deepu Alex
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Anita Bowman
- Department of Pathology, 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
| | - Debyani Chakravarty
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Lu Wang
- Department of Pathology, St Jude Children's Research Hospital, Memphis, Tennessee
| | - George Jour
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Khedoudja Nafa
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Takuo Hayashi
- Department of Human Pathology, Juntendo University School of Medicine, Tokyo, Japan
| | - Achim A Jungbluth
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Denise Frosina
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Emily Slotkin
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Neerav Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Paul Meyers
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - John H Healey
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Meera Hameed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York. .,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| |
Collapse
|
47
|
Armenia J, Wankowicz SAM, Liu D, Gao J, Kundra R, Reznik E, Chatila WK, Chakravarty D, Han GC, Coleman I, Montgomery B, Pritchard C, Morrissey C, Barbieri CE, Beltran H, Sboner A, Zafeiriou Z, Miranda S, Bielski CM, Penson AV, Tolonen C, Huang FW, Robinson D, Wu YM, Lonigro R, Garraway LA, Demichelis F, Kantoff PW, Taplin ME, Abida W, Taylor BS, Scher HI, Nelson PS, de Bono JS, Rubin MA, Sawyers CL, Chinnaiyan AM, Schultz N, Van Allen EM. Publisher Correction: The long tail of oncogenic drivers in prostate cancer. Nat Genet 2019; 51:1194. [PMID: 31152158 DOI: 10.1038/s41588-019-0451-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Collapse
Affiliation(s)
- Joshua Armenia
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Stephanie A M Wankowicz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - David Liu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jianjiong Gao
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ritika Kundra
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ed Reznik
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Walid K Chatila
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Debyani Chakravarty
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - G Celine Han
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ilsa Coleman
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Bruce Montgomery
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Colin Pritchard
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Christopher E Barbieri
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Himisha Beltran
- Department of Medicine, Division of Medical Oncology, Weill Cornell Medicine, New York, NY, USA.,Englander Institute for Precision Medicine, Weill Cornell Medical College-New York Presbyterian Hospital, New York, NY, USA.,Sandra and Edward Meyer Cancer Center at Weill Cornell Medical College, New York, NY, USA
| | - Andrea Sboner
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Zafeiris Zafeiriou
- Biomarkers Team, Division of Clinical Studies, The Institute of Cancer Research and Royal Marsden Hospital, London, UK
| | - Susana Miranda
- Biomarkers Team, Division of Clinical Studies, The Institute of Cancer Research and Royal Marsden Hospital, London, UK
| | - Craig M Bielski
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexander V Penson
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Charlotte Tolonen
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Franklin W Huang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Dan Robinson
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Yi Mi Wu
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Robert Lonigro
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Levi A Garraway
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Philip W Kantoff
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mary-Ellen Taplin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Wassim Abida
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Barry S Taylor
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Howard I Scher
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Peter S Nelson
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Medicine, University of Washington, Seattle, WA, USA
| | - Johann S de Bono
- Biomarkers Team, Division of Clinical Studies, The Institute of Cancer Research and Royal Marsden Hospital, London, UK
| | - Mark A Rubin
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.,Englander Institute for Precision Medicine, Weill Cornell Medical College-New York Presbyterian Hospital, New York, NY, USA.,Sandra and Edward Meyer Cancer Center at Weill Cornell Medical College, New York, NY, USA
| | - Charles L Sawyers
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | | | - Nikolaus Schultz
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. .,Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| |
Collapse
|
48
|
Carlo MI, Khan N, Zehir A, Patil S, Ged Y, Redzematovic A, Coskey DT, Hyman DM, Ladanyi M, Chen YB, Robson M, Hakimi AA, Lee CH, Feldman DR, Gao J, Chakravarty D, Motzer RJ, Voss MH. Comprehensive Genomic Analysis of Metastatic Non-Clear-Cell Renal Cell Carcinoma to Identify Therapeutic Targets. JCO Precis Oncol 2019; 3:1800372. [PMID: 32914011 DOI: 10.1200/po.18.00372] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/27/2018] [Indexed: 12/27/2022] Open
Abstract
PURPOSE Non-clear-cell renal cell carcinoma (nccRCC) encompasses approximately 20% of renal cell carcinomas and includes subtypes that vary in clinical and molecular biology. Compared with clear cell renal cell carcinoma, nccRCC demonstrates limited sensitivity to conventional vascular endothelial growth factor- and mammalian target of rapamycin-directed agents, indicating a need for better therapies. Characterizing the genomic landscape of metastatic nccRCC variants may help define novel therapeutic strategies. PATIENTS AND METHODS We retrospectively analyzed tumor tissue from patients with metastatic nccRCC who consented to genomic analysis of their tumor and germline DNA. A hybridization capture-based assay was used to identify single nucleotide variants and small insertions and deletions across more than 340 cancer-associated genes with germline comparison. Clinical actionability of somatic mutations was assessed using OncoKB levels of evidence. Microsatellite instability (MSI) in the tumor was investigated. RESULTS Of 116 patients included in the analysis, 57 (49%) presented with de novo metastatic disease, and 59 (51%) presented with localized disease that later metastasized. Subtype classifications included unclassified (n = 41; 35%), papillary (n = 26; 22%), chromophobe (n = 17; 15%), translocation associated (n = 13; 11%), and other (n = 19; 16%). Of all tumors, 15 (13%) had putative driver somatic alterations amenable to targeted therapies, including alterations in MET, TSC1/2, and an ALK translocation. Of 45 patients who had germline testing, 11 (24%) harbored mutations, seven of which could potentially guide therapy. Of 115 available tumors for analysis, two (1.7%) had high and six (5%) had intermediate MSI status. CONCLUSION The mutation profiles of metastatic nccRCC vary by subtype. Comprehensive analysis of somatic mutations, germline mutations, and MSI, interpreted via an annotated precision oncology knowledge base, identified potentially targetable alterations in 22% of patients, which merits additional investigation.
Collapse
Affiliation(s)
- Maria I Carlo
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nabeela Khan
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Zehir
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sujata Patil
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yasser Ged
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - David M Hyman
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Marc Ladanyi
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ying-Bei Chen
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mark Robson
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - A Ari Hakimi
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Chung-Han Lee
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Jianjiong Gao
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Martin H Voss
- Memorial Sloan Kettering Cancer Center, New York, NY
| |
Collapse
|
49
|
Walsh MF, Ritter DI, Kesserwan C, Sonkin D, Chakravarty D, Chao E, Ghosh R, Kemel Y, Wu G, Lee K, Kulkarni S, Hedges D, Mandelker D, Ceyhan-Birsoy O, Luo M, Drazer M, Zhang L, Offit K, Plon SE. Integrating somatic variant data and biomarkers for germline variant classification in cancer predisposition genes. Hum Mutat 2018; 39:1542-1552. [PMID: 30311369 PMCID: PMC6310222 DOI: 10.1002/humu.23640] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 08/29/2018] [Accepted: 08/30/2018] [Indexed: 12/20/2022]
Abstract
In its landmark paper about Standards and Guidelines for the Interpretation of Sequence Variants, the American College of Medical Genetics and Genomics (ACMG), and Association for Molecular Pathology (AMP) did not address how to use tumor data when assessing the pathogenicity of germline variants. The Clinical Genome Resource (ClinGen) established a multidisciplinary working group, the Germline/Somatic Variant Subcommittee (GSVS) with this focus. The GSVS implemented a survey to determine current practices of integrating somatic data when classifying germline variants in cancer predisposition genes. The GSVS then reviewed and analyzed available resources of relevant somatic data, and performed integrative germline variant curation exercises. The committee determined that somatic hotspots could be systematically integrated into moderate evidence of pathogenicity (PM1). Tumor RNA sequencing data showing altered splicing may be considered as strong evidence in support of germline pathogenicity (PVS1) and tumor phenotypic features such as mutational signatures be considered supporting evidence of pathogenicity (PP4). However, at present, somatic data such as focal loss of heterozygosity and mutations occurring on the alternative allele are not recommended to be systematically integrated, instead, incorporation of this type of data should take place under the advisement of multidisciplinary cancer center tumor-normal sequencing boards.
Collapse
Affiliation(s)
- Michael F Walsh
- Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | | | | | | | | | | | | | - Yelena Kemel
- Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | - Gang Wu
- St. Jude Children's Hospital, Memphis, Tennessee, USA
| | - Kristy Lee
- University of North Carolina, Chapel Hill, North Carolina, USA
| | | | - Dale Hedges
- St. Jude Children's Hospital, Memphis, Tennessee, USA
| | - Diana Mandelker
- Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | | | - Minjie Luo
- Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | - Liying Zhang
- Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | - Kenneth Offit
- Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | | |
Collapse
|
50
|
Thomas AA, Abrey LE, Terziev R, Raizer J, Martinez NL, Forsyth P, Paleologos N, Matasar M, Sauter CS, Moskowitz C, Nimer SD, DeAngelis LM, Kaley T, Grimm S, Louis DN, Cairncross JG, Panageas KS, Briggs S, Faivre G, Mohile NA, Mehta J, Jonsson P, Chakravarty D, Gao J, Schultz N, Brennan CW, Huse JT, Omuro A. Multicenter phase II study of temozolomide and myeloablative chemotherapy with autologous stem cell transplant for newly diagnosed anaplastic oligodendroglioma. Neuro Oncol 2018; 19:1380-1390. [PMID: 28472509 DOI: 10.1093/neuonc/nox086] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background Anaplastic oligodendroglioma (AO) and anaplastic oligoastrocytoma (AOA) are chemotherapy-sensitive tumors with prolonged survival after radiochemotherapy. We report a prospective trial using induction temozolomide (TMZ) followed by myeloablative high-dose chemotherapy (HDC) with autologous stem-cell transplant (ASCT) as a potential strategy to defer radiotherapy. Methods Patients with AO/AOA received 6 cycles of TMZ (200 mg/m2 × 5/28 day). Responding patients were eligible for HDC (thiotepa 250 mg/m2/day × 3 days, then busulfan 3.2 mg/kg/day × 3 days), followed by ASCT. Genomic characterization was performed using next-generation sequencing. Results Forty-one patients were enrolled; 85% had 1p/19q codeleted tumors. After induction, 26 patients were eligible for HDC-ASCT and 21 agreed to proceed. There were no unexpected adverse events or toxic deaths. After median follow-up of 66 months, 2-year progression-free survival (PFS) for transplanted patients was 86%, 5-year PFS 60%, and no patient has died. Among all 1p/19q codeleted patients (N = 33), 5-year PFS was 50% and 5-year overall survival (OS) 93%, with median time to radiotherapy not reached. Next-generation sequencing disclosed typical oligodendroglioma-related mutations, including IDH1, TERT, CIC, and FUBP1 mutations in 1p/19q codeleted patients, and glioblastoma-like signatures in 1p/19q intact patients. Aside from IDH1, potentially oncogenic/actionable mutations were variable, depicting wide molecular heterogeneity within oligodendroglial tumors. Conclusions TMZ followed by HDC-ASCT can be safely administered to patients with newly diagnosed 1p/19q codeleted AO. This strategy was associated with promising PFS and OS, suggesting that a chemotherapy-based approach may delay the need for radiotherapy and radiation-related toxicities. Raw data for further genomic and meta-analyses are publicly available at http://cbioportal.org/study?id=odg_msk_2017, accessed 6 January 2017. Clinicaltrials.gov registry NCT00588523.
Collapse
Affiliation(s)
- Alissa A Thomas
- Memorial Sloan Kettering Cancer Center, New York, New York,USA; Northwestern Memorial Hospital, Chicago, Illinois, USA; NorthShore University, Evanston, Illinois,USA; University of Calgary, Calgary, Alberta, Canada; Massachusetts General Hospital, Boston, Massachusetts, USA; MD Anderson Cancer Center, Houston, Texas, USA
| | - Lauren E Abrey
- Memorial Sloan Kettering Cancer Center, New York, New York,USA; Northwestern Memorial Hospital, Chicago, Illinois, USA; NorthShore University, Evanston, Illinois,USA; University of Calgary, Calgary, Alberta, Canada; Massachusetts General Hospital, Boston, Massachusetts, USA; MD Anderson Cancer Center, Houston, Texas, USA
| | - Robert Terziev
- Memorial Sloan Kettering Cancer Center, New York, New York,USA; Northwestern Memorial Hospital, Chicago, Illinois, USA; NorthShore University, Evanston, Illinois,USA; University of Calgary, Calgary, Alberta, Canada; Massachusetts General Hospital, Boston, Massachusetts, USA; MD Anderson Cancer Center, Houston, Texas, USA
| | - Jeffrey Raizer
- Memorial Sloan Kettering Cancer Center, New York, New York,USA; Northwestern Memorial Hospital, Chicago, Illinois, USA; NorthShore University, Evanston, Illinois,USA; University of Calgary, Calgary, Alberta, Canada; Massachusetts General Hospital, Boston, Massachusetts, USA; MD Anderson Cancer Center, Houston, Texas, USA
| | - Nina L Martinez
- Memorial Sloan Kettering Cancer Center, New York, New York,USA; Northwestern Memorial Hospital, Chicago, Illinois, USA; NorthShore University, Evanston, Illinois,USA; University of Calgary, Calgary, Alberta, Canada; Massachusetts General Hospital, Boston, Massachusetts, USA; MD Anderson Cancer Center, Houston, Texas, USA
| | - Peter Forsyth
- Memorial Sloan Kettering Cancer Center, New York, New York,USA; Northwestern Memorial Hospital, Chicago, Illinois, USA; NorthShore University, Evanston, Illinois,USA; University of Calgary, Calgary, Alberta, Canada; Massachusetts General Hospital, Boston, Massachusetts, USA; MD Anderson Cancer Center, Houston, Texas, USA
| | - Nina Paleologos
- Memorial Sloan Kettering Cancer Center, New York, New York,USA; Northwestern Memorial Hospital, Chicago, Illinois, USA; NorthShore University, Evanston, Illinois,USA; University of Calgary, Calgary, Alberta, Canada; Massachusetts General Hospital, Boston, Massachusetts, USA; MD Anderson Cancer Center, Houston, Texas, USA
| | - Matthew Matasar
- Memorial Sloan Kettering Cancer Center, New York, New York,USA; Northwestern Memorial Hospital, Chicago, Illinois, USA; NorthShore University, Evanston, Illinois,USA; University of Calgary, Calgary, Alberta, Canada; Massachusetts General Hospital, Boston, Massachusetts, USA; MD Anderson Cancer Center, Houston, Texas, USA
| | - Craig S Sauter
- Memorial Sloan Kettering Cancer Center, New York, New York,USA; Northwestern Memorial Hospital, Chicago, Illinois, USA; NorthShore University, Evanston, Illinois,USA; University of Calgary, Calgary, Alberta, Canada; Massachusetts General Hospital, Boston, Massachusetts, USA; MD Anderson Cancer Center, Houston, Texas, USA
| | - Craig Moskowitz
- Memorial Sloan Kettering Cancer Center, New York, New York,USA; Northwestern Memorial Hospital, Chicago, Illinois, USA; NorthShore University, Evanston, Illinois,USA; University of Calgary, Calgary, Alberta, Canada; Massachusetts General Hospital, Boston, Massachusetts, USA; MD Anderson Cancer Center, Houston, Texas, USA
| | - Stephen D Nimer
- Memorial Sloan Kettering Cancer Center, New York, New York,USA; Northwestern Memorial Hospital, Chicago, Illinois, USA; NorthShore University, Evanston, Illinois,USA; University of Calgary, Calgary, Alberta, Canada; Massachusetts General Hospital, Boston, Massachusetts, USA; MD Anderson Cancer Center, Houston, Texas, USA
| | - Lisa M DeAngelis
- Memorial Sloan Kettering Cancer Center, New York, New York,USA; Northwestern Memorial Hospital, Chicago, Illinois, USA; NorthShore University, Evanston, Illinois,USA; University of Calgary, Calgary, Alberta, Canada; Massachusetts General Hospital, Boston, Massachusetts, USA; MD Anderson Cancer Center, Houston, Texas, USA
| | - Thomas Kaley
- Memorial Sloan Kettering Cancer Center, New York, New York,USA; Northwestern Memorial Hospital, Chicago, Illinois, USA; NorthShore University, Evanston, Illinois,USA; University of Calgary, Calgary, Alberta, Canada; Massachusetts General Hospital, Boston, Massachusetts, USA; MD Anderson Cancer Center, Houston, Texas, USA
| | - Sean Grimm
- Memorial Sloan Kettering Cancer Center, New York, New York,USA; Northwestern Memorial Hospital, Chicago, Illinois, USA; NorthShore University, Evanston, Illinois,USA; University of Calgary, Calgary, Alberta, Canada; Massachusetts General Hospital, Boston, Massachusetts, USA; MD Anderson Cancer Center, Houston, Texas, USA
| | - David N Louis
- Memorial Sloan Kettering Cancer Center, New York, New York,USA; Northwestern Memorial Hospital, Chicago, Illinois, USA; NorthShore University, Evanston, Illinois,USA; University of Calgary, Calgary, Alberta, Canada; Massachusetts General Hospital, Boston, Massachusetts, USA; MD Anderson Cancer Center, Houston, Texas, USA
| | - J Gregory Cairncross
- Memorial Sloan Kettering Cancer Center, New York, New York,USA; Northwestern Memorial Hospital, Chicago, Illinois, USA; NorthShore University, Evanston, Illinois,USA; University of Calgary, Calgary, Alberta, Canada; Massachusetts General Hospital, Boston, Massachusetts, USA; MD Anderson Cancer Center, Houston, Texas, USA
| | - Katherine S Panageas
- Memorial Sloan Kettering Cancer Center, New York, New York,USA; Northwestern Memorial Hospital, Chicago, Illinois, USA; NorthShore University, Evanston, Illinois,USA; University of Calgary, Calgary, Alberta, Canada; Massachusetts General Hospital, Boston, Massachusetts, USA; MD Anderson Cancer Center, Houston, Texas, USA
| | - Samuel Briggs
- Memorial Sloan Kettering Cancer Center, New York, New York,USA; Northwestern Memorial Hospital, Chicago, Illinois, USA; NorthShore University, Evanston, Illinois,USA; University of Calgary, Calgary, Alberta, Canada; Massachusetts General Hospital, Boston, Massachusetts, USA; MD Anderson Cancer Center, Houston, Texas, USA
| | - Geraldine Faivre
- Memorial Sloan Kettering Cancer Center, New York, New York,USA; Northwestern Memorial Hospital, Chicago, Illinois, USA; NorthShore University, Evanston, Illinois,USA; University of Calgary, Calgary, Alberta, Canada; Massachusetts General Hospital, Boston, Massachusetts, USA; MD Anderson Cancer Center, Houston, Texas, USA
| | - Nimish A Mohile
- Memorial Sloan Kettering Cancer Center, New York, New York,USA; Northwestern Memorial Hospital, Chicago, Illinois, USA; NorthShore University, Evanston, Illinois,USA; University of Calgary, Calgary, Alberta, Canada; Massachusetts General Hospital, Boston, Massachusetts, USA; MD Anderson Cancer Center, Houston, Texas, USA
| | - Jayesh Mehta
- Memorial Sloan Kettering Cancer Center, New York, New York,USA; Northwestern Memorial Hospital, Chicago, Illinois, USA; NorthShore University, Evanston, Illinois,USA; University of Calgary, Calgary, Alberta, Canada; Massachusetts General Hospital, Boston, Massachusetts, USA; MD Anderson Cancer Center, Houston, Texas, USA
| | - Philip Jonsson
- Memorial Sloan Kettering Cancer Center, New York, New York,USA; Northwestern Memorial Hospital, Chicago, Illinois, USA; NorthShore University, Evanston, Illinois,USA; University of Calgary, Calgary, Alberta, Canada; Massachusetts General Hospital, Boston, Massachusetts, USA; MD Anderson Cancer Center, Houston, Texas, USA
| | - Debyani Chakravarty
- Memorial Sloan Kettering Cancer Center, New York, New York,USA; Northwestern Memorial Hospital, Chicago, Illinois, USA; NorthShore University, Evanston, Illinois,USA; University of Calgary, Calgary, Alberta, Canada; Massachusetts General Hospital, Boston, Massachusetts, USA; MD Anderson Cancer Center, Houston, Texas, USA
| | - Jianjiong Gao
- Memorial Sloan Kettering Cancer Center, New York, New York,USA; Northwestern Memorial Hospital, Chicago, Illinois, USA; NorthShore University, Evanston, Illinois,USA; University of Calgary, Calgary, Alberta, Canada; Massachusetts General Hospital, Boston, Massachusetts, USA; MD Anderson Cancer Center, Houston, Texas, USA
| | - Nikolaus Schultz
- Memorial Sloan Kettering Cancer Center, New York, New York,USA; Northwestern Memorial Hospital, Chicago, Illinois, USA; NorthShore University, Evanston, Illinois,USA; University of Calgary, Calgary, Alberta, Canada; Massachusetts General Hospital, Boston, Massachusetts, USA; MD Anderson Cancer Center, Houston, Texas, USA
| | - Cameron W Brennan
- Memorial Sloan Kettering Cancer Center, New York, New York,USA; Northwestern Memorial Hospital, Chicago, Illinois, USA; NorthShore University, Evanston, Illinois,USA; University of Calgary, Calgary, Alberta, Canada; Massachusetts General Hospital, Boston, Massachusetts, USA; MD Anderson Cancer Center, Houston, Texas, USA
| | - Jason T Huse
- Memorial Sloan Kettering Cancer Center, New York, New York,USA; Northwestern Memorial Hospital, Chicago, Illinois, USA; NorthShore University, Evanston, Illinois,USA; University of Calgary, Calgary, Alberta, Canada; Massachusetts General Hospital, Boston, Massachusetts, USA; MD Anderson Cancer Center, Houston, Texas, USA
| | - Antonio Omuro
- Memorial Sloan Kettering Cancer Center, New York, New York,USA; Northwestern Memorial Hospital, Chicago, Illinois, USA; NorthShore University, Evanston, Illinois,USA; University of Calgary, Calgary, Alberta, Canada; Massachusetts General Hospital, Boston, Massachusetts, USA; MD Anderson Cancer Center, Houston, Texas, USA
| |
Collapse
|