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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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Liu Y, Ho C, Yu W, Huang Y, Miller J, Gao Q, Syed M, Ma Y, Wang M, Maciag L, Petrova-Drus K, Zhu M, Yao J, Vanderbilt C, Durham B, Benhamida J, Ewalt MD, Dogan A, Roshal M, Nafa K, Arcila ME. Quantification of Measurable Residual Disease Detection by Next-Generation Sequencing-Based Clonality Testing in B-Cell and Plasma Cell Neoplasms. J Mol Diagn 2024; 26:168-178. [PMID: 38103591 PMCID: PMC10918645 DOI: 10.1016/j.jmoldx.2023.11.009] [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: 07/04/2023] [Revised: 10/27/2023] [Accepted: 11/09/2023] [Indexed: 12/19/2023] Open
Abstract
Next-generation sequencing (NGS)-based measurable residual disease (MRD) monitoring in post-treatment settings can be crucial for relapse risk stratification in patients with B-cell and plasma cell neoplasms. Prior studies have focused on validation of various technical aspects of the MRD assays, but more studies are warranted to establish the performance characteristics and enable standardization and broad utilization in routine clinical practice. Here, the authors describe an NGS-based IGH MRD quantification assay, incorporating a spike-in calibrator for monitoring B-cell and plasma cell neoplasms based on their unique IGH rearrangement status. Comparison of MRD status (positive or undetectable) by NGS and flow cytometry (FC) assays showed high concordance (91%, 471/519 cases) and overall good linear correlation in MRD quantitation, particularly for chronic lymphocytic leukemia and B-lymphoblastic leukemia/lymphoma (R = 0.85). Quantitative correlation was lower for plasma cell neoplasms, where underestimation by FC is a known limitation. No significant effects on sequencing efficiency by the spike-in calibrator were observed, with excellent inter- and intra-assay reproducibility within the authors' laboratory, and in comparison to an external laboratory, using the same assay and protocols. Assays performed both at internal and external laboratories showed highly concordant MRD detection (100%) and quantitation (R = 0.97). Overall, this NGS-based MRD assay showed highly reproducible results with quantitation that correlated well with FC MRD assessment, particularly for B-cell neoplasms.
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Affiliation(s)
- Ying Liu
- Diagnostic Molecular Pathology, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Hematopathology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Caleb Ho
- Loxo Oncology, Inc., Stamford, Connecticut
| | - Wayne Yu
- Diagnostic Molecular Pathology, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ying Huang
- Invivoscribe, Inc., San Diego, California
| | | | - Qi Gao
- Hematopathology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mustafa Syed
- Diagnostic Molecular Pathology, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yuanyuan Ma
- Diagnostic Molecular Pathology, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Meiyi Wang
- Diagnostic Molecular Pathology, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Lidia Maciag
- Diagnostic Molecular Pathology, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kseniya Petrova-Drus
- Diagnostic Molecular Pathology, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Hematopathology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Menglei Zhu
- Diagnostic Molecular Pathology, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Hematopathology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - JinJuan Yao
- Diagnostic Molecular Pathology, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Chad Vanderbilt
- Diagnostic Molecular Pathology, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Benjamin Durham
- Diagnostic Molecular Pathology, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jamal Benhamida
- Diagnostic Molecular Pathology, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mark D Ewalt
- Diagnostic Molecular Pathology, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Hematopathology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ahmet Dogan
- Hematopathology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mikhail Roshal
- Hematopathology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Khedoudja Nafa
- Diagnostic Molecular Pathology, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maria E Arcila
- Diagnostic Molecular Pathology, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Hematopathology Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.
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4
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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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5
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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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6
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Arcila ME, Patel U, Momeni-Boroujeni A, Yao J, Chan R, Chan J, Rijo I, Yu W, Chaves N, Patel H, Kakadiya S, Lachhander S, Senechal B, Riviere IC, Wang X, Sadelain M, Nafa K, Salazar P, Palomba L, Curran KJ, Park JH, Daniyan A, Borsu L. Validation of a High-Sensitivity Assay for Detection of Chimeric Antigen Receptor T-Cell Vectors Using Low-Partition Digital PCR Technology. J Mol Diagn 2023; 25:634-645. [PMID: 37330049 PMCID: PMC10488325 DOI: 10.1016/j.jmoldx.2023.06.002] [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: 10/20/2022] [Revised: 05/18/2023] [Accepted: 06/01/2023] [Indexed: 06/19/2023] Open
Abstract
Although in vivo engraftment, expansion, and persistence of chimeric antigen receptor (CAR) T cells are pivotal components of treatment efficacy, quantitative monitoring has not been implemented in routine clinical practice. We describe the development and analytical validation of a digital PCR assay for ultrasensitive detection of CAR constructs after treatment, circumventing known technical limitations of low-partitioning platforms. Primers and probes, designed for detection of axicabtagene, brexucabtagene, and Memorial Sloan Kettering CAR constructs, were employed to validate testing on the Bio-Rad digital PCR low-partitioning platform; results were compared with Raindrop, a high-partitioning system, as reference method. Bio-Rad protocols were modified to enable testing of DNA inputs as high as 500 ng. Using dual-input reactions (20 and 500 ng) and a combined analysis approach, the assay demonstrated consistent target detection around 1 × 10-5 (0.001%) with excellent specificity and reproducibility and 100% accuracy compared with the reference method. Dedicated analysis of 53 clinical samples received during validation/implementation phases showed the assay effectively enabled monitoring across multiple time points of early expansion (day 6 to 28) and long-term persistence (up to 479 days). CAR vectors were detected at levels ranging from 0.005% to 74% (vector versus reference gene copies). The highest levels observed in our cohort correlated strongly with the temporal diagnosis of grade 2 and 3 cytokine release syndrome diagnosis (P < 0.005). Only three patients with undetectable constructs had disease progression at the time of sampling.
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Affiliation(s)
- Maria E Arcila
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Utsav Patel
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Amir Momeni-Boroujeni
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - JinJuan Yao
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Roger Chan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Joe Chan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ivelise Rijo
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Wayne Yu
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nelio Chaves
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Hina Patel
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Srushti Kakadiya
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sean Lachhander
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Brigitte Senechal
- Cell Therapy and Cell Engineering Facility, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Isabelle C Riviere
- Cell Therapy and Cell Engineering Facility, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Xiuyan Wang
- Cell Therapy and Cell Engineering Facility, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michel Sadelain
- Cell Therapy and Cell Engineering Facility, 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
| | - Paulo Salazar
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Lia Palomba
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kevin J Curran
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jae H Park
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Anthony Daniyan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Laetitia Borsu
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.
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7
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Petrova-Drus K, Syed M, Yu W, Hutt K, Zlotnicki AM, Huang Y, Kamalska-Cyganik M, Maciag L, Wang M, Ma YG, Ho C, Moung C, Yao J, Nafa K, Baik J, Vanderbilt CM, Benhamida JK, Liu Y, Zhu M, Durham B, Ewalt MD, Salazar P, Rijo I, Baldi T, Mato A, Roeker LE, Roshal M, Dogan A, Arcila ME. Clonal Characterization and Somatic Hypermutation (SHM) Assessment by Next Generation Sequencing in Chronic Lymphocytic Leukemia/ Small Lymphocytic Lymphoma (CLL/SLL): A Detailed Description of the Technical Performance, Clinical Utility, and Platform Comparison. J Mol Diagn 2023; 25:352-366. [PMID: 36963483 DOI: 10.1016/j.jmoldx.2023.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 01/04/2023] [Accepted: 02/16/2023] [Indexed: 03/26/2023] Open
Abstract
Somatic hypermutation (SHM) status of the immunoglobulin heavy variable (IGHV) gene is essential for treating chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL) patients. Unlike the conventional low-throughput method, assessment of SHM by next generation sequencing (NGS) has potential for uniformity and scalability, however it lacks standardization or guidelines for routine clinical use. We critically assessed the performance of an amplicon-based NGS assay across 458 samples. Using a validation cohort (35 samples), the comparison of two platforms (Ion Torrent vs Illumina) and two primer sets (Leader vs FR1) in their ability to identify clonotypic IGHV rearrangement(s) revealed 97% concordance. The mutation rates were identical by both platforms when using the same primer set (FR1), while a slight overestimation bias (+0.326%) was found when comparing FR1 to Leader primers. However, for nearly all patients this did not affect the stratification into mutated or unmutated categories suggesting that use of FR1 may provide comparable results if Leader sequencing is not available, while also allowing for a simpler NGS laboratory workflow. In routine clinical practice (423 samples), the productive rearrangement was successfully detected by either primer set (Leader 97.7%, FR1 94.7%) and a combination of both in problematic cases reduced the failure rate to 1.2%. Higher sensitivity of the NGS-based analysis also detected a higher frequency of double IGHV rearrangements (19.1%) compared to traditional approaches.
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Affiliation(s)
- Kseniya Petrova-Drus
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY.
| | - Mustafa Syed
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Wayne Yu
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | - Monika Kamalska-Cyganik
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Lidia Maciag
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Meiyi Wang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yuanyuan G Ma
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Caleb Ho
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Christine Moung
- 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
| | - Khedoudja Nafa
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jeeyeon Baik
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Chad M Vanderbilt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jamal K Benhamida
- 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
| | - Benjamin Durham
- 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
| | - Paulo Salazar
- 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
| | - Tessara Baldi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Anthony Mato
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Lindsey E Roeker
- Department of 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
| | - Ahmet Dogan
- 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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8
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Shyr C, Blackford AL, Huang T, Ke J, Ouardaoui N, Trippa L, Syngal S, Ukaegbu C, Uno H, Nafa K, Stadler ZK, Offit K, Amos CI, Lynch PM, Chen S, Giardiello FM, Buchanan DD, Hopper JL, Jenkins MA, Southey MC, Win AK, Figueiredo JC, Braun D, Parmigiani G. A validation of models for prediction of pathogenic variants in mismatch repair genes. Genet Med 2022; 24:2155-2166. [PMID: 35997715 PMCID: PMC10312204 DOI: 10.1016/j.gim.2022.07.004] [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: 04/07/2022] [Revised: 06/30/2022] [Accepted: 07/01/2022] [Indexed: 10/15/2022] Open
Abstract
PURPOSE Models used to predict the probability of an individual having a pathogenic homozygous or heterozygous variant in a mismatch repair gene, such as MMRpro, are widely used. Recently, MMRpro was updated with new colorectal cancer penetrance estimates. The purpose of this study was to evaluate the predictive performance of MMRpro and other models for individuals with a family history of colorectal cancer. METHODS We performed a validation study of 4 models, Leiden, MMRpredict, PREMM5, and MMRpro, using 784 members of clinic-based families from the United States. Predicted probabilities were compared with germline testing results and evaluated for discrimination, calibration, and predictive accuracy. We analyzed several strategies to combine models and improve predictive performance. RESULTS MMRpro with additional tumor information (MMRpro+) and PREMM5 outperformed the other models in discrimination and predictive accuracy. MMRpro+ was the best calibrated with an observed to expected ratio of 0.98 (95% CI = 0.89-1.08). The combination models showed improvement over PREMM5 and performed similar to MMRpro+. CONCLUSION MMRpro+ and PREMM5 performed well in predicting the probability of having a pathogenic homozygous or heterozygous variant in a mismatch repair gene. They serve as useful clinical decision tools for identifying individuals who would benefit greatly from screening and prevention strategies.
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Affiliation(s)
- Cathy Shyr
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA; Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | - Amanda L Blackford
- Division of Biostatistics and Bioinformatics, Johns Hopkins School of Medicine, Baltimore, MD
| | - Theodore Huang
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA; Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | - Jianfeng Ke
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA; Department of Mathematical Sciences, Tsinghua University, Beijing, China
| | - Nofal Ouardaoui
- Department of Computer Science, School of Engineering, Tufts University, Medford, MA
| | - Lorenzo Trippa
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA; Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | - Sapna Syngal
- Cancer Genetics and Prevention Division, Dana-Farber Cancer Institute, Boston, MA; Division of Gastroenterology, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA
| | - Chinedu Ukaegbu
- Cancer Genetics and Prevention Division, Dana-Farber Cancer Institute, Boston, MA
| | - Hajime Uno
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA; McGraw/Patterson Center for Population Sciences, Dana-Farber Cancer Institute, Boston, MA
| | - Khedoudja Nafa
- Department of Pathology and Laboratory Medicine, Molecular Diagnostic Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Zsofia K Stadler
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Comprehensive Cancer Center, New York, NY; Niehaus Center for Inherited Cancer Genomics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Comprehensive Cancer Center, New York, NY; Niehaus Center for Inherited Cancer Genomics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Christopher I Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX; Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX
| | - Patrick M Lynch
- Gastroenterology, Hepatology and Nutrition, University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Francis M Giardiello
- Department of Gastroenterology and Hepatology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia; University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia; Genomic Medicine and Family Cancer Clinic, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia; University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia
| | - Melissa C Southey
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia; Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Melbourne, Victoria, Australia; Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Aung Ko Win
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jane C Figueiredo
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Danielle Braun
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA; Department of Data Science, Dana-Farber Cancer Institute, Boston, MA.
| | - Giovanni Parmigiani
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA; Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
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9
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Chu YH, Barbee J, Yang SR, Chang JC, Liang P, Mullaney K, Chan R, Salazar P, Benayed R, Offin M, Drilon A, Ladanyi M, Nafa K, Arcila ME. Clinical Utility and Performance of an Ultrarapid Multiplex RNA-Based Assay for Detection of ALK, ROS1, RET, and NTRK1/2/3 Rearrangements and MET Exon 14 Skipping Alterations. J Mol Diagn 2022; 24:642-654. [PMID: 35430374 DOI: 10.1016/j.jmoldx.2022.03.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 09/23/2021] [Revised: 01/14/2022] [Accepted: 03/03/2022] [Indexed: 11/19/2022] Open
Abstract
Several kinase fusions are established targetable drivers in lung cancers. However, rapid and comprehensive detection remains challenging because of diverse partner genes and breakpoints. We assess the clinical utility and performance of a rapid microfluidic multiplex real-time PCR-based assay for simultaneous query of fusions involving ALK, ROS1, RET, and NTRK1/2/3, as well as MET exon 14 skipping, using a 3-hour automated process. Dual analytic strategies were utilized: fusion-specific amplification and 3' to 5' expression imbalance. One-hundred and forty-three independent, formalin-fixed, paraffin-embedded tumor samples (112 surgical specimens, 31 cytologic cell blocks) were analyzed: 133 with known kinase gene alterations and 10 negative samples based on clinically validated next-generation sequencing. Testing was successful in 142 (99%) cases. The assay demonstrated a sensitivity of 97% (28/29), 100% (31/31), 92% (22/24), 81% (22/27), and 100% (20/20) for ALK, RET, ROS1, and NTRK1/2/3 rearrangements and MET exon 14 skipping alterations, respectively, with 100% specificity for all. Concordant results were achieved in specimens aged up to 5 years, with >10% tumor, and inputs of at least 9 mm2 (surgical specimens) and 9000 cells (cytologic cell blocks). The assay enables rapid screening for clinically actionable kinase alterations with quicker turnaround and lower tissue requirements compared with immunohistochemistry and molecular methods, while also circumventing the infrastructure dependencies associated with next-generation sequencing and fluorescence in situ hybridization.
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Affiliation(s)
- Ying-Hsia Chu
- Department of Pathology and Laboratory Medicine, Molecular Diagnostic Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jada Barbee
- Department of Pathology and Laboratory Medicine, Molecular Diagnostic Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Soo-Ryum Yang
- Department of Pathology and Laboratory Medicine, Molecular Diagnostic Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jason C Chang
- Department of Pathology and Laboratory Medicine, Molecular Diagnostic Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Priscilla Liang
- Department of Pathology and Laboratory Medicine, Molecular Diagnostic Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kerry Mullaney
- Department of Pathology and Laboratory Medicine, Molecular Diagnostic Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Roger Chan
- Department of Pathology and Laboratory Medicine, Molecular Diagnostic Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Paulo Salazar
- Department of Pathology and Laboratory Medicine, Molecular Diagnostic Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ryma Benayed
- Department of Pathology and Laboratory Medicine, Molecular Diagnostic Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael Offin
- Thoracic Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alexander Drilon
- Thoracic Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Marc Ladanyi
- Department of Pathology and Laboratory Medicine, Molecular Diagnostic Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Khedoudja Nafa
- Department of Pathology and Laboratory Medicine, Molecular Diagnostic Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maria E Arcila
- Department of Pathology and Laboratory Medicine, Molecular Diagnostic Service, Memorial Sloan Kettering Cancer Center, New York, New York.
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10
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Chang JC, Offin M, Falcon C, Brown D, Houck-Loomis BR, Meng F, Rudneva VA, Won HH, Amir S, Montecalvo J, Desmeules P, Kadota K, Adusumilli PS, Rusch VW, Teed S, Sabari JK, Benayed R, Nafa K, Borsu L, Li BT, Schram AM, Arcila ME, Travis WD, Ladanyi M, Drilon A, Rekhtman N. Comprehensive Molecular and Clinicopathologic Analysis of 200 Pulmonary Invasive Mucinous Adenocarcinomas Identifies Distinct Characteristics of Molecular Subtypes. Clin Cancer Res 2021; 27:4066-4076. [PMID: 33947695 PMCID: PMC8282731 DOI: 10.1158/1078-0432.ccr-21-0423] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [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: 02/03/2021] [Revised: 03/27/2021] [Accepted: 04/30/2021] [Indexed: 02/06/2023]
Abstract
PURPOSE Invasive mucinous adenocarcinoma (IMA) is a unique subtype of lung adenocarcinoma, characterized genomically by frequent KRAS mutations or specific gene fusions, most commonly involving NRG1. Comprehensive analysis of a large series of IMAs using broad DNA- and RNA-sequencing methods is still lacking, and it remains unclear whether molecular subtypes of IMA differ clinicopathologically. EXPERIMENTAL DESIGN A total of 200 IMAs were analyzed by 410-gene DNA next-generation sequencing (MSK-IMPACT; n = 136) or hotspot 8-oncogene genotyping (n = 64). Driver-negative cases were further analyzed by 62-gene RNA sequencing (MSK-Fusion) and those lacking fusions were further tested by whole-exome sequencing and whole-transcriptome sequencing (WTS). RESULTS Combined MSK-IMPACT and MSK-Fusion testing identified mutually exclusive driver alterations in 96% of IMAs, including KRAS mutations (76%), NRG1 fusions (7%), ERBB2 alterations (6%), and other less common events. In addition, WTS identified a novel NRG2 fusion (F11R-NRG2). Overall, targetable gene fusions were identified in 51% of KRAS wild-type IMAs, leading to durable responses to targeted therapy in some patients. Compared with KRAS-mutant IMAs, NRG1-rearranged tumors exhibited several more aggressive characteristics, including worse recurrence-free survival (P < 0.0001). CONCLUSIONS This is the largest molecular study of IMAs to date, where we demonstrate the presence of a major oncogenic driver in nearly all cases. This study is the first to document more aggressive characteristics of NRG1-rearranged IMAs, ERBB2 as the third most common alteration, and a novel NRG2 fusion in these tumors. Comprehensive molecular testing of KRAS wild-type IMAs that includes fusion testing is essential, given the high prevalence of alterations with established and investigational targeted therapies in this subset.
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Affiliation(s)
- Jason C Chang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael Offin
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Christina Falcon
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David Brown
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Brian R Houck-Loomis
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Fanli Meng
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Vasilisa A Rudneva
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Helen H Won
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sharon Amir
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Joseph Montecalvo
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Patrice Desmeules
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kyuichi Kadota
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Surgery, Thoracic Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Prasad S Adusumilli
- Department of Surgery, Thoracic Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Valerie W Rusch
- Department of Surgery, Thoracic Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sarah Teed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Cell Biology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Joshua K Sabari
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Khedoudja Nafa
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Laetitia Borsu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Bob T Li
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alison M Schram
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maria E Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - William D Travis
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alexander Drilon
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Early Drug Development Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Natasha Rekhtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
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11
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Rose Brannon A, Jayakumaran G, Diosdado M, Patel J, Razumova A, Hu Y, Meng F, Haque M, Sadowska J, Murphy BJ, Baldi T, Johnson I, Ptashkin R, Hasan M, Srinivasan P, Rema AB, Rijo I, Agarunov A, Won H, Perera D, Brown DN, Samoila A, Jing X, Gedvilaite E, Yang JL, Stephens DP, Dix JM, DeGroat N, Nafa K, Syed A, Li A, Lebow ES, Bowman AS, Ferguson DC, Liu Y, Mata DA, Sharma R, Yang SR, Bale T, Benhamida JK, Chang JC, Dogan S, Hameed MR, Hechtman JF, Moung C, Ross DS, Vakiani E, Vanderbilt CM, Yao J, Razavi P, Smyth LM, Chandarlapaty S, Iyer G, Abida W, Harding JJ, Krantz B, O'Reilly E, Yu HA, Li BT, Rudin CM, Diaz L, Solit DB, Arcila ME, Ladanyi M, Loomis B, Tsui D, Berger MF, Zehir A, Benayed R. Enhanced specificity of clinical high-sensitivity tumor mutation profiling in cell-free DNA via paired normal sequencing using MSK-ACCESS. Nat Commun 2021; 12:3770. [PMID: 34145282 PMCID: PMC8213710 DOI: 10.1038/s41467-021-24109-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [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] [Received: 12/02/2020] [Accepted: 05/26/2021] [Indexed: 12/13/2022] Open
Abstract
Circulating cell-free DNA from blood plasma of cancer patients can be used to non-invasively interrogate somatic tumor alterations. Here we develop MSK-ACCESS (Memorial Sloan Kettering - Analysis of Circulating cfDNA to Examine Somatic Status), an NGS assay for detection of very low frequency somatic alterations in 129 genes. Analytical validation demonstrated 92% sensitivity in de-novo mutation calling down to 0.5% allele frequency and 99% for a priori mutation profiling. To evaluate the performance of MSK-ACCESS, we report results from 681 prospective blood samples that underwent clinical analysis to guide patient management. Somatic alterations are detected in 73% of the samples, 56% of which have clinically actionable alterations. The utilization of matched normal sequencing allows retention of somatic alterations while removing over 10,000 germline and clonal hematopoiesis variants. Our experience illustrates the importance of analyzing matched normal samples when interpreting cfDNA results and highlights the importance of cfDNA as a genomic profiling source for cancer patients. Liquid biopsies allow the non-invasive detection of somatic mutations from tumours. Here, the authors develop and test MSK-ACCESS, an NGS-based clinical assay for identifying low frequency mutations in 129 genes and describe how it benefits patients in the clinic.
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Affiliation(s)
- A Rose Brannon
- 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
| | - Monica Diosdado
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Juber Patel
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anna Razumova
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yu Hu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fanli Meng
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mohammad Haque
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Justyna Sadowska
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Brian J Murphy
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tessara Baldi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ian Johnson
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ryan Ptashkin
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maysun Hasan
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Preethi Srinivasan
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Ivelise Rijo
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Aaron Agarunov
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Helen Won
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dilmi Perera
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David N Brown
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Aliaksandra Samoila
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Xiaohong Jing
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Erika Gedvilaite
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Julie L Yang
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dennis P Stephens
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jenna-Marie Dix
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nicole DeGroat
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Khedoudja Nafa
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Aijazuddin Syed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alan Li
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Emily S Lebow
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anita S Bowman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Donna C Ferguson
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ying Liu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Douglas A Mata
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rohit Sharma
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Soo-Ryum Yang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tejus Bale
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jamal K Benhamida
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jason C Chang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Snjezana Dogan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Meera R Hameed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jaclyn F Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christine Moung
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dara S Ross
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Efsevia Vakiani
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chad M Vanderbilt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - JinJuan Yao
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pedram Razavi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lillian M Smyth
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sarat Chandarlapaty
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gopa Iyer
- 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
| | - James J Harding
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Benjamin Krantz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eileen O'Reilly
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Helena A Yu
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bob T Li
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Charles M Rudin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Luis Diaz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David B Solit
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria E Arcila
- 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
| | - Brian Loomis
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dana Tsui
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael F Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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12
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Momeni-Boroujeni A, Salazar P, Zheng T, Mensah N, Rijo I, Dogan S, Yao J, Moung C, Vanderbilt C, Benhamida J, Chang J, Travis W, Rekhtman N, Ladanyi M, Nafa K, Arcila ME. Rapid EGFR Mutation Detection Using the Idylla Platform: Single-Institution Experience of 1200 Cases Analyzed by an In-House Developed Pipeline and Comparison with Concurrent Next-Generation Sequencing Results. J Mol Diagn 2020; 23:310-322. [PMID: 33346146 DOI: 10.1016/j.jmoldx.2020.11.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 10/13/2020] [Accepted: 11/17/2020] [Indexed: 12/20/2022] Open
Abstract
Mutations in the epidermal growth factor receptor (EGFR) are the most common targetable alterations in lung adenocarcinoma. To facilitate rapid testing, the Idylla EGFR assay was incorporated as a screening method before next-generation sequencing (NGS). Validation and experience using an in-house developed analysis pipeline, enhanced with a manual review algorithm is described. Results are compared with corresponding NGS results. In all, 1249 samples were studied. Validation demonstrated 98.57% (69/70) concordance with the reference methods. The limit of detection varied from 2% to 5% variant allele frequency for total EGFR quantitation cycle between 20 and 23. Of the 1179 clinical cases, 23.41% were EGFR-positive by Idylla. Concurrent NGS was successfully performed on 94.9% (799/842) requests. Concordance of Idylla with NGS was 98.62% (788/799) and 98.50% (787/799) using our in-house and Idylla analysis pipelines, respectively. Discordances involved missed mutations by both assays associated with low tumor/low input. Incorporating a manual review algorithm to supplement automated calls improved accuracy from 98.62% to 99.37% and sensitivity from 94.68% to 97.58%. Overall reporting time, from receipt of material to official clinical report, ranged from 1 to 3 days. Therefore, Idylla EGFR testing enables rapid and sensitive screening without compromising subsequent comprehensive NGS, when required. Automated calling, enhanced with a manual review algorithm, reduces false-negative calls associated with low tumor/low input samples.
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Affiliation(s)
| | - Paulo Salazar
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Tao Zheng
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nana Mensah
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ivelise Rijo
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Snjezana Dogan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - JinYuan Yao
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Christine Moung
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Chad Vanderbilt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jamal Benhamida
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jason Chang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - William Travis
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Natasha Rekhtman
- 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
| | - Khedoudja Nafa
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maria E Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
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13
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Ho C, Syed M, Roshal M, Petrova-Drus K, Moung C, Yao J, Quesada AE, Benhamida J, Vanderbilt C, Liu Y, Zhu M, Yu W, Maciag L, Wang M, Ma Y, Gao Q, Rustad EH, Hultcrantz M, Diamond BT, Zheng-Lin B, Huang Y, Hutt K, Miller JE, Dogan A, Nafa K, Landgren O, Arcila ME. Routine Evaluation of Minimal Residual Disease in Myeloma Using Next-Generation Sequencing Clonality Testing: Feasibility, Challenges, and Direct Comparison with High-Sensitivity Flow Cytometry. J Mol Diagn 2020; 23:181-199. [PMID: 33217553 PMCID: PMC7874334 DOI: 10.1016/j.jmoldx.2020.10.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 09/13/2020] [Accepted: 10/22/2020] [Indexed: 01/12/2023] Open
Abstract
The 2016 International Myeloma Working Group consensus recommendations emphasize high-sensitivity methods for minimal residual disease (MRD) detection, treatment response assessment, and prognostication. Next-generation sequencing (NGS) of IGH gene rearrangements is highly specific and sensitive, but its description in routine clinical practice and performance comparison with high-sensitivity flow cytometry (hsFC) remain limited. In this large, single-institution study including 438 samples from 251 patients, the use of NGS targeting the IGH and IGK genes for clonal characterization and monitoring, with comparison to hsFC, is described. The index clone characterization success rate was 93.6% (235/251), which depended on plasma cell (PC) cellularity, reaching 98% when PC ≥10% and below 80% when PC <5%. A total of 85% of cases were successfully characterized using leader and FR1 primer sets, and most clones showed high somatic hypermutation rates (median, 8.1%). Among monitoring samples from 124 patients, 78.6% (147/187) had detectable disease by NGS. Concordance with hsFC was 92.9% (170/183). Discordant cases encompassed 8 of 124 hsFC MRD+/NGS MRD− patients (6.5%) and 4 of 124 hsFC MRD−/NGS MRD+ patients (3.2%), all with low-level disease near detection limits for both assays. Among concordant hsFC MRD−/NGS MRD− cases, only 5 of 24 patients (20.8%) showed subsequent overt relapse at 3-year follow-up. HsFC and NGS showed similar operational sensitivity, and the choice of test may depend on practical, rather than test performance, considerations.
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Affiliation(s)
- Caleb Ho
- Hematopathology Service, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York; Diagnostic Molecular Pathology Service, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York.
| | - Mustafa Syed
- Diagnostic Molecular Pathology Service, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Mikhail Roshal
- Hematopathology Service, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Kseniya Petrova-Drus
- Hematopathology Service, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York; Diagnostic Molecular Pathology Service, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Christine Moung
- Diagnostic Molecular Pathology Service, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Jinjuan Yao
- Diagnostic Molecular Pathology Service, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Andres E Quesada
- Hematopathology Service, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York; Diagnostic Molecular Pathology Service, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Jamal Benhamida
- Diagnostic Molecular Pathology Service, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Chad Vanderbilt
- Diagnostic Molecular Pathology Service, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Ying Liu
- Hematopathology Service, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Menglei Zhu
- Hematopathology Service, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Wayne Yu
- Diagnostic Molecular Pathology Service, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Lidia Maciag
- Diagnostic Molecular Pathology Service, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Meiyi Wang
- Diagnostic Molecular Pathology Service, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Yuanyuan Ma
- Diagnostic Molecular Pathology Service, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Qi Gao
- Hematopathology Service, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Even H Rustad
- Myeloma Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Malin Hultcrantz
- Myeloma Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Benjamin T Diamond
- Myeloma Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Binbin Zheng-Lin
- Myeloma Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Ying Huang
- Invivoscribe, Inc., San Diego, California
| | - Kasey Hutt
- Invivoscribe, Inc., San Diego, California
| | | | - Ahmet Dogan
- Hematopathology Service, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Khedoudja Nafa
- Diagnostic Molecular Pathology Service, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Ola Landgren
- Myeloma Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Maria E Arcila
- Hematopathology Service, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York; Diagnostic Molecular Pathology Service, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York.
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14
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Arcila ME, Yang SR, Momeni A, Mata DA, Salazar P, Chan R, Elezovic D, Benayed R, Zehir A, Buonocore DJ, Rekhtman N, Lin O, Ladanyi M, Nafa K. Ultrarapid EGFR Mutation Screening Followed by Comprehensive Next-Generation Sequencing: A Feasible, Informative Approach for Lung Carcinoma Cytology Specimens With a High Success Rate. JTO Clin Res Rep 2020; 1:100077. [PMID: 33511359 PMCID: PMC7839984 DOI: 10.1016/j.jtocrr.2020.100077] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/01/2020] [Accepted: 07/13/2020] [Indexed: 02/07/2023] Open
Abstract
INTRODUCTION For patients with advanced NSCLC, cytologic samples may be the only diagnostic specimen available for molecular profiling. Although both rapid and comprehensive assessment are essential in this setting, an integrated multitest approach remains an important strategy in many laboratories, despite the risks and challenges when working with scant samples. In this study, we describe our experience and high success rate in using a multitest approach, focusing on the clinical validation and incorporation of ultrarapid EGFR testing using the Idylla system followed by comprehensive next-generation sequencing (NGS). METHODS Cytology samples received for routine molecular testing were included in this study. The performance characteristics of the EGFR Idylla assay were assessed; tissue suitability parameters and interpretation criteria to supplement automated mutation calling were established. The assay performance was monitored for 1 year, comparing the results with those of concurrent NGS testing by MSK-IMPACT (primarily) or MSK-AmpliSeq and MSK-Fusion solid panel in a subset of cases. RESULTS Overall, 301 samples were studied; 83 samples were included in validation (60.2% [50 of 83] were positive for EGFR mutations). Concordance with the reference method was 96.4% (80 of 83) of the samples with excellent reproducibility. The limit of detection was variable depending on the total tissue input and the specific mutation tested. Unextracted tissue inputs that maintained total EGFR cycle of quantification at less than 23 allowed all mutations to be detected if present at greater than 5% variant allele frequency. Mutations could be detected at 1% variant allele frequency with total EGFR cycle of quantification of 18. During the clinical implementation phase, 218 NSCLC samples were tested by Idylla (24.3% [53 of 218] were EGFR mutation positive). Concurrent NGS testing was requested on 165 samples and successfully performed on 96.4% (159 of 165) of the samples. The Idylla automated results were concordant with those obtained by NGS in 96.2% (153 of 159) of cases and improved to 98.7% (157 of 159) after incorporation of manual review criteria to supplement automated calling, resulting in a diagnostic sensitivity of 95.6% (95% confidence interval: 84.9%-99.5%). In general, 9% (14 of 159) of the cases tested by NGS had EGFR mutations not covered by the Idylla assay, primarily insertions in exon 19 and 20 and minor mutations cooccurring with canonical sensitizing mutations. CONCLUSIONS Comprehensive molecular testing is feasible and has a high success rate in NSCLC cytology samples when using a multitest approach. Testing with the Idylla system enables rapid and accurate determination of the EGFR status without compromising subsequent NGS testing.
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Affiliation(s)
- Maria E. Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Soo-Ryum Yang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Amir Momeni
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Douglas A. Mata
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Paulo Salazar
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Roger Chan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Daniela Elezovic
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ryma Benayed
- 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
| | - Darren J. Buonocore
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Natasha Rekhtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Oscar Lin
- 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
| | - Khedoudja Nafa
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
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15
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Zhu GG, Ramirez D, Chen W, Lu C, Wang L, Frosina D, Jungbluth A, Ntiamoah P, Nafa K, Boland PJ, Hameed MR. Chromosome 3p loss of heterozygosity and reduced expression of H3K36me3 correlate with longer relapse-free survival in sacral conventional chordoma. Hum Pathol 2020; 104:73-83. [PMID: 32795465 DOI: 10.1016/j.humpath.2020.07.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 06/30/2020] [Accepted: 07/01/2020] [Indexed: 12/26/2022]
Abstract
Conventional chordoma is a rare slow-growing malignant tumor of notochordal origin primarily arising at the base of the skull and sacrococcygeal bones. Chordoma may arise from its benign counterpart, benign notochordal cell tumors, and can also undergo dedifferentiation progressing into dedifferentiated chordoma. No study has directly compared the genomic alterations among these tumors comprising a morphologic continuum. Our prior study identified frequent chromosome 3p loss of heterozygosity and minimal deleted regions on chromosome 3 encompassing SETD2, encoding a histone methyltransferase involved in histone H3 lysine 36 trimethylation (H3K36me3). In the present study, we expanded our study to include 65 sacral conventional chordoma cases, 3 benign notochordal cell tumor cases, and 2 dedifferentiated chordoma cases using single nucleotide polymorphism (SNP) array, targeted next-generation sequencing analysis, and immunohistochemistry. We performed immunohistochemical analysis of histone, H3K36me3, and investigated whether there is any association between the clinical behavior and recurrent chromosome or aneuploidy or H3K36me3 protein expression. We found that there is increased genomic instability from benign notochordal cell tumor to conventional chordoma to dedifferentiated chordoma. The highly recurrent genomic aberration, chromosome 3p loss of heterozygosity (occurred in 70% of conventional chordomas), is correlated with longer relapse-free survival, but not with overall survival or metastasis-free survival in sacral chordoma. Chordomas demonstrate variable patterns and levels of H3K36me3 expression, and reduced expression of H3K36me3 showed marginally significant correlation with longer relapse-free survival. Copy number alterations in the genes encoding the H3K36me3 methylation transferase complex and demethylase may account for the altered H3K36me3 expression levels.
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Affiliation(s)
- Guo Gord Zhu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA; Department of Pathology, Cooper University Hospital, Cooper Medical School of Rowan University, Camden, NJ, 08003, USA
| | - Daniel Ramirez
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA; Department of Pathology, Northwell Health, Great Neck, NY, 11021, USA
| | - Wen Chen
- Department of Pathology, Washington DC VA Medical Center, Washington, DC, 20422, USA
| | - Chao Lu
- Department of Genetics & Development, Columbia University Medical Center, New York, NY, 10032, USA
| | - Lu Wang
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Denise Frosina
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Achim Jungbluth
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Peter Ntiamoah
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Khedoudja Nafa
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Patrick J Boland
- Orthopaedic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Meera R Hameed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
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16
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Benhamida JK, Hechtman JF, Nafa K, Villafania L, Sadowska J, Wang J, Wong D, Zehir A, Zhang L, Bale T, Arcila ME, Ladanyi M. Reliable Clinical MLH1 Promoter Hypermethylation Assessment Using a High-Throughput Genome-Wide Methylation Array Platform. J Mol Diagn 2019; 22:368-375. [PMID: 31881335 DOI: 10.1016/j.jmoldx.2019.11.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 10/29/2019] [Accepted: 11/18/2019] [Indexed: 12/21/2022] Open
Abstract
Clinical testing for MLH1 promoter hypermethylation status is important in the workup of patients with MLH1-deficient colorectal and uterine carcinomas when evaluating patients for Lynch syndrome. Current assays use single gene-based methods to assess promoter hypermethylation. Herein, we describe the development and report the performance of a clinical assay for MLH1 promoter hypermethylation using the Infinium methylationEPIC (850k) bead-array platform. Using four cytosine-guanine dinucleotide (CpG) sites within the MLH1 gene promoter, a qualitative MLH1 promoter hypermethylation assay was developed and validated using 63 gastrointestinal and uterine carcinoma samples of known hypermethylation status based on a pyrosequencing reference test. The array-based method achieves clinically robust and reproducible results at an analytical sensitivity level of 8%. Of importance, the 850k array contains probes targeting >850,000 additional CpG sites across the genome, covering sites in most known genes as well as important enhancer regions provided by the Encyclopedia of DNA Elements and Functional Annotation of The Mammalian Genome projects. Thus, the testing modality presented may also be applied to determine the methylation status of other clinically relevant genes or regulatory regions, potentially providing a single laboratory testing workflow for all clinical methylation assays. Furthermore, the concomitant acquisition of genome-wide methylation information provides a workflow that seamlessly enables wider translational epigenetic research.
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Affiliation(s)
- Jamal K Benhamida
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Jaclyn F Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Khedoudja Nafa
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Liliana Villafania
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Justyna Sadowska
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jiajing Wang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Donna Wong
- 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
| | - Liying Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Tejus Bale
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maria E Arcila
- 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
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17
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Suehara Y, Alex D, Bowman A, Middha S, Zehir A, Chakravarty D, Wang L, Jour G, Nafa K, Hayashi T, Jungbluth AA, Frosina D, Slotkin E, Shukla N, Meyers P, Healey JH, Hameed M, Ladanyi M. Clinical Genomic Sequencing of Pediatric and Adult Osteosarcoma Reveals Distinct Molecular Subsets with Potentially Targetable Alterations. Clin Cancer Res 2019. [PMID: 31175097 DOI: 10.1158/1078‐0432.ccr‐18‐4032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
PURPOSE Although multimodal chemotherapy has improved outcomes for patients with osteosarcoma, the prognosis for patients who present with metastatic and/or recurrent disease remains poor. In this study, we sought to define how often clinical genomic sequencing of osteosarcoma samples could identify potentially actionable alterations.Experimental Design: We analyzed genomic data from 71 osteosarcoma samples from 66 pediatric and adult patients sequenced using MSK-IMPACT, a hybridization capture-based large panel next-generation sequencing assay. Potentially actionable genetic events were categorized according to the OncoKB precision oncology knowledge base, of which levels 1 to 3 were considered clinically actionable. RESULTS We found at least one potentially actionable alteration in 14 of 66 patients (21%), including amplification of CDK4 (n = 9, 14%: level 2B) and/or MDM2 (n = 9, 14%: level 3B), and somatic truncating mutations/deletions in BRCA2 (n = 3, 5%: level 2B) and PTCH1 (n = 1, level 3B). In addition, we observed mutually exclusive patterns of alterations suggesting distinct biological subsets defined by gains at 4q12 and 6p12-21. Specifically, potentially targetable gene amplifications at 4q12 involving KIT, KDR, and PDGFRA were identified in 13 of 66 patients (20%), which showed strong PDGFRA expression by IHC. In another largely nonoverlapping subset of 14 patients (24%) with gains at 6p12-21, VEGFA amplification was identified. CONCLUSIONS We found potentially clinically actionable alterations in approximately 21% of patients with osteosarcoma. In addition, at least 40% of patients have tumors harboring PDGFRA or VEGFA amplification, representing candidate subsets for clinical evaluation of additional therapeutic options. We propose a new genomically based algorithm for directing patients with osteosarcoma to clinical trial options.
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Affiliation(s)
- Yoshiyuki Suehara
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Orthopedic Surgery, Juntendo University School of Medicine, Tokyo, Japan
| | - Deepu Alex
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Anita Bowman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sumit Middha
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Debyani Chakravarty
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Lu Wang
- Department of Pathology, St Jude Children's Research Hospital, Memphis, Tennessee
| | - George Jour
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Khedoudja Nafa
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Takuo Hayashi
- Department of Human Pathology, Juntendo University School of Medicine, Tokyo, Japan
| | - Achim A Jungbluth
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Denise Frosina
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Emily Slotkin
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Neerav Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Paul Meyers
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - John H Healey
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Meera Hameed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York. .,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
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18
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Kumar P, Uppal M, Xiao W, Dogan A, Roshal M, Gao Q, Aypar U, Zhang Y, Arcila ME, Moung C, Yao J, Nafa K, Yu W, Syed MH, Park J, Kumar A, Ho C. Clonally-Related CD5+ CLL/SLL and CD10+ high grade B-cell lymphoma suggests common neoplastic progenitor with branched disease evolution, with therapeutic implications. Leuk Lymphoma 2019; 61:460-464. [PMID: 31612754 PMCID: PMC7493823 DOI: 10.1080/10428194.2019.1675876] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Priyadarshini Kumar
- Hematopathology Service, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Manik Uppal
- Weill Cornell Medical College, New York, NY, USA
| | - Wenbin Xiao
- Hematopathology Service, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ahmet Dogan
- Hematopathology Service, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mikhail Roshal
- Hematopathology Service, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Qi Gao
- Hematopathology Service, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Umut Aypar
- Cytogenetics Service, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yanming Zhang
- Cytogenetics Service, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria E Arcila
- Hematopathology Service, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Molecular Diagnostics, Department of Pathology, Memorial Sloan Kettering Cancer Center
| | - Christine Moung
- Molecular Diagnostics, Department of Pathology, Memorial Sloan Kettering Cancer Center
| | - Jinjuan Yao
- Molecular Diagnostics, Department of Pathology, Memorial Sloan Kettering Cancer Center
| | - Khedoudja Nafa
- Molecular Diagnostics, Department of Pathology, Memorial Sloan Kettering Cancer Center
| | - Wayne Yu
- Molecular Diagnostics, Department of Pathology, Memorial Sloan Kettering Cancer Center
| | - Mustafa H Syed
- Molecular Diagnostics, Department of Pathology, Memorial Sloan Kettering Cancer Center
| | - Jae Park
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anita Kumar
- Lymphoma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Caleb Ho
- Hematopathology Service, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Molecular Diagnostics, Department of Pathology, Memorial Sloan Kettering Cancer Center
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19
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Zhu GG, Nafa K, Agaram N, Zehir A, Benayed R, Sadowska J, Borsu L, Kelly C, Tap WD, Fabbri N, Athanasian E, Boland PJ, Healey JH, Berger MF, Ladanyi M, Hameed M. Genomic Profiling Identifies Association of IDH1/IDH2 Mutation with Longer Relapse-Free and Metastasis-Free Survival in High-Grade Chondrosarcoma. Clin Cancer Res 2019; 26:419-427. [PMID: 31615936 DOI: 10.1158/1078-0432.ccr-18-4212] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 05/02/2019] [Accepted: 10/10/2019] [Indexed: 12/12/2022]
Abstract
PURPOSE Chondrosarcomas are the second most common primary malignant bone tumors. Although histologic grade is the most important factor predicting the clinical outcome of chondrosarcoma, it is subject to interobserver variability. Isocitrate dehydrogenase 1 (IDH1) and IDH2 hotspot mutations were recently found to be frequently mutated in central chondrosarcomas. However, a few published articles have been controversial regarding the association between IDH1/IDH2 mutation status and clinical outcomes in chondrosarcomas. EXPERIMENTAL DESIGN We performed hotspot sequencing of IDH1 and IDH2 genes in 89 central chondrosarcomas and targeted next-generation sequencing in 54 of them, and then correlated the IDH1/IDH2 mutation status with the patient's clinical outcome. RESULTS Although no association was discovered between IDH mutation status and the patient's overall survival, IDH1/IDH2 mutation was found to be associated with longer relapse-free and metastasis-free survival in high-grade chondrosarcomas. Genomic profiling reveals TERT gene amplification and ATRX mutation, for the first time, in addition to TERT promoter mutation in a subset (6/30, 20%) of high-grade and dedifferentiated chondrosarcomas. These abnormalities in telomere genes are concurrent with IDH1/IDH2 mutation and with CDKN2A/2B deletion or TP53 mutation, suggesting a possible association and synergy among these genes in chondrosarcoma progression. We found 21% of patients with chondrosarcoma also had histories of second malignancies unrelated to cartilaginous tumors, suggesting possible unknown genetic susceptibility to chondrosarcoma. CONCLUSIONS IDH1/IDH2 mutations are associated with longer relapse-free and metastasis-free survival in high-grade chondrosarcomas, and they tend to co-occur with TERT mutations and with CDKN2A/2B and TP53 alterations in a subset of high-grade chondrosarcomas.
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Affiliation(s)
- Guo Gord Zhu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Pathology, Cooper University Hospital, Cooper Medical School of Rowan University, Camden, New Jersey
| | - Khedoudja Nafa
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Narasimhan Agaram
- 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
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Justyna Sadowska
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Laetitia Borsu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ciara Kelly
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - William D Tap
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nicola Fabbri
- Orthopaedic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Edward Athanasian
- Orthopaedic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Patrick J Boland
- Orthopaedic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - John H Healey
- Orthopaedic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael F Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Meera Hameed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
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20
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Ptashkin RN, Benayed R, Ziegler J, Rema AB, Sadowska J, Kiecka I, Ho C, Yao J, Moung C, Petrova-Drus K, Nafa K, Batlevi C, Tallman M, Levine R, Giralt S, Younes A, Ladanyi M, Berger M, Zehir A, Arcila ME. Abstract 3409: MSK-IMPACT Heme: Validation and clinical experience of a comprehensive molecular profiling platform for hematologic malignancies. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-3409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background:
As the repertoire of molecular targeted therapies for hematologic malignancies continues to expand, so too does the opportunity for molecular profiling to inform treatment decisions. While mutations in certain genes, such as JAK2, MPL, MYD88 and BRAF have diagnostic utility, others such as FLT3, NPM1, IDH1, IDH2, DNMT3A, KIT and CEBPA have prognostic value. Here, we present the development and clinical experience of MSK-IMPACT Heme (Integrated Mutation Profiling of Actionable Cancer Targets for Hematologic malignancies), a comprehensive molecular profiling platform, utilizing hybridization capture and high coverage next generation sequencing of paired tumor and normal tissues.
Methods:
We designed custom DNA probes corresponding to all exons of 400 key oncogenes and tumor suppressor genes implicated in hematologic malignancies, including all genes that are targetable by approved and experimental therapies being investigated in clinical trials at our institution. The accuracy, precision, and sensitivity of MSK-IMPACT Heme was assessed on a validation set of 113 unique tumor samples with known SNVs and indels previously confirmed by orthogonal methods. We implemented a custom analysis pipeline to integrate the analysis of any number of normal samples with a given tumor and provide a reliable assessment of somatic alterations, even in post-transplant chimeric patients. The selection of matched nail, saliva, and/or blood tissue was determined at the time of test initiation as indicated by patient diagnosis and transplant history. The ability to detect somatic copy number alterations was demonstrated with samples previously characterized by SNP array platforms.
Results:
We sequenced 821 tumor samples, from 759 patients that represented over 50 tumor types to a mean depth of 758X. 429 patients were male (56.5%) and 20 cases were post allogeneic stem cell transplantation. The most common tumor types sequenced were Follicular lymphoma (11.9%), DLBCL (11.3%), and AML (11.0%). We identified 4,935 mutations from 732 samples. The most commonly altered genes were TP53, KMT2D, and CREBBP. Implementation of the MSK-IMPACT Heme workflow enabled the characterization of complex tumor specimens, including sorted cells and tumor samples from post-transplant chimeric patients. The joint utilization of matched patient and donor normal tissues enabled differentiation between somatic alterations and both host and donor derived common polymorphisms.
Conclusions:
The MSK-IMPACT Heme assay provides molecular profiling of hematologic malignancies with high accuracy and sensitivity. Paired analysis of tumors and patient and/or donor matched normal tissue samples enables the unambiguous detection of somatic alterations and the ability apply these data towards tumor classification, risk assessment, prognosis, disease monitoring, and treatment optimization.
Citation Format: Ryan N. Ptashkin, Ryma Benayed, John Ziegler, Anoop Balakrishnan Rema, Justyna Sadowska, Iwona Kiecka, Caleb Ho, JinJuan Yao, Christine Moung, Kseniya Petrova-Drus, Khedoudja Nafa, Connie Batlevi, Martin Tallman, Ross Levine, Sergio Giralt, Anas Younes, Marc Ladanyi, Mike Berger, Ahmet Zehir, Maria E. Arcila. MSK-IMPACT Heme: Validation and clinical experience of a comprehensive molecular profiling platform for hematologic malignancies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3409.
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Affiliation(s)
| | - Ryma Benayed
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - John Ziegler
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Iwona Kiecka
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Caleb Ho
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - JinJuan Yao
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | | | - Ross Levine
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sergio Giralt
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Anas Younes
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Marc Ladanyi
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Mike Berger
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Zehir
- Memorial Sloan Kettering Cancer Center, New York, NY
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21
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Suehara Y, Alex D, Bowman A, Middha S, Zehir A, Chakravarty D, Wang L, Jour G, Nafa K, Hayashi T, Jungbluth AA, Frosina D, Slotkin E, Shukla N, Meyers P, Healey JH, Hameed M, Ladanyi M. Clinical Genomic Sequencing of Pediatric and Adult Osteosarcoma Reveals Distinct Molecular Subsets with Potentially Targetable Alterations. Clin Cancer Res 2019; 25:6346-6356. [PMID: 31175097 DOI: 10.1158/1078-0432.ccr-18-4032] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 04/25/2019] [Accepted: 06/04/2019] [Indexed: 12/12/2022]
Abstract
PURPOSE Although multimodal chemotherapy has improved outcomes for patients with osteosarcoma, the prognosis for patients who present with metastatic and/or recurrent disease remains poor. In this study, we sought to define how often clinical genomic sequencing of osteosarcoma samples could identify potentially actionable alterations.Experimental Design: We analyzed genomic data from 71 osteosarcoma samples from 66 pediatric and adult patients sequenced using MSK-IMPACT, a hybridization capture-based large panel next-generation sequencing assay. Potentially actionable genetic events were categorized according to the OncoKB precision oncology knowledge base, of which levels 1 to 3 were considered clinically actionable. RESULTS We found at least one potentially actionable alteration in 14 of 66 patients (21%), including amplification of CDK4 (n = 9, 14%: level 2B) and/or MDM2 (n = 9, 14%: level 3B), and somatic truncating mutations/deletions in BRCA2 (n = 3, 5%: level 2B) and PTCH1 (n = 1, level 3B). In addition, we observed mutually exclusive patterns of alterations suggesting distinct biological subsets defined by gains at 4q12 and 6p12-21. Specifically, potentially targetable gene amplifications at 4q12 involving KIT, KDR, and PDGFRA were identified in 13 of 66 patients (20%), which showed strong PDGFRA expression by IHC. In another largely nonoverlapping subset of 14 patients (24%) with gains at 6p12-21, VEGFA amplification was identified. CONCLUSIONS We found potentially clinically actionable alterations in approximately 21% of patients with osteosarcoma. In addition, at least 40% of patients have tumors harboring PDGFRA or VEGFA amplification, representing candidate subsets for clinical evaluation of additional therapeutic options. We propose a new genomically based algorithm for directing patients with osteosarcoma to clinical trial options.
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Affiliation(s)
- Yoshiyuki Suehara
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Orthopedic Surgery, Juntendo University School of Medicine, Tokyo, Japan
| | - Deepu Alex
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Anita Bowman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sumit Middha
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Debyani Chakravarty
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Lu Wang
- Department of Pathology, St Jude Children's Research Hospital, Memphis, Tennessee
| | - George Jour
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Khedoudja Nafa
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Takuo Hayashi
- Department of Human Pathology, Juntendo University School of Medicine, Tokyo, Japan
| | - Achim A Jungbluth
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Denise Frosina
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Emily Slotkin
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Neerav Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Paul Meyers
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - John H Healey
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Meera Hameed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York. .,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
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22
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Liu Y, Roshal M, Xiao W, Zhang Y, Aypar U, Yu W, Nafa K, Arcila M, Moung C, Dogan A, Park J, Ho C. The t(11;14)(q13;q32)/CCND1-IGH translocation in chronic lymphocytic leukaemia/small lymphocytic lymphoma: an unusual genetic aberration during the natural clinical course. Histopathology 2019; 75:291-294. [PMID: 31021442 PMCID: PMC6662185 DOI: 10.1111/his.13885] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ying Liu
- Hematopathology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mikhail Roshal
- Hematopathology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wenbin Xiao
- Hematopathology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yanming Zhang
- Cytogenetic Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Umut Aypar
- Cytogenetic Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wayne Yu
- Molecular Diagnostics Service, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Khedoudja Nafa
- Molecular Diagnostics Service, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria Arcila
- Hematopathology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Molecular Diagnostics Service, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christine Moung
- Molecular Diagnostics Service, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ahmet Dogan
- Hematopathology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jae Park
- Lymphoma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Caleb Ho
- Hematopathology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Molecular Diagnostics Service, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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23
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Cocco E, Benhamida J, Middha S, Zehir A, Mullaney K, Shia J, Yaeger R, Zhang L, Wong D, Villafania L, Nafa K, Scaltriti M, Drilon A, Saltz L, Schram AM, Stadler ZK, Hyman DM, Benayed R, Ladanyi M, Hechtman JF. Colorectal Carcinomas Containing Hypermethylated MLH1 Promoter and Wild-Type BRAF/KRAS Are Enriched for Targetable Kinase Fusions. Cancer Res 2019; 79:1047-1053. [PMID: 30643016 DOI: 10.1158/0008-5472.can-18-3126] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 11/16/2018] [Accepted: 01/08/2019] [Indexed: 02/07/2023]
Abstract
Kinase fusions are rare and poorly characterized in colorectal carcinoma, yet they present unique opportunities for targeted therapy. In this study, we characterized kinase fusions from patients with advanced colorectal carcinoma who had MSK-IMPACT testing of their tumors between January 2014 and June 2018. Patients were analyzed for the presence of fusions, microsatellite instability (MSI), and RAS/BRAF mutations. Mismatch repair (MMR), IHC, and promoter hypermethylation status of MLH1 (MLH1ph) in microsatellite instability-high (MSI-H) colorectal carcinoma with fusions were investigated. Fusion transcripts were confirmed using a targeted RNA-seq panel assay. Of 2,314 colorectal carcinomas with MSK-IMPACT testing, 21 harbored kinase fusions. Overall 57% (12/21) of colorectal carcinoma fusions were MSI-H/MMR-D. Loss of MLH1 and MLH1ph was confirmed in all 12 and all 10 cases with available material, respectively. Fusions were present in 5% of MSI-H/MMR-D colorectal carcinoma compared with 0.4% of MSS/MMR-P colorectal carcinoma (P < 0.001) and 15% of MSI-H/MMR-D colorectal carcinoma with wild-type RAS/BRAF. Of 24 total MLH1-deficient colorectal carcinomas with MLH1ph and wild-type RAS/BRAF, 10 (42%) harbored kinase fusions. Kinase fusions in MSI-H colorectal carcinoma were associated with sporadic MLH1ph rather than with Lynch syndrome, and these patients may be eligible for kinase inhibitors, particularly following resistance or toxicity in response to immunotherapy. These findings identify a molecular subset of colorectal carcinoma with kinase fusions that may be responsive to kinase inhibitors.Significance: A high frequency of targetable kinase fusions in BRAF/RAS wild-type, MSI-H colorectal carcinoma offers a rationale for routine screening to identify patients with colorectal carcinoma with kinase fusions that may be responsive to kinase inhibitors.See related commentary by Valeri, p. 1041.
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Affiliation(s)
- Emiliano Cocco
- Human Oncology and Pathology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jamal Benhamida
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sumit Middha
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kerry Mullaney
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jinru Shia
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Rona Yaeger
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Liying Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Donna Wong
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Liliana Villafania
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Khedoudja Nafa
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maurizio Scaltriti
- Human Oncology and Pathology Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alexander Drilon
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Medical College, New York, New York
| | - Leonard Saltz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alison M Schram
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Medical College, New York, New York
| | - Zsofia K Stadler
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David M Hyman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Medical College, New York, New York
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc Ladanyi
- Human Oncology and Pathology Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jaclyn F Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
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24
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Arcila ME, Yu W, Syed M, Kim H, Maciag L, Yao J, Ho C, Petrova K, Moung C, Salazar P, Rijo I, Baldi T, Zehir A, Landgren O, Park J, Roshal M, Dogan A, Nafa K. Establishment of Immunoglobulin Heavy (IGH) Chain Clonality Testing by Next-Generation Sequencing for Routine Characterization of B-Cell and Plasma Cell Neoplasms. J Mol Diagn 2018; 21:330-342. [PMID: 30590126 DOI: 10.1016/j.jmoldx.2018.10.008] [Citation(s) in RCA: 60] [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: 03/19/2018] [Revised: 10/09/2018] [Accepted: 10/26/2018] [Indexed: 01/03/2023] Open
Abstract
Immunoglobulin heavy chain (IGH) clonality testing by next-generation sequencing (NGS) offers unique advantages over current low-throughput methods in the assessment of B-cell lineage neoplasms. Clinical use remains limited because assays are not standardized and validation/implementation guidelines are not yet developed. Herein, we describe our clinical validation and implementation of NGS IGH clonality testing and summarize our experience based on extensive routine use. NGS-based clonality testing targeting IGH FR1, FR2, FR3, and the conserved leader sequence upstream of FR1 was validated using commercially available kits. Data were analyzed by commercial and in-house-developed bioinformatics pipelines. Performance characteristics were evaluated directly comparing with capillary electrophoresis (CE) assays (BIOMED-2 primers). Assays were monitored after implementation (>1.5 years), concurrently testing by CE methods. A total of 1189 clinical samples were studied (94 validation, 1095 postimplementation). NGS showed superior performance compared with CE assays. For initial assessment, clonality detection rate was >97% for all malignancy types. Concordance with CE was 96%; discordances were related to higher sensitivity/resolution of NGS and improved detection in cases with high somatic hypermutation. Routine NGS clonality assessment is feasible and superior to existing assays, enabling accurate and specific index clone assessment and future tracking of all rearrangements in a patient sample. Successful implementation requires new standardization, validation, and implementation processes, which should be performed as a multicenter and multidisciplinary collaboration.
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Affiliation(s)
- Maria E Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Wayne Yu
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mustafa Syed
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Hannah Kim
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Lidia Maciag
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - JinJuan Yao
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Caleb Ho
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kseniya Petrova
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Christine Moung
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Paulo Salazar
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ivelise Rijo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Tessara Baldi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ahmet Zehir
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ola Landgren
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jae Park
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mikhail Roshal
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ahmet Dogan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Khedoudja Nafa
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
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25
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Middha S, Zhang L, Nafa K, Jayakumaran G, Wong D, Kim HR, Sadowska J, Berger MF, Delair DF, Shia J, Stadler Z, Klimstra DS, Ladanyi M, Zehir A, Hechtman JF. Reliable Pan-Cancer Microsatellite Instability Assessment by Using Targeted Next-Generation Sequencing Data. JCO Precis Oncol 2017; 2017. [PMID: 30211344 DOI: 10.1200/po.17.00084] [Citation(s) in RCA: 164] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Purpose Microsatellite instability (MSI)/mismatch repair (MMR) status is increasingly important in the management of patients with cancer to predict response to immune checkpoint inhibitors. We determined MSI status from large-panel clinical targeted next-generation sequencing (NGS) data across various solid cancer types. Methods The MSI statuses of 12,288 advanced solid cancers consecutively sequenced with Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets clinical NGS assay were inferred by using MSIsensor, a program that reports the percentage of unstable microsatellites as a score. Cutoff score determination and sensitivity/specificity were based on MSI polymerase chain reaction (PCR) and MMR immunohistochemistry. Results By using an MSIsensor score ≥ 10 to define MSI high (MSI-H), 83 (8%) of 996 colorectal cancers (CRCs) and 42 (16%) of 260 uterine endometrioid cancers (UECs) were MSI-H. Validation against MSI PCR and/or MMR immunohistochemistry performed for 138 (24 MSI-H, 114 microsatellite stable [MSS]) CRCs, and 40 (15 MSI-H, 25 MSS) UECs showed a concordance of 99.4%. MSIsensor also identified 68 MSI-H/MMR-deficient (MMR-D) non-CRC/UECs. Of 9,591 non-CRC/UEC tumors with MSS MSIsensor status, 456 (4.8%) had slightly elevated scores(≥3 and <10) of which 96.6% with available material were confirmed to be MSS by MSI PCR. MSI-H was also detected and confirmed in three non-CRC/UECs with low exonic mutation burden (< 20). MSIsensor correctly scored all 15 polymerase ε ultra-mutated cancers as negative for MSI. Conclusion MSI status can be reliably inferred by MSIsensor from large-panel targeted NGS data. Concurrent MSI testing by NGS is resource efficient, is potentially more sensitive for MMR-D than MSI PCR, and allows identification of MSI-H across various cancers not typically screened, as highlighted by the finding that 35% (68 of 193) of all MSI-H tumors were non-CRC/ UEC.
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Affiliation(s)
- Sumit Middha
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Liying Zhang
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Donna Wong
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Hyunjae R Kim
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | - Jinru Shia
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Marc Ladanyi
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Zehir
- Memorial Sloan Kettering Cancer Center, New York, NY
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26
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Mandelker D, Zhang L, Kemel Y, Stadler ZK, Joseph V, Zehir A, Pradhan N, Arnold A, Walsh MF, Li Y, Balakrishnan AR, Syed A, Prasad M, Nafa K, Carlo MI, Cadoo KA, Sheehan M, Fleischut MH, Salo-Mullen E, Trottier M, Lipkin SM, Lincoln A, Mukherjee S, Ravichandran V, Cambria R, Galle J, Abida W, Arcila ME, Benayed R, Shah R, Yu K, Bajorin DF, Coleman JA, Leach SD, Lowery MA, Garcia-Aguilar J, Kantoff PW, Sawyers CL, Dickler MN, Saltz L, Motzer RJ, O'Reilly EM, Scher HI, Baselga J, Klimstra DS, Solit DB, Hyman DM, Berger MF, Ladanyi M, Robson ME, Offit K. Mutation Detection in Patients With Advanced Cancer by Universal Sequencing of Cancer-Related Genes in Tumor and Normal DNA vs Guideline-Based Germline Testing. JAMA 2017; 318:825-835. [PMID: 28873162 PMCID: PMC5611881 DOI: 10.1001/jama.2017.11137] [Citation(s) in RCA: 312] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
IMPORTANCE Guidelines for cancer genetic testing based on family history may miss clinically actionable genetic changes with established implications for cancer screening or prevention. OBJECTIVE To determine the proportion and potential clinical implications of inherited variants detected using simultaneous sequencing of the tumor and normal tissue ("tumor-normal sequencing") compared with genetic test results based on current guidelines. DESIGN, SETTING, AND PARTICIPANTS From January 2014 until May 2016 at Memorial Sloan Kettering Cancer Center, 10 336 patients consented to tumor DNA sequencing. Since May 2015, 1040 of these patients with advanced cancer were referred by their oncologists for germline analysis of 76 cancer predisposition genes. Patients with clinically actionable inherited mutations whose genetic test results would not have been predicted by published decision rules were identified. Follow-up for potential clinical implications of mutation detection was through May 2017. EXPOSURE Tumor and germline sequencing compared with the predicted yield of targeted germline sequencing based on clinical guidelines. MAIN OUTCOMES AND MEASURES Proportion of clinically actionable germline mutations detected by universal tumor-normal sequencing that would not have been detected by guideline-directed testing. RESULTS Of 1040 patients, the median age was 58 years (interquartile range, 50.5-66 years), 65.3% were male, and 81.3% had stage IV disease at the time of genomic analysis, with prostate, renal, pancreatic, breast, and colon cancer as the most common diagnoses. Of the 1040 patients, 182 (17.5%; 95% CI, 15.3%-19.9%) had clinically actionable mutations conferring cancer susceptibility, including 149 with moderate- to high-penetrance mutations; 101 patients tested (9.7%; 95% CI, 8.1%-11.7%) would not have had these mutations detected using clinical guidelines, including 65 with moderate- to high-penetrance mutations. Frequency of inherited mutations was related to case mix, stage, and founder mutations. Germline findings led to discussion or initiation of change to targeted therapy in 38 patients tested (3.7%) and predictive testing in the families of 13 individuals (1.3%), including 6 for whom genetic evaluation would not have been initiated by guideline-based testing. CONCLUSIONS AND RELEVANCE In this referral population with selected advanced cancers, universal sequencing of a broad panel of cancer-related genes in paired germline and tumor DNA samples was associated with increased detection of individuals with potentially clinically significant heritable mutations over the predicted yield of targeted germline testing based on current clinical guidelines. Knowledge of these additional mutations can help guide therapeutic and preventive interventions, but whether all of these interventions would improve outcomes for patients with cancer or their family members requires further study. TRIAL REGISTRATION clinicaltrials.gov Identifier: NCT01775072.
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Affiliation(s)
| | - Liying Zhang
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yelena Kemel
- Memorial Sloan Kettering Cancer Center, New York, New York
- Sloan Kettering Institute, New York, New York
| | - Zsofia K Stadler
- Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medical College, New York, New York
| | - Vijai Joseph
- Memorial Sloan Kettering Cancer Center, New York, New York
- Sloan Kettering Institute, New York, New York
- Weill Cornell Medical College, New York, New York
| | - Ahmet Zehir
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nisha Pradhan
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Angela Arnold
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael F Walsh
- Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medical College, New York, New York
| | - Yirong Li
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | | | - Meera Prasad
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Khedoudja Nafa
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maria I Carlo
- Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medical College, New York, New York
| | - Karen A Cadoo
- Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medical College, New York, New York
| | - Meg Sheehan
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | | | - Magan Trottier
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Anne Lincoln
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Semanti Mukherjee
- Memorial Sloan Kettering Cancer Center, New York, New York
- Sloan Kettering Institute, New York, New York
| | | | - Roy Cambria
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jesse Galle
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Wassim Abida
- Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medical College, New York, New York
| | | | - Ryma Benayed
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ronak Shah
- Memorial Sloan Kettering Cancer Center, New York, New York
- Sloan Kettering Institute, New York, New York
| | - Kenneth Yu
- Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medical College, New York, New York
| | - Dean F Bajorin
- Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medical College, New York, New York
| | - Jonathan A Coleman
- Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medical College, New York, New York
| | - Steven D Leach
- Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medical College, New York, New York
| | - Maeve A Lowery
- Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medical College, New York, New York
| | - Julio Garcia-Aguilar
- Memorial Sloan Kettering Cancer Center, New York, New York
- Sloan Kettering Institute, New York, New York
- Weill Cornell Medical College, New York, New York
| | - Philip W Kantoff
- Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medical College, New York, New York
| | - Charles L Sawyers
- Memorial Sloan Kettering Cancer Center, New York, New York
- Sloan Kettering Institute, New York, New York
- Weill Cornell Medical College, New York, New York
| | - Maura N Dickler
- Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medical College, New York, New York
| | - Leonard Saltz
- Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medical College, New York, New York
| | - Robert J Motzer
- Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medical College, New York, New York
| | - Eileen M O'Reilly
- Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medical College, New York, New York
| | - Howard I Scher
- Memorial Sloan Kettering Cancer Center, New York, New York
- Sloan Kettering Institute, New York, New York
- Weill Cornell Medical College, New York, New York
| | - Jose Baselga
- Memorial Sloan Kettering Cancer Center, New York, New York
- Sloan Kettering Institute, New York, New York
- Weill Cornell Medical College, New York, New York
| | - David S Klimstra
- Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medical College, New York, New York
| | - David B Solit
- Memorial Sloan Kettering Cancer Center, New York, New York
- Sloan Kettering Institute, New York, New York
- Weill Cornell Medical College, New York, New York
| | - David M Hyman
- Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medical College, New York, New York
| | - Michael F Berger
- Memorial Sloan Kettering Cancer Center, New York, New York
- Sloan Kettering Institute, New York, New York
- Weill Cornell Medical College, New York, New York
| | - Marc Ladanyi
- Memorial Sloan Kettering Cancer Center, New York, New York
- Sloan Kettering Institute, New York, New York
| | - Mark E Robson
- Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medical College, New York, New York
| | - Kenneth Offit
- Memorial Sloan Kettering Cancer Center, New York, New York
- Sloan Kettering Institute, New York, New York
- Weill Cornell Medical College, New York, New York
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27
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Zehir A, Benayed R, Shah RH, Syed A, Middha S, Kim HR, Srinivasan P, Gao J, Chakravarty D, Devlin SM, Hellmann MD, Barron DA, Schram AM, Hameed M, Dogan S, Ross DS, Hechtman JF, DeLair DF, Yao J, Mandelker DL, Cheng DT, Chandramohan R, Mohanty AS, Ptashkin RN, Jayakumaran G, Prasad M, Syed MH, Rema AB, Liu ZY, Nafa K, Borsu L, Sadowska J, Casanova J, Bacares R, Kiecka IJ, Razumova A, Son JB, Stewart L, Baldi T, Mullaney KA, Al-Ahmadie H, Vakiani E, Abeshouse AA, Penson AV, Jonsson P, Camacho N, Chang MT, Won HH, Gross BE, Kundra R, Heins ZJ, Chen HW, Phillips S, Zhang H, Wang J, Ochoa A, Wills J, Eubank M, Thomas SB, Gardos SM, Reales DN, Galle J, Durany R, Cambria R, Abida W, Cercek A, Feldman DR, Gounder MM, Hakimi AA, Harding JJ, Iyer G, Janjigian YY, Jordan EJ, Kelly CM, Lowery MA, Morris LGT, Omuro AM, Raj N, Razavi P, Shoushtari AN, Shukla N, Soumerai TE, Varghese AM, Yaeger R, Coleman J, Bochner B, Riely GJ, Saltz LB, Scher HI, Sabbatini PJ, Robson ME, Klimstra DS, Taylor BS, Baselga J, Schultz N, Hyman DM, Arcila ME, Solit DB, Ladanyi M, Berger MF. Erratum: Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients. Nat Med 2017; 23:1004. [PMID: 28777785 DOI: 10.1038/nm0817-1004c] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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28
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Dogan S, Chute DJ, Xu B, Ptashkin RN, Chandramohan R, Casanova-Murphy J, Nafa K, Bishop JA, Chiosea SI, Stelow EB, Ganly I, Pfister DG, Katabi N, Ghossein RA, Berger MF. Frequent IDH2 R172 mutations in undifferentiated and poorly-differentiated sinonasal carcinomas. J Pathol 2017; 242:400-408. [PMID: 28493366 DOI: 10.1002/path.4915] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Revised: 04/11/2017] [Accepted: 04/25/2017] [Indexed: 12/20/2022]
Abstract
Sinonasal undifferentiated carcinoma (SNUC) is a high-grade malignancy with limited treatment options and poor outcome. A morphological spectrum of 47 sinonasal tumours including 17 (36.2%) SNUCs was analysed at genomic level. Thirty carcinomas (cohort 1) were subjected to a hybridization exon-capture next-generation sequencing assay (MSK-IMPACTTM ) to interrogate somatic variants in 279 or 410 cancer-related genes. Seventeen sinonasal tumours (cohort 2) were examined only for the presence of IDH1/2 exon 4 mutations by Sanger sequencing. IDH2 R172 single nucleotide variants were overall detected in 14 (82.4%) SNUCs, in two (20%) poorly-differentiated carcinomas with glandular/acinar differentiation, and in one of two high-grade neuroendocrine carcinomas, large cell type (HGNECs). No IDH2 mutation was detected in any of five olfactory neuroblastomas or in any of five SMARCB1-deficient carcinomas. Among 12 IDH2-mutated cases in cohort 1, five (41.7%) harboured co-existing TP53 mutations, four (33.3%) CDKN2A/2B loss-of-function alterations, four (33.3%) MYC amplification, and three (25%) had concurrent SETD2 mutations. AKT1 E17K and KIT D816V hotspot variants were each detected in one IDH2-mutated SNUC. The vast majority of SNUCs and variable proportions of other poorly-differentiated sinonasal carcinomas may be amenable to IDH2-targeted therapy. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Snjezana Dogan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Deborah J Chute
- Department of Pathology, Cleveland Clinic, Cleveland, OH, USA
| | - Bin Xu
- Department of Pathology, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Ryan N Ptashkin
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Raghu Chandramohan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Khedoudja Nafa
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Justin A Bishop
- Department of Pathology, The Johns Hopkins Hospital, Baltimore, MD, USA
| | - Simion I Chiosea
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Edward B Stelow
- Department of Pathology, University of Virginia Health System, Charlottesville, VA, USA
| | - Ian Ganly
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David G Pfister
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nora Katabi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ronald A Ghossein
- 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.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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29
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Cheng DT, Prasad M, Chekaluk Y, Benayed R, Sadowska J, Zehir A, Syed A, Wang YE, Somar J, Li Y, Yelskaya Z, Wong D, Robson ME, Offit K, Berger MF, Nafa K, Ladanyi M, Zhang L. Comprehensive detection of germline variants by MSK-IMPACT, a clinical diagnostic platform for solid tumor molecular oncology and concurrent cancer predisposition testing. BMC Med Genomics 2017; 10:33. [PMID: 28526081 PMCID: PMC5437632 DOI: 10.1186/s12920-017-0271-4] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 05/08/2017] [Indexed: 02/06/2023] Open
Abstract
Background The growing number of Next Generation Sequencing (NGS) tests is transforming the routine clinical diagnosis of hereditary cancers. Identifying whether a cancer is the result of an underlying disease-causing mutation in a cancer predisposition gene is not only diagnostic for a cancer predisposition syndrome, but also has significant clinical implications in the clinical management of patients and their families. Methods Here, we evaluated the performance of MSK-IMPACT (Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets) in detecting genetic alterations in 76 genes implicated in cancer predisposition syndromes. Output from hybridization-based capture was sequenced on an Illumina HiSeq 2500. A custom analysis pipeline was used to detect single nucleotide variants (SNVs), small insertions/deletions (indels) and copy number variants (CNVs). Results MSK-IMPACT detected all germline variants in a set of 233 unique patient DNA samples, previously confirmed by previous single gene testing. Reproducibility of variant calls was demonstrated using inter- and intra- run replicates. Moreover, in 16 samples, we identified additional pathogenic mutations other than those previously identified through a traditional gene-by-gene approach, including founder mutations in BRCA1, BRCA2, CHEK2 and APC, and truncating mutations in TP53, TSC2, ATM and VHL. Conclusions This study highlights the importance of the NGS-based gene panel testing approach in comprehensively identifying germline variants contributing to cancer predisposition and simultaneous detection of somatic and germline alterations. Electronic supplementary material The online version of this article (doi:10.1186/s12920-017-0271-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Donavan T Cheng
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, Box 36, New York, NY, 10065, USA.,Illumina Inc, Santa Clara, CA, USA
| | - Meera Prasad
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, Box 36, New York, NY, 10065, USA
| | | | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, Box 36, New York, NY, 10065, USA
| | - Justyna Sadowska
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, Box 36, New York, NY, 10065, USA
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, Box 36, New York, NY, 10065, USA
| | - Aijazuddin Syed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, Box 36, New York, NY, 10065, USA
| | - Yan Elsa Wang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, Box 36, New York, NY, 10065, USA
| | - Joshua Somar
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, Box 36, New York, NY, 10065, USA
| | - Yirong Li
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, Box 36, New York, NY, 10065, USA
| | - Zarina Yelskaya
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, Box 36, New York, NY, 10065, USA
| | - Donna Wong
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, Box 36, New York, NY, 10065, USA
| | - Mark E 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
| | - Michael F Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, Box 36, New York, NY, 10065, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Khedoudja Nafa
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, Box 36, New York, NY, 10065, USA
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, Box 36, New York, NY, 10065, USA. .,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Liying Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, Box 36, New York, NY, 10065, USA.
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30
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Zehir A, Benayed R, Shah RH, Syed A, Middha S, Kim HR, Srinivasan P, Gao J, Chakravarty D, Devlin SM, Hellmann MD, Barron DA, Schram AM, Hameed M, Dogan S, Ross DS, Hechtman JF, DeLair DF, Yao J, Mandelker DL, Cheng DT, Chandramohan R, Mohanty AS, Ptashkin RN, Jayakumaran G, Prasad M, Syed MH, Rema AB, Liu ZY, Nafa K, Borsu L, Sadowska J, Casanova J, Bacares R, Kiecka IJ, Razumova A, Son JB, Stewart L, Baldi T, Mullaney KA, Al-Ahmadie H, Vakiani E, Abeshouse AA, Penson AV, Jonsson P, Camacho N, Chang MT, Won HH, Gross BE, Kundra R, Heins ZJ, Chen HW, Phillips S, Zhang H, Wang J, Ochoa A, Wills J, Eubank M, Thomas SB, Gardos SM, Reales DN, Galle J, Durany R, Cambria R, Abida W, Cercek A, Feldman DR, Gounder MM, Hakimi AA, Harding JJ, Iyer G, Janjigian YY, Jordan EJ, Kelly CM, Lowery MA, Morris LGT, Omuro AM, Raj N, Razavi P, Shoushtari AN, Shukla N, Soumerai TE, Varghese AM, Yaeger R, Coleman J, Bochner B, Riely GJ, Saltz LB, Scher HI, Sabbatini PJ, Robson ME, Klimstra DS, Taylor BS, Baselga J, Schultz N, Hyman DM, Arcila ME, Solit DB, Ladanyi M, Berger MF. Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients. Nat Med 2017; 23:703-713. [PMID: 28481359 PMCID: PMC5461196 DOI: 10.1038/nm.4333] [Citation(s) in RCA: 2161] [Impact Index Per Article: 308.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 04/04/2017] [Indexed: 02/07/2023]
Abstract
Tumor molecular profiling is a fundamental component of precision oncology, enabling the identification of genomic alterations in genes and pathways that can be targeted therapeutically. The existence of recurrent targetable alterations across distinct histologically defined tumor types, coupled with an expanding portfolio of molecularly targeted therapies, demands flexible and comprehensive approaches to profile clinically relevant genes across the full spectrum of cancers. We established a large-scale, prospective clinical sequencing initiative using a comprehensive assay, MSK-IMPACT, through which we have compiled tumor and matched normal sequence data from a unique cohort of more than 10,000 patients with advanced cancer and available pathological and clinical annotations. Using these data, we identified clinically relevant somatic mutations, novel noncoding alterations, and mutational signatures that were shared by common and rare tumor types. Patients were enrolled on genomically matched clinical trials at a rate of 11%. To enable discovery of novel biomarkers and deeper investigation into rare alterations and tumor types, all results are publicly accessible.
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Affiliation(s)
- Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ronak H Shah
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Aijazuddin Syed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Sumit Middha
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Hyunjae R Kim
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Preethi Srinivasan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jianjiong Gao
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Debyani Chakravarty
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Sean M Devlin
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Matthew D Hellmann
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - David A Barron
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Alison M Schram
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Meera Hameed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Snjezana Dogan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Dara S Ross
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jaclyn F Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Deborah F DeLair
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - JinJuan Yao
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Diana L Mandelker
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Donavan T Cheng
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Raghu Chandramohan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Abhinita S Mohanty
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ryan N Ptashkin
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Gowtham Jayakumaran
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Meera Prasad
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Mustafa H Syed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | | | - Zhen Y Liu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Khedoudja Nafa
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Laetitia Borsu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Justyna Sadowska
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jacklyn Casanova
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ruben Bacares
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Iwona J Kiecka
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Anna Razumova
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Julie B Son
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Lisa Stewart
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Tessara Baldi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Kerry A Mullaney
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Hikmat Al-Ahmadie
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Efsevia Vakiani
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Adam A Abeshouse
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Alexander V Penson
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Philip Jonsson
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Niedzica Camacho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Matthew T Chang
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Helen H Won
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Benjamin E Gross
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ritika Kundra
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Zachary J Heins
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Hsiao-Wei Chen
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Sarah Phillips
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Hongxin Zhang
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jiaojiao Wang
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Angelica Ochoa
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jonathan Wills
- Information Systems, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Michael Eubank
- Information Systems, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Stacy B Thomas
- Information Systems, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Stuart M Gardos
- Information Systems, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Dalicia N Reales
- Clinical Research Administration, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jesse Galle
- Clinical Research Administration, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Robert Durany
- Clinical Research Administration, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Roy Cambria
- Clinical Research Administration, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Wassim Abida
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Andrea Cercek
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Darren R Feldman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Mrinal M Gounder
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - A Ari Hakimi
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - James J Harding
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Gopa Iyer
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Yelena Y Janjigian
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Emmet J Jordan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ciara M Kelly
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Maeve A Lowery
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Luc G T Morris
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Antonio M Omuro
- Department of Neurology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Nitya Raj
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Pedram Razavi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | | | - Neerav Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Tara E Soumerai
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Anna M Varghese
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Rona Yaeger
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jonathan Coleman
- Clinical Research Administration, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Bernard Bochner
- Clinical Research Administration, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Gregory J Riely
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Leonard B Saltz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Howard I Scher
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Paul J Sabbatini
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Mark E Robson
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - David S Klimstra
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Barry S Taylor
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jose Baselga
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Nikolaus Schultz
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - David M Hyman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Maria E Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - David B Solit
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Michael F Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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Syed MH, Ho C, Petrova-Drus K, Yao J, Yu W, Zehir A, Nafa K, Arcila ME. Clinical utility of clonality testing by next generation sequencing in the monitoring of B-cell and T-cell malignancies. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.7_suppl.72] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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
72 Background: Clonality testing is an integral part of the initial assessment of B and T cell malignancies. The further use of conventional clonality assays for monitoring of disease post treatment is limited by low assay sensitivity and inability to track clones based on their unique sequences. Clonality assessment by next generation sequencing (NGS) provides increased diagnostic capabilities, allowing the tracking of disease specific clones as well as the full spectrum of clonal sequences that arise in response to therapy. Here we describe our initial experience using an NGS based assay for monitoring and our comparison to conventional clonality assays and flow cytometry. Methods: DNA was extracted from hematologic samples received for routine clonality assessment including diagnostic (DS) and follow-up post therapy (PT) samples. Clonality testing was performed by conventional PCR-based assays using biomed II primers and by NGS utilizing Lymphotrack IGH FR1 and TRG kits (Invivoscribe). The amplified products were sequenced on Illumina MiSeq. For MRD assessment, we created dedicated laboratory protocols as well as in-house developed software, MSK-LymphoClone (LC), containing a data analysis pipeline, analytical tools for clonality assessment and a signout portal for easy search and retrieval of pertinent clones. Results: Samples from 48 patients were included (48 DS and 60 PT) encompassing 12 plasma cell neoplasms, 11 acute lymphoblastic leukemias, 16 mature B-cell and 9 T-cell lymphomas. All diagnostic samples showed clonal rearrangement with 100% concordance between conventional and NGS assays. Residual disease was detected in 27/60 (45%) PT samples using conventional fragment size based assays, 27/57 (47%) using flow and 38/60 (63%) using NGS. Diagnostic clonal sequences were detected in as low as 0.0019% of total reads in PT samples tested by NGS. 18/60 (30.0%) PT samples (17 patients) were disease negative by all assays; 16 patients remained disease-free (median follow-up - 2.4 months). Conclusions: NGS clonality testing is a valuable tool for monitoring patients with B and T cell neoplasms showing higher sensitivity and specificity than conventional assays.
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Affiliation(s)
| | - Caleb Ho
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - JinJuan Yao
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Wayne Yu
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Zehir
- Memorial Sloan Kettering Cancer Center, New York, NY
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Yao J, Douer D, Wang L, Arcila ME, Nafa K, Chiu A. A case of acute myeloid leukemia with e6a2 BCR-ABL fusion transcript acquired after progressing from chronic myelomonocytic leukemia. Leuk Res Rep 2017; 7:17-19. [PMID: 28275539 PMCID: PMC5328719 DOI: 10.1016/j.lrr.2017.01.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [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] [Received: 08/04/2015] [Accepted: 01/15/2017] [Indexed: 11/27/2022] Open
Abstract
Philadelphia (Ph) chromosome is a cytogenetic hallmark of chronic myeloid leukemia (CML). Most patients with CML harbor either the e13a2 or e14a2 BCR-ABL fusion product, while a small subset of the cases expresses e1a2 or e19a2 transcripts. We report a patient with chronic myelomonocytic leukemia (CMML), initially Ph chromosome negative at presentation, with rapid disease progression to acute myeloid leukemia (AML) and appearance of Ph chromosome and BCR-ABL e6a2, a very uncommon fusion transcript. The AML was refractory to treatment with subsequent emergence and dominance of a Ph negative leukemic clone. The patient expired shortly after disease progression.
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Affiliation(s)
- Jinjuan Yao
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Dan Douer
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Lu Wang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Maria E Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Khedoudja Nafa
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - April Chiu
- Department of Laboratory Medicine and Pathology Mayo Clinic, 200 First St. SW, Rochester, MN 55905, USA
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Ross DS, Zehir A, Cheng DT, Benayed R, Nafa K, Hechtman JF, Janjigian YY, Weigelt B, Razavi P, Hyman DM, Baselga J, Berger MF, Ladanyi M, Arcila ME. Next-Generation Assessment of Human Epidermal Growth Factor Receptor 2 (ERBB2) Amplification Status: Clinical Validation in the Context of a Hybrid Capture-Based, Comprehensive Solid Tumor Genomic Profiling Assay. J Mol Diagn 2016; 19:244-254. [PMID: 28027945 DOI: 10.1016/j.jmoldx.2016.09.010] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 08/02/2016] [Accepted: 09/27/2016] [Indexed: 12/31/2022] Open
Abstract
Establishing ERBB2 [human epidermal growth factor receptor 2 (HER2)] amplification status in breast and gastric carcinomas is essential to treatment selection. Immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) constitute the current standard for assessment. With further advancements in genomic medicine, new clinically relevant biomarkers are rapidly emerging and options for targeted therapy are increasing in patients with advanced disease, driving the need for comprehensive molecular profiling. Next-generation sequencing (NGS) is an attractive approach for up-front comprehensive assessment, including ERBB2 status, but the concordance with traditional methods of HER2 assessment is not well established. The Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT) assay, a hybrid capture-based NGS assay interrogating the coding regions of 410 cancer-related genes, was performed on manually macrodissected unstained sections from formalin-fixed, paraffin-embedded breast (n = 213) and gastroesophageal (n = 39) tumors submitted for clinical mutation profiling. ERBB2 status was assessed using a custom bioinformatics pipeline, and NGS results were compared to IHC and FISH. NGS ERBB2 amplification calls had an overall concordance of 98.4% (248/252) with the combined IHC/FISH results in this validation set. Discrepancies occurred in the context of low tumor content and HER2 heterogeneity. ERBB2 amplification status can be reliably determined by hybridization capture-based NGS methods, allowing efficient concurrent testing for other potentially actionable genomic alterations, particularly in limited material.
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Affiliation(s)
- Dara S Ross
- 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
| | - Donavan T Cheng
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Khedoudja Nafa
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jaclyn F Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yelena Y Janjigian
- Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Pedram Razavi
- Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David M Hyman
- Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - José Baselga
- Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael F Berger
- 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
| | - Maria E Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
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Borsu L, Intrieri J, Thampi L, Yu H, Riely G, Nafa K, Chandramohan R, Ladanyi M, Arcila ME. Clinical Application of Picodroplet Digital PCR Technology for Rapid Detection of EGFR T790M in Next-Generation Sequencing Libraries and DNA from Limited Tumor Samples. J Mol Diagn 2016; 18:903-911. [PMID: 27631691 PMCID: PMC5807920 DOI: 10.1016/j.jmoldx.2016.07.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 06/08/2016] [Accepted: 07/11/2016] [Indexed: 12/31/2022] Open
Abstract
Although next-generation sequencing (NGS) is a robust technology for comprehensive assessment of EGFR-mutant lung adenocarcinomas with acquired resistance to tyrosine kinase inhibitors, it may not provide sufficiently rapid and sensitive detection of the EGFR T790M mutation, the most clinically relevant resistance biomarker. Here, we describe a digital PCR (dPCR) assay for rapid T790M detection on aliquots of NGS libraries prepared for comprehensive profiling, fully maximizing broad genomic analysis on limited samples. Tumor DNAs from patients with EGFR-mutant lung adenocarcinomas and acquired resistance to epidermal growth factor receptor inhibitors were prepared for Memorial Sloan-Kettering-Integrated Mutation Profiling of Actionable Cancer Targets sequencing, a hybrid capture-based assay interrogating 410 cancer-related genes. Precapture library aliquots were used for rapid EGFR T790M testing by dPCR, and results were compared with NGS and locked nucleic acid-PCR Sanger sequencing (reference high sensitivity method). Seventy resistance samples showed 99% concordance with the reference high sensitivity method in accuracy studies. Input as low as 2.5 ng provided a sensitivity of 1% and improved further with increasing DNA input. dPCR on libraries required less DNA and showed better performance than direct genomic DNA. dPCR on NGS libraries is a robust and rapid approach to EGFR T790M testing, allowing most economical utilization of limited material for comprehensive assessment. The same assay can also be performed directly on any limited DNA source and cell-free DNA.
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Affiliation(s)
- Laetitia Borsu
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York.
| | - Julie Intrieri
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Linta Thampi
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Helena Yu
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Gregory Riely
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Khedoudja Nafa
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Raghu Chandramohan
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York; Human Oncology & Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Maria E Arcila
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
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Wang L, Zehir A, Nafa K, Zhou N, Berger MF, Casanova J, Sadowska J, Lu C, Allis CD, Gounder M, Chandhanayingyong C, Ladanyi M, Boland PJ, Hameed M. Genomic aberrations frequently alter chromatin regulatory genes in chordoma. Genes Chromosomes Cancer 2016; 55:591-600. [PMID: 27072194 DOI: 10.1002/gcc.22362] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 04/07/2016] [Accepted: 04/08/2016] [Indexed: 01/08/2023] Open
Abstract
Chordoma is a rare primary bone neoplasm that is resistant to standard chemotherapies. Despite aggressive surgical management, local recurrence and metastasis is not uncommon. To identify the specific genetic aberrations that play key roles in chordoma pathogenesis, we utilized a genome-wide high-resolution SNP-array and next generation sequencing (NGS)-based molecular profiling platform to study 24 patient samples with typical histopathologic features of chordoma. Matching normal tissues were available for 16 samples. SNP-array analysis revealed nonrandom copy number losses across the genome, frequently involving 3, 9p, 1p, 14, 10, and 13. In contrast, copy number gain is uncommon in chordomas. Two minimum deleted regions were observed on 3p within a ∼8 Mb segment at 3p21.1-p21.31, which overlaps SETD2, BAP1 and PBRM1. The minimum deleted region on 9p was mapped to CDKN2A locus at 9p21.3, and homozygous deletion of CDKN2A was detected in 5/22 chordomas (∼23%). NGS-based molecular profiling demonstrated an extremely low level of mutation rate in chordomas, with an average of 0.5 mutations per sample for the 16 cases with matched normal. When the mutated genes were grouped based on molecular functions, many of the mutation events (∼40%) were found in chromatin regulatory genes. The combined copy number and mutation profiling revealed that SETD2 is the single gene affected most frequently in chordomas, either by deletion or by mutations. Our study demonstrated that chordoma belongs to the C-class (copy number changes) tumors whose oncogenic signature is non-random multiple copy number losses across the genome and genomic aberrations frequently alter chromatin regulatory genes. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Lu Wang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Khedoudja Nafa
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nengyi Zhou
- 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.,Department of Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jacklyn Casanova
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Justyna Sadowska
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Chao Lu
- Department of Laboratory of Chromatin Biology and Epigenetics, the Rockefeller University, New York, NY
| | - C David Allis
- Department of Laboratory of Chromatin Biology and Epigenetics, the Rockefeller University, New York, NY
| | - Mrinal Gounder
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Patrick J Boland
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Meera Hameed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
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Jour G, Wang L, Middha S, Zehir A, Chen W, Sadowska J, Healey J, Agaram NP, Choi L, Nafa K, Hameed M. The molecular landscape of extraskeletal osteosarcoma: A clinicopathological and molecular biomarker study. J Pathol Clin Res 2015; 2:9-20. [PMID: 27499911 PMCID: PMC4858130 DOI: 10.1002/cjp2.29] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [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: 07/06/2015] [Accepted: 09/29/2015] [Indexed: 12/12/2022]
Abstract
Extraskeletal osteosarcoma (ESOSA) is a rare soft tissue neoplasm representing <5% of osteosarcomas and <1% of all soft-tissue sarcomas. Herein, we investigate the clinicopathological and molecular features of ESOSA and explore potential parameters that may affect outcome. Thirty-two cases were retrieved and histomorphology was reviewed. Clinical history and follow-up were obtained through electronic record review. DNA from formalin-fixed paraffin-embedded (FFPE) tissue was extracted and processed from 27 cases. Genome-wide DNA copy number (CN) alterations and allelic imbalances were analyzed by single nucleotide polymorphism array using Affymetrix OncoScan FFPE Assay. Massive high-throughput deep parallel sequencing was performed using a customized panel targeting 410 cancer genes. Log rank, Fisher's exact test and Cox proportional hazards were used for statistical analysis. In this series of 32 patients (male n = 12, female n = 20), the average age was 66 years (19-93) and median follow up was 24 months (range 6-120 months). Frequent genomic alterations included CN losses in tumour suppressor genes including CDKN2A (70%), TP53 (56%) and RB1 (49%). Mutations affecting methylation/demethylation, chromatin remodeling and WNT/SHH pathways were identified in 40%, 27%, and 27%, respectively. PIK3CA and TERT promoter variant mutations were identified in 11% of the cases. Cases harbouring simultaneous TP53 and RB1 biallelic CN losses were associated with worse overall survival and local recurrence (p = 0.04, p = 0.02, respectively). CDKN2A losses and positive margins were also associated with worse overall survival (p = 0.002; p = 0.03, respectively). Our findings suggest that age above 60, positive margin status, simultaneous biallelic TP53 and RB1 losses and CDKN2A loss are associated with a worse outcome in ESOSA. Comparison between conventional paediatric osteosarcoma and ESOSA shows that, while both share genetic similarities, there are notable dissimilarities and mechanistic differences in the molecular pathways involved in ESOSA.
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Affiliation(s)
- George Jour
- Department of Pathology Memorial Sloan Kettering Cancer Center New York NY USA
| | - Lu Wang
- Department of Pathology Memorial Sloan Kettering Cancer Center New York NY USA
| | - Sumit Middha
- 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
| | - Wen Chen
- Department of Pathology Memorial Sloan Kettering Cancer Center New York NY USA
| | - Justyna Sadowska
- Department of Pathology Memorial Sloan Kettering Cancer Center New York NY USA
| | - John Healey
- Department of Orthopedic Surgery Memorial Sloan Kettering Cancer Center New York NY USA
| | - Narasimhan P Agaram
- Department of Pathology Memorial Sloan Kettering Cancer Center New York NY USA
| | - Lisa Choi
- Department of Orthopedic Surgery Memorial Sloan Kettering Cancer Center New York NY USA
| | - Khedoudja Nafa
- Department of Pathology Memorial Sloan Kettering Cancer Center New York NY USA
| | - Meera Hameed
- Department of Pathology Memorial Sloan Kettering Cancer Center New York NY USA
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Naidoo J, Sima CS, Rodriguez K, Busby N, Nafa K, Ladanyi M, Riely GJ, Kris MG, Arcila ME, Yu HA. Epidermal growth factor receptor exon 20 insertions in advanced lung adenocarcinomas: Clinical outcomes and response to erlotinib. Cancer 2015; 121:3212-3220. [PMID: 26096453 DOI: 10.1002/cncr.29493] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 04/28/2015] [Accepted: 04/30/2015] [Indexed: 12/13/2022]
Abstract
BACKGROUND Epidermal growth factor receptor (EGFR) exon 20 insertions (exon20ins) represent approximately 10% of EGFR-mutant lung adenocarcinomas, and are associated with resistance to EGFR tyrosine kinase inhibitors (TKIs). Clinical outcomes in comparison with patients with sensitizing EGFR mutations are not well established. METHODS Patients with stage IV lung adenocarcinomas with EGFR exon20ins were identified through routine molecular testing. Clinicopathologic data were collected. Overall survival (OS) was measured from the diagnosis of stage IV disease, and in patients treated with EGFR TKIs, the time to progression (TTP) on erlotinib was measured. RESULTS One thousand eight hundred and eighty-two patients with stage IV lung adenocarcinomas were identified: 46 patients had EGFR exon20ins (2%), and 258 patients had an EGFR exon 19 deletion (exon19del)/L858R point mutation (14%). Among 11 patients with lung adenocarcinomas with EGFR exon20ins who received erlotinib, 3 patients (27%) had a partial response (FQEA, 1; ASV, 1; and unknown variant, 1). TTP for patients with EGFR exon20ins and patients with EGFR exon19del/L858R on erlotinib were 3 and 12 months, respectively (P < .01). Responses to chemotherapy were similar for patients with lung adenocarcinomas with EGFR exon20ins and patients with lung adenocarcinomas with EGFR exon19del/L858R. Median OS from the diagnosis of stage IV disease for patients with EGFR exon20ins and patients with EGFR exon19del/L858R was 26 months (95% confidence interval, 19 months-not reached n = 46) and 31 months (95% confidence interval, 28-33 months; n = 258), respectively (P = .53). CONCLUSIONS The majority of patients with advanced lung adenocarcinomas harboring EGFR exon20ins do not respond to EGFR TKI therapy. Standard chemotherapy should be used as first-line therapy. These patients have an OS similar to that of patients with sensitizing EGFR mutations. Individuals with certain variants such as FQEA and ASV may respond to erlotinib.
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Wang L, Zehir A, Sadowska J, Zhou N, Rosenblum M, Busam K, Agaram N, Travis W, Arcila M, Dogan S, Berger MF, Cheng DT, Ladanyi M, Nafa K, Hameed M. Consistent copy number changes and recurrent PRKAR1A mutations distinguish Melanotic Schwannomas from Melanomas: SNP-array and next generation sequencing analysis. Genes Chromosomes Cancer 2015; 54:463-471. [PMID: 26031761 DOI: 10.1002/gcc.22254] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 02/26/2015] [Accepted: 02/26/2015] [Indexed: 12/25/2022] Open
Abstract
Melanotic Schwannomas (MS) are rare tumors that share histological features with melanocytic tumors and schwannomas. However, their genetics are poorly understood. To elucidate the genetic characteristics of MS, we performed genome-wide studies in a series of cases. Twelve MS cases were available for the study. Genomic DNAs extracted from formalin-fixed paraffin embedded tumor tissues were subjected to copy number (CN) and allelic imbalance (AI) analysis by Single Nucleotide Polymorphism (SNP)-array and screened for mutations in coding exons of 341 key cancer-associated genes using a hybrid capture-based next-generation sequencing (NGS) assay. Sanger sequencing was used to further verify recurrent mutations detected by NGS study. SNP-array analysis revealed remarkably stereotypic chromosomal abnormalities in MS. Hypodiploidy was common, typically involving monosomies of chromosomes 1, 2, and 17. All 12 samples showed mutations in PRKAR1A gene, including 2 cases with 2 mutations each. The 14 mutations were scattered across PRKAR1A, and most were inactivating mutations. AI on 17q, presenting as loss of heterozygosity with or without CN losses, combined with a PRKAR1A mutation was observed in 9/12 MS cases. The remaining 3 cases included the two samples harboring two mutations in PRKAR1A. MS exhibits a stereotypic pattern of chromosomal losses. In contrast, melanomas are typically characterized by the presence of multiple CN aberrations, without demonstrable differences in the frequency of losses and gains. Inactivation of both alleles of PRKAR1A by "two hits" observed in almost all cases underscores the central role of PRKAR1A in the pathogenesis of this neoplasm. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Lu Wang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Justyna Sadowska
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Nengyi Zhou
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Marc Rosenblum
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Klaus Busam
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Narasimhan Agaram
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - William Travis
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Maria Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Snjezana Dogan
- 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.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Donavan T Cheng
- Department of Pathology, 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
| | - Khedoudja Nafa
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Meera Hameed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
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Ross DS, Zehir A, Cheng DT, Nafa K, Jour G, Razavi P, Hyman DM, Baselga J, Berger MF, Ladanyi M, Arcila ME. The clinical utility of ERBB2 amplification detection in breast carcinoma using a 341 gene hybrid capture-based next generation sequencing (NGS) assay: Comparison with standard immunohistochemistry (IHC) and Fluorescence In Situ Hybridization (FISH) assays. J Clin Oncol 2015. [DOI: 10.1200/jco.2015.33.15_suppl.604] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Dara S. Ross
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Zehir
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - George Jour
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Pedram Razavi
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Jose Baselga
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Marc Ladanyi
- Memorial Sloan Kettering Cancer Center, New York, NY
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Cheng DT, Mitchell TN, Zehir A, Shah RH, Benayed R, Syed A, Chandramohan R, Liu ZY, Won HH, Scott SN, Brannon AR, O'Reilly C, Sadowska J, Casanova J, Yannes A, Hechtman JF, Yao J, Song W, Ross DS, Oultache A, Dogan S, Borsu L, Hameed M, Nafa K, Arcila ME, Ladanyi M, Berger MF. Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT): A Hybridization Capture-Based Next-Generation Sequencing Clinical Assay for Solid Tumor Molecular Oncology. J Mol Diagn 2015; 17:251-64. [PMID: 25801821 DOI: 10.1016/j.jmoldx.2014.12.006] [Citation(s) in RCA: 1430] [Impact Index Per Article: 158.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 11/20/2014] [Accepted: 12/18/2014] [Indexed: 01/17/2023] Open
Abstract
The identification of specific genetic alterations as key oncogenic drivers and the development of targeted therapies are together transforming clinical oncology and creating a pressing need for increased breadth and throughput of clinical genotyping. Next-generation sequencing assays allow the efficient and unbiased detection of clinically actionable mutations. To enable precision oncology in patients with solid tumors, we developed Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT), a hybridization capture-based next-generation sequencing assay for targeted deep sequencing of all exons and selected introns of 341 key cancer genes in formalin-fixed, paraffin-embedded tumors. Barcoded libraries from patient-matched tumor and normal samples were captured, sequenced, and subjected to a custom analysis pipeline to identify somatic mutations. Sensitivity, specificity, reproducibility of MSK-IMPACT were assessed through extensive analytical validation. We tested 284 tumor samples with previously known point mutations and insertions/deletions in 47 exons of 19 cancer genes. All known variants were accurately detected, and there was high reproducibility of inter- and intrarun replicates. The detection limit for low-frequency variants was approximately 2% for hotspot mutations and 5% for nonhotspot mutations. Copy number alterations and structural rearrangements were also reliably detected. MSK-IMPACT profiles oncogenic DNA alterations in clinical solid tumor samples with high accuracy and sensitivity. Paired analysis of tumors and patient-matched normal samples enables unambiguous detection of somatic mutations to guide treatment decisions.
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Affiliation(s)
- Donavan T Cheng
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Talia N Mitchell
- 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
| | - Ronak H Shah
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Aijazuddin Syed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Raghu Chandramohan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Zhen Yu Liu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Helen H Won
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sasinya N Scott
- 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
| | - Catherine O'Reilly
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Justyna Sadowska
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jacklyn Casanova
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Angela Yannes
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jaclyn F Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jinjuan Yao
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Wei Song
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Dara S Ross
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alifya Oultache
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Snjezana Dogan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Laetitia Borsu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Meera Hameed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Khedoudja Nafa
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maria E Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael F Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.
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Hechtman JF, DeMatteo R, Nafa K, Chi P, Arcila ME, Dogan S, Oultache A, Chen W, Hameed M. Additional Primary Malignancies in Patients with Gastrointestinal Stromal Tumor (GIST): A Clinicopathologic Study of 260 Patients with Molecular Analysis and Review of the Literature. Ann Surg Oncol 2015; 22:2633-9. [PMID: 25564173 DOI: 10.1245/s10434-014-4332-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Indexed: 12/20/2022]
Abstract
BACKGROUND The incidence of other primary neoplasms in gastrointestinal stromal tumor (GIST) patients is relatively high. Our aim was to better characterize the clinicopathologic and molecular relationships in a cohort of GIST patients. METHODS All GIST patients with tumor samples sent for molecular testing were identified via electronic medical records. Clinicopathologic characteristics of GIST and additional primary malignancies were analyzed. RESULTS Of 260 patients, 50 (19 %) had at least one additional primary malignancy. In 33 patients, separate primary neoplasms predated their GIST diagnosis and most commonly included: prostate (n = 9), breast (n = 8), and hematologic (n = 5). Renal (n = 4) and hematologic (n = 3) malignancies were the most frequent cancers identified after GIST diagnosis. The majority (8 of 12, 66 %) of malignancies diagnosed after GIST were found incidentally. Patients who developed other malignancies after GIST more often had KIT exon 11 mutations (100 vs. 66 %, P = 0.01). In comparison to patients with only GIST, patients with a second primary neoplasm of any chronology had GISTs with increased mitotic rate (≥5 per 50 high-power fields) (P = 0.0006). Literature review revealed colorectal cancer, gastric, prostate, renal, leukemia, and desmoid-type fibromatosis as the most common secondary neoplasms. CONCLUSIONS Nineteen percent of GIST patients develop other malignancies. This is the first report to describe a relationship between additional primary malignancy and both mutation and mitotic rate of GIST. Although the basis of these relationships remains to be investigated, caution in the clinical management of GIST patients with additional lesions is warranted.
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Hechtman JF, Zehir A, Mitchell T, Borsu L, Singer S, Tap W, Oultache A, Ladanyi M, Nafa K. Novel oncogene and tumor suppressor mutations in KIT and PDGFRA wild type gastrointestinal stromal tumors revealed by next generation sequencing. Genes Chromosomes Cancer 2014; 54:177-84. [PMID: 25427437 DOI: 10.1002/gcc.22230] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 11/05/2014] [Indexed: 12/19/2022] Open
Abstract
Among gastrointestinal stromal tumors (GISTs) of 10-15% are negative for KIT and PDGFRA, and most of these cases are SDH deficient. Recent studies have provided data on additional molecular alterations such as KRAS in KIT mutant GISTs. We aimed to assess the frequency and spectrum of somatic mutations in common oncogenes as well as copy number variations in GISTs negative for KIT and PDGFRA mutations. GISTs with wild type KIT/PDGFRA were tested via next generation sequencing for somatic mutations in 341 genes. SDHB immunohistochemistry to evaluate for SDH deficiency was also performed. Of 267 GISTs tested for KIT and PDGFRA mutations, 15 were wild type, of which eight cases had material available for further testing. All eight cases had loss of SDHB expression and had various molecular alterations involving ARID1A, TP53, and other genes. One case had a KRAS G12V (c.35G>T) mutation in both the primary gastric tumor and a post-imatinib recurrence. This tumor had anaplastic features and was resistant to multiple tyrosine kinase inhibitors, ultimately resulting in cancer-related mortality within 2 years of diagnosis. In conclusion, KRAS mutations occur in rare GISTs with wild type KIT and PDGFRA. These tumors may display immunohistochemical positivity for KIT and primary resistance to tyrosine kinase inhibitors.
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Cheng DT, Cheng J, Mitchell TN, Syed A, Zehir A, Mensah NYT, Oultache A, Nafa K, Levine RL, Arcila ME, Berger MF, Hedvat CV. Detection of mutations in myeloid malignancies through paired-sample analysis of microdroplet-PCR deep sequencing data. J Mol Diagn 2014; 16:504-518. [PMID: 25017477 DOI: 10.1016/j.jmoldx.2014.05.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Revised: 04/24/2014] [Accepted: 05/09/2014] [Indexed: 01/10/2023] Open
Abstract
Amplicon-based methods for targeted resequencing of cancer genes have gained traction in the clinic as a strategy for molecular diagnostic testing. An 847-amplicon panel was designed with the RainDance DeepSeq system, covering most exons of 28 genes relevant to acute myeloid leukemia and myeloproliferative neoplasms. We developed a paired-sample analysis pipeline for variant calling and sought to assess its sensitivity and specificity relative to a set of samples with previously identified mutations. Thirty samples with known mutations in JAK2, NPM1, DNMT3A, MPL, IDH1, IDH2, CEBPA, and FLT3, were profiled and sequenced to high depth. Variant calling using an unmatched Hapmap DNA control removed a substantial number of artifactual calls regardless of algorithm used or variant class. The removed calls were nonunique, had lower variant frequencies, and tended to recur in multiple unrelated samples. Analysis of sample replicates revealed that reproducible calls had distinctly higher variant allele depths and frequencies compared to nonreproducible calls. On the basis of these differences, filters on variant frequency were chosen to select for reproducible calls. The analysis pipeline successfully retrieved the associated known variant in all tested samples and uncovered additional mutations in some samples corresponding to well-characterized hotspot mutations in acute myeloid leukemia. We have developed a paired-sample analysis pipeline capable of robust identification of mutations from microdroplet-PCR sequencing data with high sensitivity and specificity.
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Affiliation(s)
- Donavan T Cheng
- Molecular Diagnostics Service, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York.
| | - Janice Cheng
- Molecular Diagnostics Service, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Talia N Mitchell
- Molecular Diagnostics Service, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Aijazuddin Syed
- Molecular Diagnostics Service, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Ahmet Zehir
- Molecular Diagnostics Service, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Nana Yaa T Mensah
- Molecular Diagnostics Service, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Alifya Oultache
- Molecular Diagnostics Service, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Khedoudja Nafa
- Molecular Diagnostics Service, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Ross L Levine
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Maria E Arcila
- Molecular Diagnostics Service, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Michael F Berger
- Molecular Diagnostics Service, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York; Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Cyrus V Hedvat
- Molecular Diagnostics Service, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
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Lu C, Venneti S, Akalin A, Fang F, Ward PS, Dematteo RG, Intlekofer AM, Chen C, Ye J, Hameed M, Nafa K, Agaram NP, Cross JR, Khanin R, Mason CE, Healey JH, Lowe SW, Schwartz GK, Melnick A, Thompson CB. Induction of sarcomas by mutant IDH2. Genes Dev 2013; 27:1986-98. [PMID: 24065766 PMCID: PMC3792475 DOI: 10.1101/gad.226753.113] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [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] [Indexed: 02/07/2023]
Abstract
More than 50% of patients with chondrosarcomas exhibit gain-of-function mutations in either isocitrate dehydrogenase 1 (IDH1) or IDH2. In this study, we performed genome-wide CpG methylation sequencing of chondrosarcoma biopsies and found that IDH mutations were associated with DNA hypermethylation at CpG islands but not other genomic regions. Regions of CpG island hypermethylation were enriched for genes implicated in stem cell maintenance/differentiation and lineage specification. In murine 10T1/2 mesenchymal progenitor cells, expression of mutant IDH2 led to DNA hypermethylation and an impairment in differentiation that could be reversed by treatment with DNA-hypomethylating agents. Introduction of mutant IDH2 also induced loss of contact inhibition and generated undifferentiated sarcomas in vivo. The oncogenic potential of mutant IDH2 correlated with the ability to produce 2-hydroxyglutarate. Together, these data demonstrate that neomorphic IDH2 mutations can be oncogenic in mesenchymal cells.
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Affiliation(s)
- Chao Lu
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
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Dogan S, Becker JC, Rekhtman N, Tang LH, Nafa K, Ladanyi M, Klimstra DS. Use of touch imprint cytology as a simple method to enrich tumor cells for molecular analysis. Cancer Cytopathol 2013; 121:354-60. [DOI: 10.1002/cncy.21292] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 02/10/2013] [Accepted: 03/01/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Snjezana Dogan
- Department of Pathology; Memorial Sloan-Kettering Cancer Center; New York New York
| | - Jillian C. Becker
- Department of Pathology; Memorial Sloan-Kettering Cancer Center; New York New York
| | - Natasha Rekhtman
- Department of Pathology; Memorial Sloan-Kettering Cancer Center; New York New York
| | - Laura H. Tang
- Department of Pathology; Memorial Sloan-Kettering Cancer Center; New York New York
| | - Khedoudja Nafa
- Department of Pathology; Memorial Sloan-Kettering Cancer Center; New York New York
| | - Marc Ladanyi
- Department of Pathology; Memorial Sloan-Kettering Cancer Center; New York New York
| | - David S. Klimstra
- Department of Pathology; Memorial Sloan-Kettering Cancer Center; New York New York
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Arcila ME, Nafa K, Chaft JE, Rekhtman N, Lau C, Reva BA, Zakowski MF, Kris MG, Ladanyi M. EGFR exon 20 insertion mutations in lung adenocarcinomas: prevalence, molecular heterogeneity, and clinicopathologic characteristics. Mol Cancer Ther 2013; 12:220-9. [PMID: 23371856 DOI: 10.1158/1535-7163.mct-12-0620] [Citation(s) in RCA: 331] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In contrast to other primary epidermal growth factor receptor (EGFR) mutations in lung adenocarcinomas, insertions in exon 20 of EGFR have been generally associated with resistance to EGFR-tyrosine kinase inhibitors. Their molecular spectrum, clinicopathologic characteristics, and prevalence are not well established. Tumors harboring EGFR exon 20 insertions were identified through an algorithmic screen of 1,500 lung adenocarcinomas. Cases were first tested for common mutations in EGFR (exons 19 and 21) and KRAS (exon 2) and, if negative, further analyzed for EGFR exon 20 insertions. All samples underwent extended genotyping for other driver mutations in EGFR, KRAS, BRAF, ERBB2/HER2, NRAS, PIK3CA, MEK1, and AKT by mass spectrometry; a subset was evaluated for ALK rearrangements. We identified 33 EGFR exon 20 insertion cases [2.2%, 95% confidence interval (CI), 1.6-3.1], all mutually exclusive with mutations in the other genes tested (except PIK3CA). They were more common among never-smokers (P < 0.0001). There was no association with age, sex, race, or stage. Morphologically, tumors were similar to those with common EGFR mutations but with frequent solid histology. Insertions were highly variable in position and size, ranging from 3 to 12 bp, resulting in 13 different insertions, which, by molecular modeling, are predicted to have potentially different effects on erlotinib binding. EGFR exon 20 insertion testing identifies a distinct subset of lung adenocarcinomas, accounting for at least 9% of all EGFR-mutated cases, representing the third most common type of EGFR mutation after exon 19 deletions and L858R. Insertions are structurally heterogeneous with potential implications for response to EGFR inhibitors.
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Affiliation(s)
- Maria E Arcila
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA.
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Arcila ME, Chaft JE, Nafa K, Roy-Chowdhuri S, Lau C, Zaidinski M, Paik PK, Zakowski MF, Kris MG, Ladanyi M. Prevalence, clinicopathologic associations, and molecular spectrum of ERBB2 (HER2) tyrosine kinase mutations in lung adenocarcinomas. Clin Cancer Res 2012; 18:4910-8. [PMID: 22761469 DOI: 10.1158/1078-0432.ccr-12-0912] [Citation(s) in RCA: 342] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
PURPOSE Activating mutations in the tyrosine kinase domain of HER2 (ERBB2) have been described in a subset of lung adenocarcinomas (ADCs) and are mutually exclusive with EGFR and KRAS mutations. The prevalence, clinicopathologic characteristics, prognostic implications, and molecular heterogeneity of HER2-mutated lung ADCs are not well established in U.S. patients. EXPERIMENTAL DESIGN Lung ADC samples (N = 1,478) were first screened for mutations in EGFR (exons 19 and 21) and KRAS (exon 2), and negative cases were then assessed for HER2 mutations (exons 19-20) using a sizing assay and mass spectrometry. Testing for additional recurrent point mutations in EGFR, KRAS, BRAF, NRAS, PIK3CA, MEK1, and AKT was conducted by mass spectrometry. ALK rearrangements and HER2 amplification were assessed by FISH. RESULTS We identified 25 cases with HER2 mutations, representing 6% of EGFR/KRAS/ALK-negative specimens. Small insertions in exon 20 accounted for 96% (24/25) of the cases. Compared with insertions in EGFR exon 20, there was less variability, with 83% (20/24) being a 12 bp insertion causing duplication of amino acids YVMA at codon 775. Morphologically, 92% (23/25) were moderately or poorly differentiated ADC. HER2 mutation was not associated with concurrent HER2 amplification in 11 cases tested for both. HER2 mutations were more frequent among never-smokers (P < 0.0001) but there were no associations with sex, race, or stage. CONCLUSIONS HER2 mutations identify a distinct subset of lung ADCs. Given the high prevalence of lung cancer worldwide and the availability of standard and investigational therapies targeting HER2, routine clinical genotyping of lung ADC should include HER2.
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Affiliation(s)
- Maria E Arcila
- Department of Pathology, and Thoracic Oncology Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.
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Arcila ME, Nafa K, Chaft JE, Rekhtman N, Zakowski MF, Kris MG, Ladanyi M. EGFR exon 20 insertion mutations: Incidence and clinicopathologic characteristics in U.S. patients with lung adenocarcinoma. J Clin Oncol 2012. [DOI: 10.1200/jco.2012.30.15_suppl.10560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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
10560 Background: Activating insertion mutations in exon 20 of EGFR are reported in a small subset of lung adenocarcinomas (ADC). In contrast to the classic EGFR mutations, they appear to confer primary resistance to currently approved EGFR tyrosine kinase inhibitors. Their incidence and clinicopathologic features are not well established. Methods: Lung ADCs (n=1500) were screened for major activating mutations in EGFR (exons 19 and 21) and KRAS (exon 2). Negative cases were tested for EGFR exon 20 insertions by a PCR-based sizing assay. Extended testing for additional recurrent point mutations in EGFR, KRAS, BRAF, NRAS, PIK3CA, MEK1 and AKT was performed in all cases by Sequenom mass spectrometry. A subset of cases was also tested for ALK rearrangements by FISH. Results: We identified 32cases withEGFRexon 20 insertions, accounting for 11% of all EGFR mutations. EGFRexon 20 insertions were mutually exclusive with the other genetic alterations tested except for PIK3CA mutations. The incidence was higher among never-smokers (p<0.0001) but there was no association with sex, ethnic origin or stage at diagnosis. Insertions were 3, 6, 9 or 12bp; 9bp insertions were most common (50%, 16/32). Morphologically, 90% of tumors were moderate to poorly differentiated with a predominant mixed ADC phenotype. Conclusions: EGFR exon 20 testing may identify a unique subset of EGFR mutant lung ADCs which is significantly larger than previously reported, making this the third most common type of EGFR mutation after exon 19 deletions and L858R. This population could potentially benefit from alternate targeted therapies, many of which are currently in clinical development.
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Affiliation(s)
| | | | | | | | | | - Mark G. Kris
- Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Marc Ladanyi
- Memorial Sloan-Kettering Cancer Center, New York, NY
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He M, Capelletti M, Nafa K, Yun CH, Arcila ME, Miller VA, Ginsberg MS, Zhao B, Kris MG, Eck MJ, Jänne PA, Ladanyi M, Oxnard GR. EGFR exon 19 insertions: a new family of sensitizing EGFR mutations in lung adenocarcinoma. Clin Cancer Res 2012. [PMID: 22190593 DOI: 10.1158/1078-0432.ccr-11-2361.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Epidermal growth factor receptor (EGFR) genotyping is now standard in the management of advanced lung adenocarcinoma, as this biomarker predicts marked benefit from treatment with EGFR tyrosine kinase inhibitors (TKI). EGFR exon 19 insertions are a poorly described family of EGFR mutations, and their association with EGFR-TKI sensitivity in lung adenocarcinoma is uncertain. EXPERIMENTAL DESIGN Patients with lung cancers harboring EGFR exon 19 insertions were studied. The predicted effects of the insertions on the structure of the EGFR protein were examined, and EGFR exon 19 insertions were introduced into Ba/F3 cells to assess oncogenicity and in vitro sensitivity to EGFR-TKIs. In patients receiving TKI, response magnitude was assessed with serial computed tomographic (CT) measurement. RESULTS Twelve tumors harboring EGFR exon 19 insertions were identified; patients were predominately female (92%) and never-smokers (75%). The 11 specimens available for full sequencing all showed an 18-bp insertion that resulted in the substitution of a Pro for Leu at residue 747. The mutant EGFR transformed the Ba/F3 cells, which were then sensitive to EGFR-TKI. Six patients with measurable disease received TKI and five had a response on serial CT. CONCLUSIONS EGFR exon 19 insertions are a newly appreciated family of EGFR-TKI-sensitizing mutations, and patients with tumors harboring these mutations should be treated with EGFR-TKI. While these mutations may be missed through the use of some mutation-specific assays, the addition of PCR product size analysis to multigene assays allows sensitive detection of both exon 19 insertion and deletion mutations.
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Affiliation(s)
- Mai He
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
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Strom RG, Shvartsbeyn M, Rosenblum MK, Hameed MR, Nafa K, Mikolaenko I, Babu RP. Melanocytic tumor with GNA11 p.Q209L mutation mimicking a foramen magnum meningioma. Clin Neurol Neurosurg 2012; 114:1197-200. [PMID: 22421249 DOI: 10.1016/j.clineuro.2012.02.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Revised: 02/09/2012] [Accepted: 02/19/2012] [Indexed: 10/28/2022]
Affiliation(s)
- Russell G Strom
- Department of Neurosurgery, NYU Langone Medical Center, New York, NY, United States.
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