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Ceyhan-Birsoy O, Fiala E, Rana S, Sheehan M, Kennedy J, Yelskaya Z, Rai V, Li Y, Yang C, Wong D, Rijo I, Casanova J, Somar J, Mehta N, Park H, Ostafi S, Arora K, Padunan A, Ewalt MD, Aypar U, Terraf P, Misyura M, Haque S, Behr GG, Haque T, Sulis M, Geyer MB, Forlenza C, Thompson MC, Carlo M, Latham A, Liu Y, Zehir A, Brannon R, Berger M, Diaz LA, Dogan A, Ladanyi M, Petrova-Drus K, Nafa K, Offit K, Arcila M, Stadler ZK, Walsh MF, Mandelker D. Universal germline genetic testing in patients with hematologic malignancies using DNA isolated from nail clippings. Haematologica 2024. [PMID: 38572560 DOI: 10.3324/haematol.2024.285055] [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] [Received: 02/02/2024] [Indexed: 04/05/2024] Open
Abstract
Not available.
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Affiliation(s)
- Ozge Ceyhan-Birsoy
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Elise Fiala
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Satshil Rana
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Margaret Sheehan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jennifer Kennedy
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Zarina Yelskaya
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Vikas Rai
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yirong Li
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ciyu Yang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Donna Wong
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ivelise Rijo
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jacklyn Casanova
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Joshua Somar
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nikita Mehta
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Hyeonjin Park
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Silvana Ostafi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kanika Arora
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Angelika Padunan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mark D Ewalt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Umut Aypar
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Panieh Terraf
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Maksym Misyura
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sofia Haque
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Gerald G Behr
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Tamanna Haque
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Maria Sulis
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mark B Geyer
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Christopher Forlenza
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Meghan C Thompson
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Maria 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
| | - Ying Liu
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Zehir
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Rose Brannon
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael Berger
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Luis A Diaz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Dogan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Marc Ladanyi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kseniya Petrova-Drus
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Khedoudja Nafa
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Maria Arcila
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Zsofia K Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY.
| | - Michael F Walsh
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY.
| | - Diana Mandelker
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY.
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Krystel-Whittemore M, Petrova-Drus K, Ptashkin RN, Ewalt MD, Yao J, Liu Y, Zhu M, Benhamida J, Durham B, Kumar J, Nafa K, Kiecka I, Bowman AS, Gedvilaite E, Casanova J, Lin YT, Mohanty AS, Rana S, Rema AB, Rijo I, Chaves N, Salazar P, Yun A, Lachhander S, Wang W, Haque MS, Xiao W, Roshal M, Giralt S, Salles G, Rampal R, Stein EM, Perales MA, Horwitz S, Jakubowski A, Ponce D, Markova A, Birsoy O, Mandelker D, Mantha S, Dogan A, Benayed R, Ladanyi M, Berger MF, Brannon AR, Zehir A, Vanderbilt C, Arcila ME. Cell-free DNA from nail clippings as source of normal control for genomic studies in hematologic malignancies. Haematologica 2024. [PMID: 38450530 DOI: 10.3324/haematol.2024.285054] [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] [Received: 01/12/2024] [Indexed: 03/08/2024] Open
Abstract
Comprehensive genomic sequencing is becoming a critical component in the assessment of hematologic malignancies, with broad implications for patient management. In this context, unequivocally discriminating somatic from germline events is challenging but greatly facilitated by matched analysis of tumor:normal pairs. In contrast to solid tumors, conventional sources of normal control (peripheral blood, buccal swabs, saliva) could be highly involved by the neoplastic process, rendering them unsuitable. In this work we describe our real-world experience using cell free DNA (cfDNA) isolated from nail clippings as an alternate source of normal control, through the dedicated review of 2,610 tumor:nail pairs comprehensively sequenced by MSK-IMPACT-heme. Overall, we find nail cfDNA is a robust source of germline control for paired genomic studies. In a subset of patients, nail DNA may have tumor DNA contamination, reflecting unique attributes of the hematologic disease and transplant history. Contamination is generally low level, but significantly more common among patients with myeloid neoplasms (20.5%; 304/1482) compared to lymphoid diseases (5.4%; 61/1128) and particularly enriched in myeloproliferative neoplasms with marked myelofibrosis. When identified in patients with lymphoid and plasma-cell neoplasms, mutations commonly reflected a myeloid profile and correlated with a concurrent/evolving clonal myeloid neoplasm. For nails collected after allogeneic stem-cell transplantation, donor DNA was identified in 22% (11/50). In this cohort, an association with recent history of graft-vs-host disease was identified. These findings should be considered as a potential limitation for the use of nail as normal control but could also provide important diagnostic information regarding the disease process.
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Affiliation(s)
| | - Kseniya Petrova-Drus
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ryan N Ptashkin
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mark D Ewalt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - JinJuan Yao
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ying Liu
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Menglei Zhu
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jamal Benhamida
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Benjamin Durham
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jyoti Kumar
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Khedoudja Nafa
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Iwona Kiecka
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Anita S Bowman
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Erika Gedvilaite
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jacklyn Casanova
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yun-Te Lin
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Abhinita S Mohanty
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Satshil Rana
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Anoop Balakrishnan Rema
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ivelise Rijo
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nelio Chaves
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Paulo Salazar
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Anita Yun
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sean Lachhander
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Wei Wang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mohammad S Haque
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Wenbin Xiao
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mikhail Roshal
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sergio Giralt
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Gilles Salles
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Raajit Rampal
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Eytan M Stein
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Steven Horwitz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ann Jakubowski
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Doris Ponce
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Alina Markova
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ozge Birsoy
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Diana Mandelker
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Simon Mantha
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Dogan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ryma Benayed
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Marc Ladanyi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael F Berger
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - A Rose Brannon
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Zehir
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Chad Vanderbilt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Maria E Arcila
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY.
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Yang SR, Gedvilaite E, Ptashkin R, Chang J, Ziegler J, Mata DA, Villafania LB, Nafa K, Hechtman JF, Benayed R, Zehir A, Benhamida J, Arcila ME, Mandelker D, Rudin CM, Paik PK, Drilon A, Schoenfeld AJ, Ladanyi M. Microsatellite Instability and Mismatch Repair Deficiency Define a Distinct Subset of Lung Cancers Characterized by Smoking Exposure, High Tumor Mutational Burden, and Recurrent Somatic MLH1 Inactivation. J Thorac Oncol 2024; 19:409-424. [PMID: 37838086 PMCID: PMC10939956 DOI: 10.1016/j.jtho.2023.10.004] [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: 08/05/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 10/16/2023]
Abstract
INTRODUCTION Microsatellite instability (MSI) and mismatch repair (MMR) deficiency represent a distinct oncogenic process and predict response to immune checkpoint inhibitors (ICIs). The clinicopathologic features of MSI-high (MSI-H) and MMR deficiency (MMR-D) in lung cancers remain poorly characterized. METHODS MSI status from 5171 patients with NSCLC and 315 patients with SCLC was analyzed from targeted next-generation sequencing data using two validated bioinformatic pipelines. RESULTS MSI-H and MMR-D were identified in 21 patients with NSCLC (0.41%) and six patients with SCLC (1.9%). Notably, all patients with NSCLC had a positive smoking history, including 11 adenocarcinomas. Compared with microsatellite stable cases, MSI-H was associated with exceptionally high tumor mutational burden (37.4 versus 8.5 muts/Mb, p < 0.0001), MMR mutational signatures (43% versus 0%, p < 0.0001), and somatic biallelic alterations in MLH1 (52% versus 0%, p < 0.0001). Loss of MLH1 and PMS2 expression by immunohistochemistry was found in MLH1 altered and wild-type cases. Similarly, the majority of patients with MSI-H SCLC had evidence of MLH1 inactivation, including two with MLH1 promoter hypermethylation. A single patient with NSCLC with a somatic MSH2 mutation had Lynch syndrome as confirmed by the presence of a germline MSH2 mutation. Among patients with advanced MSI-H lung cancers treated with ICIs, durable clinical benefit was observed in three of eight patients with NSCLC and two of two patients with SCLC. In NSCLC, STK11, KEAP1, and JAK1 were mutated in nonresponders but wild type in responders. CONCLUSIONS We present a comprehensive clinicogenomic landscape of MSI-H lung cancers and reveal that MSI-H defines a rare subset of lung cancers associated with smoking, high tumor mutational burden, and MLH1 inactivation. Although durable clinical benefit to ICI was observed in some patients, the broad range of responses suggests that clinical activity may be modulated by co-mutational landscapes.
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Affiliation(s)
- Soo-Ryum Yang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Erika Gedvilaite
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ryan Ptashkin
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jason Chang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - John Ziegler
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Douglas A Mata
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Liliana B Villafania
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Khedoudja Nafa
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jaclyn F Hechtman
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ryma Benayed
- 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
| | - Jamal Benhamida
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maria E Arcila
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Diana Mandelker
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Charles M Rudin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Paul K Paik
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alexander Drilon
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Adam J Schoenfeld
- Department of Medicine, 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
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Zehir A, Nardi V, Konnick EQ, Lockwood CM, Long TA, Sidiropoulos N, Souers RJ, Vasalos P, Lindeman NI, Moncur JT. SPOT/Dx Pilot Reanalysis and College of American Pathologists Proficiency Testing for KRAS and NRAS Demonstrate Excellent Laboratory Performance. Arch Pathol Lab Med 2024; 148:139-148. [PMID: 37776255 DOI: 10.5858/arpa.2023-0322-cp] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/11/2023] [Indexed: 10/02/2023]
Abstract
CONTEXT.— The Sustainable Predictive Oncology Therapeutics and Diagnostics quality assurance pilot study (SPOT/Dx pilot) on molecular oncology next-generation sequencing (NGS) reportedly demonstrated performance limitations of NGS laboratory-developed tests, including discrepancies with a US Food and Drug Administration-approved companion diagnostic. The SPOT/Dx pilot methods differ from those used in proficiency testing (PT) programs. OBJECTIVE.— To reanalyze SPOT/Dx pilot data using PT program methods and compare to PT program data.Also see p. 136. DESIGN.— The College of American Pathologists (CAP) Molecular Oncology Committee reanalyzed SPOT/Dx pilot data applying PT program methods, adjusting for confounding conditions, and compared them to CAP NGS PT program performance (2019-2022). RESULTS.— Overall detection rates of KRAS and NRAS single-nucleotide variants (SNVs) and multinucleotide variants (MNVs) by SPOT/Dx pilot laboratories were 96.8% (716 of 740) and 81.1% (129 of 159), respectively. In CAP PT programs, the overall detection rates for the same SNVs and MNVs were 97.2% (2671 of 2748) and 91.8% (1853 of 2019), respectively. In 2022, the overall detection rate for 5 KRAS and NRAS MNVs in CAP PT programs was 97.3% (1161 of 1193). CONCLUSIONS.— CAP PT program data demonstrate that laboratories consistently have high detection rates for KRAS and NRAS variants. The SPOT/Dx pilot has multiple design and analytic differences with established PT programs. Reanalyzed pilot data that adjust for confounding conditions demonstrate that laboratories proficiently detect SNVs and less successfully detect rare to never-observed MNVs. The SPOT/Dx pilot results are not generalizable to all molecular oncology testing and should not be used to market products or change policy affecting all molecular oncology testing.
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Affiliation(s)
- Ahmet Zehir
- From the Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York (Zehir)
| | - Valentina Nardi
- the Department of Pathology, Massachusetts General Hospital, Mass General Brigham, Harvard Medical School, Boston (Nardi)
| | - Eric Q Konnick
- the Department of Laboratory Medicine and Pathology, University of Washington, Seattle (Konnick, Lockwood)
| | - Christina M Lockwood
- the Department of Laboratory Medicine and Pathology, University of Washington, Seattle (Konnick, Lockwood)
| | - Thomas A Long
- Biostatistics (Long, Souers) Departments, College of American Pathologists, Northfield, Illinois
| | - Nikoletta Sidiropoulos
- Pathology and Laboratory Medicine, University of Vermont Medical Center, Larner College of Medicine at the University of Vermont, Burlington (Sidiropoulos)
| | - Rhona J Souers
- Biostatistics (Long, Souers) Departments, College of American Pathologists, Northfield, Illinois
| | - Patricia Vasalos
- Proficiency Testing (Vasalos) Departments, College of American Pathologists, Northfield, Illinois
| | - Neal I Lindeman
- the Department of Pathology, Weill Cornell Medicine, New York, New York (Lindeman)
| | - Joel T Moncur
- the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Moncur)
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5
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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.
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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
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6
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Vega DM, Yee LM, McShane LM, Williams PM, Chen L, Vilimas T, Fabrizio D, Funari V, Newberg J, Bruce LK, Chen SJ, Baden J, Carl Barrett J, Beer P, Butler M, Cheng JH, Conroy J, Cyanam D, Eyring K, Garcia E, Green G, Gregersen VR, Hellmann MD, Keefer LA, Lasiter L, Lazar AJ, Li MC, MacConaill LE, Meier K, Mellert H, Pabla S, Pallavajjalla A, Pestano G, Salgado R, Samara R, Sokol ES, Stafford P, Budczies J, Stenzinger A, Tom W, Valkenburg KC, Wang XZ, Weigman V, Xie M, Xie Q, Zehir A, Zhao C, Zhao Y, Stewart MD, Allen J. Erratum to "Aligning tumor mutational burden (TMB) quantification across diagnostic platforms: phase II of the Friends of Cancer Research TMB Harmonization Project": [Annals of Oncology 32 (2021) 1626-1636]. Ann Oncol 2024; 35:145. [PMID: 37558578 DOI: 10.1016/j.annonc.2023.07.005] [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] [Indexed: 08/11/2023] Open
Affiliation(s)
- D M Vega
- Friends of Cancer Research, Washington
| | - L M Yee
- National Cancer Institute, Bethesda
| | | | - P M Williams
- Molecular Characterization Laboratory, Frederick National Lab for Cancer Research, Leidos Biomedical Research Inc., Frederick
| | - L Chen
- Molecular Characterization Laboratory, Frederick National Lab for Cancer Research, Leidos Biomedical Research Inc., Frederick
| | - T Vilimas
- Molecular Characterization Laboratory, Frederick National Lab for Cancer Research, Leidos Biomedical Research Inc., Frederick
| | | | - V Funari
- NeoGenomics Laboratories, Aliso Viejo, USA
| | | | - L K Bruce
- NeoGenomics Laboratories, Aliso Viejo, USA
| | | | - J Baden
- Bristol Myers Squibb Co., Princeton
| | | | - P Beer
- European Organisation for Research and Treatment of Cancer, Brussels, Belgium
| | - M Butler
- LGC Clinical Diagnostics, Gaithersburg
| | | | | | - D Cyanam
- Clinical Sequencing Division, Thermo Fisher Scientific, Ann Arbor
| | - K Eyring
- Intermountain Precision Genomics, St. George
| | - E Garcia
- Brigham and Women's Hospital, Boston, USA
| | - G Green
- Bristol Myers Squibb Co., Princeton
| | | | - M D Hellmann
- Memorial Sloan Kettering Cancer Center, New York
| | | | - L Lasiter
- Friends of Cancer Research, Washington
| | - A J Lazar
- The University of Texas MD Anderson Cancer Center, Houston
| | - M-C Li
- National Cancer Institute, Bethesda
| | | | - K Meier
- Illumina Inc, Clinical Genomics, San Diego
| | | | | | | | | | - R Salgado
- European Organisation for Research and Treatment of Cancer, Brussels, Belgium
| | | | | | - P Stafford
- Caris Life Sciences Inc, Phoenix, Arizona, USA
| | - J Budczies
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - A Stenzinger
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - W Tom
- Clinical Sequencing Division, Thermo Fisher Scientific, Ann Arbor
| | | | - X Z Wang
- EMD Serono Research and Development Institute, Inc., Billerica
| | | | - M Xie
- AstraZeneca Pharmaceuticals LP, Waltham, USA
| | - Q Xie
- General Dynamics Information Technology, Inc., Columbia, USA
| | - A Zehir
- Memorial Sloan Kettering Cancer Center, New York
| | - C Zhao
- Illumina Inc, Clinical Genomics, San Diego
| | - Y Zhao
- National Cancer Institute, Bethesda
| | | | - J Allen
- Friends of Cancer Research, Washington
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7
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Wang T, Askan G, Ozcan K, Rana S, Zehir A, Bhanot UK, Yantiss RK, Rao DS, Wahl SJ, Bagci P, Balci S, Balachandran V, Jarnagin WR, Adsay NV, Klimstra DS, Basturk O. Tumoral Intraductal Neoplasms of the Bile Ducts Comprise Morphologically and Genetically Distinct Entities. Arch Pathol Lab Med 2023; 147:1390-1401. [PMID: 36821179 DOI: 10.5858/arpa.2022-0343-oa] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2022] [Indexed: 02/24/2023]
Abstract
CONTEXT.— Tumoral (grossly visible) intraductal neoplasms of the bile ducts are still being characterized. OBJECTIVE.— To investigate their morphologic, immunohistochemical, and molecular features. DESIGN.— Forty-one cases were classified as gastric-, intestinal-, pancreatobiliary-type intraductal papillary neoplasm (IPN), intraductal oncocytic papillary neoplasm (IOPN), or intraductal tubulopapillary neoplasm (ITPN) on the basis of histology. All neoplasms were subjected to targeted next-generation sequencing. RESULTS.— The mean age at diagnosis was 69 years (42-81 years); male to female ratio was 1.3. Most neoplasms (n = 23, 56%) were extrahepatic/large (mean size, 4.6 cm). The majority (n = 32, 78%) contained high-grade dysplasia, and 68% (n = 28) revealed invasion. All gastric-type IPNs (n = 9) and most ITPNs/IOPNs showed consistent colabeling for CK7/MUC6, which was less common among others (P = .004). Intestinal-type IPNs (n = 5) showed higher rates of CK20 expression than others (P < .001). Overall, the most commonly mutated genes included TP53 and APC, while copy number variants affected ELF3 and CDKN2A/B. All gastric-type IPNs contained an alteration affecting the Wnt signaling pathway; 7 of 9 (78%) showed aberrations in the MAPK pathway. Mutations in APC and KRAS were common in gastric-type IPNs as compared with others (P = .01 for both). SMAD4 was more frequently mutated in intestinal-type IPNs (P = .02). Pancreatobiliary-type IPNs (n = 14) exhibited frequent alterations in tumor suppressor genes including TP53, CDKN2A/B, and ARID2 (P = .04, P = .01 and P = .002, respectively). Of 6 IOPNs analyzed, 3 (50%) revealed ATP1B1-PRKACB fusion. ITPNs (n = 6) showed relatively few recurrent genetic aberrations. Follow-up information was available for 38 patients (median, 58.5 months). The ratio of disease-related deaths was higher for the cases with invasion (56% versus 10%). CONCLUSIONS.— Tumoral intraductal neoplasms of the bile ducts, similar to their counterparts in the pancreas, are morphologically and genetically heterogeneous.
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Affiliation(s)
- Tao Wang
- From the Department of Pathology and Laboratory Medicine (Wang, Askan, Ozcan, Rana, Zehir, Bhanot, Rao, Klimstra, Basturk), Memorial Sloan Kettering Cancer Center, New York, New York
| | - Gokce Askan
- From the Department of Pathology and Laboratory Medicine (Wang, Askan, Ozcan, Rana, Zehir, Bhanot, Rao, Klimstra, Basturk), Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kerem Ozcan
- From the Department of Pathology and Laboratory Medicine (Wang, Askan, Ozcan, Rana, Zehir, Bhanot, Rao, Klimstra, Basturk), Memorial Sloan Kettering Cancer Center, New York, New York
| | - Satshil Rana
- From the Department of Pathology and Laboratory Medicine (Wang, Askan, Ozcan, Rana, Zehir, Bhanot, Rao, Klimstra, Basturk), Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ahmet Zehir
- From the Department of Pathology and Laboratory Medicine (Wang, Askan, Ozcan, Rana, Zehir, Bhanot, Rao, Klimstra, Basturk), Memorial Sloan Kettering Cancer Center, New York, New York
| | - Umeshkumar K Bhanot
- From the Department of Pathology and Laboratory Medicine (Wang, Askan, Ozcan, Rana, Zehir, Bhanot, Rao, Klimstra, Basturk), Memorial Sloan Kettering Cancer Center, New York, New York
| | - Rhonda K Yantiss
- Department of Pathology, Weill Cornell Medicine, New York, New York (Yantiss)
| | - Deepthi S Rao
- From the Department of Pathology and Laboratory Medicine (Wang, Askan, Ozcan, Rana, Zehir, Bhanot, Rao, Klimstra, Basturk), Memorial Sloan Kettering Cancer Center, New York, New York
| | - Samuel J Wahl
- Department of Pathology, Lenox Hill Hospital, New York, New York (Wahl)
| | - Pelin Bagci
- Department of Pathology, Marmara University Hospital, Istanbul, Turkey (Bagci)
| | - Serdar Balci
- Department of Pathology, Memorial Healthcare Group, Istanbul, Turkey (Balci)
| | - Vinod Balachandran
- The Department of Surgery (Balachandran, Jarnagin), Memorial Sloan Kettering Cancer Center, New York, New York
| | - William R Jarnagin
- The Department of Surgery (Balachandran, Jarnagin), Memorial Sloan Kettering Cancer Center, New York, New York
| | - N Volkan Adsay
- The Department of Pathology, Koç University Hospital and Koç University Research Center for Translational Medicine (KUTTAM), Istanbul, Turkey (Adsay)
| | - David S Klimstra
- From the Department of Pathology and Laboratory Medicine (Wang, Askan, Ozcan, Rana, Zehir, Bhanot, Rao, Klimstra, Basturk), Memorial Sloan Kettering Cancer Center, New York, New York
| | - Olca Basturk
- From the Department of Pathology and Laboratory Medicine (Wang, Askan, Ozcan, Rana, Zehir, Bhanot, Rao, Klimstra, Basturk), Memorial Sloan Kettering Cancer Center, New York, New York
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8
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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.
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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.
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9
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Franch-Expósito S, Mehine M, Ptashkin RN, Bolton KL, Bandlamudi C, Srinivasan P, Zhang L, Goodell MA, Gedvilaite E, Menghrajani K, Sánchez-Vela P, Mandelker D, Comen E, Norton L, Benayed R, Gao T, Papaemmanuil E, Taylor B, Levine R, Offit K, Stadler Z, Berger MF, Zehir A. Associations Between Cancer Predisposition Mutations and Clonal Hematopoiesis in Patients With Solid Tumors. JCO Precis Oncol 2023; 7:e2300070. [PMID: 37561983 PMCID: PMC10581611 DOI: 10.1200/po.23.00070] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/31/2023] [Accepted: 07/05/2023] [Indexed: 08/12/2023] Open
Abstract
PURPOSE Clonal hematopoiesis (CH), the expansion of clones in the hematopoietic system, has been linked to different internal and external features such as aging, genetic ancestry, smoking, and oncologic treatment. However, the interplay between mutations in known cancer predisposition genes and CH has not been thoroughly examined in patients with solid tumors. METHODS We used prospective tumor-blood paired sequencing data from 46,906 patients who underwent Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT) testing to interrogate the associations between CH and rare pathogenic or likely pathogenic (P/LP) germline variants. RESULTS We observed an enrichment of CH-positive patients among those carrying P/LP germline mutations and identified a significant association between P/LP germline variants in ATM and CH. Germline and CH comutation patterns in ATM, TP53, and CHEK2 suggested biallelic inactivation as a potential mediator of clonal expansion. Moreover, we observed that CH-PPM1D mutations, similar to somatic tumor-associated PPM1D mutations, were depleted in patients with P/LP germline mutations in the DNA damage response (DDR) genes ATM, CHEK2, and TP53. Patients with solid tumors and harboring P/LP germline mutations, CH mutations, and mosaicism chromosomal alterations might be at an increased risk of developing secondary leukemia while germline variants in TP53 were identified as an independent risk factor (hazard ratio, 36; P < .001) for secondary leukemias. CONCLUSION Our results suggest a close relationship between inherited variants and CH mutations within the DDR genes in patients with solid tumors. Associations identified in this study might translate into enhanced clinical surveillance for CH and associated comorbidities in patients with cancer harboring these germline mutations.
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Affiliation(s)
- Sebastià Franch-Expósito
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Miika Mehine
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ryan N. Ptashkin
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- C2i Genomics, New York, NY
| | - Kelly L. Bolton
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Chaitanya Bandlamudi
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Preethi Srinivasan
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Natera Inc, San Carlos, CA
| | - Linda Zhang
- Department of Molecular and Cellular Biology, Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX
| | - Margaret A. Goodell
- Department of Molecular and Cellular Biology, Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX
| | - Erika Gedvilaite
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kamal Menghrajani
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Pablo Sánchez-Vela
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Diana Mandelker
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Elizabeth Comen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Larry Norton
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ryma Benayed
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Precision Medicine and Biosamples, AstraZeneca, New York, NY
| | - Teng Gao
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | - Elli Papaemmanuil
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Barry Taylor
- 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 Cancer Center, New York, NY
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ross Levine
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Zsofia Stadler
- 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 and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Zehir
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Precision Medicine and Biosamples, AstraZeneca, New York, NY
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10
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Hagemann IS, Zehir A, Suarez CJ, Furtado LV, Halley J, Kane M, Mot N, Vasalos P, Moncur JT, Konnick EQ. In silico approaches to proficiency testing: Considerations for continued feasibility. J Mol Diagn 2023:S1525-1578(23)00079-X. [PMID: 37088136 DOI: 10.1016/j.jmoldx.2023.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/30/2023] [Accepted: 04/10/2023] [Indexed: 04/25/2023] Open
Affiliation(s)
- Ian S Hagemann
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Carlos J Suarez
- Department of Pathology, Stanford University, Stanford, California
| | - Larissa V Furtado
- Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jaimie Halley
- Proficiency Testing, College of American Pathologists, Northfield, Illinois
| | - Megan Kane
- Proficiency Testing, College of American Pathologists, Northfield, Illinois
| | - Nicole Mot
- Proficiency Testing, College of American Pathologists, Northfield, Illinois
| | - Patricia Vasalos
- Proficiency Testing, College of American Pathologists, Northfield, Illinois
| | - Joel T Moncur
- Office of the Director, Joint Pathology Center, Silver Spring, MD
| | - Eric Q Konnick
- Department of Laboratory Medicine, University of Washington, Seattle, Washington.
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11
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Tao J, Vela PS, Safonov A, Ferraro E, Exposito SF, Menghrajani K, Ptashkin R, Comen E, Braunstein LZ, Robson ME, Chandarlapaty S, Reis-Filho J, Berger M, Zehir A, Norton L, Levine R, Razavi P. Abstract P4-02-18: Impact of clonal hematopoiesis on disease progression following CDK4/6 inhibitor therapy. Cancer Res 2023. [DOI: 10.1158/1538-7445.sabcs22-p4-02-18] [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: 03/06/2023]
Abstract
Abstract
Background Clonal Hematopoiesis (CH) is a well-established risk factor for adverse clinical outcomes including all-cause mortality, cardiovascular disease, and progression to hematologic malignancies. The presence of CH has been shown to adversely impact overall survival in non-hematologic cancers, however whether CH modulates response to specific therapies in breast cancer is not known. Here we investigate the impact of CH mutations on disease progression in patients with metastatic estrogen receptor (ER) positive breast cancer undergoing treatment with first line CDK4/6 inhibitors and endocrine therapy (CDK4/6i+ET). Methods We analyzed data from a well annotated cohort of patients with ER+ breast cancer who received endocrine therapy and CDK4/6 inhibitors. All patients underwent prospective tumor and matched WBC sequencing utilizing the MSK-IMPACT assay. CH variants were detected in blood samples utilizing the well-validated variant detection and filtration pipeline of MSK-IMPACT. CH mutations were defined as putative drivers (CH-PD) or non-putative drivers (CH) as previously described. To ensure the presence of CH at the time of therapy initiation, only patients who had CH sampling performed from 6 months before through 4 months after initiation of CDK4/6i+ET were included. We compared progression free survival (PFS) in patients with and without CH, as well as by CH-PD status and DNMT3A CH mutations. We investigated clinical covariates including type of endocrine therapy, receipt of prior neoadjuvant or adjuvant chemotherapy, and age at start of CDK4/6i+ET. Results The final cohort was comprised of 378 patients, of whom 135 (35.7%) had CH. The median time between sample collection and CDK4/6i+ET initiation was 0 (IQR -0.79 to 0.47 months). Patients with CH were older at time of therapy initiation (median 63.0 versus 54.7 years, p < 0.001). There were no significant differences between groups in terms of endocrine therapy (aromatase inhibitor or fulvestrant), prior chemotherapy, and time from CH sample collection to CDK4/6i+ET start. Univariate Cox-proportional hazard analysis did not reveal a difference between progression free survival and overall CH (HR 0.96, 95% CI 0.75 – 1.23, p = 0.76), CH-PD (HR 1.05, 0.77 – 1.43, p = 0.77), or DNMT3A mutations (HR 1.12, 0.80 – 1.60, p = 0.52) compared to patients without CH. Interestingly, age less than 60 years was found to be associated with PFS outcome (univariate HR 1.57, 1.22 – 2.01, p = 0.0004). Multivariate analysis adjusted for endocrine therapy partner and age at CDK4/6i+ET therapy did not reveal an association between outcome and overall CH (HR 1.07, 0.83 – 1.39, p = 0.59). In patients younger than age 60, presence of overall CH did not confer a significant PFS difference (HR 0.90, 0.63 – 1.29, p = 0.57). In the subset of patients older than 60 (n = 168) presence of CH conferred numerically, but not statistically, significant shorter PFS (HR 1.41 [0.96 – 2.09], p = 0.08). In this population, CH-PD conferred a shorter PFS (HR 1.75, 1.12 – 2.72, p = 0.02). Conclusion We found that CH, CH-PD and DNMT3A CH mutations did not affect PFS among metastatic ER+ breast cancer patients treated with first line CDK4/6 inhibitors. Younger age was associated with increased risk of progression, warranting further investigation. In the subset of patients with age older than 60, CH-PD conferred a shorter PFS. Further data, incorporating records of dose reductions, will be presented at the meeting.
Citation Format: Jacqueline Tao, Pablo Sanchez Vela, Anton Safonov, Emanuela Ferraro, Sebastia Franch Exposito, Kamal Menghrajani, Ryan Ptashkin, Elizabeth Comen, Lior Z. Braunstein, Mark E. Robson, Sarat Chandarlapaty, Jorge Reis-Filho, Michael Berger, Ahmet Zehir, Larry Norton, Ross Levine, Pedram Razavi. Impact of clonal hematopoiesis on disease progression following CDK4/6 inhibitor therapy [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P4-02-18.
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Affiliation(s)
| | | | | | | | | | | | - Ryan Ptashkin
- 7Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | | | | | | | | | | | - Michael Berger
- 13Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ahmet Zehir
- 14Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | | | - Ross Levine
- 16Memorial Sloan Kettering Cancer Center, New York, New York, USA
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12
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Marinoff AE, Spurr LF, Fong C, Li YY, Forrest SJ, Ward A, Doan D, Corson L, Mauguen A, Pinto N, Maese L, Colace S, Macy ME, Kim A, Sabnis AJ, Applebaum MA, Laetsch TW, Glade-Bender J, Weiser DA, Anderson M, Crompton BD, Meyers P, Zehir A, MacConaill L, Lindeman N, Nowak JA, Ladanyi M, Church AJ, Cherniack AD, Shukla N, Janeway KA. Clinical Targeted Next-Generation Panel Sequencing Reveals MYC Amplification Is a Poor Prognostic Factor in Osteosarcoma. JCO Precis Oncol 2023; 7:e2200334. [PMID: 36996377 PMCID: PMC10531050 DOI: 10.1200/po.22.00334] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 10/11/2022] [Accepted: 01/09/2023] [Indexed: 04/01/2023] Open
Abstract
PURPOSE Osteosarcoma risk stratification, on the basis of the presence of metastatic disease at diagnosis and histologic response to chemotherapy, has remained unchanged for four decades, does not include genomic features, and has not facilitated treatment advances. We report on the genomic features of advanced osteosarcoma and provide evidence that genomic alterations can be used for risk stratification. MATERIALS AND METHODS In a primary analytic patient cohort, 113 tumor and 69 normal samples from 92 patients with high-grade osteosarcoma were sequenced with OncoPanel, a targeted next-generation sequencing assay. In this primary cohort, we assessed the genomic landscape of advanced disease and evaluated the correlation between recurrent genomic events and outcome. We assessed whether prognostic associations identified in the primary cohort were maintained in a validation cohort of 86 patients with localized osteosarcoma tested with MSK-IMPACT. RESULTS In the primary cohort, 3-year overall survival (OS) was 65%. Metastatic disease, present in 33% of patients at diagnosis, was associated with poor OS (P = .04). The most frequently altered genes in the primary cohort were TP53, RB1, MYC, CCNE1, CCND3, CDKN2A/B, and ATRX. Mutational signature 3 was present in 28% of samples. MYC amplification was associated with a worse 3-year OS in both the primary cohort (P = .015) and the validation cohort (P = .012). CONCLUSION The most frequently occurring genomic events in advanced osteosarcoma were similar to those described in prior reports. MYC amplification, detected with clinical targeted next-generation sequencing panel tests, is associated with poorer outcomes in two independent cohorts.
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Affiliation(s)
- Amanda E. Marinoff
- Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA
- Harvard Medical School, Boston, MA
- Pediatric Hematology/Oncology, UCSF Benioff Children's Hospital, San Francisco, CA
| | - Liam F. Spurr
- Broad Institute of Harvard and MIT, Boston, MA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Pritzker School of Medicine, Biological Sciences Division, The University of Chicago, Chicago, IL
| | - Christina Fong
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yvonne Y. Li
- Harvard Medical School, Boston, MA
- Broad Institute of Harvard and MIT, Boston, MA
| | - Suzanne J. Forrest
- Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA
- Harvard Medical School, Boston, MA
| | - Abigail Ward
- Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA
| | - Duong Doan
- Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA
| | - Laura Corson
- Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA
| | - Audrey Mauguen
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Navin Pinto
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Washington, Seattle, WA
| | - Luke Maese
- University of Utah, Huntsman Cancer Institute, and Primary Children's Hospital, Salt Lake City, UT
| | - Susan Colace
- Pediatric Hematology/Oncology/Blood and Marrow Transplant, Nationwide Children's Hospital, Columbus, OH
| | - Margaret E. Macy
- Department of Pediatric Hematology/Oncology, University of Colorado and The Center for Cancer and Blood Disorders, Colorado Children's Hospital, Denver, CO
| | - AeRang Kim
- Center for Cancer and Blood Disorders, Children's National Medical Center, Washington, DC
| | - Amit J. Sabnis
- Pediatric Hematology/Oncology, UCSF Benioff Children's Hospital, San Francisco, CA
| | | | - Theodore W. Laetsch
- Division of Oncology, Department of Pediatrics, Children’s Hospital of Philadelphia and University of Pennsylvania, Philadelphia, PA
| | - Julia Glade-Bender
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Daniel A. Weiser
- Department of Pediatric Hematology/Oncology, Children's Hospital at Montefiore, New York, NY
| | - Megan Anderson
- Harvard Medical School, Boston, MA
- Department of Orthopedic Surgery, Boston Children's Hospital, Boston, MA
| | - Brian D. Crompton
- Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA
- Harvard Medical School, Boston, MA
| | - Paul Meyers
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Zehir
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Laura MacConaill
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Neal Lindeman
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Jonathan A. Nowak
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Alanna J. Church
- Harvard Medical School, Boston, MA
- Department of Pathology, Boston Children's Hospital, Boston, MA
| | - Andrew D. Cherniack
- Harvard Medical School, Boston, MA
- Broad Institute of Harvard and MIT, Boston, MA
| | - Neerav Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Katherine A. Janeway
- Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA
- Harvard Medical School, Boston, MA
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13
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Diplas BH, Ptashkin R, Chou JF, Sabwa S, Foote MB, Rousseau B, Argilés G, White JR, Stewart CM, Bolton K, Chalasani SB, Desai AM, Goldberg Z, Gu P, Li J, Shcherba M, Zervoudakis A, Cercek A, Yaeger R, Segal NH, Ilson DH, Ku GY, Zehir A, Capanu M, Janjigian YY, Diaz LA, Maron SB. Clinical Importance of Clonal Hematopoiesis in Metastatic Gastrointestinal Tract Cancers. JAMA Netw Open 2023; 6:e2254221. [PMID: 36729457 PMCID: PMC9896303 DOI: 10.1001/jamanetworkopen.2022.54221] [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] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 12/12/2022] [Indexed: 02/03/2023] Open
Abstract
Importance Clonal hematopoiesis (CH) has been associated with development of atherosclerosis and leukemia and worse survival among patients with cancer; however, the association with cancer therapy efficacy, in particular immune checkpoint blockade (ICB), and toxicity has not yet been established. Given the widespread use of ICB and the critical role hematopoietic stem cell-derived lymphocytes play in mediating antitumor responses, CH may be associated with therapeutic efficacy and hematologic toxicity. Objective To determine the association between CH and outcomes, hematologic toxicity, and therapeutic efficacy in patients with metastatic gastrointestinal tract cancers being treated with systemic therapy, both in the first-line metastatic treatment setting and in ICB. Design, Setting, and Participants This retrospective cohort study included 633 patients with stage IV colorectal (CRC) and esophagogastric (EGC) cancer who were treated with first-line chemotherapy and/or ICB at Memorial Sloan Kettering Cancer Center. Patients underwent matched tumor and peripheral blood DNA sequencing using the Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets next-generation sequencing assay between January 1, 2006, and December 31, 2020. Exposures Clonal hematopoiesis-related genetic alterations were identified by next-generation sequencing of patients' tumor and normal blood buffy coat samples, with a subset of these CH alterations annotated as likely putative drivers (CH-PD) based upon previously established criteria. Main Outcomes and Measures Patients with CH and CH-PD in peripheral blood samples were identified, and these findings were correlated with survival outcomes (progression-free survival [PFS] and overall survival [OS]) during first-line chemotherapy and ICB, as well as baseline white blood cell levels and the need for granulocyte colony-stimulating factor (G-CSF) support. Results Among the 633 patients included in the study (390 men [61.6%]; median age, 58 [IQR, 48-66] years), the median age was 52 (IQR, 45-63) years in the CRC group and 61 (IQR, 53-69) years in the EGC group. In the CRC group, 161 of 301 patients (53.5%) were men, compared with 229 of 332 patients (69.0%) in the EGC group. Overall, 62 patients (9.8%) were Asian, 45 (7.1%) were Black or African American, 482 (76.1%) were White, and 44 (7.0%) were of unknown race or ethnicity. Presence of CH was identified in 115 patients with EGC (34.6%) and 83 with CRC (27.6%), with approximately half of these patients harboring CH-PD (CRC group, 44 of 83 [53.0%]; EGC group, 55 of 115 [47.8%]). Patients with EGC and CH-PD exhibited a significantly worse median OS of 16.0 (95% CI, 11.6-22.3) months compared with 21.6 (95% CI, 19.6-24.3) months for those without CH-PD (P = .01). For patients with CRC and EGC, CH and CH-PD were not associated with PFS differences in patients undergoing ICB or first-line chemotherapy. Neither CH nor CH-PD were correlated with baseline leukocyte levels or increased need for G-CSF support. Conclusions and Relevance These findings suggest CH and CH-PD are not directly associated with the treatment course of patients with metastatic gastrointestinal tract cancer receiving cancer-directed therapy.
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Affiliation(s)
- Bill H. Diplas
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ryan Ptashkin
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Joanne F. Chou
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Shalom Sabwa
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael B. Foote
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Benoit Rousseau
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Guillem Argilés
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Caitlin M. Stewart
- Meyer Cancer Center, Weill Cornell Medicine, New York, New York
- New York Genome Center, New York, New York
| | - Kelly Bolton
- Department of Medicine, Washington University Medical School, St Louis, Missouri
| | - Sree B. Chalasani
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Avni M. Desai
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Zoe Goldberg
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ping Gu
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jia Li
- 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
| | - Alice Zervoudakis
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Andrea Cercek
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Rona Yaeger
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Neil H. Segal
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David H. Ilson
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Geoffrey Y. Ku
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marinela Capanu
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yelena Y. Janjigian
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Luis A. Diaz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Steven B. Maron
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
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14
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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.
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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
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15
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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.
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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
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16
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Liu YL, Maio A, Kemel Y, Salo-Mullen EE, Sheehan M, Tejada PR, Trottier M, Arnold AG, Fleischut MH, Latham A, Carlo MI, Murciano-Goroff YR, Walsh MF, Mandelker D, Mehta N, Bandlamudi C, Arora K, Zehir A, Berger MF, Solit DB, Aghajanian C, Diaz LA, Robson ME, Brown CL, Offit K, Hamilton JG, Stadler ZK. Disparities in cancer genetics care by race/ethnicity among pan-cancer patients with pathogenic germline variants. Cancer 2022; 128:3870-3879. [PMID: 36041233 PMCID: PMC10335605 DOI: 10.1002/cncr.34434] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 04/12/2022] [Revised: 06/27/2022] [Accepted: 06/30/2022] [Indexed: 11/09/2022]
Abstract
BACKGROUND Germline risk assessment is increasing as part of cancer care; however, disparities in subsequent genetic counseling are unknown. METHODS Pan-cancer patients were prospectively consented to tumor-normal sequencing via custom next generation sequencing panel (Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets) inclusive of germline analysis of ≥76 genes from January 2015 through December 2019 (97.5% research nonbillable) with protocol for genetics referral. Rates of pathogenic/likely pathogenic germline variants (PVs) and downstream counseling were compared across ancestry groups (mutually exclusive groups based on self-reported race/ethnicity and Ashkenazi Jewish [AJ] heritage) using nonparametric tests and multivariable logistic regression models. RESULTS Among 15,775 patients (59.6%, non-Hispanic [NH]-White; 15.7%, AJ; 20.5%, non-White [6.9%, Asian; 6.8%, Black/African American (AA); 6.7%, Hispanic; 0.1%, Other], and 4.2%, unknown), 2663 (17%) had a PV. Non-White patients had a lower PV rate (n = 433, 13.4%) compared to NH-Whites (n = 1451, 15.4%) and AJ patients (n = 683, 27.6%), p < .01, with differences in mostly moderate and low/recessive/uncertain penetrance variants. Among 2239 patients with new PV, 1652 (73.8%) completed recommended genetic counseling. Non-White patients had lower rates of genetic counseling (67.7%) than NH-White (73.7%) and AJ patients (78.8%), p < .01, with lower rates occurring in Black/AA (63%) compared to NH-White patients, even after adjustment for confounders (odds ratio, 0.60; 95% confidence interval, 0.37-0.97; p = .036). Non-White, particularly Black/AA and Asian, probands had a trend toward lower rates and numbers of at-risk family members being seen for counseling/genetic testing. CONCLUSIONS Despite minimizing barriers to genetic testing, non-White patients were less likely to receive recommended cancer genetics follow-up, with potential implications for oncologic care, cancer risk reduction, and at-risk family members. LAY SUMMARY Genetic testing is becoming an important part of cancer care, and we wanted to see if genetics care was different between individuals of different backgrounds. We studied 15,775 diverse patients with cancer who had genetic testing using a test called MSK-IMPACT that was covered by research funding. Clinically important genetic findings were high in all groups. However, Black patients were less likely to get recommended counseling compared to White patients. Even after removing many roadblocks, non-White and especially Black patients were less likely to get recommended genetics care, which may affect their cancer treatments and families.
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Affiliation(s)
- Ying L Liu
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Anna Maio
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Yelena Kemel
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Erin E Salo-Mullen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Margaret Sheehan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Prince Ray Tejada
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Magan Trottier
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Angela G Arnold
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | | | - Alicia Latham
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Maria I Carlo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Yonina R Murciano-Goroff
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Michael F Walsh
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Diana Mandelker
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Nikita Mehta
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Chaitanya Bandlamudi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Kanika Arora
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ahmet Zehir
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- AstraZeneca, New York, New York, USA
| | - Michael F Berger
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - David B Solit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Carol Aghajanian
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Luis A Diaz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Mark E Robson
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Carol L Brown
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Obstetrics and Gynecology, Weill Cornell Medical College, New York, New York, USA
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
| | - Jada G Hamilton
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Psychiatry and Behavioral Sciences, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Psychiatry, Weill Cornell Medical College, New York, New York, USA
| | - Zsofia K Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Medicine, Weill Cornell Medical College, New York, New York, USA
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17
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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.
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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.
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18
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Nacev BA, Sanchez-Vega F, Smith S, Antonescu C, Rosenbaum E, Shi H, Tang C, Socci N, Rana S, Gularte-Merida R, Zehir A, Gounder M, Bowler T, Luthra A, Jadeja B, Okada A, Strong J, Stoller J, Chan J, Chi P, D'Angelo S, Dickson M, Kelly C, Keohan ML, Movva S, Thornton K, Meyers P, Wexler L, Slotkin E, Bender JG, Shukla N, Hensley M, Healey J, La Quaglia M, Alektiar K, Crago A, Yoon S, Untch B, Chiang S, Agaram N, Hameed M, Berger M, Solit D, Schultz N, Ladanyi M, Singer S, Tap W. Abstract PR012: Targeted sequencing of 2,138 bone and soft tissue sarcomas reveals commonly altered pathways, subtype-independent genetic clusters, and potential therapeutic targets. Clin Cancer Res 2022. [DOI: 10.1158/1557-3265.sarcomas22-pr012] [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
A hallmark of sarcomas is genetic, biologic, and clinical heterogeneity, which is a challenge for preclinical development of therapeutic targets, clinical trial design, and patient care. Because sarcomas comprise over 100 subtypes, a broad comparative genetic analysis of subtypes has been lacking and sarcoma genetic studies have by necessity focused on one or a few subtypes. We will report the results of a comprehensive analysis of somatic genetic alterations detected by a targeted sequencing platform in a single institution cohort of 2,138 patient-specific samples of soft tissue and bone sarcoma representing 45 distinct pathological entities. We determined subtype-specific mutation and copy number (arm and gene level) events with a focus on pathways in which there are therapeutic targets under clinical or preclinical investigation. The most commonly altered pathways are cell cycle control, TP53, PI3K, receptor tyrosine kinase/RAS, and epigenetic regulators (e.g. >40% of uterine leiomyosarcoma [n=165], undifferentiated pleomorphic sarcoma [UPS, n=145] and pleomorphic liposarcoma [n=22]). Subtype-specific associations in rare subtypes include TERT amplification in 41% of intimal sarcoma (n=18) and alterations in chromatin remodeling and histone modifying complexes in uterine adenosarcoma (43% and 36%, respectively; n=14). Epigenetic pathway alterations in common sarcomas were also noted, including an increased frequency of oncogenic alterations in epigenetic regulators in dedifferentiated liposarcoma (DDLS; n=167) (25%) vs. well differentiated liposarcoma (8%; n=48). We evaluated rates of whole genome doubling (WGD), which in subtypes such as UPS and osteosarcoma (n=129) were >45%, which is more frequent than many carcinomas. WGD associated with worse overall survival in metastatic (p=0.042) but not primary samples (p=0.391). Among specific subtypes, WGD was associated with worse overall survival in metastatic UPS (p=0.022). Unsupervised clustering of samples based on genetic features revealed that in some cases sarcomas are more similar to individual tumors of distinct histology than to other sarcomas of the same subtype. For example, UPS and soft tissue leiomyosarcoma (n=125) segregated into multiple genetic clusters (high entropy) compared to others with low entropy (DDLS), which could have implications for future clinical trial interpretation and/or design. We also determined the subtype-specific rate of tumor mutation burden, which was overall low compared to many carcinomas, but notably varied between and within subtypes, with some having a long tail in the upper range of the distribution. Lastly, we assessed targetable alterations on a subtype-specific basis. Together with other ‘multiomic’ approaches, we anticipate this work will motivate preclinical studies of subtype-specific sarcoma biology and potential therapeutic targets and will inform efforts to interpret outcomes in sarcoma clinical trials with respect to underlying genetic subtypes.
Citation Format: Benjamin A. Nacev, Francisco Sanchez-Vega, Shaleigh Smith, Cristina Antonescu, Evan Rosenbaum, Hongyu Shi, Cerise Tang, Nicholas Socci, Satshil Rana, Rodrigo Gularte-Merida, Ahmet Zehir, Mrinal Gounder, Timothy Bowler, Anisha Luthra, Bhumika Jadeja, Azusa Okada, Jonathan Strong, Jake Stoller, Jason Chan, Ping Chi, Sandra D'Angelo, Mark Dickson, Ciara Kelly, Mary Louise Keohan, Sujana Movva, Katherine Thornton, Paul Meyers, Leonard Wexler, Emily Slotkin, Julia Glade Bender, Neerav Shukla, Martee Hensley, John Healey, Michael La Quaglia, Kaled Alektiar, Aimee Crago, Sam Yoon, Brian Untch, Sarah Chiang, Narasimhan Agaram, Meera Hameed, Michael Berger, David Solit, Nikolaus Schultz, Marc Ladanyi, Samuel Singer, William Tap. Targeted sequencing of 2,138 bone and soft tissue sarcomas reveals commonly altered pathways, subtype-independent genetic clusters, and potential therapeutic targets [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr PR012.
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Affiliation(s)
| | | | | | | | | | - Hongyu Shi
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Cerise Tang
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Satshil Rana
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Ahmet Zehir
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Anisha Luthra
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Azusa Okada
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Jake Stoller
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jason Chan
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ping Chi
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Mark Dickson
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ciara Kelly
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Sujana Movva
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Paul Meyers
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Emily Slotkin
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Neerav Shukla
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - John Healey
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Aimee Crago
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sam Yoon
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Brian Untch
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sarah Chiang
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Meera Hameed
- 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
| | - Samuel Singer
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - William Tap
- 1Memorial Sloan Kettering Cancer Center, New York, NY
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19
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Elkrief A, Ogura K, Bowman AS, Koche RP, Benayed R, Mauguen A, Mattar MS, Khodos I, de Stanchina E, Meyers PA, Healey JH, Tap WD, Shukla N, Hameed M, Zehir A, Sawyers C, Bose R, Slotkin E, Ladanyi M. Abstract B023: Prospective clinical genomic profiling of ewing sarcoma: ERF and FGFR1 mutations as recurrent secondary alterations of potential biological and therapeutic relevance. Clin Cancer Res 2022. [DOI: 10.1158/1557-3265.sarcomas22-b023] [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
Background: Ewing Sarcoma (ES) is a primitive sarcoma defined by EWSR1–ETS fusions as the primary driver alteration. To expand our understanding of the genetic and molecular characterization of ES, we conducted a comprehensive analysis of clinical genomic profiling data on tumors from 113 patients using the MSK-IMPACT platform (Integrated Mutation Profiling of Actionable Cancer Targets). Methods: The dataset consisted of ES patients prospectively tested with the FDA-cleared MSK-IMPACT large panel, hybrid capture-based NGS assay. To assess the functional significance of ERF loss, we generated ES cell lines with increased expression of ERF as well as lines with knockdown of ERF. We assessed cell viability, clonogenic growth, and motility and performed transcriptomic and epigenetic analyses. Finally, we validated our findings in vivo using cell line xenografts. Results: Unlike previous ES genomic cohorts, ours included more adult patients (>18 years of age) and more patients with advanced stage at presentation. TP53, STAG2, and CDKN2A were the most common alterations and were associated with worse overall survival at 5-years. Notably, 3% had activating FGFR1 alterations (1 amplification and 2 hotspot activating kinase domain mutations). Mining data generated using a targeted RNAseq assay that includes FGFR1 based on the Archer Anchored Multiplex PCR technology, FGFR1 was highly expressed in the ES cohort (N=42). The 2 patients with activating FGFR1 mutations had relatively high expression of FGFR1. The second novel subset of patients in our cohort were defined by recurrent secondary alterations in ERF, which encodes an ETS domain transcriptional repressor, in 7% of patients (5 truncating mutations, 1 deep deletion, 2 missense mutations). ERF alterations were non-overlapping with STAG2 alterations, suggesting a potentially important biologic role in ES. As the functional significance of FGFR1 mutation in ES has been previously studied, we focused our functional studies on the role of ERF status in ES. In vitro, increased expression of ERF decreased tumor cell growth, colony formation, and motility in two ES cell lines, while ERF loss induced cellular proliferation and clonogenic growth. Transcriptomic analysis of cell lines with ERF loss revealed increased expression of genes and pathways associated with aggressive tumor biology, and epigenetic, chromatin-based studies revealed that ERF competes with EWSR1-FLI1 at ETS binding sites. Conclusion: Our study reveals a previously unexplored role of ERF loss-of-function in ES. Older age in our cohort, and a higher proportion of patients with advanced disease at presentation, could potentially explain the finding of ERF alterations which were associated with aggressive tumor biology in our preclinical studies. Our functional analyses of how ERF modulates EWSR1-FLI1 oncogenicity may open a new window into the pathobiology of ES. Moreover, our data suggest that 3% of ES patients harbor activating FGFR1 mutations, the first targetable kinase alteration in this sarcoma.
Citation Format: Arielle Elkrief, Koichi Ogura, Anita S. Bowman, Richard P. Koche, Ryma Benayed, Audrey Mauguen, Marissa S. Mattar, Inna Khodos, Elisa de Stanchina, Paul A. Meyers, John H. Healey, William D. Tap, Neerav Shukla, Meera Hameed, Ahmet Zehir, Charles Sawyers, Rohit Bose, Emily Slotkin, Marc Ladanyi. Prospective clinical genomic profiling of ewing sarcoma: ERF and FGFR1 mutations as recurrent secondary alterations of potential biological and therapeutic relevance [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr B023.
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Affiliation(s)
| | - Koichi Ogura
- 1Memorial Sloan Kettering Cancer Center, New York, NY,
| | | | | | - Ryma Benayed
- 1Memorial Sloan Kettering Cancer Center, New York, NY,
| | | | | | - Inna Khodos
- 1Memorial Sloan Kettering Cancer Center, New York, NY,
| | | | | | | | | | - Neerav Shukla
- 1Memorial Sloan Kettering Cancer Center, New York, NY,
| | - Meera Hameed
- 1Memorial Sloan Kettering Cancer Center, New York, NY,
| | - Ahmet Zehir
- 1Memorial Sloan Kettering Cancer Center, New York, NY,
| | | | - Rohit Bose
- 2University of California, San Francisco (UCSF), San Francisco, CA
| | - Emily Slotkin
- 1Memorial Sloan Kettering Cancer Center, New York, NY,
| | - Marc Ladanyi
- 1Memorial Sloan Kettering Cancer Center, New York, NY,
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20
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Ceyhan-Birsoy O, Jayakumaran G, Kemel Y, Misyura M, Aypar U, Jairam S, Yang C, Li Y, Mehta N, Maio A, Arnold A, Salo-Mullen E, Sheehan M, Syed A, Walsh M, Carlo M, Robson M, Offit K, Ladanyi M, Reis-Filho JS, Stadler ZK, Zhang L, Latham A, Zehir A, Mandelker D. Diagnostic yield and clinical relevance of expanded genetic testing for cancer patients. Genome Med 2022; 14:92. [PMID: 35971132 PMCID: PMC9377129 DOI: 10.1186/s13073-022-01101-2] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 08/03/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genetic testing (GT) for hereditary cancer predisposition is traditionally performed on selected genes based on established guidelines for each cancer type. Recently, expanded GT (eGT) using large hereditary cancer gene panels uncovered hereditary predisposition in a greater proportion of patients than previously anticipated. We sought to define the diagnostic yield of eGT and its clinical relevance in a broad cancer patient population over a 5-year period. METHODS A total of 17,523 cancer patients with a broad range of solid tumors, who received eGT at Memorial Sloan Kettering Cancer Center between July 2015 to April 2020, were included in the study. The patients were unselected for current GT criteria such as cancer type, age of onset, and/or family history of disease. The diagnostic yield of eGT was determined for each cancer type. For 9187 patients with five common cancer types frequently interrogated for hereditary predisposition (breast, colorectal, ovarian, pancreatic, and prostate cancer), the rate of pathogenic/likely pathogenic (P/LP) variants in genes that have been associated with each cancer type was analyzed. The clinical implications of additional findings in genes not known to be associated with a patients' cancer type were investigated. RESULTS 16.7% of patients in a broad cancer cohort had P/LP variants in hereditary cancer predisposition genes identified by eGT. The diagnostic yield of eGT in patients with breast, colorectal, ovarian, pancreatic, and prostate cancer was 17.5%, 15.3%, 24.2%, 19.4%, and 15.9%, respectively. Additionally, 8% of the patients with five common cancers had P/LP variants in genes not known to be associated with the patient's current cancer type, with 0.8% of them having such a variant that confers a high risk for another cancer type. Analysis of clinical and family histories revealed that 74% of patients with variants in genes not associated with their current cancer type but which conferred a high risk for another cancer did not meet the current GT criteria for the genes harboring these variants. One or more variants of uncertain significance were identified in 57% of the patients. CONCLUSIONS Compared to targeted testing approaches, eGT can increase the yield of detection of hereditary cancer predisposition in patients with a range of tumors, allowing opportunities for enhanced surveillance and intervention. The benefits of performing eGT should be weighed against the added number of VUSs identified with this approach.
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Affiliation(s)
- Ozge Ceyhan-Birsoy
- 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
| | - Yelena Kemel
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maksym Misyura
- 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
| | - Sowmya Jairam
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ciyu Yang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yirong Li
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nikita Mehta
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anna Maio
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Angela Arnold
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Erin Salo-Mullen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Margaret Sheehan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Aijazuddin Syed
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael Walsh
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria Carlo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mark Robson
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kenneth Offit
- 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
| | - Jorge S Reis-Filho
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zsofia K Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Liying Zhang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Present Address: Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Alicia Latham
- Department of Medicine, 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.
- Present Address: Precision Medicine and Biosamples, Oncology R&D, AstraZeneca, New York, NY, USA.
| | - Diana Mandelker
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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21
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Ogura K, Elkrief A, Bowman AS, Koche RP, de Stanchina E, Benayed R, Mauguen A, Mattar MS, Khodos I, Meyers PA, Healey JH, Tap WD, Hameed M, Zehir A, Shukla N, Sawyers C, Bose R, Slotkin E, Ladanyi M. Prospective Clinical Genomic Profiling of Ewing Sarcoma: ERF and FGFR1 Mutations as Recurrent Secondary Alterations of Potential Biologic and Therapeutic Relevance. JCO Precis Oncol 2022; 6:e2200048. [PMID: 35952322 PMCID: PMC9384944 DOI: 10.1200/po.22.00048] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ewing sarcoma (ES) is a primitive sarcoma defined by EWSR1-ETS fusions as the primary driver alteration. To better define the landscape of cooperating secondary genetic alterations in ES, we analyzed clinical genomic profiling data of 113 patients with ES, a cohort including more adult patients (> 18 years) and more patients with advanced stage at presentation than previous genomic cohorts.
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Affiliation(s)
- Koichi Ogura
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Arielle Elkrief
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Anita S Bowman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Richard P Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Elisa de Stanchina
- Anti-tumor Assessment Core Facility, Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY.,AstraZeneca Pharmaceuticals, Wilmington, DE
| | - Audrey Mauguen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Marissa S Mattar
- Anti-tumor Assessment Core Facility, Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Inna Khodos
- Anti-tumor Assessment Core Facility, Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Paul A Meyers
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - John H Healey
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Surgery, Orthopaedic Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | - William D Tap
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Meera Hameed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY.,AstraZeneca Pharmaceuticals, Wilmington, DE
| | - Neerav Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Charles Sawyers
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY.,HHMI, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Rohit Bose
- Department of Anatomy, University of California, San Francisco, San Francisco, CA.,Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA.,Department of Urology, University of California, San Francisco, San Francisco, CA.,Benioff Initiative for Prostate Cancer Research, Helen Diller Family Comprehensive Cancer Center, San Francisco, CA
| | - Emily Slotkin
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
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22
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Mukherjee S, Bandlamudi C, Hellmann MD, Kemel Y, Drill E, Rizvi H, Tkachuk K, Khurram A, Walsh MF, Zauderer MG, Mandelker D, Topka S, Zehir A, Srinivasan P, Selvan ME, Carlo MI, Cadoo KA, Latham A, Hamilton JG, Liu YL, Lipkin SM, Belhadj S, Bond GL, Gümüş ZH, Klein RJ, Ladanyi M, Solit DB, Robson ME, Jones DR, Kris MG, Vijai J, Stadler ZK, Amos CI, Taylor BS, Berger MF, Rudin CM, Offit K. Germline Pathogenic Variants Impact Clinicopathology of Advanced Lung Cancer. Cancer Epidemiol Biomarkers Prev 2022; 31:1450-1459. [PMID: 35477182 PMCID: PMC9250622 DOI: 10.1158/1055-9965.epi-21-1287] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 11/09/2021] [Revised: 01/31/2022] [Accepted: 04/25/2022] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND The genetic factors that modulate risk for developing lung cancer have not been fully defined. Here, we sought to determine the prevalence and clinical significance of germline pathogenic/likely pathogenic variants (PV) in patients with advanced lung cancer. METHODS We studied clinical and tumor characteristics of germline PV in 5,118 patients who underwent prospective genomic profiling using paired tumor-normal tissue samples in 468 cancer genes. RESULTS Germline PV in high/moderate-penetrance genes were observed in 222 (4.3%) patients; of these, 193 patients had PV in DNA damage repair (DDR) pathway genes including BRCA2 (n = 54), CHEK2 (n = 30), and ATM (n = 26) that showed high rate of biallelic inactivation in tumors. BRCA2 heterozygotes with lung adenocarcinoma were more likely to be never smokers and had improved survival compared with noncarriers. Fourteen patients with germline PV in lung cancer predisposing genes (TP53, EGFR, BAP1, and MEN1) were diagnosed at younger age compared with noncarriers, and of tumor suppressors, 75% demonstrated biallelic inactivation in tumors. A significantly higher proportion of germline PV in high/moderate-penetrance genes were detected in high-risk patients who had either a family history of any cancer, multiple primary tumors, or early age at diagnosis compared with unselected patients (10.5% vs. 4.1%; P = 1.7e-04). CONCLUSIONS These data underscore the biological and clinical importance of germline mutations in highly penetrant DDR genes as a risk factor for lung cancer. IMPACT The family members of lung cancer patients harboring PV in cancer predisposing genes should be referred for genetic counseling and may benefit from proactive surveillance.
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Affiliation(s)
| | | | | | - Yelena Kemel
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Esther Drill
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Hira Rizvi
- Memorial Sloan Kettering Cancer Center, United States
| | - Kaitlyn Tkachuk
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Aliya Khurram
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Michael F Walsh
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | | | - Diana Mandelker
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Sabine Topka
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Ahmet Zehir
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | | | | | - Maria I Carlo
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Karen A Cadoo
- St. James’s Hospital, Trinity College Dublin, Trinity St. James’s Cancer Institute, Dublin 8, Ireland
| | - Alicia Latham
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY, United States
| | - Jada G Hamilton
- Memorial Sloan Kettering Cancer Center, New York, New York, United States
| | - Ying L Liu
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | | | - Sami Belhadj
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Gareth L Bond
- University of Birmingham, Birmingham, United Kingdom
| | - Zeynep H Gümüş
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Robert J Klein
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Marc Ladanyi
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - David B Solit
- Memorial Sloan Kettering Cancer Center, New York, New York, United States
| | - Mark E Robson
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - David R Jones
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Mark G Kris
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Joseph Vijai
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Zsofia K Stadler
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY, United States
| | | | - Barry S Taylor
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Michael F Berger
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Charles M Rudin
- Memorial Sloan Kettering Cancer Center, New York, New York, United States
| | - Kenneth Offit
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
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23
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Kotecha RR, Gedvilaite E, Ptashkin R, Knezevic A, Murray S, Johnson I, Shapnik N, Feldman DR, Carlo MI, Shah NJ, Dunigan M, Huberman K, Benayed R, Zehir A, Berger MF, Ladanyi M, Tsui DWY, Motzer RJ, Lee CH, Voss MH. Matched Molecular Profiling of Cell-Free DNA and Tumor Tissue in Patients With Advanced Clear Cell Renal Cell Carcinoma. JCO Precis Oncol 2022; 6:e2200012. [PMID: 35797508 PMCID: PMC9489165 DOI: 10.1200/po.22.00012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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
PURPOSE The clinical utility of cell-free DNA (cfDNA) as a biomarker for advanced clear cell renal cell carcinoma (ccRCC) remains unclear. We evaluated the validity of cfDNA-based genomic profiling in a large cohort of patients with ccRCC with matched next-generation sequencing (NGS) from primary tumor tissues. MATERIALS AND METHODS We performed paired NGS of tumor DNA and plasma cfDNA using the MSK-IMPACT platform in 110 patients with metastatic ccRCC. Tissues were profiled for variants and copy number alterations with germline comparison. Manual cross-genotyping between cfDNA and tumor tissue was performed. Deep sequencing with a higher sensitivity platform, MSK-ACCESS, was performed on a subset of cfDNA samples. Clinical data and radiographic tumor volumes were assessed to correlate cfDNA yield with treatment response and disease burden. RESULTS Tumor tissue MSK-IMPACT testing identified 582 genomic alterations (GAs) across the cohort. Using standard thresholds for de novo variant calling in cfDNA, only 24 GAs were found by MSK-IMPACT in cfDNA in 7 of 110 patients (6%). With manual cross-genotyping, 210 GAs were detectable below thresholds in 74 patients (67%). Intrapatient concordance with tumor tissue was limited, including VHL (31.6%), PBRM1 (24.1%), and TP53 (52.9%). cfDNA profiling did not identify 3p loss because of low tumor fractions. Tumor volume was associated with cfDNA allele frequency, and VHL concordance was superior for patients with greater disease burden. CONCLUSION cfDNA-based NGS profiling yielded low detection rates in this metastatic ccRCC cohort. Concordance with tumor profiling was low, even for truncal mutations such as VHL, and some findings in peripheral blood may represent clonal hematopoiesis. Routine cfDNA panel testing is not supported, and its application in biomarker efforts must account for these limitations.
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Affiliation(s)
- Ritesh R Kotecha
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Erika Gedvilaite
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ryan Ptashkin
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Andrea Knezevic
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Samuel Murray
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ian Johnson
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Natalie Shapnik
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Darren R Feldman
- 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
| | - Neil J Shah
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Marisa Dunigan
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kety Huberman
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Michael F Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Dana W Y Tsui
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Robert J Motzer
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Chung-Han Lee
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Martin H Voss
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
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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.
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Affiliation(s)
| | | | | | | | - Calvin Lu
- 1Memorial Sloan Kettering, New York, NY
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25
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DiNapoli SE, Spence C, Gedvilaite E, Bowman A, Diosdado M, Razumova A, Tsui D, Salles GA, Batlevi C, von Keudell G, Ptashkin R, Zehir A, Berger M, Brannon AR, Benayed R, Arcila M. Abstract 56: MSK-ACCESS Heme: A cell-free DNA next-generation sequencing assay to identify somatic alterations in patients with lymphoma. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-56] [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
Next-generation sequencing of cell-free DNA (cfDNA) can be used to noninvasively assess and monitor patients with lymphoma. Here, we describe the preliminary validation of MSK-ACCESS Heme (Memorial Sloan Kettering-Analysis of Circulating cfDNA to Examine Somatic Status), a cfDNA assay that employs unique molecular indexing and ultra-deep sequencing to detect somatic alterations in 117 genes related to hematologic malignancies. To our knowledge, this is the first report of a clinical-grade cfDNA assay developed specifically for hematologic malignancies.
Overall assay performance was assessed using 53 validation samples (26 normal samples and 27 cfDNA samples with somatic variants). Initial accuracy studies showed excellent correlation with the reference next-generation sequencing method (MSK-ACCESS Solid), detecting 32/32 (100%) of expected variants with a variant allele frequency over 1%. The limit of detection was assessed using standard samples, with detection of variants down to 0.5% variant allele frequency. Results were highly concordant in both inter- and intra-assay reproducibility studies.
Overall, these data indicate that MSK-ACCESS Heme is a robust cfDNA-based assay that can be used to detect variants at low frequency with high reproducibility. Future work sequencing additional samples will be performed to further assess the performance of the panel.
Citation Format: Sara E. DiNapoli, Coleman Spence, Erika Gedvilaite, Anita Bowman, Monica Diosdado, Anna Razumova, Dana Tsui, Gilles A. Salles, Connie Batlevi, Gottfried von Keudell, Ryan Ptashkin, Ahmet Zehir, Michael Berger, A Rose Brannon, Ryma Benayed, Maria Arcila. MSK-ACCESS Heme: A cell-free DNA next-generation sequencing assay to identify somatic alterations in patients with lymphoma [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 56.
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Affiliation(s)
| | | | | | - Anita Bowman
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Anna Razumova
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Dana Tsui
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | - Ryan Ptashkin
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Zehir
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Ryma Benayed
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Maria Arcila
- 1Memorial Sloan Kettering Cancer Center, New York, NY
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26
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Nacev BA, Sanchez-Vega F, Smith SA, Antonescu CR, Rosenbaum E, Shi H, Tang C, Socci ND, Rana S, Gularte-Mérida R, Zehir A, Gounder MM, Bowler TG, Luthra A, Jadeja B, Okada A, Strong JA, Stoller J, Chan JE, Chi P, D'Angelo SP, Dickson MA, Kelly CM, Keohan ML, Movva S, Thornton K, Meyers PA, Wexler LH, Slotkin EK, Glade Bender JL, Shukla NN, Hensley ML, Healey JH, La Quaglia MP, Alektiar KM, Crago AM, Yoon SS, Untch BR, Chiang S, Agaram NP, Hameed MR, Berger MF, Solit DB, Schultz N, Ladanyi M, Singer S, Tap WD. Clinical sequencing of soft tissue and bone sarcomas delineates diverse genomic landscapes and potential therapeutic targets. Nat Commun 2022; 13:3405. [PMID: 35705560 PMCID: PMC9200818 DOI: 10.1038/s41467-022-30453-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [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: 10/18/2021] [Accepted: 05/02/2022] [Indexed: 02/02/2023] Open
Abstract
The genetic, biologic, and clinical heterogeneity of sarcomas poses a challenge for the identification of therapeutic targets, clinical research, and advancing patient care. Because there are > 100 sarcoma subtypes, in-depth genetic studies have focused on one or a few subtypes. Herein, we report a comparative genetic analysis of 2,138 sarcomas representing 45 pathological entities. This cohort is prospectively analyzed using targeted sequencing to characterize subtype-specific somatic alterations in targetable pathways, rates of whole genome doubling, mutational signatures, and subtype-agnostic genomic clusters. The most common alterations are in cell cycle control and TP53, receptor tyrosine kinases/PI3K/RAS, and epigenetic regulators. Subtype-specific associations include TERT amplification in intimal sarcoma and SWI/SNF alterations in uterine adenosarcoma. Tumor mutational burden, while low compared to other cancers, varies between and within subtypes. This resource will improve sarcoma models, motivate studies of subtype-specific alterations, and inform investigations of genetic factors and their correlations with treatment response.
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Affiliation(s)
- Benjamin A Nacev
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, 10065, NY, USA
- The Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, 10065, NY, USA
| | - Francisco Sanchez-Vega
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
| | - Shaleigh A Smith
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
| | - Cristina R Antonescu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
| | - Evan Rosenbaum
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, 10065, NY, USA
| | - Hongyu Shi
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
| | - Cerise Tang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
- Physiology, Biophysics and Systems Biology Graduate Program, Weill Cornell Medical College, New York, 10065, NY, USA
| | - Nicholas D Socci
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
- Bioinformatics Core, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
| | - Satshil Rana
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
| | | | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
| | - Mrinal M Gounder
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, 10065, NY, USA
| | - Timothy G Bowler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
| | - Anisha Luthra
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
| | - Bhumika Jadeja
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
| | - Azusa Okada
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
| | - Jonathan A Strong
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
| | - Jake Stoller
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
| | - Jason E Chan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
| | - Ping Chi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, 10065, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
| | - Sandra P D'Angelo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, 10065, NY, USA
| | - Mark A Dickson
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, 10065, NY, USA
| | - Ciara M Kelly
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, 10065, NY, USA
| | - Mary Louise Keohan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, 10065, NY, USA
| | - Sujana Movva
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, 10065, NY, USA
| | - Katherine Thornton
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, 10065, NY, USA
| | - Paul A Meyers
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
| | - Leonard H Wexler
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
| | - Emily K Slotkin
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
| | - Julia L Glade Bender
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
| | - Neerav N Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
| | - Martee L Hensley
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, 10065, NY, USA
| | - John H Healey
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
| | - Michael P La Quaglia
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
- Department of Surgery, Weill Cornell Medical College, New York, 10065, NY, USA
| | - Kaled M Alektiar
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
| | - Aimee M Crago
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
- Department of Surgery, Weill Cornell Medical College, New York, 10065, NY, USA
| | - Sam S Yoon
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
- Department of Surgery, Weill Cornell Medical College, New York, 10065, NY, USA
| | - Brian R Untch
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
- Department of Surgery, Weill Cornell Medical College, New York, 10065, NY, USA
| | - Sarah Chiang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
| | - Narasimhan P Agaram
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
| | - Meera R Hameed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
| | - Michael F Berger
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
| | - David B Solit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, 10065, NY, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
| | - Nikolaus Schultz
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
| | - Samuel Singer
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA.
- Department of Surgery, Weill Cornell Medical College, New York, 10065, NY, USA.
| | - William D Tap
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA.
- Department of Medicine, Weill Cornell Medical College, New York, 10065, NY, USA.
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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.
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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
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28
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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.
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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
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29
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Shukla N, Levine MF, Gundem G, Domenico D, Spitzer B, Bouvier N, Arango-Ossa JE, Glodzik D, Medina-Martínez JS, Bhanot U, Gutiérrez-Abril J, Zhou Y, Fiala E, Stockfisch E, Li S, Rodriguez-Sanchez MI, O'Donohue T, Cobbs C, Roehrl MHA, Benhamida J, Iglesias Cardenas F, Ortiz M, Kinnaman M, Roberts S, Ladanyi M, Modak S, Farouk-Sait S, Slotkin E, Karajannis MA, Dela Cruz F, Glade Bender J, Zehir A, Viale A, Walsh MF, Kung AL, Papaemmanuil E. Feasibility of whole genome and transcriptome profiling in pediatric and young adult cancers. Nat Commun 2022; 13:2485. [PMID: 35585047 PMCID: PMC9117241 DOI: 10.1038/s41467-022-30233-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 04/21/2022] [Indexed: 02/07/2023] Open
Abstract
The utility of cancer whole genome and transcriptome sequencing (cWGTS) in oncology is increasingly recognized. However, implementation of cWGTS is challenged by the need to deliver results within clinically relevant timeframes, concerns about assay sensitivity, reporting and prioritization of findings. In a prospective research study we develop a workflow that reports comprehensive cWGTS results in 9 days. Comparison of cWGTS to diagnostic panel assays demonstrates the potential of cWGTS to capture all clinically reported mutations with comparable sensitivity in a single workflow. Benchmarking identifies a minimum of 80× as optimal depth for clinical WGS sequencing. Integration of germline, somatic DNA and RNA-seq data enable data-driven variant prioritization and reporting, with oncogenic findings reported in 54% more patients than standard of care. These results establish key technical considerations for the implementation of cWGTS as an integrated test in clinical oncology. Cancer whole-genome and transcriptome sequencing (cWGTS) has been challenging to implement in clinical settings. Here, the authors develop a workflow to deliver robust cWGTS analyses and reports within clinically-relevant timeframes for paediatric, adolescent and young adult solid tumour patients.
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Affiliation(s)
- N Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M F Levine
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - G Gundem
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - D Domenico
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - B Spitzer
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - N Bouvier
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - J E Arango-Ossa
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - D Glodzik
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - J S Medina-Martínez
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - U Bhanot
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Precision Pathology Biobanking Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - J Gutiérrez-Abril
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Y Zhou
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - E Fiala
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - E Stockfisch
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - S Li
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - T O'Donohue
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - C Cobbs
- Integrated Genomics Operation Core, Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M H A Roehrl
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Precision Pathology Biobanking Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - J Benhamida
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - F Iglesias Cardenas
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M Ortiz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M Kinnaman
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - S Roberts
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - S Modak
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - S Farouk-Sait
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - E Slotkin
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M A Karajannis
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - F Dela Cruz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - J Glade Bender
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - A Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - A Viale
- Integrated Genomics Operation Core, Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M F Walsh
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - A L Kung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - E Papaemmanuil
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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30
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Vanderbilt CM, Bowman AS, Middha S, Petrova-Drus K, Tang YW, Chen X, Wang Y, Chang J, Rekhtman N, Busam KJ, Gupta S, Hameed M, Arcila ME, Ladanyi M, Berger MF, Dogan S, Zehir A. Defining Novel DNA Virus-Tumor Associations and Genomic Correlates Using Prospective Clinical Tumor/Normal Matched Sequencing Data. J Mol Diagn 2022; 24:515-528. [PMID: 35331965 PMCID: PMC9127461 DOI: 10.1016/j.jmoldx.2022.01.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/27/2021] [Accepted: 01/31/2022] [Indexed: 12/11/2022] Open
Abstract
This study is the largest analysis of DNA viruses in solid tumors with associated genomics. To achieve this, a novel method for discovery of DNA viruses from matched tumor/normal next-generation sequencing samples was developed and validated. This method performed comparably to reference methods for the detection of high-risk (HR) human papilloma virus (HPV) (area under the receiver operating characteristic curve = 0.953). After virus identification in 48,148 consecutives samples from 42,846 unique patients, novel virus tumor associations were established by segregating tumor types to determine whether each DNA virus was enriched in each of the tumor types compared with the remaining cohort. All firmly established solid tumor-virus associations (eg, HR HPV in cervical cancer) were confirmed, and the novel associations discovered included: human herpes virus 6 in neuroblastoma, human herpes virus 7 in esophagogastric cancer, and HPV42 in digital papillary adenocarcinoma. These associations were confirmed in an independent validation cohort. HR HPV- and Epstein-Barr virus-associated tumors showed newly discovered genomic associations, including a lower tumor mutation burden. The study demonstrated the ability to study the role of DNA viruses in human cancer from clinical genomics data and established the largest cohort that can be utilized as a validation set for future discovery efforts.
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Affiliation(s)
- Chad M Vanderbilt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Anita S Bowman
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sumit Middha
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kseniya Petrova-Drus
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yi-Wei Tang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Xin Chen
- Atila Biosystems Inc., Mountain View, California
| | | | - Jason Chang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Natasha Rekhtman
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Klaus J Busam
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sounak Gupta
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Meera Hameed
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maria E Arcila
- Department of Pathology and Laboratory Medicine, 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
| | - Michael F Berger
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Snjezana Dogan
- 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
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31
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Spitzer B, Rutherford KD, Gundem G, McGovern EM, Millard NE, Arango Ossa JE, Cheung IY, Gao T, Levine MF, Zhang Y, Medina-Martínez JS, Feng Y, Ptashkin RN, Bolton KL, Farnoud N, Zhou Y, Patel MA, Asimomitis G, Cobbs CC, Mohibullah N, Huberman KH, Arcilla ME, Kushner BH, Modak S, Kung AL, Zehir A, Levine RL, Armstrong SA, Cheung NKV, Papaemmanuil E. Bone Marrow Surveillance of Pediatric Cancer Survivors Identifies Clones that Predict Therapy-Related Leukemia. Clin Cancer Res 2022; 28:1614-1627. [PMID: 35078859 PMCID: PMC9983778 DOI: 10.1158/1078-0432.ccr-21-2451] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 10/01/2021] [Accepted: 01/20/2022] [Indexed: 01/25/2023]
Abstract
PURPOSE Therapy-related myelodysplastic syndrome and acute leukemias (t-MDS/AL) are a major cause of nonrelapse mortality among pediatric cancer survivors. Although the presence of clonal hematopoiesis (CH) in adult patients at cancer diagnosis has been implicated in t-MDS/AL, there is limited published literature describing t-MDS/AL development in children. EXPERIMENTAL DESIGN We performed molecular characterization of 199 serial bone marrow samples from 52 patients treated for high-risk neuroblastoma, including 17 with t-MDS/AL (transformation), 14 with transient cytogenetic abnormalities (transient), and 21 without t-MDS/AL or cytogenetic alterations (neuroblastoma-treated control). We also evaluated for CH in a cohort of 657 pediatric patients with solid tumor. RESULTS We detected at least one disease-defining alteration in all cases at t-MDS/AL diagnosis, most commonly TP53 mutations and KMT2A rearrangements, including involving two novel partner genes (PRDM10 and DDX6). Backtracking studies identified at least one t-MDS/AL-associated mutation in 13 of 17 patients at a median of 15 months before t-MDS/AL diagnosis (range, 1.3-32.4). In comparison, acquired mutations were infrequent in the transient and control groups (4/14 and 1/21, respectively). The relative risk for development of t-MDS/AL in the presence of an oncogenic mutation was 8.8 for transformation patients compared with transient. Unlike CH in adult oncology patients, TP53 mutations were only detectable after initiation of cancer therapy. Last, only 1% of pediatric patients with solid tumor evaluated had CH involving myeloid genes. CONCLUSIONS These findings demonstrate the clinical relevance of identifying molecular abnormalities in predicting development of t-MDS/AL and should guide the formation of intervention protocols to prevent this complication in high-risk pediatric patients.
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Affiliation(s)
- Barbara Spitzer
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center New York, NY,Department of Pediatrics, Weill Cornell Medical College, New York, NY
| | - Kayleigh D. Rutherford
- Center for Computational Oncology, Department of Epidemiology and Statistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Gunes Gundem
- Center for Computational Oncology, Department of Epidemiology and Statistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Erin M. McGovern
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nathan E. Millard
- Division of Hematology/Oncology, Department of Pediatrics, Seattle Children’s Hospital, Seattle, WA
| | - Juan E. Arango Ossa
- Center for Computational Oncology, Department of Epidemiology and Statistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Irene Y. Cheung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center New York, NY
| | - Teng Gao
- Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA
| | - Max F. Levine
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center New York, NY,Center for Computational Oncology, Department of Epidemiology and Statistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yanming Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Juan S. Medina-Martínez
- Center for Computational Oncology, Department of Epidemiology and Statistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yi Feng
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center New York, NY
| | - Ryan N. Ptashkin
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kelly L. Bolton
- Division of Oncology, Department of Medicine, Washington University, St. Louis, MO
| | - Noushin Farnoud
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yangyu Zhou
- Center for Computational Oncology, Department of Epidemiology and Statistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Minal A. Patel
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Georgios Asimomitis
- Center for Computational Oncology, Department of Epidemiology and Statistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Cassidy C. Cobbs
- Integrated Genomics Core, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Neeman Mohibullah
- Integrated Genomics Core, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kety H. Huberman
- Integrated Genomics Core, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Maria E. Arcilla
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Brian H. Kushner
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center New York, NY
| | - Shakeel Modak
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center New York, NY
| | - Andrew L. Kung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center New York, NY
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ross L. Levine
- Human Oncology and Oncogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Scott A. Armstrong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Nai Kong V. Cheung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center New York, NY
| | - Elli Papaemmanuil
- Center for Computational Oncology, Department of Epidemiology and Statistics, Memorial Sloan Kettering Cancer Center, New York, NY
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32
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Rosenbaum E, Antonescu CR, Smith S, Bradic M, Kashani D, Richards AL, Donoghue M, Kelly CM, Nacev B, Chan JE, Chi P, Dickson MA, Keohan ML, Gounder MM, Movva S, Avutu V, Thornton K, Zehir A, Bowman AS, Singer S, Tap W, D'Angelo S. Clinical, genomic, and transcriptomic correlates of response to immune checkpoint blockade-based therapy in a cohort of patients with angiosarcoma treated at a single center. J Immunother Cancer 2022; 10:jitc-2021-004149. [PMID: 35365586 PMCID: PMC8977792 DOI: 10.1136/jitc-2021-004149] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/12/2022] [Indexed: 12/15/2022] Open
Abstract
Background Angiosarcoma is a histologically and molecularly heterogeneous vascular neoplasm with aggressive clinical behavior. Emerging data suggests that immune checkpoint blockade (ICB) is efficacious against some angiosarcomas, particularly cutaneous angiosarcoma of the head and neck (CHN). Methods Patients with histologically confirmed angiosarcoma treated with ICB-based therapy at a comprehensive cancer center were retrospectively identified. Clinical characteristics and the results of targeted exome sequencing, transcriptome sequencing, and immunohistochemistry analyses were examined for correlation with clinical benefit. Durable clinical benefit was defined as a progression-free survival (PFS) of ≥16 weeks. Results For the 35 patients included in the analyses, median PFS and median overall survival (OS) from the time of first ICB-based treatment were 11.9 (95% CI 7.4 to 31.9) and 42.5 (95% CI 19.6 to 114.2) weeks, respectively. Thirteen patients (37%) had PFS ≥16 weeks. Clinical factors associated with longer PFS and longer OS in multivariate analyses were ICB plus other therapy regimens, CHN disease, and white race. Three of 10 patients with CHN angiosarcoma evaluable for tumor mutational burden (TMB) had a TMB ≥10. Five of six patients with CHN angiosarcoma evaluable for mutational signature analysis had a dominant mutational signature associated with ultraviolet (UV) light. No individual gene or genomic pathway was significantly associated with PFS or OS; neither were TMB or UV signature status. Analyses of whole transcriptomes from nine patient tumor samples found upregulation of angiogenesis, inflammatory response, and KRAS signaling pathways, among others, in patients with PFS ≥16 weeks, as well as higher levels of cytotoxic T cells, dendritic cells, and natural killer cells. Patients with PFS <16 weeks had higher numbers of cancer-associated fibroblasts. Immunohistochemistry findings for 12 patients with baseline samples available suggest that neither PD-L1 expression nor presence of tumor-infiltrating lymphocytes at baseline appears necessary for a response to ICB-based therapy. Conclusions ICB-based therapy benefits only a subset of angiosarcoma patients. Patients with CHN angiosarcoma are more likely to have PFS ≥16 weeks, a dominant UV mutational signature, and higher TMB than angiosarcomas arising from other primary sites. However, clinical benefit was seen in other angiosarcomas also and was not restricted to tumors with a high TMB, a dominant UV signature, PD-L1 expression, or presence of tumor infiltrating lymphocytes at baseline.
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Affiliation(s)
- Evan Rosenbaum
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York, USA .,Department of Medicine, Weill Cornell Medical College, New York City, New York, USA
| | - Cristina R Antonescu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | - Shaleigh Smith
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Martina Bradic
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel Kashani
- Department of Medicine, SUNY Downstate Medical Center, New York City, New York, USA
| | - Allison L Richards
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mark Donoghue
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ciara M Kelly
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York, USA.,Department of Medicine, Weill Cornell Medical College, New York City, New York, USA
| | - Benjamin Nacev
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York, USA.,Department of Medicine, Weill Cornell Medical College, New York City, New York, USA
| | - Jason E Chan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York, USA.,Department of Medicine, Weill Cornell Medical College, New York City, New York, USA
| | - Ping Chi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York, USA.,Department of Medicine, Weill Cornell Medical College, New York City, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mark A Dickson
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York, USA.,Department of Medicine, Weill Cornell Medical College, New York City, New York, USA
| | - Mary L Keohan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York, USA.,Department of Medicine, Weill Cornell Medical College, New York City, New York, USA
| | - Mrinal M Gounder
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York, USA.,Department of Medicine, Weill Cornell Medical College, New York City, New York, USA
| | - Sujana Movva
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York, USA.,Department of Medicine, Weill Cornell Medical College, New York City, New York, USA
| | - Viswatej Avutu
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York, USA.,Department of Medicine, Weill Cornell Medical College, New York City, New York, USA
| | - Katherine Thornton
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York, USA.,Department of Medicine, Weill Cornell Medical College, New York City, New York, USA
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | - Anita S Bowman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | - Samuel Singer
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | - William Tap
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York, USA.,Department of Medicine, Weill Cornell Medical College, New York City, New York, USA
| | - Sandra D'Angelo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York, USA.,Department of Medicine, Weill Cornell Medical College, New York City, New York, USA
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33
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Gularte-Mérida R, Smith S, Bowman AS, da Cruz Paula A, Chatila W, Bielski CM, Vyas M, Borsu L, Zehir A, Martelotto LG, Shia J, Yaeger R, Fang F, Gardner R, Luo R, Schatz MC, Shen R, Weigelt B, Sánchez-Vega F, Reis-Filho JS, Hechtman JF. Same-Cell Co-Occurrence of RAS Hotspot and BRAF V600E Mutations in Treatment-Naive Colorectal Cancer. JCO Precis Oncol 2022; 6:e2100365. [PMID: 35235413 PMCID: PMC8906458 DOI: 10.1200/po.21.00365] [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
PURPOSE Mitogen-activated protein kinase pathway-activating mutations occur in the majority of colorectal cancer (CRC) cases and show mutual exclusivity. We identified 47 epidermal growth factor receptor/BRAF inhibitor-naive CRC patients with dual RAS hotspot/BRAF V600E mutations (CRC-DD) from a cohort of 4,561 CRC patients with clinical next-generation sequencing results. We aimed to define the molecular phenotypes of the CRC-DD and to test if the dual RAS hotspot/BRAF V600E mutations coexist within the same cell. MATERIALS AND METHODS We developed a single-cell genotyping method with a mutation detection rate of 96.3% and a genotype prediction accuracy of 92.1%. Mutations in the CRC-DD cohort were analyzed for clonality, allelic imbalance, copy number, and overall survival. RESULTS Application of single-cell genotyping to four CRC-DD revealed the co-occurrence of both mutations in the following percentages of cells per case: NRAS G13D/KRAS G12C, 95%; KRAS G12D/NRAS G12V, 48%; BRAF V600E/KRAS G12D, 44%; and KRAS G12D/NRAS G13V, 14%, respectively. Allelic imbalance favoring the oncogenic allele was less frequent in CRC-DD (24 of 76, 31.5%, somatic mutations) compared with a curated cohort of CRC with a single-driver mutation (CRC-SD; 119 of 232 mutations, 51.3%; P = .013). Microsatellite instability-high status was enriched in CRC-DD compared with CRC-SD (23% v 11.4%, P = .028). Of the seven CRC-DD cases with multiregional sequencing, five retained both driver mutations throughout all sequenced tumor sites. Both CRC-DD cases with discordant multiregional sequencing were microsatellite instability-high. CONCLUSION Our findings indicate that dual-driver mutations occur in a rare subset of CRC, often within the same tumor cells and across multiple tumor sites. Their presence and a lower rate of allelic imbalance may be related to dose-dependent signaling within the mitogen-activated protein kinase pathway.
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Affiliation(s)
- Rodrigo Gularte-Mérida
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY,Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY,Rodrigo Gularte Mérida, PhD, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY 10065; e-mail:
| | - Shaleigh Smith
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Anita S. Bowman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Walid Chatila
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Craig M. Bielski
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Monika Vyas
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA
| | - Laetitia Borsu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Jinru Shia
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Rona Yaeger
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Fang Fang
- Flow Cytometry Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Rui Gardner
- Flow Cytometry Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ruibang Luo
- Department of Computer Science, John Hopkins University, Baltimore, MD
| | - Michael C. Schatz
- Department of Computer Science, John Hopkins University, Baltimore, MD
| | - Ronglai Shen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Francisco Sánchez-Vega
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jorge S. Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jaclyn F. Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
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Safonov A, Bandlamudi C, de Lara PT, Ferraro E, Derakhshan F, Will M, Donoghue M, Selenica P, Drago J, Rosen E, dos Anjos C, Walsh E, Comen EA, Ahmed M, Acevedo B, Zehir A, Berger MF, Solit D, Norton L, Shen R, Stadler Z, Powell S, Reis-Filho JS, Chandarlapaty S, Robson M, Razavi P. Abstract GS4-08: Comprehensive genomic profiling of patients with breast cancer identifies germline-somatic interactions mediating therapy resistance. Cancer Res 2022. [DOI: 10.1158/1538-7445.sabcs21-gs4-08] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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
Background: Germline genetic alterations are established mediators of breast carcinogenesis, often giving rise to specific forms of genomic instability. BRCA1/2 pathogenic variants (PVs) are emblematic of this phenomenon through their induction of homologous recombination deficiency. While specific patterns of genomic instability may sensitize cancers to therapies such as PARP inhibitors (PARPi) or platinum chemotherapy, their implications for lineage-directed therapies such as endocrine therapy (ET) or CDK4/6 inhibitors (CDK4/6i) are unknown. Herein, we systematically investigated the patterns of association of germline alterations with specific somatic alterations and explored the resulting effect on clinical outcomes. Methods: Patients who underwent germline and matched tumor tissue sequencing utilizing MSK-IMPACT from April 2014 to May 2021 and had available germline analysis results were included. The final analysis presented at SABCS will include 6000 tumors from 5,150 patients, anonymized according to established institutional IRB guidelines to allow for germline analysis on the full cohort. We analyzed genomic data to inform the full spectrum of somatic and germline mutations, ploidy, and allele-specific copy number to determine loss of heterozygosity (LOH). We performed gene- and pathway-level enrichment analyses between somatic variants and germline PVs. Univariable and multivariable Cox proportional hazards models were constructed to assess the association of therapy-specific progression-free survival (PFS) with select germline PVs and germline-somatic interactions. Results: The preliminary analysis includes 2,798 tumors from 2,242 patients with germline and somatic sequencing results. The most frequent germline PVs were: BRCA2 (n = 81), BRCA1 (n = 67), CHEK2 (n = 57), ATM (n = 32), PALB2 (n = 19). The cohort robustly confirmed previously established relationships such as mutual exclusivity of gATM and TP53 variants (OR 0.10, 95% CI 0.032 - 0.33, q = 0.005). Alterations of TP53 were seen in 83% (56/67) of gBRCA1 patients; however, this did not achieve significance when adjusted for receptor subtype (OR 3.90, 95% CI 1.34-11.38, q = 0.15). The size of the cohort allowed discovery of several novel relationships. For instance, gBRCA2 loss was associated with alterations in TGF-B pathway components (OR 3.58, 95% CI 1.70 - 7.56, q = 0.002), potentially relevant to metastatic disease progression. PIK3CA mutations were significantly less prevalent in both gBRCA2 (OR 0.52, 95% CI 0.31 - 0.87, q = 0.063) and gBRCA1 PVs (OR 0.21, 95% CI 0.085 - 0.51, q = 0.014). Our analysis uncovered a strong association between gBRCA2 and somatic RB1 pathogenic alterations (OR 3.58, 95% CI 1.70 - 7.56, q = 0.011), with most variants (80%) encountered in metastatic gBRCA2 tumors. Given the essential role of RB1 in CDK4/6i response, we investigated the effect of BRCA2 status on clinical efficacy of CDK4/6i-ET. Strikingly, gBRCA2 PVs were significantly associated with inferior PFS (HR 2.17, 95% CI 1.46-3.22, p < 0.001) on first line treatment with CDK4/6i-ET. We posited the enrichment of somatic RB1 loss as a potential mechanism of resistance to CDK4/6i. Given the proximity of RB1 to BRCA2 on chromosome 13, we hypothesized that co-LOH of BRCA2 and RB1 predisposes the cancer cells to bi-allelic loss under therapeutic pressure of CDK4/6i. Indeed, 18/26 gBRCA2 (69.2%) tumors evaluable for allele-specific copy number had evidence of RB1 LOH. Discussion: Analysis of germline-somatic interactions yielded novel associations relevant to breast cancer progression and treatment resistance. Among these, we demonstrated BRCA2 carriers to have inferior outcomes to first line CDK4/6i-ET with potential implications for optimal first line therapy and sequencing of CDK4/6i vs PARPi in this patient population.
Citation Format: Anton Safonov, Chai Bandlamudi, Paulino Tallón de Lara, Emanuela Ferraro, Fatemeh Derakhshan, Marie Will, Mark Donoghue, Pier Selenica, Joshua Drago, Ezra Rosen, Carlos dos Anjos, Elaine Walsh, Elizabeth A Comen, Mehnaj Ahmed, Barbara Acevedo, Ahmet Zehir, Michael F Berger, David Solit, Larry Norton, Ronglai Shen, Zsofia Stadler, Simon Powell, Jorge S Reis-Filho, Sarat Chandarlapaty, Mark Robson, Pedram Razavi. Comprehensive genomic profiling of patients with breast cancer identifies germline-somatic interactions mediating therapy resistance [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr GS4-08.
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Affiliation(s)
- Anton Safonov
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | - Marie Will
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mark Donoghue
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Pier Selenica
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Joshua Drago
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ezra Rosen
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Elaine Walsh
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Mehnaj Ahmed
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Ahmet Zehir
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - David Solit
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Larry Norton
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ronglai Shen
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Simon Powell
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Mark Robson
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Pedram Razavi
- Memorial Sloan Kettering Cancer Center, New York, NY
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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.
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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.
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Pareja F, Ptashkin RN, Brown DN, Derakhshan F, Selenica P, da Silva EM, Gazzo AM, Da Cruz Paula A, Breen K, Shen R, Marra A, Zehir A, Benayed R, Berger MF, Ceyhan-Birsoy O, Jairam S, Sheehan M, Patel U, Kemel Y, Casanova-Murphy J, Schwartz CJ, Vahdatinia M, Comen E, Borsu L, Pei X, Riaz N, Abramson DH, Weigelt B, Walsh MF, Hadjantonakis AK, Ladanyi M, Offit K, Stadler ZK, Robson ME, Reis-Filho JS, Mandelker D. Cancer Causative Mutations Occurring in Early Embryogenesis. Cancer Discov 2021; 12:949-957. [DOI: 10.1158/2159-8290.cd-21-1110] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/21/2021] [Accepted: 12/20/2021] [Indexed: 11/16/2022]
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Vega DM, Yee LM, McShane LM, Williams PM, Chen L, Vilimas T, Fabrizio D, Funari V, Newberg J, Bruce LK, Chen SJ, Baden J, Carl Barrett J, Beer P, Butler M, Cheng JH, Conroy J, Cyanam D, Eyring K, Garcia E, Green G, Gregersen VR, Hellmann MD, Keefer LA, Lasiter L, Lazar AJ, Li MC, MacConaill LE, Meier K, Mellert H, Pabla S, Pallavajjalla A, Pestano G, Salgado R, Samara R, Sokol ES, Stafford P, Budczies J, Stenzinger A, Tom W, Valkenburg KC, Wang XZ, Weigman V, Xie M, Xie Q, Zehir A, Zhao C, Zhao Y, Stewart MD, Allen J. Aligning tumor mutational burden (TMB) quantification across diagnostic platforms: phase II of the Friends of Cancer Research TMB Harmonization Project. Ann Oncol 2021; 32:1626-1636. [PMID: 34606929 DOI: 10.1016/j.annonc.2021.09.016] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 09/21/2021] [Accepted: 09/26/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Tumor mutational burden (TMB) measurements aid in identifying patients who are likely to benefit from immunotherapy; however, there is empirical variability across panel assays and factors contributing to this variability have not been comprehensively investigated. Identifying sources of variability can help facilitate comparability across different panel assays, which may aid in broader adoption of panel assays and development of clinical applications. MATERIALS AND METHODS Twenty-nine tumor samples and 10 human-derived cell lines were processed and distributed to 16 laboratories; each used their own bioinformatics pipelines to calculate TMB and compare to whole exome results. Additionally, theoretical positive percent agreement (PPA) and negative percent agreement (NPA) of TMB were estimated. The impact of filtering pathogenic and germline variants on TMB estimates was assessed. Calibration curves specific to each panel assay were developed to facilitate translation of panel TMB values to whole exome sequencing (WES) TMB values. RESULTS Panel sizes >667 Kb are necessary to maintain adequate PPA and NPA for calling TMB high versus TMB low across the range of cut-offs used in practice. Failure to filter out pathogenic variants when estimating panel TMB resulted in overestimating TMB relative to WES for all assays. Filtering out potential germline variants at >0% population minor allele frequency resulted in the strongest correlation to WES TMB. Application of a calibration approach derived from The Cancer Genome Atlas data, tailored to each panel assay, reduced the spread of panel TMB values around the WES TMB as reflected in lower root mean squared error (RMSE) for 26/29 (90%) of the clinical samples. CONCLUSIONS Estimation of TMB varies across different panels, with panel size, gene content, and bioinformatics pipelines contributing to empirical variability. Statistical calibration can achieve more consistent results across panels and allows for comparison of TMB values across various panel assays. To promote reproducibility and comparability across assays, a software tool was developed and made publicly available.
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Affiliation(s)
- D M Vega
- Friends of Cancer Research, Washington, USA
| | - L M Yee
- National Cancer Institute, Bethesda, USA
| | | | - P M Williams
- Molecular Characterization Laboratory, Frederick National Lab for Cancer Research, Leidos Biomedical Research Inc., Frederick, USA
| | - L Chen
- Molecular Characterization Laboratory, Frederick National Lab for Cancer Research, Leidos Biomedical Research Inc., Frederick, USA
| | - T Vilimas
- Molecular Characterization Laboratory, Frederick National Lab for Cancer Research, Leidos Biomedical Research Inc., Frederick, USA
| | - D Fabrizio
- Foundation Medicine Inc., Cambridge, USA
| | - V Funari
- NeoGenomics Laboratories, Aliso Viejo, USA
| | - J Newberg
- Foundation Medicine Inc., Cambridge, USA
| | - L K Bruce
- NeoGenomics Laboratories, Aliso Viejo, USA
| | | | - J Baden
- Bristol Myers Squibb Co., Princeton, USA
| | | | - P Beer
- European Organisation for Research and Treatment of Cancer, Brussels, Belgium
| | - M Butler
- LGC Clinical Diagnostics, Gaithersburg, USA
| | | | | | - D Cyanam
- Clinical Sequencing Division, Thermo Fisher Scientific, Ann Arbor, USA
| | - K Eyring
- Intermountain Precision Genomics, St. George, USA
| | - E Garcia
- Brigham and Women's Hospital, Boston, USA
| | - G Green
- Bristol Myers Squibb Co., Princeton, USA
| | | | - M D Hellmann
- Memorial Sloan Kettering Cancer Center, New York, USA
| | - L A Keefer
- Personal Genome Diagnostics, Baltimore, USA
| | - L Lasiter
- Friends of Cancer Research, Washington, USA
| | - A J Lazar
- The University of Texas MD Anderson Cancer Center, Houston, USA
| | - M-C Li
- National Cancer Institute, Bethesda, USA
| | | | - K Meier
- Illumina Inc, Clinical Genomics, San Diego, USA
| | | | | | | | | | - R Salgado
- European Organisation for Research and Treatment of Cancer, Brussels, Belgium
| | | | - E S Sokol
- Foundation Medicine Inc., Cambridge, USA
| | | | - J Budczies
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - A Stenzinger
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - W Tom
- Clinical Sequencing Division, Thermo Fisher Scientific, Ann Arbor, USA
| | | | - X Z Wang
- EMD Serono Research and Development Institute, Inc., Billerica, USA
| | | | - M Xie
- AstraZeneca Pharmaceuticals LP, Waltham, USA
| | - Q Xie
- General Dynamics Information Technology, Inc., Columbia, USA
| | - A Zehir
- Memorial Sloan Kettering Cancer Center, New York, USA
| | - C Zhao
- Illumina Inc, Clinical Genomics, San Diego, USA
| | - Y Zhao
- National Cancer Institute, Bethesda, USA
| | - M D Stewart
- Friends of Cancer Research, Washington, USA.
| | - J Allen
- Friends of Cancer Research, Washington, USA
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38
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Sabnis HS, Shulman DS, Mizukawa B, Bouvier N, Zehir A, Fangusaro J, Fabrizio VA, Whitlow C, Winchester M, Agresta L, Turpin B, Wechsler DS, DuBois SG, Glade-Bender J, Castellino SM, Shukla N. Multicenter Analysis of Genomically Targeted Single Patient Use Requests for Pediatric Neoplasms. J Clin Oncol 2021; 39:3822-3828. [PMID: 34591650 PMCID: PMC9851705 DOI: 10.1200/jco.21.01213] [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: 01/22/2023] Open
Abstract
PURPOSE The US Food and Drug Administration-expanded access program (EAP) uses a single patient use (SPU) mechanism to provide patient access to investigational agents in situations where no satisfactory or comparable therapy is available. Genomic profiling of de novo and relapsed or refractory childhood cancer has led to increased identification of new drug targets in the last decade. The aim of this study is to examine the SPU experience for genomically targeted therapies in patients with pediatric cancer. PATIENTS AND METHODS All genomically targeted therapeutic SPUs obtained over a 5-year period were evaluated at four large pediatric cancer programs. Data were collected on the type of neoplasm, agents requested, corresponding molecularly informed targets, and clinical outcomes. RESULTS A total of 45 SPUs in 44 patients were identified. Requests were predominantly made for CNS and solid tumors (84.4%) compared with hematologic malignancies (15.6%). Lack of an available clinical trial was the main reason for SPU initiation (64.4%). The median time from US Food and Drug Administration submission to approval was 3 days (range, 0-12 days) and from Institutional Review Board submission to approval was 5 days (range, 0-50 days). Objective tumor response was seen in 39.5% (15 of 38) of all evaluable SPUs. Disease progression was the primary reason for discontinuation of drug (66.7%) followed by toxicity (13.3%). CONCLUSION SPU requests remain an important mechanism for pediatric access to genomically targeted agents given the limited availability of targeted clinical trials for children with high-risk neoplasms. Furthermore, this subset of SPUs resulted in a substantial number of objective tumor responses. The development of a multi-institutional data registry of SPUs may enable systematic review of toxicity and clinical outcomes and provide evidence-based access to new drugs in rare pediatric cancers.
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Affiliation(s)
- Himalee S. Sabnis
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA,Emory University School of Medicine, Department of Pediatrics, Atlanta, GA,Himalee S. Sabnis, MD, MSc, The Aflac Cancer & Blood Disorders Center, Children's Healthcare of Atlanta, Emory University, 426J Emory Children's Center, 2015 Uppergate Dr, Atlanta, GA 30322; e-mail:
| | - David S. Shulman
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA
| | - Benjamin Mizukawa
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH,University of Cincinnati College of Medicine, Cincinnati OH
| | - Nancy Bouvier
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jason Fangusaro
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA,Emory University School of Medicine, Department of Pediatrics, Atlanta, GA
| | - Vanessa A. Fabrizio
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Chanta Whitlow
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA
| | - Marilyn Winchester
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Laura Agresta
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH,University of Cincinnati College of Medicine, Cincinnati OH
| | - Brian Turpin
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH,University of Cincinnati College of Medicine, Cincinnati OH
| | - Daniel S. Wechsler
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA,Emory University School of Medicine, Department of Pediatrics, Atlanta, GA
| | - Steven G. DuBois
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA
| | - Julia Glade-Bender
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sharon M. Castellino
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA,Emory University School of Medicine, Department of Pediatrics, Atlanta, GA
| | - Neerav Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
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39
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Liu YL, Cadoo KA, Mukherjee S, Khurram A, Tkachuk K, Kemel Y, Maio A, Belhadj S, Carlo MI, Latham A, Walsh MF, Dubard-Gault ME, Wang Y, Brannon AR, Salo-Mullen E, Sheehan M, Fiala E, Devolder B, Dandiker S, Mandelker D, Zehir A, Ladanyi M, Berger MF, Solit DB, Bandlamudi C, Ravichandran V, Bajorin DF, Stadler ZK, Robson ME, Vijai J, Seshan V, Offit K. Multiple Primary Cancers in Patients Undergoing Tumor-Normal Sequencing Define Novel Associations. Cancer Epidemiol Biomarkers Prev 2021; 31:362-371. [PMID: 34810208 DOI: 10.1158/1055-9965.epi-21-0820] [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] [Received: 07/02/2021] [Revised: 10/07/2021] [Accepted: 11/18/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Cancer survivors are developing more subsequent tumors. We sought to characterize patients with multiple (≥2) primary cancers (MPC) to assess associations and genetic mechanisms. METHODS Patients were prospectively consented (01/2013-02/2019) to tumor-normal sequencing via a custom targeted panel (MSK-IMPACT). A subset consented to return of results of ≥76 cancer predisposition genes. International Agency for Research on Cancer (IARC) 2004 rules for defining MPC were applied. Tumor pairs were created to assess relationships between cancers. Age-adjusted, sex-specific, standardized incidence ratios (SIR) for first to second cancer event combinations were calculated using SEER rates, adjusting for confounders and time of ascertainment. Associations were made with germline and somatic variants. RESULTS Of 24,241 patients, 4,340 had MPC (18%); 20% were synchronous. Most (80%) had two primaries; however, 4% had ≥4 cancers. SIR analysis found lymphoma-lung, lymphoma-uterine, breast-brain, and melanoma-lung pairs in women and prostate-mesothelioma, prostate-sarcoma, melanoma-stomach, and prostate-brain pairs in men in excess of expected after accounting for synchronous tumors, known inherited cancer syndromes, and environmental exposures. Of 1,580 (36%) patients who received germline results, 324 (21%) had 361 pathogenic/likely pathogenic variants (PV), 159 (44%) in high penetrance genes. Of tumor samples analyzed, 55% exhibited loss of heterozygosity at the germline variant. In those with negative germline findings, melanoma, prostate, and breast cancers were common. CONCLUSIONS We identified tumor pairs without known predisposing mutations that merit confirmation and will require novel strategies to elucidate genetic mechanisms of shared susceptibilities. IMPACT If verified, patients with MPC with novel phenotypes may benefit from targeted cancer surveillance.
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Affiliation(s)
- Ying L Liu
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York. .,Department of Medicine, Weill Cornell Medical College, New York, New York
| | | | - Semanti Mukherjee
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Aliya Khurram
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kaitlyn Tkachuk
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yelena Kemel
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Sloan Kettering Institute, Memorial Sloan Kettering New York, New York
| | - Anna Maio
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sami Belhadj
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Sloan Kettering Institute, Memorial Sloan Kettering New York, New York
| | - Maria I Carlo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Alicia Latham
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Michael F Walsh
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Marianne E Dubard-Gault
- Division of Medical Genetics in the Department of Medicine, University of Washington, Seattle, Washington
| | - Yuhan Wang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - A Rose Brannon
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Erin Salo-Mullen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Margaret Sheehan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Elise Fiala
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Bryan Devolder
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sita Dandiker
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Diana Mandelker
- 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
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael F Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.,Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David B Solit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Chaitanya Bandlamudi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.,Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Vignesh Ravichandran
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Dean F Bajorin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Zsofia K Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Mark E Robson
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Joseph Vijai
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Venkatraman Seshan
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Weill Cornell Medical College, New York, New York
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40
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Srinivasan P, Bandlamudi C, Jonsson P, Kemel Y, Chavan SS, Richards AL, Penson AV, Bielski CM, Fong C, Syed A, Jayakumaran G, Prasad M, Hwee J, Sumer SO, de Bruijn I, Li X, Gao J, Schultz N, Cambria R, Galle J, Mukherjee S, Vijai J, Cadoo KA, Carlo MI, Walsh MF, Mandelker D, Ceyhan-Birsoy O, Shia J, Zehir A, Ladanyi M, Hyman DM, Zhang L, Offit K, Robson ME, Solit DB, Stadler ZK, Berger MF, Taylor BS. The context-specific role of germline pathogenicity in tumorigenesis. Nat Genet 2021; 53:1577-1585. [PMID: 34741162 PMCID: PMC8957388 DOI: 10.1038/s41588-021-00949-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [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] [Received: 11/16/2020] [Accepted: 09/09/2021] [Indexed: 11/08/2022]
Abstract
Human cancers arise from environmental, heritable and somatic factors, but how these mechanisms interact in tumorigenesis is poorly understood. Studying 17,152 prospectively sequenced patients with cancer, we identified pathogenic germline variants in cancer predisposition genes, and assessed their zygosity and co-occurring somatic alterations in the concomitant tumors. Two major routes to tumorigenesis were apparent. In carriers of pathogenic germline variants in high-penetrance genes (5.1% overall), lineage-dependent patterns of biallelic inactivation led to tumors exhibiting mechanism-specific somatic phenotypes and fewer additional somatic oncogenic drivers. Nevertheless, 27% of cancers in these patients, and most tumors in patients with pathogenic germline variants in lower-penetrance genes, lacked particular hallmarks of tumorigenesis associated with the germline allele. The dependence of tumors on pathogenic germline variants is variable and often dictated by both penetrance and lineage, a finding with implications for clinical management.
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Affiliation(s)
- Preethi Srinivasan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Stanford University School of Medicine, Palo Alto, CA, USA
| | - Chaitanya Bandlamudi
- Department of Pathology, 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
| | - Philip Jonsson
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yelena Kemel
- Robert and Kate Niehaus Center for Inherited Cancer Genomics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shweta S Chavan
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Allison L Richards
- 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
- 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
- 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
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Aijazuddin Syed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gowtham Jayakumaran
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Meera Prasad
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jason Hwee
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Selcuk Onur Sumer
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ino de Bruijn
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Xiang Li
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 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
- Department of Epidemiology and Biostatistics, 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
| | - Roy Cambria
- Research and Technology Management, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jesse Galle
- Research and Technology Management, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Semanti Mukherjee
- 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
| | - 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
| | - Karen A Cadoo
- 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
| | - Maria I Carlo
- 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
| | - Michael F Walsh
- 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
| | - Diana Mandelker
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ozge Ceyhan-Birsoy
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jinru Shia
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ahmet Zehir
- 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
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David M Hyman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Loxo Oncology, Stamford, CT, USA
| | - Liying Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 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
| | - Mark E Robson
- 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
| | - 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
| | - Michael F Berger
- Department of Pathology, 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.
| | - Barry S Taylor
- 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
- Loxo Oncology, Stamford, CT, USA
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41
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Carter AB, Abruzzo LV, Hirschhorn JW, Jones D, Jordan DC, Nassiri M, Ogino S, Patel NR, Suciu CG, Temple-Smolkin RL, Zehir A, Roy S. Electronic Health Records and Genomics: Perspectives from the Association for Molecular Pathology Electronic Health Record (EHR) Interoperability for Clinical Genomics Data Working Group. J Mol Diagn 2021; 24:1-17. [PMID: 34656760 DOI: 10.1016/j.jmoldx.2021.09.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 09/14/2021] [Accepted: 09/28/2021] [Indexed: 02/09/2023] Open
Abstract
The use of genomics in medicine is expanding rapidly, but information systems are lagging in their ability to support genomic workflows both from the laboratory and patient-facing provider perspective. The complexity of genomic data, the lack of needed data standards, and lack of genomic fluency and functionality as well as several other factors have contributed to the gaps between genomic data generation, interoperability, and utilization. These gaps are posing significant challenges to laboratory and pathology professionals, clinicians, and patients in the ability to generate, communicate, consume, and use genomic test results. The Association for Molecular Pathology Electronic Health Record Working Group was convened to assess the challenges and opportunities and to recommend solutions on ways to resolve current problems associated with the display and use of genomic data in electronic health records.
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Affiliation(s)
- Alexis B Carter
- The Electronic Health Record Interoperability for Clinical Genomics Data Working Group of the Informatics Subdivision, Association for Molecular Pathology, Rockville, Maryland; Children's Healthcare of Atlanta, Atlanta, Georgia.
| | - Lynne V Abruzzo
- The Electronic Health Record Interoperability for Clinical Genomics Data Working Group of the Informatics Subdivision, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Wexner Medical Center, The Ohio State University, Columbus, Ohio
| | - Julie W Hirschhorn
- The Electronic Health Record Interoperability for Clinical Genomics Data Working Group of the Informatics Subdivision, Association for Molecular Pathology, Rockville, Maryland; Medical University of South Carolina, Charleston, South Carolina
| | - Dan Jones
- The Electronic Health Record Interoperability for Clinical Genomics Data Working Group of the Informatics Subdivision, Association for Molecular Pathology, Rockville, Maryland; The Ohio State University Comprehensive Cancer Center, James Cancer Hospital and Solove Research Institute, Columbus, Ohio
| | | | - Mehdi Nassiri
- The Electronic Health Record Interoperability for Clinical Genomics Data Working Group of the Informatics Subdivision, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Shuji Ogino
- The Electronic Health Record Interoperability for Clinical Genomics Data Working Group of the Informatics Subdivision, Association for Molecular Pathology, Rockville, Maryland; Brigham & Women's Hospital, Boston, Massachusetts; Harvard Medical School, Boston, Massachusetts; Harvard T.H. Chan School of Public Health, Boston, Massachusetts; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Nimesh R Patel
- The Electronic Health Record Interoperability for Clinical Genomics Data Working Group of the Informatics Subdivision, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Rhode Island Hospital and Alpert Medical School of Brown University, Providence, Rhode Island
| | - Christopher G Suciu
- The Electronic Health Record Interoperability for Clinical Genomics Data Working Group of the Informatics Subdivision, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri; Institute for Informatics, Washington University School of Medicine, St. Louis, Missouri
| | | | - Ahmet Zehir
- The Electronic Health Record Interoperability for Clinical Genomics Data Working Group of the Informatics Subdivision, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Somak Roy
- The Electronic Health Record Interoperability for Clinical Genomics Data Working Group of the Informatics Subdivision, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
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42
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Bolton KL, Koh Y, Foote MB, Im H, Jee J, Sun CH, Safonov A, Ptashkin R, Moon JH, Lee JY, Jung J, Kang CK, Song KH, Choe PG, Park WB, Kim HB, Oh MD, Song H, Kim S, Patel M, Derkach A, Gedvilaite E, Tkachuk KA, Wiley BJ, Chan IC, Braunstein LZ, Gao T, Papaemmanuil E, Esther Babady N, Pessin MS, Kamboj M, Diaz LA, Ladanyi M, Rauh MJ, Natarajan P, Machiela MJ, Awadalla P, Joseph V, Offit K, Norton L, Berger MF, Levine RL, Kim ES, Kim NJ, Zehir A. Clonal hematopoiesis is associated with risk of severe Covid-19. Nat Commun 2021; 12:5975. [PMID: 34645798 PMCID: PMC8514469 DOI: 10.1038/s41467-021-26138-6] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [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: 04/13/2021] [Accepted: 09/10/2021] [Indexed: 01/08/2023] Open
Abstract
Acquired somatic mutations in hematopoietic stem and progenitor cells (clonal hematopoiesis or CH) are associated with advanced age, increased risk of cardiovascular and malignant diseases, and decreased overall survival. These adverse sequelae may be mediated by altered inflammatory profiles observed in patients with CH. A pro-inflammatory immunologic profile is also associated with worse outcomes of certain infections, including SARS-CoV-2 and its associated disease Covid-19. Whether CH predisposes to severe Covid-19 or other infections is unknown. Among 525 individuals with Covid-19 from Memorial Sloan Kettering (MSK) and the Korean Clonal Hematopoiesis (KoCH) consortia, we show that CH is associated with severe Covid-19 outcomes (OR = 1.85, 95%=1.15-2.99, p = 0.01), in particular CH characterized by non-cancer driver mutations (OR = 2.01, 95% CI = 1.15-3.50, p = 0.01). We further explore the relationship between CH and risk of other infections in 14,211 solid tumor patients at MSK. CH is significantly associated with risk of Clostridium Difficile (HR = 2.01, 95% CI: 1.22-3.30, p = 6×10-3) and Streptococcus/Enterococcus infections (HR = 1.56, 95% CI = 1.15-2.13, p = 5×10-3). These findings suggest a relationship between CH and risk of severe infections that warrants further investigation.
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Affiliation(s)
- Kelly L Bolton
- Department of Medicine, Washington University, St Louis, MO, USA.
| | - Youngil Koh
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
- Genome Opinion Inc., Seoul, Korea
- Center for Precision Medicine, Seoul National University Hospital, Seoul, Korea
| | - Michael B Foote
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Justin Jee
- 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
| | - Ryan Ptashkin
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joon Ho Moon
- Department of Internal Medicine, Kyungpook National University Hospital, School of Medicine, Kyungpook National University, Daegu, Korea
| | - Ji Yeon Lee
- Department of Internal Medicine, National Medical Center, Seoul, Korea
| | - Jongtak Jung
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Chang Kyung Kang
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
| | - Kyoung-Ho Song
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Pyoeng Gyun Choe
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
| | - Wan Beom Park
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
| | - Hong Bin Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Myoung-Don Oh
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
| | - Han Song
- Genome Opinion Inc., Seoul, Korea
| | | | - Minal Patel
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andriy Derkach
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Erika Gedvilaite
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kaitlyn A Tkachuk
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Brian J Wiley
- Department of Medicine, Washington University, St Louis, MO, USA
| | - Ireaneus C Chan
- Department of Medicine, Washington University, St Louis, MO, USA
| | - Lior Z Braunstein
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Teng Gao
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Center for Computational Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elli Papaemmanuil
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Center for Computational Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - N Esther Babady
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Melissa S Pessin
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mini Kamboj
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Luis A Diaz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael J Rauh
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada
| | - Pradeep Natarajan
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | | | - Vijai Joseph
- Clinical Genetics Research Lab, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kenneth Offit
- Clinical Genetics Research Lab, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Larry Norton
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael F Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Center for Computational Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ross L Levine
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eu Suk Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea.
| | - Nam Joong Kim
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea.
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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Zehir A, Berger MF. A quick guide for clinical oncology. Nat Cancer 2021; 2:998-999. [PMID: 35121881 DOI: 10.1038/s43018-021-00273-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Michael F Berger
- Department of Pathology, 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.
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Chui MH, Chang JC, Zhang Y, Zehir A, Schram AM, Konner J, Drilon AE, Da Cruz Paula A, Weigelt B, Grisham RN. Spectrum of BRAF Mutations and Gene Rearrangements in Ovarian Serous Carcinoma. JCO Precis Oncol 2021; 5:PO.21.00055. [PMID: 34568720 PMCID: PMC8457847 DOI: 10.1200/po.21.00055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 05/28/2021] [Accepted: 07/27/2021] [Indexed: 01/08/2023] Open
Abstract
Low-grade serous carcinoma (LGSC) is a rare type of ovarian cancer, which commonly arises from serous borderline tumor (SBT) and is characterized by frequent activating mutations in the mitogen-activated protein kinase pathway, including BRAF. The BRAF V600E mutation is associated with improved prognosis in SBT and LGSC, and responses to BRAF inhibitor therapy have been reported. We sought to characterize the clinicopathologic and molecular features of BRAF-driven tubo-ovarian and primary peritoneal serous tumors. METHODS Retrospective analysis of our institutional cohort of SBTs (n = 22), LGSCs (n = 119) and high-grade serous carcinomas (HGSCs, n = 1,290) subjected to targeted massively parallel sequencing was performed to identify cases with BRAF genetic alterations. Putative BRAF rearrangements were confirmed using targeted RNA sequencing and/or fluorescence in situ hybridization (FISH). BRAFV600E oncoprotein expression was assessed by immunohistochemistry on selected cases. RESULTS BRAF somatic genetic alterations were identified in 29 of 1,431 (2%) serous tumors and included mutations (n = 24), gene rearrangements (n = 3), and amplification (n = 2). BRAF mutations were more frequent in SBTs (7 of 22; 32%) compared with LGSCs (11 of 119; 9%, P = .009) and HGSCs (6 of 1,290; 0.5%; P < .0001, SBT/LGSC v HGSC). The BRAF V600E hotspot mutation was most common (n = 16); however, other BRAF driver mutations were also detected (n = 8). BRAF mutations were often clonal or truncal in SBTs and LGSCs, but subclonal in most HGSCs. Pathogenic BRAF gene fusions were identified in LGSCs (n = 2) and HGSC (n = 1) and involved distinct fusion partners (AGK, MKRN1, and AGAP3). Three patients with BRAF-mutant LGSC were treated with targeted mitogen-activated protein kinase inhibitors, one of whom was maintained on therapy for over 3 years with clinical benefit. CONCLUSION Recognition of BRAF alterations beyond V600E mutation in LGSC may have clinical implications for appropriate targeted therapy selection.
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Affiliation(s)
- M Herman Chui
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jason C Chang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yanming Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Zehir
- Department of Computational Biology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Alison M Schram
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Jason Konner
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Alexander E Drilon
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Medicine, Weill Cornell Medical College, New York, NY
| | | | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Rachel N Grisham
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Medicine, Weill Cornell Medical College, New York, NY
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Chui MH, Yang C, Mehta N, Rai V, Zehir A, Momeni Boroujeni A, Ladanyi M, Mandelker D. Somatic intronic TP53 c.375+5G mutations are a recurrent but under-recognized mode of TP53 inactivation. J Pathol Clin Res 2021; 8:14-18. [PMID: 34505757 PMCID: PMC8682938 DOI: 10.1002/cjp2.242] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/18/2021] [Accepted: 08/21/2021] [Indexed: 11/30/2022]
Abstract
TP53 is one of the most ubiquitously altered genes in human cancer. The biological impact of rare variants, particularly those located within noncoding regions, remains poorly understood. From interrogation of clinical massively parallel sequencing data from over 55,000 tumors, which included 23,330 tumors with known TP53 mutations, TP53 intron 4 nucleotide substitutions at position c.375+5G were identified in 45 tumors (0.2% of TP53‐mutated cancers), comprising cancers of different organ sites. Loss‐of‐heterozygosity or a second‐hit somatic TP53 mutation was observed in 34 of 40 (85%) informative cases. RT‐PCR analysis showed the c.375+5G>T variant to be associated with aberrantly spliced TP53 mRNA transcripts with concomitant loss of the normal transcript. Immunohistochemical staining for p53 was performed on a representative subset of tumors with TP53 c.375+5G variants (n = 14), all of which showed loss of protein expression (100%; n = 13 complete loss, n = 1 subclonal loss). Our data are consistent with classification of TP53 c.375+5G variants as deleterious intronic mutations that interfere with proper mRNA splicing, ultimately resulting in loss of expression of functional p53 protein. The clinical scenario of a tumor with loss of p53 immunohistochemical staining, yet lacking a detectable TP53 exonic mutation, should therefore prompt consideration of splice‐altering intronic variants.
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Affiliation(s)
- M Herman Chui
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ciyu Yang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nikita Mehta
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Vikas Rai
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ahmet Zehir
- 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
| | - Diana Mandelker
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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Thomas S, Lichtenberg T, Dang K, Fitzsimons M, Grossman RL, Kundra R, Lavery JA, Lenoue-Newton ML, Panageas KS, Sawyers C, Schultz ND, Sirintrapun SJ, Topaloglu U, Welch A, Yu T, Zehir A, Gardos S. Linked Entity Attribute Pair (LEAP): A Harmonization Framework for Data Pooling. JCO Clin Cancer Inform 2021; 4:691-699. [PMID: 32755461 PMCID: PMC7469618 DOI: 10.1200/cci.20.00037] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE As data-sharing projects become increasingly frequent, so does the need to map data elements between multiple classification systems. A generic, robust, shareable architecture will result in increased efficiency and transparency of the mapping process, while upholding the integrity of the data. MATERIALS AND METHODS The American Association for Cancer Research’s Genomics Evidence Neoplasia Information Exchange (GENIE) collects clinical and genomic data for precision cancer medicine. As part of its commitment to open science, GENIE has partnered with the National Cancer Institute’s Genomic Data Commons (GDC) as a secondary repository. After initial efforts to submit data from GENIE to GDC failed, we realized the need for a solution to allow for the iterative mapping of data elements between dynamic classification systems. We developed the Linked Entity Attribute Pair (LEAP) database framework to store and manage the term mappings used to submit data from GENIE to GDC. RESULTS After creating and populating the LEAP framework, we identified 195 mappings from GENIE to GDC requiring remediation and observed a 28% reduction in effort to resolve these issues, as well as a reduction in inadvertent errors. These results led to a decrease in the time to map between OncoTree, the cancer type ontology used by GENIE, and International Classification of Disease for Oncology, 3rd Edition, used by GDC, from several months to less than 1 week. CONCLUSION The LEAP framework provides a streamlined mapping process among various classification systems and allows for reusability so that efforts to create or adjust mappings are straightforward. The ability of the framework to track changes over time streamlines the process to map data elements across various dynamic classification systems.
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Affiliation(s)
- Stacy Thomas
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Tara Lichtenberg
- Center for Translational Data Science, University of Chicago, Chicago, IL
| | | | - Michael Fitzsimons
- Center for Translational Data Science, University of Chicago, Chicago, IL.,University of Illinois at Chicago, Chicago, IL
| | - Robert L Grossman
- Center for Translational Data Science, University of Chicago, Chicago, IL
| | - Ritika Kundra
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jessica A Lavery
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Katherine S Panageas
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Charles Sawyers
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nikolaus D Schultz
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Umit Topaloglu
- Cancer Biology, Wake Forest University School of Medicine, Winston Salem, NC
| | - Angelica Welch
- Information Systems, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Stuart Gardos
- Information Systems, Memorial Sloan Kettering Cancer Center, New York, NY
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Merino DM, McShane LM, Fabrizio D, Funari V, Chen SJ, White JR, Wenz P, Baden J, Barrett JC, Chaudhary R, Chen L, Chen WS, Cheng JH, Cyanam D, Dickey JS, Gupta V, Hellmann M, Helman E, Li Y, Maas J, Papin A, Patidar R, Quinn KJ, Rizvi N, Tae H, Ward C, Xie M, Zehir A, Zhao C, Dietel M, Stenzinger A, Stewart M, Allen J. Establishing guidelines to harmonize tumor mutational burden (TMB): in silico assessment of variation in TMB quantification across diagnostic platforms: phase I of the Friends of Cancer Research TMB Harmonization Project. J Immunother Cancer 2021; 8:jitc-2019-000147. [PMID: 32217756 PMCID: PMC7174078 DOI: 10.1136/jitc-2019-000147] [Citation(s) in RCA: 281] [Impact Index Per Article: 93.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/11/2020] [Indexed: 12/13/2022] Open
Abstract
Background Tumor mutational burden (TMB), defined as the number of somatic mutations per megabase of interrogated genomic sequence, demonstrates predictive biomarker potential for the identification of patients with cancer most likely to respond to immune checkpoint inhibitors. TMB is optimally calculated by whole exome sequencing (WES), but next-generation sequencing targeted panels provide TMB estimates in a time-effective and cost-effective manner. However, differences in panel size and gene coverage, in addition to the underlying bioinformatics pipelines, are known drivers of variability in TMB estimates across laboratories. By directly comparing panel-based TMB estimates from participating laboratories, this study aims to characterize the theoretical variability of panel-based TMB estimates, and provides guidelines on TMB reporting, analytic validation requirements and reference standard alignment in order to maintain consistency of TMB estimation across platforms. Methods Eleven laboratories used WES data from The Cancer Genome Atlas Multi-Center Mutation calling in Multiple Cancers (MC3) samples and calculated TMB from the subset of the exome restricted to the genes covered by their targeted panel using their own bioinformatics pipeline (panel TMB). A reference TMB value was calculated from the entire exome using a uniform bioinformatics pipeline all members agreed on (WES TMB). Linear regression analyses were performed to investigate the relationship between WES and panel TMB for all 32 cancer types combined and separately. Variability in panel TMB values at various WES TMB values was also quantified using 95% prediction limits. Results Study results demonstrated that variability within and between panel TMB values increases as the WES TMB values increase. For each panel, prediction limits based on linear regression analyses that modeled panel TMB as a function of WES TMB were calculated and found to approximately capture the intended 95% of observed panel TMB values. Certain cancer types, such as uterine, bladder and colon cancers exhibited greater variability in panel TMB values, compared with lung and head and neck cancers. Conclusions Increasing uptake of TMB as a predictive biomarker in the clinic creates an urgent need to bring stakeholders together to agree on the harmonization of key aspects of panel-based TMB estimation, such as the standardization of TMB reporting, standardization of analytical validation studies and the alignment of panel-based TMB values with a reference standard. These harmonization efforts should improve consistency and reliability of panel TMB estimates and aid in clinical decision-making.
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Affiliation(s)
| | | | | | | | | | | | - Paul Wenz
- Clinical Genomics, Illumina Inc, San Diego, California, USA
| | | | - J Carl Barrett
- Translational Medicine, Oncology Research and Early Development, AstraZeneca Pharmaceuticals LP, Boston, Massachusetts, USA
| | - Ruchi Chaudhary
- Clinical Sequencing Division, Thermo Fisher Scientific, Ann Arbor, Michigan, USA
| | - Li Chen
- Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | | | | | - Dinesh Cyanam
- Clinical Sequencing Division, Thermo Fisher Scientific, Ann Arbor, Michigan, USA
| | | | | | | | - Elena Helman
- Bioinformatics, Guardant Health Inc, Redwood City, California, USA
| | - Yali Li
- Foundation Medicine Inc, Cambridge, Massachusetts, USA
| | - Joerg Maas
- Quality in Pathology (QuIP), Berlin, Germany
| | | | - Rajesh Patidar
- Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Katie J Quinn
- Bioinformatics, Guardant Health Inc, Redwood City, California, USA
| | - Naiyer Rizvi
- Division of Hematology/Oncology, Department of Medicine, Columbia University, New York, New York, USA
| | | | | | - Mingchao Xie
- AstraZeneca Pharmaceuticals LP, Waltham, Massachusetts, USA
| | - Ahmet Zehir
- Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Chen Zhao
- Clinical Genomics, Illumina Inc, San Diego, California, USA
| | | | - Albrecht Stenzinger
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Baden-Württemberg, Germany
| | | | - Jeff Allen
- Friends of Cancer Research, Washington, DC, USA
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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.
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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
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da Silva EM, Fix DJ, Sebastiao APM, Selenica P, Ferrando L, Kim SH, Stylianou A, Da Cruz Paula A, Pareja F, Smith ES, Zehir A, Konner JA, Cadoo K, Reis-Filho JS, Abu-Rustum NR, Mueller JJ, Weigelt B, Park KJ. Mesonephric and mesonephric-like carcinomas of the female genital tract: molecular characterization including cases with mixed histology and matched metastases. Mod Pathol 2021; 34:1570-1587. [PMID: 33772212 PMCID: PMC8343944 DOI: 10.1038/s41379-021-00799-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [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: 01/08/2021] [Revised: 02/24/2021] [Accepted: 03/02/2021] [Indexed: 12/13/2022]
Abstract
Mesonephric carcinoma of the cervix is a rare tumor derived from Wolffian remnants. Mesonephric-like carcinomas of the ovary and endometrium, while morphologically similar, do not have obvious Wolffian derivation. Here, we sought to characterize the repertoire of genetic alterations in primary mesonephric and mesonephric-like carcinomas, in the distinct histologic components of mixed cases, as well as in matched primary tumors and metastases. DNA from microdissected tumor and normal tissue from mesonephric carcinomas (cervix, n = 8) and mesonephric-like carcinomas (ovarian n = 15, endometrial n = 13) were subjected to sequencing targeting 468 cancer-related genes. The histologically distinct components of four cases with mixed histology and four primary tumors and their matched metastases were microdissected and analyzed separately. Mesonephric-like carcinomas were underpinned by somatic KRAS mutations (25/28, 89%) akin to mesonephric carcinomas (8/8, 100%), but also harbored genetic alterations more frequently reported in Müllerian tumors. Mesonephric-like carcinomas that lacked KRAS mutations harbored NRAS (n = 2, ovary) or BRAF (n = 1, endometrium) hotspot mutations. PIK3CA mutations were identified in both mesonephric-like (8/28, 28%) and mesonephric carcinomas (2/8, 25%). Only mesonephric-like tumors harbored CTNNB1 hotspot (4/28, 14%) and PTEN (3/13, 23%) mutations. Copy number analysis revealed frequent gains of chromosomes 1q and 10 in both mesonephric (87% 1q; 50% chromosome 10) and mesonephric-like tumors (89% 1q; 43% chromosome 10). Chromosome 12 gains were more frequent in ovarian mesonephric-like carcinomas, and losses of chromosome 9 were more frequent in mesonephric than in mesonephric-like carcinomas (both p = 0.01, Fisher's exact test). The histologically distinct components of four mixed cases were molecularly related and shared similar patterns of genetic alterations. The progression from primary to metastatic lesions involved the acquisition of additional mutations, and/or shifts from subclonal to clonal mutations. Our findings suggest that mesonephric-like carcinomas are derived from a Müllerian substrate with differentiation along Wolffian/mesonephric lines.
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Affiliation(s)
- Edaise M da Silva
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel J Fix
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology, Hackensack University Medical Center, Hackensack, NJ, USA
| | - Ana Paula Martins Sebastiao
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medical Pathology, Federal University of Parana, Curitiba, PR, Brazil
| | - Pier Selenica
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lorenzo Ferrando
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Internal Medicine, University of Genoa, Genoa, Italy
| | - Sarah H Kim
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anthe Stylianou
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Arnaud Da Cruz Paula
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fresia Pareja
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Evan S Smith
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jason A Konner
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Karen Cadoo
- Department of Medicine, 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
| | - Nadeem R Abu-Rustum
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jennifer J Mueller
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Kay J Park
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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50
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Ceyhan-Birsoy O, Selenica P, Chui MH, Jayakumaran G, Ptashkin R, Misyura M, Aypar U, Jairam S, Yang C, Li Y, Mehta N, Kemel Y, Salo-Mullen E, Maio A, Sheehan M, Zehir A, Carlo M, Latham A, Stadler Z, Robson M, Offit K, Ladanyi M, Walsh M, Reis-Filho JS, Mandelker D. Paired Tumor-Normal Sequencing Provides Insights Into the TP53-Related Cancer Spectrum in Patients With Li-Fraumeni Syndrome. J Natl Cancer Inst 2021; 113:1751-1760. [PMID: 34240179 PMCID: PMC9891110 DOI: 10.1093/jnci/djab117] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 04/12/2021] [Accepted: 07/01/2021] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Genetic testing for Li-Fraumeni syndrome (LFS) is performed by using blood specimens from patients selected based on phenotype-dependent guidelines. This approach is problematic for understanding the LFS clinical spectrum because patients with nonclassical presentations are missed, clonal hematopoiesis-related somatic blood alterations cannot be distinguished from germline variants, and unrelated tumors cannot be differentiated from those driven by germline TP53 defects. METHODS To provide insights into the LFS-related cancer spectrum, we analyzed paired tumor-blood DNA sequencing results in 17 922 patients with cancer and distinguished clonal hematopoiesis-related, mosaic, and germline TP53 variants. Loss of heterozygosity and TP53 mutational status were assessed in tumors, followed by immunohistochemistry for p53 expression on a subset to identify those lacking biallelic TP53 inactivation. RESULTS Pathogenic/likely pathogenic TP53 variants were identified in 50 patients, 12 (24.0%) of which were clonal hematopoiesis related and 4 (8.0%) of which were mosaic. Twelve (35.3%) of 34 patients with germline TP53 variants did not meet LFS testing criteria. Loss of heterozygosity of germline TP53 variant was observed in 96.0% (95% confidence interval [CI] = 79.7% to 99.9%) of core LFS spectrum-type tumors vs 45.5% (95% CI = 16.8% to 76.6%) of other tumors and 91.3% (95% CI = 72.0% to 98.9%) of tumors from patients who met LFS testing criteria vs 61.5% (95% CI = 31.6% to 86.1%) of tumors from patients who did not. Tumors retaining the wild-type TP53 allele exhibited wild-type p53 expression. CONCLUSIONS Our results indicate that some TP53 variants identified in blood-only sequencing are not germline and a substantial proportion of patients with LFS are missed based on current testing guidelines. Additionally, a subset of tumors from patients with LFS do not have biallelic TP53 inactivation and may represent cancers unrelated to their germline TP53 defect.
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Affiliation(s)
- Ozge Ceyhan-Birsoy
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pier Selenica
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M Herman Chui
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gowtham Jayakumaran
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ryan Ptashkin
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maksym Misyura
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Umut Aypar
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sowmya Jairam
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ciyu Yang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yirong Li
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nikita Mehta
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yelena Kemel
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Erin Salo-Mullen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anna Maio
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Margaret Sheehan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria Carlo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alicia Latham
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zsofia Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mark Robson
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael Walsh
- Department of Medicine, 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
| | - Diana Mandelker
- Correspondence to: Diana Mandelker, MD, PhD, Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA (e-mail: )
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