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Tsai HK, Sabbagh MF, Montesion M, Williams EA, Arbini A, Boué DR, Harris EM, Wachter F, Grimmett L, Place AE, Lucas F, Nardi V, Kim AS, Brugnara C, Degar B, Pollard J, Harris MH, Bledsoe JR. Acute promyelocytic leukemia with torque teno mini virus (TTMV)::RARA fusion: an approach to screening and diagnosis. Mod Pathol 2024:100509. [PMID: 38704030 DOI: 10.1016/j.modpat.2024.100509] [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: 03/22/2024] [Accepted: 04/20/2024] [Indexed: 05/06/2024]
Abstract
Acute promyelocytic leukemia (APL) with variant RARA translocation is linked to over 15 partner genes. Recent publications encompassing six cases have expanded the spectrum of RARA partners to torque teno mini virus (TTMV). This entity is likely under-recognized due to lack of clinician and pathologist familiarity, inability to detect the fusion using routine testing modalities, and informatic challenges in its recognition within next-generation sequencing (NGS) data. We describe a clinicopathologic approach and provide necessary tools to screen and diagnose APL with TTMV::RARA using existing clinical DNA or RNA-based NGS assays, which led to identification of four cases, all without other known cytogenetic/molecular drivers. One was identified prospectively and three retrospectively, including two from custom automated screening of multiple data sets (50 257 cases of hematopoietic malignancy, including 4809 acute myeloid leukemia (AML)/myeloid sarcoma/APL cases). Two cases presented as myeloid sarcoma, including one with multiple relapses after AML-type chemotherapy and hematopoietic stem cell transplant (HSCT). Two cases presented as leukemia, had a poor response to induction chemotherapy, but achieved remission upon re-induction (including all-trans retinoic acid (ATRA) in one case) and subsequent HSCT. Neoplastic cells demonstrated features of APL including frequent azurophilic granules and dim/absent CD34 and HLA-DR expression. RARA rearrangement was not detected by karyotype or FISH. Custom analysis of NGS fusion panel data identified TTMV::RARA rearrangements, and in the prospectively identified case, facilitated monitoring in sequential bone marrow samples. APL with TTMV::RARA is a rare leukemia with a high rate of treatment failure in described cases. The diagnosis should be considered in leukemias with features of APL that lack detectable RARA fusions and other drivers, and may be confirmed by appropriate NGS tests with custom informatics. Incorporation of ATRA may have a role in treatment but requires accurate recognition of the fusion for appropriate classification as APL.
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Affiliation(s)
- Harrison K Tsai
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Mark F Sabbagh
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| | | | - Erik A Williams
- Department of Pathology and Laboratory Medicine, University of Miami, Sylvester Comprehensive Cancer Center, and Jackson Memorial Hospitals, Miami, FL, USA; Foundation Medicine Inc., Boston, MA, USA.
| | - Arnaldo Arbini
- Department of Pathology, NYU Grossman School of Medicine, New York City, NY, USA.
| | - Daniel R Boué
- Department of Pathology & Laboratory Medicine, Nationwide Children's Hospital and The Ohio State University, Columbus, OH, USA.
| | - Emily M Harris
- Dana Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA.
| | - Franziska Wachter
- Dana Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA.
| | - Leslie Grimmett
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Andrew E Place
- Dana Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA.
| | - Fabienne Lucas
- Department of Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Valentina Nardi
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| | - Annette S Kim
- Department of Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Carlo Brugnara
- Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Barbara Degar
- Dana Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA.
| | - Jessica Pollard
- Dana Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, USA.
| | - Marian H Harris
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Jacob R Bledsoe
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, USA.
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2
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AlJabban A, Paik H, Aster JC, Berliner N, Brouillard J, Brown JR, Burns KH, Castillo JJ, Card J, Dal Cin P, DeAngelo DJ, Dorfman DM, Ebert BL, Garcia JS, Jacobson CA, Lakhani H, Laubach JP, Ligon AH, Lindeman NI, Lindsley RC, Lovitch SB, Luskin MR, Morgan EA, Nowak A, Petrides A, Pinkus GS, Pozdnyakova O, Steensma DP, Stone RM, Weinberg OK, Winer ES, Kim AS. Optimization of Advanced Molecular Genetic Testing Utilization in Hematopathology: A Goldilocks Approach to Bone Marrow Testing. JCO Oncol Pract 2024; 20:220-227. [PMID: 37683132 DOI: 10.1200/op.23.00217] [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: 04/10/2023] [Revised: 06/13/2023] [Accepted: 07/10/2023] [Indexed: 09/10/2023] Open
Abstract
PURPOSE This study investigated the effectiveness of algorithmic testing in hematopathology at the Brigham and Women's Hospital and Dana-Farber Cancer Institute (DFCI). The algorithm was predicated on test selection after an initial pathologic evaluation to maximize cost-effective testing, especially for expensive molecular and cytogenetic assays. MATERIALS AND METHODS Standard ordering protocols (SOPs) for 17 disease categories were developed and encoded in a decision support application. Six months of retrospective data from application beta testing was obtained and compared with actual testing practices during that timeframe. In addition, 2 years of prospective data were also obtained from patients at one community satellite site. RESULTS A total of 460 retrospective cases (before introduction of algorithmic testing) and 109 prospective cases (following introduction) were analyzed. In the retrospective data, 61.7% of tests (509 of 825) were concordant with the SOPs while 38.3% (316 of 825) were overordered and 30.8% (227 of 736) of SOP-recommended tests were omitted. In the prospective data, 98.8% of testing was concordant (244 of 247 total tests) with only 1.2% overordered tests (3 of 247) and 7.6% omitted tests (20 of 264 SOP-recommended tests; overall P < .001). The cost of overordered tests before implementing SOP indicates a potential annualized saving of $1,347,520 in US dollars (USD) in overordered testing at Brigham and Women's Hospital/DFCI. Only two of 316 overordered tests (0.6%) returned any additional information, both for extremely rare clinical circumstances. CONCLUSION Implementation of SOPs dramatically improved test ordering practices, with a just right number of ancillary tests that minimizes cost and has no significant impact on acquiring key informative test results.
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Affiliation(s)
- Ali AlJabban
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Henry Paik
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
- Enterprise Research IS (ERIS), Digital, Mass General Brigham, Boston, MA
| | - Jon C Aster
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Nancy Berliner
- Harvard Medical School, Boston, MA
- Division of Hematology, Brigham and Women's Hospital, Boston, MA
| | | | - Jennifer R Brown
- Harvard Medical School, Boston, MA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Kathleen H Burns
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
- Harvard Medical School, Boston, MA
- Department of Pathology, Dana-Farber Cancer Institute, Boston, MA
| | - Jorge J Castillo
- Harvard Medical School, Boston, MA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - James Card
- Department of Quality and Safety, Dana-Farber Cancer Institute, Boston, MA
| | - Paola Dal Cin
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Daniel J DeAngelo
- Harvard Medical School, Boston, MA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - David M Dorfman
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
| | - Benjamin L Ebert
- Harvard Medical School, Boston, MA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Jacqueline S Garcia
- Harvard Medical School, Boston, MA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Caron A Jacobson
- Harvard Medical School, Boston, MA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Hakim Lakhani
- Department of Quality and Safety, Dana-Farber Cancer Institute, Boston, MA
| | - Jacob P Laubach
- Harvard Medical School, Boston, MA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Azra H Ligon
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
- Harvard Medical School, Boston, MA
- Department of Pathology, Dana-Farber Cancer Institute, Boston, MA
| | - Neal I Lindeman
- Department of Pathology, Weill Cornell Medicine, New York, NY
| | - R Coleman Lindsley
- Harvard Medical School, Boston, MA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Scott B Lovitch
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Marlise R Luskin
- Harvard Medical School, Boston, MA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Elizabeth A Morgan
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Andrew Nowak
- Department of Performance Improvement, Stanford Medicine Children's Health, Stanford, CA
| | - Athena Petrides
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
- Enterprise Research IS (ERIS), Digital, Mass General Brigham, Boston, MA
| | - Geraldine S Pinkus
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Olga Pozdnyakova
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - David P Steensma
- Novartis Institutes for BioMedical Research (NIBR), Cambridge, MA
| | - Richard M Stone
- Harvard Medical School, Boston, MA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Olga K Weinberg
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX
| | - Eric S Winer
- Harvard Medical School, Boston, MA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Annette S Kim
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
- Harvard Medical School, Boston, MA
- Department of Pathology, Dana-Farber Cancer Institute, Boston, MA
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3
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Kim AS. Reply to B. Chin-Yee et al. JCO Oncol Pract 2024; 20:302-304. [PMID: 38193727 DOI: 10.1200/op.23.00692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 10/27/2023] [Indexed: 01/10/2024] Open
Affiliation(s)
- Annette S Kim
- Annette S. Kim, MD, University of Michigan, Department of Pathology, Ann Arbor, MI
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Sadigh S, DeAngelo DJ, Garcia JS, Hasserjian RP, Hergott CB, Lane AA, Lovitch SB, Lucas F, Luskin MR, Morgan EA, Pinkus GS, Pozdnyakova O, Rodig SJ, Shanmugam V, Tsai HK, Winer ES, Zemmour D, Kim AS. Cutaneous Manifestations of Myeloid Neoplasms Exhibit Broad and Divergent Morphologic and Immunophenotypic Features but Share Ancestral Clonal Mutations With Bone Marrow. Mod Pathol 2024; 37:100352. [PMID: 37839675 DOI: 10.1016/j.modpat.2023.100352] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 08/14/2023] [Accepted: 09/20/2023] [Indexed: 10/17/2023]
Abstract
In this study, we performed a comprehensive molecular analysis of paired skin and peripheral blood/bone marrow (BM) samples from 17 patients with cutaneous myeloid or cutaneous histiocytic-dendritic neoplasms. The cutaneous manifestations included 10 patients with cutaneous acute myeloid leukemia (c-AML), 2 patients with full or partial Langerhans cell differentiation, 2 patients with blastic plasmacytoid dendritic cell neoplasms (BPDCN), 1 patient with both Langerhans cell differentiation and BPDCN, and 2 patients with full or partial indeterminate dendritic cell differentiation. Seven of the 10 c-AML patients (70%) exhibited concurrent or subsequent marrow involvement by acute myeloid leukemia, with all 7 cases (100%) demonstrating shared clonal mutations in both the skin and BM. However, clonal relatedness was documented in one additional case that never had any BM involvement. Nevertheless, NPM1 mutations were identified in 7 of the 10 (70%) of these c-AML cases while one had KMT2A rearrangement and one showed inv(16). All 3 patients (100%) with Langerhans cell neoplasms, 2 patients with BPDCN (100%), and one of the 2 patients (50%) with other cutaneous dendritic cell neoplasms also demonstrated shared mutations between the skin and concurrent or subsequent myeloid neoplasms. Both BM and c-AML shared identical founding drivers, with a predominance of NPM1, DNMT3A, and translocations associated with monocytic differentiation, with common cutaneous-only mutations involving genes in the signal transduction and epigenetic pathways. Cutaneous histiocytic-dendritic neoplasms shared founding drivers in ASXL1, TET2, and/or SRSF2. However, in the Langerhans cell histiocytosis or histiocytic sarcoma cases, there exist recurrent secondary RAS pathway hits, whereas cutaneous BPDCN cases exhibit copy number or structural variants. These results enrich and broaden our understanding of clonally related cutaneous manifestations of myeloid neoplasms and further illuminate the highly diverse spectrum of morphologic and immunophenotypic features they exhibit.
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Affiliation(s)
- Sam Sadigh
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Daniel J DeAngelo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jacqueline S Garcia
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Robert P Hasserjian
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Christopher B Hergott
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Andrew A Lane
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Scott B Lovitch
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Fabienne Lucas
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Marlise R Luskin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Elizabeth A Morgan
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Geraldine S Pinkus
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Olga Pozdnyakova
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Scott J Rodig
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Vignesh Shanmugam
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Harrison K Tsai
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Eric S Winer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - David Zemmour
- Department of Pathology, The University of Chicago, Chicago, Illinois
| | - Annette S Kim
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts; Now with Department of Pathology, University of Michigan, Ann Arbor, Michigan.
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5
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Paolino J, Dimitrov B, Winger BA, Sandoval-Perez A, Rangarajan AV, Ocasio-Martinez N, Tsai HK, Li Y, Robichaud AL, Khalid D, Hatton C, Gillani R, Polonen P, Dilig A, Gotti G, Kavanagh J, Adhav AA, Gow S, Tsai J, Li YD, Ebert BL, Van Allen EM, Bledsoe J, Kim AS, Tasian SK, Cooper SL, Cooper TM, Hijiya N, Sulis ML, Shukla NN, Magee JA, Mullighan CG, Burke MJ, Luskin MR, Mar BG, Jacobson MP, Harris MH, Stegmaier K, Place AE, Pikman Y. Integration of Genomic Sequencing Drives Therapeutic Targeting of PDGFRA in T-Cell Acute Lymphoblastic Leukemia/Lymphoblastic Lymphoma. Clin Cancer Res 2023; 29:4613-4626. [PMID: 37725576 PMCID: PMC10872648 DOI: 10.1158/1078-0432.ccr-22-2562] [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: 08/16/2022] [Revised: 05/22/2023] [Accepted: 09/12/2023] [Indexed: 09/21/2023]
Abstract
PURPOSE Patients with relapsed or refractory T-cell acute lymphoblastic leukemia (T-ALL) or lymphoblastic lymphoma (T-LBL) have limited therapeutic options. Clinical use of genomic profiling provides an opportunity to identify targetable alterations to inform therapy. EXPERIMENTAL DESIGN We describe a cohort of 14 pediatric patients with relapsed or refractory T-ALL enrolled on the Leukemia Precision-based Therapy (LEAP) Consortium trial (NCT02670525) and a patient with T-LBL, discovering alterations in platelet-derived growth factor receptor-α (PDGFRA) in 3 of these patients. We identified a novel mutation in PDGFRA, p.D842N, and used an integrated structural modeling and molecular biology approach to characterize mutations at D842 to guide therapeutic targeting. We conducted a preclinical study of avapritinib in a mouse patient-derived xenograft (PDX) model of FIP1L1-PDGFRA and PDGFRA p.D842N leukemia. RESULTS Two patients with T-ALL in the LEAP cohort (14%) had targetable genomic alterations affecting PDGFRA, a FIP1-like 1 protein/PDGFRA (FIP1L1-PDGFRA) fusion and a novel mutation in PDGFRA, p.D842N. The D842N mutation resulted in PDGFRA activation and sensitivity to tested PDGFRA inhibitors. In a T-ALL PDX model, avapritinib treatment led to decreased leukemia burden, significantly prolonged survival, and even cured a subset of mice. Avapritinib treatment was well tolerated and yielded clinical benefit in a patient with refractory T-ALL. CONCLUSIONS Refractory T-ALL has not been fully characterized. Alterations in PDGFRA or other targetable kinases may inform therapy for patients with refractory T-ALL who otherwise have limited treatment options. Clinical genomic profiling, in real time, is needed for fully informed therapeutic decision making.
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Affiliation(s)
- Jonathan Paolino
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA
| | - Boris Dimitrov
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Beth Apsel Winger
- Department of Pediatrics, Division of Hematology/Oncology, Benioff Children’s Hospital and the Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA
| | - Angelica Sandoval-Perez
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA
| | - Amith Vikram Rangarajan
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA
| | | | | | - Yuting Li
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
| | | | - Delan Khalid
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Charlie Hatton
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Riaz Gillani
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA
| | - Petri Polonen
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
| | | | - Giacomo Gotti
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
- Pediatrics, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
| | - Julia Kavanagh
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Asmani A. Adhav
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Sean Gow
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Jonathan Tsai
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA
| | - Yen Der Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Benjamin L. Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | | | - Jacob Bledsoe
- Department of Pathology, Boston Children’s Hospital, Boston, MA
| | - Annette S. Kim
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA
| | - Sarah K. Tasian
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, and Department of Pediatrics and Abramson Cancer Center at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Stacy L. Cooper
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD
| | - Todd M. Cooper
- Seattle Children's Hospital, Cancer and Blood Disorders Center, Seattle, WA
| | - Nobuko Hijiya
- Division of Pediatric Hematology/Oncology/Stem Cell Transplantation, Columbia University Irving Medical Center, New York, NY
| | - Maria Luisa Sulis
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Neerav N. Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jeffrey A. Magee
- Division of Pediatric Hematology/Oncology, Washington University/St. Louis Children's Hospital, St. Louis, MO
| | | | - Michael J. Burke
- Medical College of Wisconsin, Children’s Hospital of Wisconsin, Milwaukee, WI
| | - Marlise R. Luskin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | | | - Matthew P. Jacobson
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA
| | | | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA
| | - Andrew E. Place
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA
| | - Yana Pikman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA
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6
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Lucas F, O'Keefe TE, Banks N, Bledsoe J, Kim AS, Sadigh S. Old links revisited: Co-occurring thymoma and Castleman disease. Am J Hematol 2023; 98:1497-1498. [PMID: 36794925 DOI: 10.1002/ajh.26885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023]
Affiliation(s)
- Fabienne Lucas
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Thomas E O'Keefe
- Department of Pathology, Saint Elizabeth's Medical Center, Boston, Massachusetts, USA
| | - Nadia Banks
- Department of Pathology, Saint Elizabeth's Medical Center, Boston, Massachusetts, USA
| | - Jacob Bledsoe
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Department of Pathology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Annette S Kim
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Sam Sadigh
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
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7
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Tsai HK, Gogakos T, Lip V, Tsai JM, Li YD, Fisch AS, Weiss J, Yang W, Grimmett L, DiToro D, Schaefer EJ, Lindsley RC, Tran TH, Caron M, Langlois S, Sinnett D, Pikman Y, Nardi V, Kim AS, Silverman LB, Harris MH. Outlier Expression of Isoforms by Targeted or Total RNA Sequencing Identifies Clinically Significant Genomic Variants in Hematolymphoid Tumors. J Mol Diagn 2023; 25:665-681. [PMID: 37419244 PMCID: PMC10488324 DOI: 10.1016/j.jmoldx.2023.06.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 04/14/2023] [Accepted: 06/01/2023] [Indexed: 07/09/2023] Open
Abstract
Recognition of aberrant gene isoforms due to DNA events can impact risk stratification and molecular classification of hematolymphoid tumors. In myelodysplastic syndromes, KMT2A partial tandem duplication (PTD) was one of the top adverse predictors in the International Prognostic Scoring System-Molecular study. In B-cell acute lymphoblastic leukemia (B-ALL), ERG isoforms have been proposed as markers of favorable-risk DUX4 rearrangements, whereas deletion-mediated IKZF1 isoforms are associated with adverse prognosis and have been extended to the high-risk IKZF1plus signature defined by codeletions, including PAX5. In this limited study, outlier expression of isoforms as markers of IKZF1 intragenic or 3' deletions, DUX4 rearrangements, or PAX5 intragenic deletions were 92.3% (48/52), 90% (9/10), or 100% (9/9) sensitive, respectively, and 98.7% (368/373), 100% (35/35), or 97.1% (102/105) specific, respectively, by targeted RNA sequencing, and 84.0% (21/25), 85.7% (6/7), or 81.8% (9/11) sensitive, respectively, and 98.2% (109/111), 98.4% (127/129), or 98.7% (78/79) specific, respectively, by total RNA sequencing. Comprehensive split-read analysis identified expressed DNA breakpoints, cryptic splice sites associated with IKZF1 3' deletions, PTD of IKZF1 exon 5 spanning N159Y in B-ALL with mutated IKZF1 N159Y, and truncated KMT2A-PTD isoforms. Outlier isoforms were also effective targeted RNA markers for PAX5 intragenic amplifications (B-ALL), KMT2A-PTD (myeloid malignant cancers), and rare NOTCH1 intragenic deletions (T-cell acute lymphoblastic leukemia). These findings support the use of outlier isoform analysis as a robust strategy for detecting clinically significant DNA events.
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Affiliation(s)
- Harrison K Tsai
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.
| | - Tasos Gogakos
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Va Lip
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jonathan M Tsai
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Yen-Der Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Adam S Fisch
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jonathan Weiss
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Weiping Yang
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Leslie Grimmett
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Daniel DiToro
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Eva J Schaefer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - R Coleman Lindsley
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Thai Hoa Tran
- Division of Pediatric Hematology-Oncology, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Quebec, Canada; Immune Diseases and Cancers Axis, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Quebec, Canada
| | - Maxime Caron
- Immune Diseases and Cancers Axis, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Quebec, Canada
| | - Sylvie Langlois
- Immune Diseases and Cancers Axis, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Quebec, Canada
| | - Daniel Sinnett
- Division of Pediatric Hematology-Oncology, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Quebec, Canada; Immune Diseases and Cancers Axis, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Quebec, Canada
| | - Yana Pikman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Valentina Nardi
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Annette S Kim
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Lewis B Silverman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Marian H Harris
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts.
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8
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Lee TD, Aisner DL, David MP, Eno CC, Gagan J, Gocke CD, Guseva NV, Haley L, Jajosky AN, Jones D, Mansukhani MM, Mroz P, Murray SS, Newsom KJ, Paulson V, Roy S, Rushton C, Segal JP, Senaratne TN, Siddon AJ, Starostik P, Van Ziffle JAG, Wu D, Xian RR, Yohe S, Kim AS. Current clinical practices and challenges in molecular testing: a GOAL Consortium Hematopathology Working Group report. Blood Adv 2023; 7:4599-4607. [PMID: 37236162 PMCID: PMC10425685 DOI: 10.1182/bloodadvances.2023010149] [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: 03/07/2023] [Revised: 05/02/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
While molecular testing of hematologic malignancies is now standard of care, there is variability in practice and testing capabilities between different academic laboratories, with common questions arising on how to best meet clinical expectations. A survey was sent to hematopathology subgroup members of the Genomics Organization for Academic Laboratories consortium to assess current and future practice and potentially establish a reference for peer institutions. Responses were received from 18 academic tertiary-care laboratories regarding next-generation sequencing (NGS) panel design, sequencing protocols and metrics, assay characteristics, laboratory operations, case reimbursement, and development plans. Differences in NGS panel size, use, and gene content were reported. Gene content for myeloid processes was reported to be generally excellent, while genes for lymphoid processes were less well covered. The turnaround time (TAT) for acute cases, including acute myeloid leukemia, was reported to range from 2 to 7 calendar days to 15 to 21 calendar days, with different approaches to achieving rapid TAT described. To help guide NGS panel design and standardize gene content, consensus gene lists based on current and future NGS panels in development were generated. Most survey respondents expected molecular testing at academic laboratories to continue to be viable in the future, with rapid TAT for acute cases likely to remain an important factor. Molecular testing reimbursement was reported to be a major concern. The results of this survey and subsequent discussions improve the shared understanding of differences in testing practices for hematologic malignancies between institutions and will help provide a more consistent level of patient care.
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Affiliation(s)
- Thomas D. Lee
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA
| | - Dara L. Aisner
- Department of Pathology, University of Colorado, Aurora, CO
| | - Marjorie P. David
- Department of Pathology and Laboratory Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX
| | - Celeste C. Eno
- Department of Pathology and Lab Medicine, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Jeffrey Gagan
- Department of Pathology, University of Texas Southwestern, Dallas, TX
| | - Christopher D. Gocke
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | | | - Lisa Haley
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Audrey N. Jajosky
- Department of Pathology & Laboratory Medicine, University of Rochester Medical Center, Rochester, NY
| | - Daniel Jones
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH
| | - Mahesh M. Mansukhani
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Pawel Mroz
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN
| | - Sarah S. Murray
- Department of Pathology, University of California San Diego, La Jolla, CA
| | - Kimberly J. Newsom
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL
| | - Vera Paulson
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Somak Roy
- Department of Pathology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Chase Rushton
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at University of Pennsylvania, Philadelphia, PA
| | | | - T. Niroshini Senaratne
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA
| | - Alexa J. Siddon
- Departments of Laboratory Medicine & Pathology, Yale School of Medicine, New Haven, CT
| | - Petr Starostik
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL
| | | | - David Wu
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Rena R. Xian
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Sophia Yohe
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN
| | - Annette S. Kim
- Department of Pathology, Brigham and Women’s Hospital/Harvard Medical School, Boston, MA
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9
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Mayerhofer C, Sedrak MS, Hopkins JO, Li T, Tayob N, Faggen MG, Sinclair NF, Chen WY, Parsons HA, Mayer EL, Lange PB, Basta AS, Perilla-Glen A, Lederman RI, Wong AR, Tiwari A, McAllister SS, Mittendorf EA, Gibson CJ, Burstein HJ, Kim AS, Freedman RA, Miller PG. Clonal hematopoiesis in older patients with breast cancer receiving chemotherapy. J Natl Cancer Inst 2023; 115:981-988. [PMID: 37042724 PMCID: PMC10407695 DOI: 10.1093/jnci/djad065] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/10/2023] [Accepted: 04/05/2023] [Indexed: 04/13/2023] Open
Abstract
BACKGROUND The expansion of hematopoietic stem cells carrying recurrent somatic mutations, termed clonal hematopoiesis (CH), is common in elderly individuals and is associated with increased risk of myeloid malignancy and all-cause mortality. Though chemotherapy is a known risk factor for developing CH, how myelosuppressive therapies affect the short-term dynamics of CH remains incompletely understood. Most studies have been limited by retrospective design, heterogeneous patient populations, varied techniques to identifying CH, and analysis of single timepoints. METHODS We examined serial samples from 40 older women with triple-negative or hormone receptor-positive breast cancer treated on the prospective ADjuVANt Chemotherapy in the Elderly trial to evaluate the prevalence and dynamics of CH at baseline and throughout chemotherapy (6 and 12 weeks). RESULTS CH was detected in 44% of patients at baseline and in 53% at any timepoint. Baseline patient characteristics were not associated with CH. Over the course of treatment, mutations exhibited a variety of dynamics, including emergence, expansion, contraction, and disappearance. All mutations in TP53 (n = 3) and PPM1D (n = 4), genes that regulate the DNA damage response, either became detectable or expanded over the course of treatment. Neutropenia was more common in patients with CH, particularly when the mutations became detectable during treatment, and CH was significantly associated with cyclophosphamide dose reductions and holds (P = .02). CONCLUSIONS Our study shows that CH is common, dynamic, and of potential clinical significance in this population. Our results should stimulate larger efforts to understand the biological and clinical importance of CH in solid tumor malignancies. TRIAL REGISTRATION ClinicalTrials.gov (https://clinicaltrials.gov/ct2/show/NCT03858322). Clinical trial registration number: NCT03858322.
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Affiliation(s)
- Christina Mayerhofer
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA, USA
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Mina S Sedrak
- Department of Medical Oncology and Therapeutics Research, City of Hope, Duarte, CA, USA
| | - Judith O Hopkins
- Novant Health Cancer Institute/SCOR NCORP, Winston Salem, NC, USA
| | - Tianyu Li
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nabihah Tayob
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Meredith G Faggen
- Dana-Farber Brigham Cancer Center at South Shore Hospital, South Weymouth, MA, USA
| | - Natalie F Sinclair
- Dana-Farber Brigham Cancer Center at Milford Regional Medical Center, Milford, MA, USA
| | - Wendy Y Chen
- Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
| | - Heather A Parsons
- Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
| | - Erica L Mayer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
| | - Paulina B Lange
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ameer S Basta
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Ruth I Lederman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Andrew R Wong
- Department of Medical Oncology and Therapeutics Research, City of Hope, Duarte, CA, USA
| | - Abhay Tiwari
- Department of Medical Oncology and Therapeutics Research, City of Hope, Duarte, CA, USA
| | - Sandra S McAllister
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA, USA
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Hematology Division, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Elizabeth A Mittendorf
- Harvard Medical School, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
- Division of Breast Surgery, Department of Surgery, Brigham and Women’s Hospital, Boston, MA, USA
| | - Christopher J Gibson
- Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Harold J Burstein
- Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
| | - Annette S Kim
- Brigham and Women’s Hospital, Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Rachel A Freedman
- Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, MA, USA
| | - Peter G Miller
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
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10
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Wild RA, Edwards RK, Zhao D, Hansen KR, Kim AS, Wrenn DS. Highly Atherogenic Lipid Particles are Associated with Preeclampsia After Successful Fertility Treatment for Obese Women who have Unexplained Infertility. Reprod Sci 2023; 30:2495-2502. [PMID: 36813973 PMCID: PMC10442456 DOI: 10.1007/s43032-023-01197-w] [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: 08/19/2022] [Accepted: 02/08/2023] [Indexed: 02/24/2023]
Abstract
Atherogenic dyslipidemia-before or during pregnancy-may contribute to preeclampsia and subsequent cardiovascular disease risk. We performed a nested case-control study to further understand dyslipidemia associated with preeclampsia. The cohort consisted of participants in the randomized clinical trial "Improving Reproductive Fitness Through Pretreatment with Lifestyle Modification in Obese Women with Unexplained Infertility" (FIT-PLESE). FIT-PLESE was designed to study the effect of a pre-fertility treatment 16-week randomized lifestyle intervention program (Nutrisystem diet + exercise + orlistat vs. training alone) on improvement in live birth rate among obese women with unexplained infertility. Of the 279 patients in FIT-PLESE, 80 delivered a viable infant. Maternal serum was analyzed across five visits: before and after lifestyle interventions and also at three pregnancy visits (16, 24, and 32 weeks gestation). Apolipoprotein lipids were measured in a blinded fashion using ion mobility. Cases were those who developed preeclampsia. Controls also had a live birth but did not develop preeclampsia. Generalized linear and mixed models with repeated measures were used to compare the mean lipoprotein lipid levels of the two groups across all visits. Complete data were available for 75 pregnancies, and preeclampsia developed in 14.5% of the pregnancies. Cholesterol/high-density lipoprotein (HDL) ratios (p < 0.003), triglycerides (p = 0.012), and triglyceride/HDL ratios, all adjusted for BMI, were worse in patients with preeclampsia (p < 0.001). Subclasses a, b, and c of highly atherogenic, very small, low-density lipoprotein (LDL) particles were higher during pregnancy for the preeclamptic women (p < 0.05). Very small LDL particle subclass d levels were significantly greater only at 24 weeks (p = 0.012). The role of highly atherogenic, very small LDL particle excess in the pathophysiology of preeclampsia awaits further investigation.
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Affiliation(s)
- R A Wild
- Department of Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Biostatistics and Clinical Epidemiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
| | - R K Edwards
- Department of Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - D Zhao
- Biostatistics and Clinical Epidemiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - K R Hansen
- Department of Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - A S Kim
- Department of Obstetrics and Gynecology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - D S Wrenn
- Quest Diagnostics, Secaucus, NJ, USA
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11
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AlJabban A, Evans MG, Fell GG, Guccione JP, Edwards RA, Pinkus GS, Padera RF, Pozdnyakova O, Kim AS. Autopsy findings from patients diagnosed with COVID-19 demonstrate unique morphological patterns in bone marrow and lymph node. J Clin Pathol 2023:jcp-2023-208875. [PMID: 37290912 DOI: 10.1136/jcp-2023-208875] [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: 03/07/2023] [Accepted: 04/30/2023] [Indexed: 06/10/2023]
Abstract
AIMS The identification of haemophagocytosis in bone marrow (BM) is recurrently identified in patients with severe COVID-19. These initial COVID-19 autopsy studies have afforded valuable insight into the pathophysiology of this disease; however, only a limited number of case series have focused on lymphoid or haematopoietic tissues. METHODS BM and lymph node (LN) specimens were obtained from adult autopsies performed between 1 April 2020 and 1 June 2020, for which the decedent had tested positive for SARS-CoV-2. Tissue sections (H&E, CD3, CD20, CD21, CD138, CD163, MUM1, kappa/lambda light chains in situ hybridisation) were examined by two haematopathologists, who recorded morphological features in a blinded fashion. Haemophagocytic lymphohistiocytosis (HLH) was assessed based on HLH 2004 criteria. RESULTS The BM demonstrated a haemophagocytic pattern in 9 out of 25 patients (36%). The HLH pattern was associated with longer hospitalisation, BM plasmacytosis, LN follicular hyperplasia and lower aspartate aminotransferase (AST), as well as ferritin at demise. LN examination showed increased plasmacytoid cells in 20 of 25 patients (80%). This pattern was associated with a low absolute monocyte count at diagnosis, lower white cell count and lower absolute neutrophil count at demise, and lower ferritin and AST at demise. CONCLUSIONS Autopsy results demonstrate distinct morphological patterns in BM, with or without haemophagocytic macrophages, and in LN, with or without increased plasmacytoid cells. Since only a minority of patients met diagnostic criteria for HLH, the observed BM haemophagocytic macrophages may be more indicative of an overall inflammatory state.
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Affiliation(s)
- Ali AlJabban
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Department of Clinical Investigation, Harvard Medical School, Boston, Massachusetts, USA
| | - Mark G Evans
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Geoffrey G Fell
- Department of Biostatistics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Jack P Guccione
- Los Angeles County Department of Medical Examiner-Coroner, Los Angeles, California, USA
| | - Robert A Edwards
- Department of Pathology and Laboratory Medicine, University of California Irvine, Irvine, California, USA
| | - Geraldine S Pinkus
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Robert F Padera
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Olga Pozdnyakova
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Annette S Kim
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
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12
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Smagulova АМ, Kukhar YV, Glotova ТI, Glotov AG, Kim AS. First record of Trichophyton benhamiae isolated from domestic cats in Russia. Med Mycol Case Rep 2023; 40:16-21. [PMID: 36910893 PMCID: PMC9995281 DOI: 10.1016/j.mmcr.2023.01.001] [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: 07/05/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 02/12/2023] Open
Abstract
We report a first case of Trichophyton benhamiae isolation from domestic cats in Russia. Genetically affiliated to European strains T. benhamiae were deposited in NCBI. T. benhamiae strains formed zonal cream-colored colonies, with reversum pigmentation ranging from intensive yellow to orange-brown in one and orange-brown to chocolate in the second strain. Mycelium is colorless, hyphae are septated, rapidly aging with the formation of arthrospores and microconidia. The formation of macroconidia was recorded after 48 hours. A favorable outcome of treatment was recorded after two weeks.
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Affiliation(s)
- А М Smagulova
- Research Platform Agricultural Biotechnology NJSC "Kazakh Agrotechnical University Named after S. Seifullin", Nur-Sultan, Kazakhstan
| | - Ye V Kukhar
- Research Platform Agricultural Biotechnology NJSC "Kazakh Agrotechnical University Named after S. Seifullin", Nur-Sultan, Kazakhstan
| | - Т I Glotova
- Laboratory of Biotechnology, The Diagnostic Institute of Experimental Veterinary Science of Siberia and Far East Siberian Federal Scientific Center for Agrobiotechnologies of the Russian Academy of Sciences (SFSCA RAS), Russia
| | - A G Glotov
- Laboratory of Biotechnology, The Diagnostic Institute of Experimental Veterinary Science of Siberia and Far East Siberian Federal Scientific Center for Agrobiotechnologies of the Russian Academy of Sciences (SFSCA RAS), Russia
| | - A S Kim
- Private Practicing Veterinarian, Novosibirsk, Russia
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13
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Naeem A, Utro F, Wang Q, Cha J, Vihinen M, Martindale S, Zhou Y, Ren Y, Tyekucheva S, Kim AS, Fernandes SM, Saksena G, Rhrissorrakrai K, Levovitz C, Danysh BP, Slowik K, Jacobs RA, Davids MS, Lederer JA, Zain R, Smith CIE, Leshchiner I, Parida L, Getz G, Brown JR. Pirtobrutinib targets BTK C481S in ibrutinib-resistant CLL but second-site BTK mutations lead to resistance. Blood Adv 2023; 7:1929-1943. [PMID: 36287227 PMCID: PMC10202739 DOI: 10.1182/bloodadvances.2022008447] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/26/2022] [Accepted: 10/09/2022] [Indexed: 11/20/2022] Open
Abstract
Covalent inhibitors of Bruton tyrosine kinase (BTK) have transformed the therapy of chronic lymphocytic leukemia (CLL), but continuous therapy has been complicated by the development of resistance. The most common resistance mechanism in patients whose disease progresses on covalent BTK inhibitors (BTKis) is a mutation in the BTK 481 cysteine residue to which the inhibitors bind covalently. Pirtobrutinib is a highly selective, noncovalent BTKi with substantial clinical activity in patients whose disease has progressed on covalent BTKi, regardless of BTK mutation status. Using in vitro ibrutinib-resistant models and cells from patients with CLL, we show that pirtobrutinib potently inhibits BTK-mediated functions including B-cell receptor (BCR) signaling, cell viability, and CCL3/CCL4 chemokine production in both BTK wild-type and C481S mutant CLL cells. We demonstrate that primary CLL cells from responding patients on the pirtobrutinib trial show reduced BCR signaling, cell survival, and CCL3/CCL4 chemokine secretion. At time of progression, these primary CLL cells show increasing resistance to pirtobrutinib in signaling inhibition, cell viability, and cytokine production. We employed longitudinal whole-exome sequencing on 2 patients whose disease progressed on pirtobrutinib and identified selection of alternative-site BTK mutations, providing clinical evidence that secondary BTK mutations lead to resistance to noncovalent BTKis.
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MESH Headings
- Humans
- Agammaglobulinaemia Tyrosine Kinase
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Chemokine CCL4/genetics
- Chemokine CCL4/therapeutic use
- Drug Resistance, Neoplasm/genetics
- Protein Kinase Inhibitors/pharmacology
- Protein Kinase Inhibitors/therapeutic use
- Pyrimidines/pharmacology
- Pyrimidines/therapeutic use
- Mutation
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Affiliation(s)
- Aishath Naeem
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Cancer Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
| | | | - Qing Wang
- Department of Laboratory Medicine, Biomolecular and Cellular Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, SE-141 86, Huddinge, Sweden
| | - Justin Cha
- Cancer Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
| | - Mauno Vihinen
- Department of Experimental Medical Science, Lund University, SE-221 84, Lund, Sweden
| | - Stephen Martindale
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Yinglu Zhou
- Department of Data Sciences, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA
| | - Yue Ren
- Department of Data Sciences, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA
| | - Svitlana Tyekucheva
- Department of Data Sciences, Dana-Farber Cancer Institute, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA
| | - Annette S. Kim
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA
| | - Stacey M. Fernandes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Gordon Saksena
- Cancer Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
| | | | | | - Brian P. Danysh
- Cancer Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
| | - Kara Slowik
- Cancer Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
| | - Raquel A. Jacobs
- Cancer Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
| | - Matthew S. Davids
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA
| | | | - Rula Zain
- Department of Laboratory Medicine, Biomolecular and Cellular Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, SE-141 86, Huddinge, Sweden
- Centre for Rare Diseases, Department of Clinical Genetics, Karolinska University Hospital, SE-171 76, Stockholm, Sweden
| | - C. I. Edvard Smith
- Department of Laboratory Medicine, Biomolecular and Cellular Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, SE-141 86, Huddinge, Sweden
| | - Ignaty Leshchiner
- Cancer Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
| | | | - Gad Getz
- Cancer Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
- Department of Pathology, Harvard Medical School, Boston, MA
- Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, MA
| | - Jennifer R. Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Cancer Program, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA
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14
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Fathi AT, Kim HT, Soiffer RJ, Levis MJ, Li S, Kim AS, DeFilipp Z, El-Jawahri A, McAfee SL, Brunner AM, Amrein PC, Mims AS, Knight LW, Kelley D, Bottoms AS, Perry LH, Wahl JL, Brock J, Breton E, Marchione DM, Ho VT, Chen YB. Multi-center phase I trial of Ivosidenib as Maintenance Treatment following Allogeneic Hematopoietic Cell Transplantation for IDH1-Mutated Acute Myeloid Leukemia. Clin Cancer Res 2023:725127. [PMID: 37014667 DOI: 10.1158/1078-0432.ccr-23-0182] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/24/2023] [Accepted: 03/31/2023] [Indexed: 04/05/2023]
Abstract
PURPOSE IDH1 (isocitrate dehydrogenase 1) mutations occur in 5-10% of patients with acute myeloid leukemia (AML). Ivosidenib is an IDH1 inhibitor, approved for use in patients with IDH1-mutated AML. PATIENTS AND METHODS We conducted a multi-center, phase I trial of maintenance ivosidenib following allogeneic hematopoietic cell transplantation (HCT) in patients with IDH1-mutated AML. Ivosidenib was initiated between days 30 and 90 following HCT and continued for up to twelve 28-day cycles. The first dose level was 500mg daily, with level reduction to 250mg daily, if needed, in a 3x3 de-escalation design. Ten additional patients would then receive the maximum tolerated (MTD) or recommended phase 2 dose (RP2D). The primary endpoint was establishing the MTD or RP2D of ivosidenib. RESULTS Eighteen patients were enrolled, of whom 16 initiated post-HCT ivosidenib. One dose limiting toxicity, grade(g) 3 QTc prolongation, was observed. The RP2D was established at 500mg daily. Attributable g≥3 adverse events were uncommon, with the most common being QTc prolongation in 2 patients. Eight patients discontinued maintenance, with only one due to adverse event. Six-month cumulative incidence (CI) of gII-IV aGVHD was 6.3%, and two-year CI of all cGVHD was 63%. Two-year CI of relapse and non-relapse mortality (NRM) were 19% and 0%, respectively. Two-year progression-free (PFS) was 81%, and two-year overall survival (OS) was 88%. CONCLUSIONS Ivosidenib is safe and well-tolerated as maintenance therapy following HCT. Cumulative incidence of relapse and NRM, as well as estimations of PFS and OS, were promising in this phase 1 study.
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Affiliation(s)
- Amir T Fathi
- Massachusetts General Hospital / Harvard Medical School, Boston, MA, United States
| | | | | | - Mark J Levis
- Johns Hopkins University, Baltimore, MD, United States
| | - Shuli Li
- Dana-Farber Cancer Institute, Harvard School of Public Health, United States
| | - Annette S Kim
- Brigham and Women's Hospital/Harvard Medical School, Boston, MA, United States
| | | | - Areej El-Jawahri
- Massachusetts General Hospital / Harvard Medical School, Boston, MA, United States
| | - Steve L McAfee
- Massachusetts General Hospital, Boston, MA, United States
| | | | | | - Alice S Mims
- The Ohio State University, Columbus, Ohio, United States
| | - Laura W Knight
- Massachusetts General Hospital, Boston, MA, United States
| | | | | | | | | | | | - Elayne Breton
- Johns Hopkins Sidney Kimmel Comprehensive Cancer Center, Baltimore, United States
| | | | - Vincent T Ho
- Dana-Farber Cancer Institute, Boston, MA, United States
| | - Yi-Bin Chen
- Massachusetts General Hospital Cancer Center, Boston, MA, United States
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15
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Lampson BL, Gupta A, Tyekucheva S, Mashima K, Petráčková A, Wang Z, Wojciechowska N, Shaughnessy CJ, Baker PO, Fernandes SM, Shupe S, Machado JH, Fardoun R, Kim AS, Brown JR. Rare Germline ATM Variants Influence the Development of Chronic Lymphocytic Leukemia. J Clin Oncol 2023; 41:1116-1128. [PMID: 36315919 PMCID: PMC9928739 DOI: 10.1200/jco.22.00269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 11/07/2022] Open
Abstract
PURPOSE Germline missense variants of unknown significance in cancer-related genes are increasingly being identified with the expanding use of next-generation sequencing. The ataxia telangiectasia-mutated (ATM) gene on chromosome 11 has more than 1,000 germline missense variants of unknown significance and is a tumor suppressor. We aimed to determine if rare germline ATM variants are more frequent in chronic lymphocytic leukemia (CLL) compared with other hematologic malignancies and if they influence the clinical characteristics of CLL. METHODS We identified 3,128 patients (including 825 patients with CLL) in our hematologic malignancy clinic who had received clinical-grade sequencing of the entire coding region of ATM. We ascertained the comparative frequencies of germline ATM variants in categories of hematologic neoplasms, and, in patients with CLL, we determined whether these variants affected CLL-associated characteristics such as somatic 11q deletion. RESULTS Rare germline ATM variants are present in 24% of patients with CLL, significantly greater than that in patients with other lymphoid malignancies (16% prevalence), myeloid disease (15%), or no hematologic neoplasm (14%). Patients with CLL with germline ATM variants are younger at diagnosis and twice as likely to have 11q deletion. The ATM variant p.L2307F is present in 3% of patients with CLL, is associated with a three-fold increase in rates of somatic 11q deletion, and is a hypomorph in cell-based assays. CONCLUSION Germline ATM variants cluster within CLL and affect the phenotype of CLL that develops, implying that some of these variants (such as ATM p.L2307F) have functional significance and should not be ignored. Further studies are needed to determine whether these variants affect the response to therapy or account for some of the inherited risk of CLL.
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Affiliation(s)
- Benjamin L. Lampson
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Aditi Gupta
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | | | - Kiyomi Mashima
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Anna Petráčková
- Department of Immunology, Palacký University, Olomouc, Czech Republic
| | - Zixu Wang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA
| | - Natalia Wojciechowska
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
- Current Address: Wrocław Medical University, Wrocław, Poland
| | - Conner J. Shaughnessy
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Peter O. Baker
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Stacey M. Fernandes
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Samantha Shupe
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - John-Hanson Machado
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Rayan Fardoun
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Annette S. Kim
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
| | - Jennifer R. Brown
- Division of Hematologic Malignancies and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
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16
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Haakenstad EK, Brais LK, Bertram A, Kruse A, Gentile A, Freedman RA, Lindeman NI, Kozyreva ON, Sanz-Altamira P, Lathan CS, Hassett MJ, Cerami E, Kim AS, Manning D, Nowak J, Giannakis M, Lindsley RC, Hahn WC, Johnson BE, McCleary NJ. Defining equitable genomic testing uptake in gastrointestinal oncology: Ensuring capture of demographic data. J Clin Oncol 2023. [DOI: 10.1200/jco.2023.41.4_suppl.794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
794 Background: Tumor genomic testing (GT) has increased diagnostic accuracy and treatment options for patients (pts) with cancer. Dana-Farber Cancer Institute (DFCI) has made GT accessible as an institute-supported research effort for >10 yrs. We estimate 50% standard therapies and 15-35% clinical trials in Gastrointestinal Cancer Clinic (GCC) require GT to determine eligibility. Pts in GCC with certain cancers are eligible for GT as a clinical test – these include metastatic/locally advanced colorectal, gastric, pancreatic, or biliary cancers. Clinical testing requires CLIA lab certification and insurance reimbursement; research does not. Herein we ID gaps in our GT database. Methods: We reviewed data on GT uptake in GCC between 4/2015 - 6/2022. 20,096 pts were captured by the GT tracking system. Data included: testing ordered and completed (proportion, type, time to receiving tissue for testing [TR], time to testing completion [TC]). Demographic data is not captured in the tracking system; matching unique patient identifiers with electronic health record is pending. Results: Most pts received GT (57.6%); 12% were not eligible; 30.4% declined consent. Most testing was completed (67.6%), but 21.3% of tests failed (45.5% of these from insufficient tissue). Research testing (71%) comprised most tests, but clinical tests were completed faster (median 34 days research vs 20 days clinical). Ampullary (91%), anal (90%), colon (90%) had highest completion rates; pancreatic (59%), hepatocellular carcinoma (56%) had lowest (from insufficient viable tumor in submitted specimens). Conclusions: GCC has a robust recruitment program that has yielded high GT uptake. Given the frequency that GT is used for treatment and trials, building a demographically representative dataset is crucial, especially for pts with largest burden of morbidity and mortality from cancer. We ID'd data gaps in the GT tracking system, which lacks demographics and reason for not testing. Demographic data is available in the electronic health record but does not speak with the GT tracking system so this analysis is not routinely done. Ability to visualize this data is important to ensure equitable GT uptake. Future efforts will focus on improving rates of consent in genomics databases and cancer clinical trials. Genomic testing at Dana-Farber Cancer Institute Gastrointestinal Cancer Center, 4/2015 – 6/2022.[Table: see text]
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17
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Raman HS, Kim SE, DeAngelo DJ, Stevenson KE, Neuberg D, Winer ES, Wadleigh M, Garcia JS, Kim AS, Stone RM, Ho VT, Luskin MR. Intensity of induction regimen and outcomes among adults with Ph+ALL undergoing allogeneic hematopoietic stem cell transplantation. Leuk Res 2023; 125:107004. [PMID: 36577290 DOI: 10.1016/j.leukres.2022.107004] [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: 10/24/2022] [Revised: 12/13/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
Tyrosine kinase inhibitors (TKIs) are essential for the treatment of Philadelphia chromosome-positive acute lymphoblastic leukemia (Ph+ ALL) and have allowed for effective, low intensity induction regimens including no or minimal chemotherapy. Whether the use of low intensity induction regimens impacts outcomes after allogeneic hematopoietic stem cell transplant (alloHCT) is less understood. We identified consecutive adult patients with Ph+ ALL undergoing alloHCT in first complete remission (CR1) at our center from 2010 to 2021 and examined the impact of pre-transplant induction intensity on outcomes. Among the 87 identified patients, 44 (51%) received low intensity induction and 43 (49%) received induction with high intensity chemotherapy. Patients receiving low intensity induction were older (median age 60 vs. 47 years, p < 0.01). Following induction, measurable residual disease (MRD) negativity by BCR::ABL1 RT-PCR was similar in the low and high intensity induction cohorts (54% and 52% respectively). Receipt of reduced intensity transplant conditioning was not associated with intensity of induction regimen (39% vs. 19% in low vs. high, respectively, p = 0.06). At a median follow-up of 21 months from transplant, there was no difference between low and high intensity induction with respect to 2-year disease-free survival (58% vs. 56%), 2-year overall survival (62% vs. 63%), 2-year cumulative incidence of relapse (9% vs. 17%), and 2-year non-relapse mortality (33% vs. 29%). We also found no difference in outcomes when patients were segmented by both induction and conditioning regimen intensities. Our retrospective analysis suggests that induction intensity does not impact post-transplant outcomes among patients with Ph+ ALL transplanted in CR1.
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Affiliation(s)
- Hari S Raman
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
| | - Se Eun Kim
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Daniel J DeAngelo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
| | | | - Donna Neuberg
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Eric S Winer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Martha Wadleigh
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Jacqueline S Garcia
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Annette S Kim
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.
| | - Richard M Stone
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Vincent T Ho
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Marlise R Luskin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
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18
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Hergott CB, Dal Cin P, Hornick JL, Winer ES, Carrasco RD, Kim AS. Characteristic nuclear membrane ALK reactivity in chronic myelomonocytic leukemia with RANBP2-ALK fusion. Am J Hematol 2023; 98:365-367. [PMID: 33491794 DOI: 10.1002/ajh.26107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 01/17/2021] [Indexed: 01/13/2023]
Affiliation(s)
| | - Paola Dal Cin
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Jason L Hornick
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Eric S Winer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Ruben D Carrasco
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Annette S Kim
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
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19
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Duncavage EJ, Bagg A, Hasserjian RP, DiNardo CD, Godley LA, Iacobucci I, Jaiswal S, Malcovati L, Vannucchi AM, Patel KP, Arber DA, Arcila ME, Bejar R, Berliner N, Borowitz MJ, Branford S, Brown AL, Cargo CA, Döhner H, Falini B, Garcia-Manero G, Haferlach T, Hellström-Lindberg E, Kim AS, Klco JM, Komrokji R, Lee-Cheun Loh M, Loghavi S, Mullighan CG, Ogawa S, Orazi A, Papaemmanuil E, Reiter A, Ross DM, Savona M, Shimamura A, Skoda RC, Solé F, Stone RM, Tefferi A, Walter MJ, Wu D, Ebert BL, Cazzola M. Genomic profiling for clinical decision making in myeloid neoplasms and acute leukemia. Blood 2022; 140:2228-2247. [PMID: 36130297 PMCID: PMC10488320 DOI: 10.1182/blood.2022015853] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [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: 06/06/2022] [Accepted: 08/27/2022] [Indexed: 11/20/2022] Open
Abstract
Myeloid neoplasms and acute leukemias derive from the clonal expansion of hematopoietic cells driven by somatic gene mutations. Although assessment of morphology plays a crucial role in the diagnostic evaluation of patients with these malignancies, genomic characterization has become increasingly important for accurate diagnosis, risk assessment, and therapeutic decision making. Conventional cytogenetics, a comprehensive and unbiased method for assessing chromosomal abnormalities, has been the mainstay of genomic testing over the past several decades and remains relevant today. However, more recent advances in sequencing technology have increased our ability to detect somatic mutations through the use of targeted gene panels, whole-exome sequencing, whole-genome sequencing, and whole-transcriptome sequencing or RNA sequencing. In patients with myeloid neoplasms, whole-genome sequencing represents a potential replacement for both conventional cytogenetic and sequencing approaches, providing rapid and accurate comprehensive genomic profiling. DNA sequencing methods are used not only for detecting somatically acquired gene mutations but also for identifying germline gene mutations associated with inherited predisposition to hematologic neoplasms. The 2022 International Consensus Classification of myeloid neoplasms and acute leukemias makes extensive use of genomic data. The aim of this report is to help physicians and laboratorians implement genomic testing for diagnosis, risk stratification, and clinical decision making and illustrates the potential of genomic profiling for enabling personalized medicine in patients with hematologic neoplasms.
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Affiliation(s)
- Eric J. Duncavage
- Department of Pathology and Immunology, Washington University, St. Louis, MO
| | - Adam Bagg
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA
| | | | - Courtney D. DiNardo
- Division of Cancer Medicine, Department of Leukemia, MD Anderson Cancer Center, Houston, TX
| | - Lucy A. Godley
- Section of Hematology and Oncology, Departments of Medicine and Human Genetics, The University of Chicago, Chicago, IL
| | - Ilaria Iacobucci
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | | | - Luca Malcovati
- Department of Molecular Medicine, University of Pavia & Fondazione IRCCS Policlinico S. Matteo, Pavia, Italy
| | - Alessandro M. Vannucchi
- Department of Hematology, Center Research and Innovation of Myeloproliferative Neoplasms, University of Florence and Azienda Ospedaliero-Universitaria Careggi, Florence, Italy
| | - Keyur P. Patel
- Division of Pathology/Lab Medicine, Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Maria E. Arcila
- Department of Pathology, Memorial Sloan Lettering Cancer Center, New York, NY
| | - Rafael Bejar
- Division of Hematology and Oncology, University of California San Diego, La Jolla, CA
| | - Nancy Berliner
- Division of Hematology, Brigham and Women’s Hospital, Harvard University, Boston, MA
| | - Michael J. Borowitz
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD
- Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Susan Branford
- Department of Genetics and Molecular Pathology, Center for Cancer Biology, SA Pathology, Adelaide, Australia
| | - Anna L. Brown
- Department of Pathology, South Australia Heath Alliance, Adelaide, Australia
| | - Catherine A. Cargo
- Haematological Malignancy Diagnostic Service, St James’s University Hospital, Leeds, United Kingdom
| | - Hartmut Döhner
- Department of Internal Medicine III, Ulm University Hospital, Ulm, Germany
| | - Brunangelo Falini
- Department of Hematology, CREO, University of Perugia, Perugia, Italy
| | | | | | - Eva Hellström-Lindberg
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Annette S. Kim
- Department of Pathology, Brigham and Women’s Hospital, Harvard University, Boston, MA
| | - Jeffery M. Klco
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Rami Komrokji
- Department of Malignant Hematology, Moffitt Cancer Center, Tampa, FL
| | - Mignon Lee-Cheun Loh
- Department of Pediatrics, Ben Towne Center for Childhood Cancer Research, Seattle Children’s Hospital, University of Washington, Seattle, WA
| | - Sanam Loghavi
- Division of Pathology/Lab Medicine, Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Seishi Ogawa
- University of Kyoto School of Medicine, Kyoto, Japan
| | - Attilio Orazi
- Department of Pathology, Texas Tech University Health Sciences Center, El Paso, TX
| | | | - Andreas Reiter
- University Hospital Mannheim, Heidelberg University, Mannheim, Germany
| | - David M. Ross
- Haematology Directorate, SA Pathology, Adelaide, Australia
| | - Michael Savona
- Department of Medicine, Vanderbilt University, Nashville, TN
| | - Akiko Shimamura
- Dana Farber/Boston Children’s Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA
| | - Radek C. Skoda
- Department of Biomedicine, University Hospital Basel, Basel, Switzerland
| | - Francesc Solé
- MDS Group, Institut de Recerca contra la Leucèmia Josep Carreras, Barcelona, Spain
| | - Richard M. Stone
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | | | | | - David Wu
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Benjamin L. Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Mario Cazzola
- Division of Hematology, Fondazione IRCCS Policlinico San Matteo, University of Pavia, Pavia, Italy
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20
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Miller PG, Fell GG, Foy BH, Scherer AK, Gibson CJ, Sperling AS, Burugula BB, Nakao T, Uddin MM, Warren H, Bry L, Pozdnyakova O, Frigault MJ, Bick AG, Neuberg D, Higgins JM, Mansour MK, Natarajan P, Kim AS, Kitzman JO, Ebert BL. Clonal hematopoiesis of indeterminate potential and risk of death from COVID-19. Blood 2022; 140:1993-1997. [PMID: 36096050 PMCID: PMC9474399 DOI: 10.1182/blood.2022018052] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/05/2022] [Indexed: 01/07/2023] Open
Abstract
Two Letters to Blood address the risks of COVID-19 in populations with precursors of hematological disease. In the first article, Miller and colleagues report on whether clonal hematopoiesis of intermediate potential (CHIP) is associated with adverse outcomes with COVID-19, finding no association between CHIP and 28-day mortality while providing data indirectly linking IL-6 signaling and patient outcomes. In the second article, Ho and colleagues investigate the outcomes of patients with monoclonal gammopathy of undetermined significance (MGUS) with COVID-19, reporting that one-fourth had a severe infection and that on multivariable analysis, adverse outcomes are more likely if immunoparesis is present.
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Affiliation(s)
- Peter G Miller
- Center for Cancer Research and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA
| | - Geoffrey G Fell
- Department of Data Sciences, Dana Farber Cancer Institute, Boston, MA
| | - Brody H Foy
- Department of Pathology & Center for Systems Biology, Massachusetts General Hospital, Boston, MA
- Department of Systems Biology, Harvard Medical School, Boston, MA
| | - Allison K Scherer
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | | | - Adam S Sperling
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Bala B Burugula
- Department of Human Genetics, University of Michigan, Ann Arbor, MI
| | - Tetsushi Nakao
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Division of Cardiology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Md M Uddin
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
| | - Hailey Warren
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA
| | - Lynn Bry
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
| | - Olga Pozdnyakova
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
| | - Matthew J Frigault
- Center for Cancer Research and Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA
| | - Alex G Bick
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Donna Neuberg
- Department of Data Sciences, Dana Farber Cancer Institute, Boston, MA
| | - John M Higgins
- Department of Pathology & Center for Systems Biology, Massachusetts General Hospital, Boston, MA
- Department of Systems Biology, Harvard Medical School, Boston, MA
| | - Michael K Mansour
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Pradeep Natarajan
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA
- Department of Medicine, Harvard Medical School, Boston, MA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
| | - Annette S Kim
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
| | - Jacob O Kitzman
- Department of Human Genetics, University of Michigan, Ann Arbor, MI
| | - Benjamin L Ebert
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA
- Howard Hughes Medical Institute, Bethesda, MD
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21
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Abstract
Molecular diagnostics inhabit an increasingly central role in characterizing hematopoietic malignancies. This brief review summarizes the genomic targets important for many major categories of hematopoietic neoplasia by focusing on disease pathogenesis. In myeloid disease, recurrent mutations in key functional classes drive clonal hematopoiesis, on which additional variants can specify clinical presentation and accelerate progression. Lymphoblastic leukemias are frequently initiated by oncogenic fusions that block lymphoid maturation while, in concert with additional mutations, driving proliferation. The links between genetic aberrations and lymphoma patient outcomes have been clarified substantially through the clustering of genomic profiles. Finally, the addition of next-generation sequencing strategies to cytogenetics is refining risk stratification for plasma cell myeloma. In all categories, molecular diagnostics shed light on the unique mechanistic underpinnings of each individual malignancy, thereby empowering more rational, personalized care for these patients.
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Affiliation(s)
- Christopher B Hergott
- Department of Pathology, Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Annette S Kim
- Department of Pathology, Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA.
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22
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Kim AS, Pozdnyakova O. SOHO State of the Art Updates and Next Questions | Myeloid/Lymphoid Neoplasms with Eosinophilia and Gene Rearrangements: Diagnostic Pearls and Pitfalls. Clin Lymphoma Myeloma Leuk 2022; 22:643-651. [PMID: 35478091 DOI: 10.1016/j.clml.2022.03.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/05/2022] [Accepted: 03/15/2022] [Indexed: 06/14/2023]
Abstract
The myeloid and/or lymphoid neoplasms with eosinophilia and gene rearrangement (MLN-Eos) are a rare group of hematopoietic neoplasms with diverse and often perplexing presentations that can cause challenges, and even potential pitfalls, for the diagnostic pathologist. However, accurate diagnosis of this group of disorders is of the utmost importance, since the presence of specific gene rearrangements dictates targeted patient therapy. The goal of this review is to discuss the current literature, including emergence of novel molecular data, and equip pathologists and clinicians with morphologic and immunophenotypic clues for diagnosing this challenging group of hematopoietic neoplasms.
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Affiliation(s)
- Annette S Kim
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA.
| | - Olga Pozdnyakova
- Department of Pathology, Brigham and Women's Hospital, Boston, MA
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23
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Pollard JA, Furutani E, Liu S, Esrick E, Cohen LE, Bledsoe J, Liu CW, Lu K, de Haro MJR, Surrallés J, Malsch M, Kuniholm A, Galvin A, Armant M, Kim AS, Ballotti K, Moreau L, Zhou Y, Babushok D, Boulad F, Carroll C, Hartung H, Hont A, Nakano T, Olson T, Sze SG, Thompson AA, Wlodarski MW, Gu X, Libermann TA, D’Andrea A, Grompe M, Weller E, Shimamura A. Metformin for treatment of cytopenias in children and young adults with Fanconi anemia. Blood Adv 2022; 6:3803-3811. [PMID: 35500223 PMCID: PMC9631552 DOI: 10.1182/bloodadvances.2021006490] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 04/15/2022] [Indexed: 11/26/2022] Open
Abstract
Fanconi anemia (FA), a genetic DNA repair disorder characterized by marrow failure and cancer susceptibility. In FA mice, metformin improves blood counts and delays tumor development. We conducted a single institution study of metformin in nondiabetic patients with FA to determine feasibility and tolerability of metformin treatment and to assess for improvement in blood counts. Fourteen of 15 patients with at least 1 cytopenia (hemoglobin < 10 g/dL; platelet count < 100 000 cells/µL; or an absolute neutrophil count < 1000 cells/µL) were eligible to receive metformin for 6 months. Median patient age was 9.4 years (range 6.0-26.5 ). Thirteen of 14 subjects (93%) tolerated maximal dosing for age; 1 subject had dose reduction for grade 2 gastrointestinal symptoms. No subjects developed hypoglycemia or metabolic acidosis. No subjects had dose interruptions caused by toxicity, and no grade 3 or higher adverse events attributed to metformin were observed. Hematologic response based on modified Myelodysplastic Syndrome International Working Group criteria was observed in 4 of 13 evaluable patients (30.8%; 90% confidence interval, 11.3-57.3). Median time to response was 84.5 days (range 71-128 days). Responses were noted in neutrophils (n = 3), platelets (n = 1), and red blood cells (n = 1). No subjects met criteria for disease progression or relapse during treatment. Correlative studies explored potential mechanisms of metformin activity in FA. Plasma proteomics showed reduction in inflammatory pathways with metformin. Metformin is safe and tolerable in nondiabetic patients with FA and may provide therapeutic benefit. This trial was registered at as #NCT03398824.
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Affiliation(s)
- Jessica A. Pollard
- Pediatric Hematology-Oncology, Boston Children’s Hospital, Boston, MA
- Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Elissa Furutani
- Pediatric Hematology-Oncology, Boston Children’s Hospital, Boston, MA
- Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Shanshan Liu
- Biostatistics and Research Design Center, Institutional Centers for Clinical and Translational Research, Harvard Medical School, Boston, MA
| | - Erica Esrick
- Pediatric Hematology-Oncology, Boston Children’s Hospital, Boston, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Laurie E. Cohen
- Department of Pediatrics, Harvard Medical School, Boston, MA
- Department of Endocrinology, and
| | - Jacob Bledsoe
- Department of Pathology, Boston Children’s Hospital, Boston, MA
| | - Chih-Wei Liu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Kun Lu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Maria Jose Ramirez de Haro
- Joint Research Unit UAB-Sant Pau Biomedical Research Institute,Institut de Recerca Hospital de la Santa Creu i Sant Pau-IIB Sant Pau, Universitat Autònoma de Barcelona, Barcelona Spain
- Center for Biomedical Network Research on Rare Diseases, Madrid, Spain
| | - Jordi Surrallés
- Joint Research Unit UAB-Sant Pau Biomedical Research Institute,Institut de Recerca Hospital de la Santa Creu i Sant Pau-IIB Sant Pau, Universitat Autònoma de Barcelona, Barcelona Spain
- Center for Biomedical Network Research on Rare Diseases, Madrid, Spain
| | - Maggie Malsch
- Pediatric Hematology-Oncology, Boston Children’s Hospital, Boston, MA
- Clinical Research Operations Center, Institutional Centers for Clinical and Translational Research, Boston Children’s Hospital, Boston, MA
| | - Ashley Kuniholm
- Clinical Research Operations Center, Institutional Centers for Clinical and Translational Research, Boston Children’s Hospital, Boston, MA
| | - Ashley Galvin
- Clinical Research Operations Center, Institutional Centers for Clinical and Translational Research, Boston Children’s Hospital, Boston, MA
| | - Myriam Armant
- Trans Laboratory, Boston Children’s Hospital, Boston, MA
| | - Annette S. Kim
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Kaitlyn Ballotti
- Pediatric Hematology-Oncology, Boston Children’s Hospital, Boston, MA
| | - Lisa Moreau
- Comprehensive Center for Fanconi Anemia, Dana-Farber Cancer Institute, Boston, MA
| | - Yu Zhou
- Pediatric Hematology-Oncology, Boston Children’s Hospital, Boston, MA
| | - Daria Babushok
- Division of Hematology-Oncology, University of Pennsylvania, Philadelphia, PA
| | - Farid Boulad
- Pediatric Hematology-Oncology, Memorial Sloan-Kettering Cancer Center, New York, NY
| | - Clint Carroll
- Pediatric Hematology-Oncology, The Children's Hospital at TriStar Centennial, Nashville, TN
| | - Helge Hartung
- Pediatric Hematology-Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Amy Hont
- Pediatric Hematology-Oncology, Children’s National Medical Center, Washington, DC
| | - Taizo Nakano
- Pediatric Hematology-Oncology, Children’s Hospital Colorado, Denver, CO
| | - Tim Olson
- Pediatric Hematology-Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Sei-Gyung Sze
- Department of Pediatrics, Maine Medical Center, Tufts University School of Medicine, Portland, ME
| | - Alexis A. Thompson
- Pediatric Hematology-Oncology, Ann and Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL
| | - Marcin W. Wlodarski
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN
| | - Xuesong Gu
- Beth Israel Deaconess Medical Center Genomics, Proteomics, Bioinformatics and Systems Biology Center, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Towia A. Libermann
- Beth Israel Deaconess Medical Center Genomics, Proteomics, Bioinformatics and Systems Biology Center, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Alan D’Andrea
- Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Markus Grompe
- Oregon Stem Cell Center, Department of Pediatrics, Papé Family Institute, Oregon Health and Science University, Portland, OR; and
| | - Edie Weller
- Department of Pediatrics, Harvard Medical School, Boston, MA
- Biostatistics and Research Design Center, Institutional Centers for Clinical and Translational Research, Harvard Medical School, Boston, MA
| | - Akiko Shimamura
- Pediatric Hematology-Oncology, Boston Children’s Hospital, Boston, MA
- Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
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24
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Aziz-Bose R, Wachter F, Chiarle R, Lindeman NI, Kim AS, Degar BA, Davies K, Pikman Y. Rapid next-generation sequencing aids in diagnosis of transient abnormal myelopoiesis in a phenotypically normal newborn. Blood Adv 2022; 6:2893-2896. [PMID: 35090166 PMCID: PMC9092404 DOI: 10.1182/bloodadvances.2021006865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 01/18/2022] [Indexed: 11/24/2022] Open
Affiliation(s)
- Rahela Aziz-Bose
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA
| | - Franziska Wachter
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA
| | - Roberto Chiarle
- Harvard Medical School, Boston, MA
- Department of Pathology, Boston Children’s Hospital, Boston, MA; and
| | - Neal I. Lindeman
- Harvard Medical School, Boston, MA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA
| | - Annette S. Kim
- Harvard Medical School, Boston, MA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA
| | - Barbara A. Degar
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA
| | - Kimberly Davies
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA
| | - Yana Pikman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA
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25
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Bruehl FK, Kim AS, Li MM, Lindeman NI, Moncur JT, Souers RJ, Vasalos P, Voelkerding KV, Xian RR, Surrey LF. Tiered Somatic Variant Classification Adoption Has Increased Worldwide With Some Practice Differences Based on Location and Institutional Setting. Arch Pathol Lab Med 2022; 146:822-832. [PMID: 34979564 DOI: 10.5858/arpa.2021-0179-cp] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2021] [Indexed: 11/06/2022]
Abstract
CONTEXT.— The 2017 Association for Molecular Pathology/American Society of Clinical Oncology/College of American Pathologists (CAP) tier classification guideline provides a framework to standardize interpretation and reporting of somatic variants. OBJECTIVE.— To evaluate the adoption and performance of the 2017 guideline among laboratories performing somatic next-generation sequencing (NGS). DESIGN.— A survey was distributed to laboratories participating in NGS CAP proficiency testing for solid tumors (NGSST) and hematologic malignancies (NGSHM). RESULTS.— Worldwide, 64.4% (152 of 236) of NGSST and 66.4% (87 of 131) of NGSHM participants used tier classification systems, of which the 2017 guideline was used by 84.9% (129 of 152) of NGSST and 73.6% (64 of 87) of NGSHM participants. The 2017 guideline was modified by 24.4% (30 of 123) of NGSST and 21.7% (13 of 60) of NGSHM laboratories. Laboratories implementing the 2017 guideline were satisfied or very satisfied (74.2% [89 of 120] NGSST and 69.5% [41 of 59] NGSHM), and the impression of tier classification reproducibility was high (mean of 3.9 [NGSST] and 3.6 [NGSHM] on a 5-point scale). Of nonusers, 35.2% (38 of 108) of NGSST and 39.4% (26 of 66) of NGSHM laboratories were planning implementation. For future guideline revisions, respondents favored including variants to monitor disease (63.9% [78 of 122] NGSST, 80.0% [48 of 60] NGSHM) and germline variants (55.3% [63 of 114] NGSST, 75.0% [45 of 60] NGSHM). Additional subtiers were not favored by academic laboratories compared to nonacademic laboratories (P < .001 NGSST and P = .02 NGSHM). CONCLUSIONS.— The 2017 guideline has been implemented by more than 50.0% of CAP laboratories. While most laboratories using the 2017 guideline report satisfaction, thoughtful guideline modifications may further enhance the quality, reproducibility, and clinical utility of the 2017 guideline for tiered somatic variant classification.
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Affiliation(s)
- Frido K Bruehl
- From Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio (Bruehl)
| | - Annette S Kim
- The Departments of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts (Kim, Lindeman)
| | - Marilyn M Li
- The Department of Pathology and Laboratory Medicine, Perelman School of Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania (Li, Surrey)
| | - Neal I Lindeman
- The Departments of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts (Kim, Lindeman)
| | - Joel T Moncur
- The Joint Pathology Center, Office of the Director, Silver Spring, Maryland (Moncur), College of American Pathologists, Northfield, Illinois
| | - Rhona J Souers
- Biostatistics Department (Souers), College of American Pathologists, Northfield, Illinois
| | - Patricia Vasalos
- Proficiency Testing (Vasalos), College of American Pathologists, Northfield, Illinois
| | | | - Rena R Xian
- The Department of Pathology and Oncology, School of Medicine, Johns Hopkins University, Baltimore, Maryland (Xian)
| | - Lea F Surrey
- The Department of Pathology and Laboratory Medicine, Perelman School of Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania (Li, Surrey)
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26
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Garcia JS, Kim HT, Murdock HM, Cutler CS, Brock J, Gooptu M, Ho VT, Koreth J, Nikiforow S, Romee R, Shapiro R, Loschi F, Ryan J, Fell G, Karp HQ, Lucas F, Kim AS, Potter D, Mashaka T, Stone RM, DeAngelo DJ, Letai A, Lindsley RC, Soiffer RJ, Antin JH. Adding venetoclax to fludarabine/busulfan RIC transplant for high-risk MDS and AML is feasible, safe, and active. Blood Adv 2021; 5:5536-5545. [PMID: 34614506 PMCID: PMC8714724 DOI: 10.1182/bloodadvances.2021005566] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 08/20/2021] [Indexed: 01/03/2023] Open
Abstract
Adding the selective BCL-2 inhibitor venetoclax to reduced-intensity conditioning chemotherapy (fludarabine and busulfan [FluBu2]) may enhance antileukemic cytotoxicity and thereby reduce the risk of posttransplant relapse. This phase 1 study investigated the recommended phase 2 dose (RP2D) of venetoclax, a BCL-2 selective inhibitor, when added to FluBu2 in adult patients with high-risk acute myeloid leukemia (AML), myelodysplastic syndromes (MDS), and MDS/myeloproliferative neoplasms (MPN) undergoing transplant. Patients received dose-escalated venetoclax (200-400 mg daily starting day -8 for 6-7 doses) in combination with fludarabine 30 mg/m2 per day for 4 doses and busulfan 0.8 mg/kg twice daily for 8 doses on day -5 to day -2 (FluBu2). Transplant related-toxicity was evaluated from the first venetoclax dose on day -8 to day 28. Twenty-two patients were treated. At study entry, 5 patients with MDS and MDS/MPN had 5% to 10% marrow blasts, and 18 (82%) of 22 had a persistent detectable mutation. Grade 3 adverse events included mucositis, diarrhea, and liver transaminitis (n = 3 each). Neutrophil/platelet recovery and acute/chronic graft-versus-host-disease rates were similar to those of standard FluBu2. No dose-limiting toxicities were observed. The RP2D of venetoclax was 400 mg daily for 7 doses. With a median follow-up of 14.7 months (range, 8.6-24.8 months), median overall survival was not reached, and progression-free survival was 12.2 months (95% confidence interval, 6.0-not estimable). In patients with high-risk AML, MDS, and MDS/MPN, adding venetoclax to FluBu2 was feasible and safe. To further address relapse risk, assessment of maintenance therapy after venetoclax plus FluBu2 transplant is ongoing. This study was registered at clinicaltrials.gov as #NCT03613532.
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Affiliation(s)
| | - Haesook T. Kim
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA; and
| | | | | | | | | | | | | | | | | | | | | | | | - Geoffrey Fell
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA; and
| | | | - Fabienne Lucas
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA
| | - Annette S. Kim
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA
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27
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Wang SA, Ok CY, Kim AS, Lucas F, Morgan EA, Thakral B, Patel S, Nardi V, Patel KM, Weinberg OK, Hasserjian RP. Myelodysplastic syndromes with no somatic mutations detected by next-generation sequencing display similar features to myelodysplastic syndromes with detectable mutations. Am J Hematol 2021; 96:E420-E423. [PMID: 34416041 DOI: 10.1002/ajh.26325] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 08/02/2021] [Accepted: 08/09/2021] [Indexed: 11/10/2022]
Affiliation(s)
- Sa A. Wang
- Department of Hematopathology MD Anderson Cancer Center Houston Texas USA
| | - Chi Young Ok
- Department of Hematopathology MD Anderson Cancer Center Houston Texas USA
| | - Annette S. Kim
- Department of Pathology Brigham & Women's Hospital Boston Massachusetts USA
| | - Fabienne Lucas
- Department of Pathology Brigham & Women's Hospital Boston Massachusetts USA
| | | | - Beenu Thakral
- Department of Hematopathology MD Anderson Cancer Center Houston Texas USA
| | - Sanjay Patel
- Department of Pathology Weill‐Cornell Medical Center New York New York USA
| | - Valentina Nardi
- Department of Pathology Massachusetts General Hospital Boston Massachusetts USA
| | - Keyur M. Patel
- Department of Hematopathology MD Anderson Cancer Center Houston Texas USA
| | - Olga K. Weinberg
- Department of Pathology University of Texas Southwestern Medical Center Dallas Texas USA
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28
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Stockslager MA, Malinowski S, Touat M, Yoon JC, Geduldig J, Mirza M, Kim AS, Wen PY, Chow KH, Ligon KL, Manalis SR. Functional drug susceptibility testing using single-cell mass predicts treatment outcome in patient-derived cancer neurosphere models. Cell Rep 2021; 37:109788. [PMID: 34610309 DOI: 10.1016/j.celrep.2021.109788] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [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: 01/13/2021] [Revised: 08/17/2021] [Accepted: 09/10/2021] [Indexed: 02/07/2023] Open
Abstract
Functional precision medicine aims to match individual cancer patients to optimal treatment through ex vivo drug susceptibility testing on patient-derived cells. However, few functional diagnostic assays have been validated against patient outcomes at scale because of limitations of such assays. Here, we describe a high-throughput assay that detects subtle changes in the mass of individual drug-treated cancer cells as a surrogate biomarker for patient treatment response. To validate this approach, we determined ex vivo response to temozolomide in a retrospective cohort of 69 glioblastoma patient-derived neurosphere models with matched patient survival and genomics. Temozolomide-induced changes in cell mass distributions predict patient overall survival similarly to O6-methylguanine-DNA methyltransferase (MGMT) promoter methylation and may aid in predictions in gliomas with mismatch-repair variants of unknown significance, where MGMT is not predictive. Our findings suggest cell mass is a promising functional biomarker for cancers and drugs that lack genomic biomarkers.
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Affiliation(s)
- Max A Stockslager
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Seth Malinowski
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Mehdi Touat
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA; Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neurologie 2-Mazarin, Paris, France
| | - Jennifer C Yoon
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Jack Geduldig
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Mahnoor Mirza
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Annette S Kim
- Department of Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Patrick Y Wen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA USA
| | - Kin-Hoe Chow
- Center for Patient-Derived Models, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Keith L Ligon
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA; Department of Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, USA; Center for Patient-Derived Models, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Scott R Manalis
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Koch Institute for Integrative Cancer Research, Cambridge, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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29
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Sadigh S, Kim AS. Molecular Pathology of Myeloid Neoplasms: Molecular Pattern Recognition. Surg Pathol Clin 2021; 14:517-528. [PMID: 34373100 DOI: 10.1016/j.path.2021.05.013] [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] [Indexed: 10/20/2022]
Abstract
Despite the apparent complexity of the molecular genetic underpinnings of myeloid neoplasms, most myeloid mutational profiles can be understood within a simple framework. Somatic mutations accumulate in hematopoietic stem cells with aging and toxic insults, termed clonal hematopoiesis. These "old stem cells" mutations, predominantly in the epigenetic and RNA spliceosome pathways, act as "founding" driver mutations leading to a clonal myeloid neoplasm when sufficient in number and clone size. Subsequent mutations can create the genetic flavor of the myeloid neoplasm ("backseat" drivers) due to their enrichment in certain entities or act as progression events ("aggressive" drivers) during clonal evolution.
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Affiliation(s)
- Sam Sadigh
- Department of Pathology, Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, USA
| | - Annette S Kim
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA 02115, USA.
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30
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Nardi V, Tsuchiya KD, Kim AS, Bean LJH, Halley JG, Long TA, Szelinger S, Vasalos P, Thorson JA, Moyer AM, Moncur JT. Next-Generation Sequencing Somatic and Germline Assay Troubleshooting Guide Derived From Proficiency Testing Data. Arch Pathol Lab Med 2021; 146:451-461. [PMID: 34424952 DOI: 10.5858/arpa.2020-0842-cp] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/27/2021] [Indexed: 11/06/2022]
Abstract
CONTEXT.— Next-generation sequencing-based assays are increasingly used in clinical molecular laboratories to detect somatic variants in solid tumors and hematologic malignancies and to detect constitutional variants. Proficiency testing data are potential sources of information about challenges in performing these assays. OBJECTIVE.— To examine the most common sources of unacceptable results from the College of American Pathologists Next-Generation Sequencing Bioinformatics, Hematological Malignancies, Solid Tumor, and Germline surveys, and provide recommendations on how to avoid these pitfalls and improve performance. DESIGN.— The College of American Pathologists next-generation sequencing somatic and germline proficiency testing survey results from 2016 to 2019 were analyzed to identify the most common causes of unacceptable results. RESULTS.— On somatic and germline proficiency testing surveys, 95.9% (18 815/19 623) and 97.8% (33 890/34 641) of all variants were correctly identified, respectively. The most common causes of unacceptable results related to sequencing were false-negative errors in genomic regions that were difficult to sequence because of high GC content. False-positive errors occurred in the context of homopolymers and pseudogenes. Recurrent errors in variant annotation were seen for dinucleotide and duplication variants and included unacceptable transcript selection and outdated variant nomenclature. A small percentage of preanalytic or postanalytic errors were attributed to specimen swaps and transcription errors. CONCLUSIONS.— Laboratories demonstrate overall excellent performance for detecting variants in both somatic and germline proficiency testing surveys. Proficiency testing survey results highlight infrequent, but recurrent, analytic and nonanalytic challenges in performing next- generation sequencing-based assays and point to remedies to help laboratories improve performance.
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Affiliation(s)
- Valentina Nardi
- From the Department of Pathology, Massachusetts General Hospital, Boston (Nardi)
| | - Karen D Tsuchiya
- Department of Laboratories, Seattle Children's Hospital, Seattle, Washington (Tsuchiya)
| | - Annette S Kim
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts (Kim)
| | - Lora J H Bean
- Department of Pathology, PerkinElmer Genomics, Pittsburgh, Pennsylvania (Bean)
| | - Jaimie G Halley
- Proficiency Testing (Halley, Szelenger, Vasalos), Northfield, Illinois
| | | | | | - Patricia Vasalos
- Proficiency Testing (Halley, Szelenger, Vasalos), Northfield, Illinois
| | - John A Thorson
- College of American Pathologists, Northfield, Illinois; Department of Pathology, UC San Diego, Del Mar, California (Thorson)
| | - Ann M Moyer
- Department of Laboratory Medicine and Pathology, Mayo Clinc, Rochester, Minnesota (Moyer)
| | - Joel T Moncur
- the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Moncur)
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31
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Wang D, Lin M, Utz B, Bosompem A, Guo Y, Daneshbod Y, Alford CE, Nettles SA, Scher J, Gagne EY, O'Neill M, Barrow L, Wojciechowska N, Keegan J, Mosse CA, Lederer JA, Kim AS. miR-378-3p Knockdown Recapitulates Many of the Features of Myelodysplastic Syndromes. Am J Pathol 2021; 191:2009-2022. [PMID: 34364880 PMCID: PMC8579243 DOI: 10.1016/j.ajpath.2021.07.006] [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] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 06/26/2021] [Accepted: 07/08/2021] [Indexed: 11/19/2022]
Abstract
Myelodysplastic syndromes (MDS) are clonal neoplasms of the hematopoietic stem cell that result in aberrant differentiation of hematopoietic lineages due to a wide range of underlying genetic, epigenetic, and other causes. Despite the myriad etiologies, there is a recognizable MDS phenotype that has been associated with microRNA (miRNA) aberrant expression. A model of aberrant myeloid maturation mimicking MDS that is seen in MDS has been created using a stable knockdown of miR-378-3p. This model exhibited a transcriptional profile that indicates aberrant maturation and function, showed immunophenotypic and morphologic dysplasia, and displays the aberrant growth and function that characterizes MDS. Moreover, aberrant signal transduction in response to stimulation was demonstrated that is specific to the stage of myeloid maturation and mimics that seen in MDS patient samples using mass cytometry (CyTOF). The aberrant signaling, immunophenotypic changes, cellular growth, and colony formation ability seen in this myeloid model could be reversed with azacytidine (AZA) albeit without significant improvement of neutrophil function.
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Affiliation(s)
- Dahai Wang
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Miao Lin
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Begum Utz
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Amma Bosompem
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Yan Guo
- Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Yahya Daneshbod
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Catherine E Alford
- Department of Pathology, Tennessee Valley Healthcare System, Veterans Affairs, Nashville, Tennessee
| | - Sabin A Nettles
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jonathan Scher
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Emma Y Gagne
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Maria O'Neill
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Lia Barrow
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Natalia Wojciechowska
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Joshua Keegan
- Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Claudio A Mosse
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee; Department of Pathology, Tennessee Valley Healthcare System, Veterans Affairs, Nashville, Tennessee
| | - James A Lederer
- Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Annette S Kim
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee.
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Raman HS, Shanmugam V, Li J, Steensma DP, Kim AS, Luskin MR. NPM1-mutant acute myeloid leukemia relapsing as acute lymphoblastic leukemia with clonal persistence of IDH1 mutation. Leuk Lymphoma 2021; 62:1790-1792. [PMID: 33586600 DOI: 10.1080/10428194.2021.1881510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Hari S Raman
- Harvard Medical School, Boston, MA, USA.,Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Vignesh Shanmugam
- Harvard Medical School, Boston, MA, USA.,Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Jingwei Li
- Harvard Medical School, Boston, MA, USA.,Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - David P Steensma
- Harvard Medical School, Boston, MA, USA.,Dana-Farber Cancer Institute, Boston, MA, USA
| | - Annette S Kim
- Harvard Medical School, Boston, MA, USA.,Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Marlise R Luskin
- Harvard Medical School, Boston, MA, USA.,Dana-Farber Cancer Institute, Boston, MA, USA
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Pozdnyakova O, Connell NT, Battinelli EM, Connors JM, Fell G, Kim AS. Clinical Significance of CBC and WBC Morphology in the Diagnosis and Clinical Course of COVID-19 Infection. Am J Clin Pathol 2021; 155:364-375. [PMID: 33269374 PMCID: PMC7799218 DOI: 10.1093/ajcp/aqaa231] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [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: 12/26/2022] Open
Abstract
Objectives To investigate the clinical significance of numeric and morphologic peripheral blood (PB) changes in coronavirus disease 2019 (COVID-19)–positive patients in predicting the outcome, as well as to compare these changes between critically ill COVID-19–positive and COVID-19–negative patients. Methods The study included 90 COVID-19–positive (51 intensive care unit [ICU] and 39 non-ICU) patients and 30 COVID-19–negative ICU patients. We collected CBC parameters (both standard and research) and PB morphologic findings, which were independently scored by two hematopathologists. Results All patients with COVID-19 demonstrated striking numeric and morphologic WBC changes, which were different between mild and severe disease states. More severe disease was associated with significant neutrophilia and lymphopenia, which was intensified in critically ill patients. Abnormal WBC morphology, most pronounced in monocytes and lymphocytes, was associated with more mild disease; the changes were lost with disease progression. Between COVID-19–positive and COVID-19–negative ICU patients, significant differences in morphology-associated research parameters were indicative of changes due to the severe acute respiratory syndrome coronavirus 2 virus, including higher RNA content in monocytes, lower RNA content in lymphocytes, and smaller hypogranular neutrophils. Conclusions Hospitalized patients with COVID-19 should undergo a comprehensive daily CBC with manual WBC differential to monitor for numerical and morphologic changes predictive of poor outcome and signs of disease progression.
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Affiliation(s)
- Olga Pozdnyakova
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA
- Division of Hematology, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Nathan T Connell
- Division of Hematology, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Elisabeth M Battinelli
- Division of Hematology, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Jean M Connors
- Division of Hematology, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
- Harvard Medical School, Boston, MA
| | - Geoffrey Fell
- Department of Statistics, Dana Farber Cancer Institute, Boston, MA
| | - Annette S Kim
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA
- Division of Hematology, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
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Pikman Y, Tasian SK, Sulis ML, Stevenson K, Blonquist TM, Apsel Winger B, Cooper TM, Pauly M, Maloney KW, Burke MJ, Brown PA, Gossai N, McNeer JL, Shukla NN, Cole PD, Kahn JM, Chen J, Barth MJ, Magee JA, Gennarini L, Adhav AA, Clinton CM, Ocasio-Martinez N, Gotti G, Li Y, Lin S, Imamovic A, Tognon CE, Patel T, Faust HL, Contreras CF, Cremer A, Cortopassi WA, Garrido Ruiz D, Jacobson MP, Dharia NV, Su A, Robichaud AL, Saur Conway A, Tarlock K, Stieglitz E, Place AE, Puissant A, Hunger SP, Kim AS, Lindeman NI, Gore L, Janeway KA, Silverman LB, Tyner JW, Harris MH, Loh ML, Stegmaier K. Matched Targeted Therapy for Pediatric Patients with Relapsed, Refractory, or High-Risk Leukemias: A Report from the LEAP Consortium. Cancer Discov 2021; 11:1424-1439. [PMID: 33563661 DOI: 10.1158/2159-8290.cd-20-0564] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 11/25/2020] [Accepted: 01/14/2021] [Indexed: 11/16/2022]
Abstract
Despite a remarkable increase in the genomic profiling of cancer, integration of genomic discoveries into clinical care has lagged behind. We report the feasibility of rapid identification of targetable mutations in 153 pediatric patients with relapsed/refractory or high-risk leukemias enrolled on a prospective clinical trial conducted by the LEAP Consortium. Eighteen percent of patients had a high confidence Tier 1 or 2 recommendation. We describe clinical responses in the 14% of patients with relapsed/refractory leukemia who received the matched targeted therapy. Further, in order to inform future targeted therapy for patients, we validated variants of uncertain significance, performed ex vivo drug-sensitivity testing in patient leukemia samples, and identified new combinations of targeted therapies in cell lines and patient-derived xenograft models. These data and our collaborative approach should inform the design of future precision medicine trials. SIGNIFICANCE: Patients with relapsed/refractory leukemias face limited treatment options. Systematic integration of precision medicine efforts can inform therapy. We report the feasibility of identifying targetable mutations in children with leukemia and describe correlative biology studies validating therapeutic hypotheses and novel mutations.See related commentary by Bornhauser and Bourquin, p. 1322.This article is highlighted in the In This Issue feature, p. 1307.
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Affiliation(s)
- Yana Pikman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts
| | - Sarah K Tasian
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Pediatrics and Abramson Cancer Center at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Maria Luisa Sulis
- Division of Pediatric Hematology/Oncology/Stem Cell Transplantation, Columbia University Irving Medical Center, New York, New York
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kristen Stevenson
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Traci M Blonquist
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Beth Apsel Winger
- Department of Pediatrics, Division of Hematology/Oncology, Benioff Children's Hospital and the Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Todd M Cooper
- Seattle Children's Hospital, Cancer and Blood Disorders Center, Seattle, Washington
| | - Melinda Pauly
- Division of Hematology/Oncology, Emory University, Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, Georgia
| | - Kelly W Maloney
- Children's Hospital Colorado, University of Colorado Cancer Center, Aurora, Colorado
| | - Michael J Burke
- Medical College of Wisconsin, Children's Hospital of Wisconsin, Milwaukee, Wisconsin
| | | | - Nathan Gossai
- Center for Cancer and Blood Disorders, Children's Minnesota, Minneapolis, Minnesota
| | | | - Neerav N Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Peter D Cole
- Children's Hospital at Montefiore, Bronx, New York
- Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey
| | - Justine M Kahn
- Division of Pediatric Hematology/Oncology/Stem Cell Transplantation, Columbia University Irving Medical Center, New York, New York
| | - Jing Chen
- Division of Pediatric Hematology/Oncology/Stem Cell Transplantation, Columbia University Irving Medical Center, New York, New York
- Children's Cancer Institute, Joseph M. Sanzari Children's Hospital, Hackensack University Medical Center, Hackensack, New Jersey
| | | | - Jeffrey A Magee
- Division of Pediatric Hematology/Oncology, Washington University/St. Louis Children's Hospital, St. Louis, Missouri
| | | | - Asmani A Adhav
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Catherine M Clinton
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Giacomo Gotti
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Yuting Li
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Shan Lin
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Alma Imamovic
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts
| | - Cristina E Tognon
- Division of Hematology and Medical Oncology, Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Tasleema Patel
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Haley L Faust
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Cristina F Contreras
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Anjali Cremer
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- University Hospital Frankfurt, Department of Hematology/Oncology, Frankfurt/Main, Germany
| | - Wilian A Cortopassi
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California
| | - Diego Garrido Ruiz
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California
| | - Matthew P Jacobson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California
| | - Neekesh V Dharia
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts
| | - Angela Su
- INSERM UMR 944, IRSL, St Louis Hospital, Paris, France
| | - Amanda L Robichaud
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Amy Saur Conway
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Katherine Tarlock
- Seattle Children's Hospital, Cancer and Blood Disorders Center, Seattle, Washington
| | - Elliot Stieglitz
- Department of Pediatrics, Division of Hematology/Oncology, Benioff Children's Hospital and the Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Andrew E Place
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts
| | | | - Stephen P Hunger
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Department of Pediatrics and Abramson Cancer Center at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Annette S Kim
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Neal I Lindeman
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Lia Gore
- Children's Hospital Colorado, University of Colorado Cancer Center, Aurora, Colorado
| | - Katherine A Janeway
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts
| | - Lewis B Silverman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts
| | - Jeffrey W Tyner
- Division of Hematology and Medical Oncology, Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
| | - Marian H Harris
- Department of Pathology, Boston Children's Hospital, Boston, Massachusetts
| | - Mignon L Loh
- Department of Pediatrics, Division of Hematology/Oncology, Benioff Children's Hospital and the Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts
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Zhang BM, Keegan A, Li P, Lindeman NI, Nagarajan R, Routbort MJ, Vasalos P, Kim AS, Merker JD. An Overview of Characteristics of Clinical Next-Generation Sequencing-Based Testing for Hematologic Malignancies. Arch Pathol Lab Med 2021; 145:1110-1116. [PMID: 33450747 DOI: 10.5858/arpa.2019-0661-cp] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/23/2020] [Indexed: 11/06/2022]
Abstract
CONTEXT.— With the increasing integration of molecular alterations into the evaluation of hematologic malignancies (HM), somatic mutation profiling by next-generation sequencing (NGS) has become a common clinical testing strategy. Limited data are available about the characteristics of these assays. OBJECTIVE.— To describe assay characteristics, specimen requirements, and reporting practices for NGS-based HM testing using College of American Pathologists proficiency testing survey data. DESIGN.— The College of American Pathologists NGS Hematologic Malignancies Survey (NGSHM) results from 78 laboratories were used to determine laboratory practices in NGS-based HM testing. RESULTS.— The majority of laboratories performed tumor-only (88.5% [69 of 78]), targeted sequencing of cancer genes or mutation hotspots (98.7% [77 of 78]); greater than 90% performed testing on fresh bone marrow and peripheral blood. The majority of laboratories reported a 5% lower limit of detection for single-nucleotide variants (73.1% [57 of 78]) and small insertions and deletions (50.6% [39 of 77]). A majority of laboratories used benchtop sequencers and custom enrichment approaches. CONCLUSIONS.— This manuscript summarizes the characteristics of clinical NGS-based testing for the detection of somatic variants in HM. These data may be broadly useful to inform laboratory practice and quality management systems, regulation, and oversight of NGS testing, and precision medicine efforts using a data-driven approach.
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Affiliation(s)
- Bing M Zhang
- From the Department of Pathology, Stanford University School of Medicine, Stanford, California (Zhang)
| | - Alissa Keegan
- the Department of Pathology, Brigham and Women's Hospital, Harvard University, Boston, Massachusetts (Keegan, Lindeman, Kim).,Current or past members of the College of American Pathologists, Molecular Oncology Committee are Keegan, Kim, Lindeman, Merker, Nagarajan, Routbort, Vasalos (staff). Merker and Kim contributed equally and are co-senior authors of this work
| | - Peng Li
- ARUP Laboratories, Department of Pathology, University of Utah, Salt Lake City, Utah (Li)
| | - Neal I Lindeman
- the Department of Pathology, Brigham and Women's Hospital, Harvard University, Boston, Massachusetts (Keegan, Lindeman, Kim).,Current or past members of the College of American Pathologists, Molecular Oncology Committee are Keegan, Kim, Lindeman, Merker, Nagarajan, Routbort, Vasalos (staff). Merker and Kim contributed equally and are co-senior authors of this work
| | - Rakesh Nagarajan
- PierianDx, St Louis, Missouri (Nagarajan).,Current or past members of the College of American Pathologists, Molecular Oncology Committee are Keegan, Kim, Lindeman, Merker, Nagarajan, Routbort, Vasalos (staff). Merker and Kim contributed equally and are co-senior authors of this work
| | - Mark J Routbort
- the Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston (Routbort).,Current or past members of the College of American Pathologists, Molecular Oncology Committee are Keegan, Kim, Lindeman, Merker, Nagarajan, Routbort, Vasalos (staff). Merker and Kim contributed equally and are co-senior authors of this work
| | - Patricia Vasalos
- Proficiency Testing, College of American Pathologists, Northfield, Illinois (Vasalos).,Current or past members of the College of American Pathologists, Molecular Oncology Committee are Keegan, Kim, Lindeman, Merker, Nagarajan, Routbort, Vasalos (staff). Merker and Kim contributed equally and are co-senior authors of this work
| | - Annette S Kim
- the Department of Pathology, Brigham and Women's Hospital, Harvard University, Boston, Massachusetts (Keegan, Lindeman, Kim).,Current or past members of the College of American Pathologists, Molecular Oncology Committee are Keegan, Kim, Lindeman, Merker, Nagarajan, Routbort, Vasalos (staff). Merker and Kim contributed equally and are co-senior authors of this work
| | - Jason D Merker
- the Departments of Pathology and Laboratory Medicine & Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill (Merker).,Current or past members of the College of American Pathologists, Molecular Oncology Committee are Keegan, Kim, Lindeman, Merker, Nagarajan, Routbort, Vasalos (staff). Merker and Kim contributed equally and are co-senior authors of this work
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Kim AS, Boyko NV, Stagnieva IV, Panchenko SN. [Small salivary glands in the paratonsillar space in children]. Vestn Otorinolaringol 2021; 86:41-45. [PMID: 33720650 DOI: 10.17116/otorino20218601141] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Was to study the changes in the small salivary glands in chronic tonsillitis and paratonsillar abscess in children. A histological examination of the palatine tonsils of 22 children aged 5 to 14 years old who had a paratonsillar abscess and 18 children suffering from chronic tonsillitis was carried out. Fragments of small salivary glands, located both superficially, in the mucous membrane between the stratified squamous non-keratinizing epithelium and the lymphoid tissue of the palatine tonsils, and between the muscles of the amygdala were found in 42 of the 80 (52.5%) tonsils studied. Along with the unchanged glandular structure, 26 (61.9%) samples revealed areas of destruction foci in small salivary glands with signs of inflammatory and compensatory regenerative activity. The presence of separate interlobular ducts of the salivary glands with pronounced periductal lymph - macrophage infiltration was noted. The subepithelial lymph-macrophage infiltrates found in the lamina propria are associated with the exit of the excretory ducts of the salivary glands to the surface of the mucous membrane. Many thin-walled veins are surrounded by perivascular lymphocellular infiltrates. The inflammatory and post-inflammatory changes in the small salivary glands revealed by us in children with chronic tonsillitis do not exclude their participation in the pathogenesis of paratonsillitis. At the same time, inflammation in the salivary gland can be both primary, as a result of its infection with live microorganisms from the tissues of the tonsil, and secondary, due to the compression of the excretory ducts by the edematous tissue of the tonsil in acute tonsillitis.
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Affiliation(s)
- A S Kim
- Rostov State Medical University, Rostov-on-Don, Russia
| | - N V Boyko
- Rostov State Medical University, Rostov-on-Don, Russia
| | - I V Stagnieva
- Rostov State Medical University, Rostov-on-Don, Russia
| | - S N Panchenko
- Rostov State Medical University, Rostov-on-Don, Russia
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Bhatt S, Pioso MS, Olesinski EA, Yilma B, Ryan JA, Mashaka T, Leutz B, Adamia S, Zhu H, Kuang Y, Mogili A, Louissaint A, Bohl SR, Kim AS, Mehta AK, Sanghavi S, Wang Y, Morris E, Halilovic E, Paweletz CP, Weinstock DM, Garcia JS, Letai A. Reduced Mitochondrial Apoptotic Priming Drives Resistance to BH3 Mimetics in Acute Myeloid Leukemia. Cancer Cell 2020; 38:872-890.e6. [PMID: 33217342 PMCID: PMC7988687 DOI: 10.1016/j.ccell.2020.10.010] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 08/04/2020] [Accepted: 10/07/2020] [Indexed: 12/20/2022]
Abstract
Acquired resistance to BH3 mimetic antagonists of BCL-2 and MCL-1 is an important clinical problem. Using acute myelogenous leukemia (AML) patient-derived xenograft (PDX) models of acquired resistance to BCL-2 (venetoclax) and MCL-1 (S63845) antagonists, we identify common principles of resistance and persistent vulnerabilities to overcome resistance. BH3 mimetic resistance is characterized by decreased mitochondrial apoptotic priming as measured by BH3 profiling, both in PDX models and human clinical samples, due to alterations in BCL-2 family proteins that vary among cases, but not to acquired mutations in leukemia genes. BCL-2 inhibition drives sequestered pro-apoptotic proteins to MCL-1 and vice versa, explaining why in vivo combinations of BCL-2 and MCL-1 antagonists are more effective when concurrent rather than sequential. Finally, drug-induced mitochondrial priming measured by dynamic BH3 profiling (DBP) identifies drugs that are persistently active in BH3 mimetic-resistant myeloblasts, including FLT-3 inhibitors and SMAC mimetics.
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Affiliation(s)
- Shruti Bhatt
- Department of Medical Oncology, Dana-Farber Cancer Institute, 440 Brookline Avenue, M430, Boston, MA 02215, USA; Harvard Medical School, Boston, MA, USA; Department of Pharmacy, National University of Singapore, Singapore
| | - Marissa S Pioso
- Department of Medical Oncology, Dana-Farber Cancer Institute, 440 Brookline Avenue, M430, Boston, MA 02215, USA; Harvard Medical School, Boston, MA, USA
| | - Elyse Anne Olesinski
- Department of Medical Oncology, Dana-Farber Cancer Institute, 440 Brookline Avenue, M430, Boston, MA 02215, USA; Harvard Medical School, Boston, MA, USA
| | - Binyam Yilma
- Department of Medical Oncology, Dana-Farber Cancer Institute, 440 Brookline Avenue, M430, Boston, MA 02215, USA; Harvard Medical School, Boston, MA, USA
| | - Jeremy A Ryan
- Department of Medical Oncology, Dana-Farber Cancer Institute, 440 Brookline Avenue, M430, Boston, MA 02215, USA; Harvard Medical School, Boston, MA, USA
| | - Thelma Mashaka
- Department of Medical Oncology, Dana-Farber Cancer Institute, 440 Brookline Avenue, M430, Boston, MA 02215, USA; Harvard Medical School, Boston, MA, USA
| | - Buon Leutz
- Department of Bioinformatics and Data Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Sophia Adamia
- Department of Medical Oncology, Dana-Farber Cancer Institute, 440 Brookline Avenue, M430, Boston, MA 02215, USA
| | - Haoling Zhu
- Department of Medical Oncology, Dana-Farber Cancer Institute, 440 Brookline Avenue, M430, Boston, MA 02215, USA
| | - Yanan Kuang
- Department of Bioinformatics and Data Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Abhishek Mogili
- Department of Bioinformatics and Data Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Abner Louissaint
- Department of Medical Oncology, Dana-Farber Cancer Institute, 440 Brookline Avenue, M430, Boston, MA 02215, USA
| | - Stephan R Bohl
- Department of Medical Oncology, Dana-Farber Cancer Institute, 440 Brookline Avenue, M430, Boston, MA 02215, USA; Harvard Medical School, Boston, MA, USA
| | - Annette S Kim
- Harvard Medical School, Boston, MA, USA; Brigham and Women's Hospital, Boston, MA, USA
| | - Anita K Mehta
- Breast Tumor Immunology Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sneha Sanghavi
- Novartis Institutes for BioMedical Research, Inc., Cambridge, MA, USA
| | - Youzhen Wang
- Novartis Institutes for BioMedical Research, Inc., Cambridge, MA, USA
| | - Erick Morris
- Novartis Institutes for BioMedical Research, Inc., Cambridge, MA, USA
| | - Ensar Halilovic
- Novartis Institutes for BioMedical Research, Inc., Cambridge, MA, USA
| | - Cloud P Paweletz
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David M Weinstock
- Department of Medical Oncology, Dana-Farber Cancer Institute, 440 Brookline Avenue, M430, Boston, MA 02215, USA; Harvard Medical School, Boston, MA, USA
| | - Jacqueline S Garcia
- Department of Medical Oncology, Dana-Farber Cancer Institute, 440 Brookline Avenue, M430, Boston, MA 02215, USA
| | - Anthony Letai
- Department of Medical Oncology, Dana-Farber Cancer Institute, 440 Brookline Avenue, M430, Boston, MA 02215, USA; Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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Abstract
OBJECTIVES At a discussion on molecular/cytogenetic education for hematopathology fellows at the 2018 Society for Hematopathology Program Directors Meeting, consensus was that fellows should understand basic principles and indications for and limitations of molecular/cytogenetic testing used in routine practice. Fellows should also be adept at integrating results of such testing for rendering a final diagnosis. To aid these consensus goals, representatives from the Society for Hematopathology and the Association for Molecular Pathology formed a working group to devise a molecular/cytogenetic curriculum for hematopathology fellow education. CURRICULUM SUMMARY The curriculum includes a primer on cytogenetics and molecular techniques. The bulk of the curriculum reviews the molecular pathology of individual malignant hematologic disorders, with applicable molecular/cytogenetic testing for each and following the 2017 World Health Organization classification of hematologic neoplasms. Benign hematologic disorders and bone marrow failure syndromes are also discussed briefly. Extensive tables are used to summarize genetics of individual disorders and appropriate methodologies. CONCLUSIONS This curriculum provides an overview of the current understanding of the molecular biology of hematologic disorders and appropriate ancillary testing for their evaluation. The curriculum may be used by program directors for training hematopathology fellows or by practicing hematopathologists.
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Affiliation(s)
- Rose C Beck
- Department of Pathology, University Hospitals of Cleveland, Case Western Reserve University, Cleveland, OH (Society for Hematopathology Representative)
| | - Annette S Kim
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA (Association for Molecular Pathology Representative)
| | - Rashmi S Goswami
- Department of Laboratory Medicine and Molecular Diagnostics, Sunnybrook Health Sciences Centre, and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Olga K Weinberg
- Department of Pathology, Boston Children’s Hospital, Boston, MA
| | - Cecilia C S Yeung
- Department of Pathology, University of Washington, and Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA
| | - Mark D Ewalt
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora
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Tsai HK, Brackett DG, Szeto D, Frazier R, MacLeay A, Davineni P, Manning DK, Garcia E, Lindeman NI, Le LP, Lennerz JK, Gibson CJ, Lindsley RC, Kim AS, Nardi V. Targeted Informatics for Optimal Detection, Characterization, and Quantification of FLT3 Internal Tandem Duplications Across Multiple Next-Generation Sequencing Platforms. J Mol Diagn 2020; 22:1162-1178. [PMID: 32603763 PMCID: PMC7479488 DOI: 10.1016/j.jmoldx.2020.06.006] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/27/2020] [Accepted: 06/08/2020] [Indexed: 01/09/2023] Open
Abstract
Assessment of internal tandem duplications in FLT3 (FLT3-ITDs) and their allelic ratio (AR) is recommended by clinical guidelines for diagnostic workup of acute myeloid leukemia and traditionally performed through capillary electrophoresis (CE). Although significant progress has been made integrating FLT3-ITD detection within contemporary next-generation sequencing (NGS) panels, AR estimation is not routinely part of clinical NGS practice because of inherent biases and challenges. In this study, data from multiple NGS platforms—anchored multiplex PCR (AMP), amplicon [TruSeq Custom Amplicon (TSCA)], and hybrid-capture—were analyzed through a custom algorithm, including platform-specific measures of AR. Sensitivity and specificity of NGS for FLT3-ITD status relative to CE were 100% (42/42) and 99.4% (1076/1083), respectively, by AMP on an unselected cohort and 98.1% (53/54) and 100% (48/48), respectively, by TSCA on a selected cohort. Primer analysis identified criteria for ITDs to escape detection by TSCA, estimated to occur in approximately 9% of unselected ITDs. Allelic fractions under AMP or TSCA were highly correlated to CE, with linear regression slopes near 1 for ITDs not duplicating primers, and systematically underestimated for ITDs duplicating a primer. Bias was alleviated in AMP through simple adjustments. This article provides an approach for targeted computational FLT3-ITD analysis for NGS data from multiple platforms; AMP was found capable of near perfect sensitivity and specificity with relatively accurate estimates of ARs.
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Affiliation(s)
- Harrison K Tsai
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Diane G Brackett
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - David Szeto
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Ryan Frazier
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Allison MacLeay
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Phani Davineni
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Danielle K Manning
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Elizabeth Garcia
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Neal I Lindeman
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Long P Le
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Jochen K Lennerz
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Christopher J Gibson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - R Coleman Lindsley
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Annette S Kim
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts.
| | - Valentina Nardi
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts.
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Bustoros MW, Cibulskis C, Dowdell T, Gavrilov S, Boehner C, Yesil J, Labkoff SE, Mehr S, Park J, Pistofidis RS, Manier S, Kim AS, Ligon KL, Lennon N, Adalsteinsson V, Wilkinson J, Ghobrial IM, Auclair D. Abstract A38: A novel clinical-grade liquid biopsy platform for multiple myeloma. Clin Cancer Res 2020. [DOI: 10.1158/1557-3265.liqbiop20-a38] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Direct-to-patient (DTP) multiple myeloma (MM) research studies have been launched recently, including PCROWD (NCT02269592), PROMISE (NCT03689595), and the MMRF CureCloud Research Initiative (NCT03657251), aimed at enrolling thousands of individuals from whom comprehensive molecular and immune analyses will be generated from blood specimens and the resulting data aggregated with the correlating clinical information. To support the molecular characterization of liquid biopsies for such DTP efforts, a myeloma-specific hybrid selection panel was developed that captures 70 commonly altered genes. The assay detects somatic point mutations and indels present in a patient’s circulating-free DNA (cfDNA). For this MM 70-Gene cfDNA Assay, samples are received as blood in a Streck’s tube and DNA is extracted from buffy coat using magnetic bead-based chemistry. Coverage sequencing (80,000x depth) is performed and duplex BAM files are generated with UMI alignment and de-duplication. As will be presented, MM blood specimens present a unique challenge as circulating MM cells are often present at significant levels in the buffy coat blood fraction used as the source of normal genomic DNA. The performance of the 70-Gene cfDNA Assay was thoroughly validated in order to establish the sensitivity, specificity, and reproducibility of the technical approach. First, the reference genomic DNA from unrelated healthy individuals was sequenced in replicate at deep coverage. Next, two cohorts were used, one from Dana-Farber and one from the MMRF CureCloud pilot. For both cohorts, tumor DNA samples from bone marrow aspirates (BMAs) with matched normal DNA from blood were sequenced on an orthogonal platform and compared to results from the MM 70-Gene Assay on cfDNA extracted from the same individuals. The yield of extracted cfDNA ranged from 6 ng to 80 ng, and about two third of cases yielded enough material to attempt sequencing, with failures coming mostly from individuals in remission. As will be presented, there was a very strong correlation between BMA and cfDNA and additional events could actually be detected in the blood that were not seen in the BMAs. Because this MM 70-Gene cfDNA Assay may potentially be used by treating physicians for management of care, a clinical-grade (CLIA) pipeline was established. For that CLIA pipeline, the variants reported are a subset of all the events detected by the MM 70-Gene Assay. The events detected in the assay are reviewed by a Genomic Tumor Board within the appropriate subset of territory predefined for reporting. The territory limitations are defined by the Genomic Tumor Board knowledgebase of actionable genomic territory available. In summary, we have developed a robust and very sensitive clinical-grade next-gen liquid biopsy sequencing platform allowing for less invasive monitoring of MM disease genomics that can be used to complement other more classical approaches and to help support direct-to-patient Initiatives.
Citation Format: Mark W. Bustoros, Carrie Cibulskis, Teni Dowdell, Svetlana Gavrilov, Cody Boehner, Jennifer Yesil, Steven E. Labkoff, Shaadi Mehr, Jihye Park, Romanos Sklavenitis Pistofidis, Salomon Manier, Annette S. Kim, Keith L. Ligon, Niall Lennon, Viktor Adalsteinsson, Jane Wilkinson, Irene M. Ghobrial, Daniel Auclair. A novel clinical-grade liquid biopsy platform for multiple myeloma [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr A38.
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Affiliation(s)
| | | | | | | | | | | | | | - Shaadi Mehr
- 3Multiple Myeloma Research Foundation, Norwalk, CT,
| | - Jihye Park
- 1Dana-Farber Cancer Institute, Boston, MA,
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Craig JW, Hasserjian RP, Kim AS, Aster JC, Pinkus GS, Hornick JL, Steensma DP, Coleman Lindsley R, DeAngelo DJ, Morgan EA. Detection of the KIT D816V mutation in myelodysplastic and/or myeloproliferative neoplasms and acute myeloid leukemia with myelodysplasia-related changes predicts concurrent systemic mastocytosis. Mod Pathol 2020; 33:1135-1145. [PMID: 31896808 DOI: 10.1038/s41379-019-0447-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/16/2019] [Accepted: 12/16/2019] [Indexed: 12/20/2022]
Abstract
Greater than 90% of cases of systemic mastocytosis (SM) harbor pathogenic KIT mutations, particularly KITD816V. Prognostically-significant pathogenic KIT mutations also occur in 30-40% of core binding factor-associated acute myeloid leukemia (CBF-AML), but are uncommonly associated with concurrent SM. By comparison, the occurrence of SM in other myeloid neoplasms bearing pathogenic KIT mutations, particularly those with a chronic course, is poorly understood. Review of clinical next-generation sequencing (NGS) performed at our institutions in patients with known or suspected hematologic malignancies over an 8-year period revealed 64 patients with both a pathogenic KIT mutation detected at one or more timepoints and available bone marrow biopsy materials. Patients with KITD816V-mutated myelodysplastic syndromes (MDS), myeloproliferative neoplasms (MPN), or overlap MDS/MPN (n = 22) accounted for approximately one-third of our cohort (34%). Comprehensive morphologic and immunophenotypic characterization revealed that nearly all cases (n = 20, 91%) exhibited concurrent SM. In contrast, of the 18 patients (28%) with AML and KITD816V, only eight (44%) showed evidence of SM at any point in their disease course (p = 0.0021); of these eight, the AML component was characterized as AML with myelodysplasia-related changes (AML-MRC) in all but one instance (n = 7, 87%). Twelve patients (19%) had pathogenic KIT mutations other than p.D816V, all in the setting of AML (CFB-AML, n = 7; AML, not otherwise specified, n = 2; AML-MRC, n = 1; acute promyelocytic leukemia, n = 1); only two of these patients (17%), both with CBF-AML, exhibited concurrent SM. The remaining 12 patients (19%) had SM without evidence of an associated hematological neoplasm (AHN). For nearly one-third of the 30 SM-AHN patients in our cohort (n = 9, 30%), the SM component of their disease was not initially clinicopathologically recognized. We propose that identification of the KITD816V mutation in patients diagnosed with MDS, MPN, MDS/MPN, or AML-MRC should trigger reflex testing for SM.
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Affiliation(s)
- Jeffrey W Craig
- Department of Pathology and Laboratory Medicine, BC Cancer Agency, Vancouver, BC, Canada
| | - Robert P Hasserjian
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Annette S Kim
- Harvard Medical School, Boston, MA, USA.,Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Jon C Aster
- Harvard Medical School, Boston, MA, USA.,Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Geraldine S Pinkus
- Harvard Medical School, Boston, MA, USA.,Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Jason L Hornick
- Harvard Medical School, Boston, MA, USA.,Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - David P Steensma
- Harvard Medical School, Boston, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - R Coleman Lindsley
- Harvard Medical School, Boston, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Daniel J DeAngelo
- Harvard Medical School, Boston, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Elizabeth A Morgan
- Harvard Medical School, Boston, MA, USA. .,Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.
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Luskin MR, Kim AS, Patel SS, Wright K, LeBoeuf NR, Lane AA. Evidence for separate transformation to acute myeloid leukemia and blastic plasmacytoid dendritic cell neoplasm from a shared ancestral hematopoietic clone. Leuk Lymphoma 2020; 61:2258-2261. [PMID: 32366145 DOI: 10.1080/10428194.2020.1755856] [Citation(s) in RCA: 2] [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] [Indexed: 01/25/2023]
Affiliation(s)
- Marlise R Luskin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Annette S Kim
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sanjay S Patel
- Division of Hematopathology, Department of Pathology, Weill Cornell Medical College, New York, NY, USA
| | - Kyle Wright
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Nicole R LeBoeuf
- Department of Dermatology, Center for Cutaneous Oncology, Dana-Farber/Brigham and Women's Cancer Center, Harvard Medical School, Boston, MA, USA
| | - Andrew A Lane
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
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Keegan A, Bridge JA, Lindeman NI, Long TA, Merker JD, Moncur JT, Montgomery ND, Nagarajan R, Rothberg PG, Routbort MJ, Vasalos P, Xian R, Kim AS. Proficiency Testing of Standardized Samples Shows High Interlaboratory Agreement for Clinical Next Generation Sequencing-Based Hematologic Malignancy Assays With Survey Material-Specific Differences in Variant Frequencies. Arch Pathol Lab Med 2020; 144:959-966. [PMID: 31986076 DOI: 10.5858/arpa.2019-0352-cp] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT.— As laboratories increasingly turn from single-analyte testing in hematologic malignancies to next-generation sequencing-based panel testing, there is a corresponding need for proficiency testing to ensure adequate performance of these next-generation sequencing assays for optimal patient care. OBJECTIVE.— To report the performance of laboratories on proficiency testing from the first 4 College of American Pathologists Next-Generation Sequencing Hematologic Malignancy surveys. DESIGN.— College of American Pathologists proficiency testing results for 36 different engineered variants and/or allele fractions as well as a sample with no pathogenic variants were analyzed for accuracy and associated assay performance characteristics. RESULTS.— The overall sensitivity observed for all variants was 93.5% (2190 of 2341) with 99.8% specificity (22 800 of 22 840). The false-negative rate was 6.5% (151 of 2341), and the largest single cause of these errors was difficulty in identifying variants in the sequence of CEBPA that is rich in cytosines and guanines. False-positive results (0.18%; 40 of 22 840) were most likely the result of preanalytic or postanalytic errors. Interestingly, the variant allele fractions were almost uniformly lower than the engineered fraction (as measured by digital polymerase chain reaction). Extensive troubleshooting identified a multifactorial cause for the low variant allele fractions, a result of an interaction between the linearized nature of the plasmid and the Illumina TruSeq chemistry. CONCLUSIONS.— Laboratories demonstrated an overall accuracy of 99.2% (24 990 of 25 181) with 99.8% specificity and 93.5% sensitivity when examining 36 clinically relevant somatic single-nucleotide variants with a variant allele fraction of 10% or greater. The data also highlight an issue with artificial linearized plasmids as survey material for next-generation sequencing.
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Affiliation(s)
- Alissa Keegan
- From the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Keegan, Lindeman, and Kim); the Departments of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), ollege of American Pathologists, Northfield, Illinois; the UNC Lineberger Comprehensive Cancer Center (Dr Merker) and the Department of Pathology and Laboratory Medicine (Dr Montgomery), University of North Carolina, Chapel Hill; the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, PierianDx, St Louis, Missouri (Dr Nagarajan); the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center, Rochester, New York (Dr Rothberg); the Department of Hematopathology, MD Anderson Cancer Center, Houston, Texas (Dr Routbort); and the Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland (Dr Xian)
| | - Julia A Bridge
- From the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Keegan, Lindeman, and Kim); the Departments of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), ollege of American Pathologists, Northfield, Illinois; the UNC Lineberger Comprehensive Cancer Center (Dr Merker) and the Department of Pathology and Laboratory Medicine (Dr Montgomery), University of North Carolina, Chapel Hill; the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, PierianDx, St Louis, Missouri (Dr Nagarajan); the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center, Rochester, New York (Dr Rothberg); the Department of Hematopathology, MD Anderson Cancer Center, Houston, Texas (Dr Routbort); and the Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland (Dr Xian)
| | - Neal I Lindeman
- From the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Keegan, Lindeman, and Kim); the Departments of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), ollege of American Pathologists, Northfield, Illinois; the UNC Lineberger Comprehensive Cancer Center (Dr Merker) and the Department of Pathology and Laboratory Medicine (Dr Montgomery), University of North Carolina, Chapel Hill; the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, PierianDx, St Louis, Missouri (Dr Nagarajan); the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center, Rochester, New York (Dr Rothberg); the Department of Hematopathology, MD Anderson Cancer Center, Houston, Texas (Dr Routbort); and the Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland (Dr Xian)
| | - Thomas A Long
- From the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Keegan, Lindeman, and Kim); the Departments of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), ollege of American Pathologists, Northfield, Illinois; the UNC Lineberger Comprehensive Cancer Center (Dr Merker) and the Department of Pathology and Laboratory Medicine (Dr Montgomery), University of North Carolina, Chapel Hill; the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, PierianDx, St Louis, Missouri (Dr Nagarajan); the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center, Rochester, New York (Dr Rothberg); the Department of Hematopathology, MD Anderson Cancer Center, Houston, Texas (Dr Routbort); and the Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland (Dr Xian)
| | - Jason D Merker
- From the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Keegan, Lindeman, and Kim); the Departments of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), ollege of American Pathologists, Northfield, Illinois; the UNC Lineberger Comprehensive Cancer Center (Dr Merker) and the Department of Pathology and Laboratory Medicine (Dr Montgomery), University of North Carolina, Chapel Hill; the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, PierianDx, St Louis, Missouri (Dr Nagarajan); the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center, Rochester, New York (Dr Rothberg); the Department of Hematopathology, MD Anderson Cancer Center, Houston, Texas (Dr Routbort); and the Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland (Dr Xian)
| | - Joel T Moncur
- From the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Keegan, Lindeman, and Kim); the Departments of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), ollege of American Pathologists, Northfield, Illinois; the UNC Lineberger Comprehensive Cancer Center (Dr Merker) and the Department of Pathology and Laboratory Medicine (Dr Montgomery), University of North Carolina, Chapel Hill; the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, PierianDx, St Louis, Missouri (Dr Nagarajan); the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center, Rochester, New York (Dr Rothberg); the Department of Hematopathology, MD Anderson Cancer Center, Houston, Texas (Dr Routbort); and the Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland (Dr Xian)
| | - Nathan D Montgomery
- From the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Keegan, Lindeman, and Kim); the Departments of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), ollege of American Pathologists, Northfield, Illinois; the UNC Lineberger Comprehensive Cancer Center (Dr Merker) and the Department of Pathology and Laboratory Medicine (Dr Montgomery), University of North Carolina, Chapel Hill; the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, PierianDx, St Louis, Missouri (Dr Nagarajan); the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center, Rochester, New York (Dr Rothberg); the Department of Hematopathology, MD Anderson Cancer Center, Houston, Texas (Dr Routbort); and the Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland (Dr Xian)
| | - Rakesh Nagarajan
- From the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Keegan, Lindeman, and Kim); the Departments of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), ollege of American Pathologists, Northfield, Illinois; the UNC Lineberger Comprehensive Cancer Center (Dr Merker) and the Department of Pathology and Laboratory Medicine (Dr Montgomery), University of North Carolina, Chapel Hill; the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, PierianDx, St Louis, Missouri (Dr Nagarajan); the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center, Rochester, New York (Dr Rothberg); the Department of Hematopathology, MD Anderson Cancer Center, Houston, Texas (Dr Routbort); and the Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland (Dr Xian)
| | - Paul G Rothberg
- From the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Keegan, Lindeman, and Kim); the Departments of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), ollege of American Pathologists, Northfield, Illinois; the UNC Lineberger Comprehensive Cancer Center (Dr Merker) and the Department of Pathology and Laboratory Medicine (Dr Montgomery), University of North Carolina, Chapel Hill; the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, PierianDx, St Louis, Missouri (Dr Nagarajan); the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center, Rochester, New York (Dr Rothberg); the Department of Hematopathology, MD Anderson Cancer Center, Houston, Texas (Dr Routbort); and the Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland (Dr Xian)
| | - Mark J Routbort
- From the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Keegan, Lindeman, and Kim); the Departments of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), ollege of American Pathologists, Northfield, Illinois; the UNC Lineberger Comprehensive Cancer Center (Dr Merker) and the Department of Pathology and Laboratory Medicine (Dr Montgomery), University of North Carolina, Chapel Hill; the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, PierianDx, St Louis, Missouri (Dr Nagarajan); the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center, Rochester, New York (Dr Rothberg); the Department of Hematopathology, MD Anderson Cancer Center, Houston, Texas (Dr Routbort); and the Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland (Dr Xian)
| | - Patricia Vasalos
- From the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Keegan, Lindeman, and Kim); the Departments of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), ollege of American Pathologists, Northfield, Illinois; the UNC Lineberger Comprehensive Cancer Center (Dr Merker) and the Department of Pathology and Laboratory Medicine (Dr Montgomery), University of North Carolina, Chapel Hill; the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, PierianDx, St Louis, Missouri (Dr Nagarajan); the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center, Rochester, New York (Dr Rothberg); the Department of Hematopathology, MD Anderson Cancer Center, Houston, Texas (Dr Routbort); and the Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland (Dr Xian)
| | - Rena Xian
- From the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Keegan, Lindeman, and Kim); the Departments of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), ollege of American Pathologists, Northfield, Illinois; the UNC Lineberger Comprehensive Cancer Center (Dr Merker) and the Department of Pathology and Laboratory Medicine (Dr Montgomery), University of North Carolina, Chapel Hill; the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, PierianDx, St Louis, Missouri (Dr Nagarajan); the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center, Rochester, New York (Dr Rothberg); the Department of Hematopathology, MD Anderson Cancer Center, Houston, Texas (Dr Routbort); and the Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland (Dr Xian)
| | - Annette S Kim
- From the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Keegan, Lindeman, and Kim); the Departments of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), ollege of American Pathologists, Northfield, Illinois; the UNC Lineberger Comprehensive Cancer Center (Dr Merker) and the Department of Pathology and Laboratory Medicine (Dr Montgomery), University of North Carolina, Chapel Hill; the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, PierianDx, St Louis, Missouri (Dr Nagarajan); the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center, Rochester, New York (Dr Rothberg); the Department of Hematopathology, MD Anderson Cancer Center, Houston, Texas (Dr Routbort); and the Department of Pathology, Johns Hopkins School of Medicine, Baltimore, Maryland (Dr Xian)
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Kim AS, Bartley AN, Bridge JA, Kamel-Reid S, Lazar AJ, Lindeman NI, Long TA, Merker JD, Rai AJ, Rimm DL, Rothberg PG, Vasalos P, Moncur JT. Comparison of Laboratory-Developed Tests and FDA-Approved Assays for BRAF, EGFR, and KRAS Testing. JAMA Oncol 2019; 4:838-841. [PMID: 29242895 DOI: 10.1001/jamaoncol.2017.4021] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Importance The debate about the role of the Food and Drug Administration (FDA) in the regulation of laboratory-developed tests (LDTs) has focused attention on the analytical performance of all clinical laboratory testing. This study provides data comparing the performance of LDTs and FDA-approved companion diagnostics (FDA-CDs) in proficiency testing (PT) provided by the College of American Pathologists Molecular Oncology Committee. Objective To compare the analytical performance of LDTs and FDA-CDs on well-characterized PT samples and to compare the practice characteristics of laboratories using these assays. Design, Setting, and Participants This comparison of PT responses examines the performance of laboratories participating in the College of American Pathologists PT for 3 oncology analytes for which both FDA-CDs and LDTs are used: BRAF, EGFR, and KRAS. A total of 6897 PT responses were included: BRAF (n = 2524; 14 PT samples), EGFR (n = 2216; 11 PT samples), and KRAS (n = 2157, 10 PT samples). US Food and Drug Administration companion diagnostics and LDTs are compared for both accuracy and preanalytic practices of the laboratories. Main Outcomes and Measures As per the College of American Pathologists PT standards, results were scored and the percentages of acceptable responses for each analyte were compared. These were also broken down by the specific variants tested, by kit manufacturer for laboratories using commercial reagents, and by preanalytic practices. Results From analysis of 6897 PT responses, this study demonstrates that both LDTs and FDA-CDs have excellent performance overall, with both test types exceeding 97% accuracy for all 3 genes (BRAF, EGFR, and KRAS) combined. Rare variant-specific differences did not consistently favor LDTs or FDA-CDs. Additionally, more than 60% of participants using an FDA-CD reported adapting their assay from the approved procedure to allow for a greater breadth of sample types, minimum tumor content, and instrumentation, changing the classification of their assay from FDA-CD to LDT. Conclusions This study demonstrates the high degree of accuracy and comparable performance of both LDTs and FDA-CDs for 3 oncology analytes. More significantly, the majority of laboratories using FDA-CDs have modified the scope of their assay to allow for more clinical practice variety, rendering them LDTs. These findings support both the excellent and equivalent performance of both LDTs and FDA-CDs in clinical diagnostic testing.
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Affiliation(s)
- Annette S Kim
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | | | | | | | | | - Neal I Lindeman
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Thomas A Long
- College of American Pathologists, Northfield, Illinois
| | | | - Alex J Rai
- Columbia University Medical Center, New York, New York
| | - David L Rimm
- Yale University School of Medicine, New Haven, Connecticut
| | - Paul G Rothberg
- Strong Memorial Hospital, University of Rochester Medical Center, Rochester, New York
| | | | - Joel T Moncur
- Walter Reed National Military Medical Center, Bethesda, Maryland
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Soma LA, Kovach AE, Siddon AJ, Beck R, Gibson SE, Swerdlow SH, Kim AS, Wu D, Jones D, Cook JR, Prakash S, Rosado F, Crane G, Bradley K, Weinberg OK, Sargent RL. Molecular and Cytogenetic Education in Hematopathology Fellowship. Am J Clin Pathol 2019; 152:438-445. [PMID: 31141139 DOI: 10.1093/ajcp/aqz048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES Given the increased complexity of molecular and cytogenetic testing (MOL-CG), the Society for Hematopathology Education Committee (SH-EC) was interested in determining what the current expectations are for MOL-CG education in hematopathology (HP) fellowship training. METHODS The SH-EC sent a questionnaire to HP fellowship program directors (HP-PDs) covering MOL-CG training curricula, test menus, faculty background, teaching, and sign-out roles. These findings were explored via a panel-based discussion at the 2018 SH-EC meeting for HP-PDs. RESULTS HP fellows are expected to understand basic principles, nomenclature, and indications for and limitations of testing. Interpretation of common assays is within that scope, but not necessarily proficiency in technical troubleshooting of testing or analysis of complex raw data. CONCLUSIONS The consensus was that HP fellows should understand the components of MOL-CG testing necessary to incorporate those results into an accurate, clinically relevant, and integrated HP report.
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Affiliation(s)
- Lorinda A Soma
- Department of Laboratory Medicine, University of Washington School of Medicine, Seattle
| | - Alexandra E Kovach
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center and Monroe Carell Jr Children’s Hospital at Vanderbilt, Nashville, TN
| | - Alexa J Siddon
- Department of Laboratory Medicine, Yale University, New Haven, CT
| | - Rose Beck
- Department of Pathology, University Hospitals of Cleveland/Case Western Reserve University, Cleveland, OH
| | - Sarah E Gibson
- Department of Laboratory Medicine and Pathology, Mayo Clinic Arizona, Phoenix
| | - Steven H Swerdlow
- Department of Anatomic and Clinical Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Annette S Kim
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA
| | - David Wu
- Department of Laboratory Medicine, University of Washington School of Medicine, Seattle
| | - Dan Jones
- Department of Pathology, The Ohio State University, Columbus
| | - James R Cook
- Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH
| | - Sonam Prakash
- Department of Laboratory Medicine, University of California, San Francisco
| | - Flavia Rosado
- Department of Pathology, University of Texas Southwestern, Dallas
| | - Genevieve Crane
- Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY
| | - Kyle Bradley
- Department of Pathology and Laboratory Medicine, Emory University Hospital, Atlanta, GA
| | - Olga K Weinberg
- Department of Pathology, Boston Children’s Hospital, Boston, MA
| | - Rachel L Sargent
- Oncology Diagnostics, Janssen Research and Development, Spring House, PA
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Crombie JL, Venkateswaran R, Kim AS, Vaidya A, Fisher DC. Bad to the Bone. N Engl J Med 2019; 381:e9. [PMID: 31340097 DOI: 10.1056/nejmimc1810061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Moncur JT, Bartley AN, Bridge JA, Kamel-Reid S, Lazar AJ, Lindeman NI, Long TA, Merker JD, Rai AJ, Rimm DL, Rothberg PG, Vasalos P, Kim AS. Performance Comparison of Different Analytic Methods in Proficiency Testing for Mutations in the BRAF, EGFR, and KRAS Genes: A Study of the College of American Pathologists Molecular Oncology Committee. Arch Pathol Lab Med 2019; 143:1203-1211. [PMID: 30969158 DOI: 10.5858/arpa.2018-0396-cp] [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] [Indexed: 11/06/2022]
Abstract
CONTEXT.— The performance of laboratory testing has recently come under increased scrutiny as part of important and ongoing debates on regulation and reimbursement. To address this critical issue, this study compares the performance of assay methods, using either commercial kits or assays designed and implemented by single laboratories ("home brews"), including next-generation sequencing methods, on proficiency testing provided by the College of American Pathologists Molecular Oncology Committee. OBJECTIVE.— To compare the performance of different assay methods on College of American Pathologists proficiency testing for variant analysis of 3 common oncology analytes: BRAF, EGFR, and KRAS. DESIGN.— There were 6897 total responses across 35 different proficiency testing samples interrogating 13 different variants as well as wild-type sequences for BRAF, EGFR, and KRAS. Performance was analyzed by test method, kit manufacturer, variants tested, and preanalytic and postanalytic practices. RESULTS.— Of 26 reported commercial kits, 23 achieved greater than 95% accuracy. Laboratory-developed tests with no kit specified demonstrated 96.8% or greater accuracy across all 3 analytes (1123 [96.8%] acceptable of 1160 total responses for BRAF; 848 [97.5%] acceptable of 870 total responses for EGFR; 942 [97.0%] acceptable of 971 total responses for KRAS). Next-generation sequencing platforms (summed across all analytes and 2 platforms) demonstrated 99.4% accuracy for these analytes (165 [99.4%] acceptable of 166 total next-generation sequencing responses). Slight differences in performance were noted among select commercial assays, dependent upon the particular design and specificity of the assay. Wide differences were noted in the lower limits of neoplastic cellularity laboratories accepted for testing. CONCLUSIONS.— These data demonstrate the high degree of accuracy and comparable performance across all laboratories, regardless of methodology. However, care must be taken in understanding the diagnostic specificity and reported analytic sensitivity of individual methods.
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Affiliation(s)
- Joel T Moncur
- From the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, St Joseph Mercy Hospital, Ypsilanti, Michigan (Dr Bartley); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); the Department of Pathology, University Health Network, University of Toronto, Toronto, Ontario, Canada (Dr Kamel-Reid); the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Lazar); the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Lindeman and Kim); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), College of American Pathologists, Northfield, Illinois; the Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill (Dr Merker); the Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York (Dr Rai); the Department of Pathology, Yale University School of Medicine, New Haven, Connecticut (Dr Rimm); and the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center and Pathology and Laboratory Medicine, Molecular Diagnostic Laboratory, Rochester, New York (Dr Rothberg). Dr Moncur is employed by the US Army. The identification of specific products or scientific instrumentation is considered an integral part of the scientific endeavor and does not constitute endorsement or implied endorsement on the part of the authors, the Department of Defense, or any component agency. The views expressed in this article are those of the authors and do not reflect the official policy of the Department of Army/Navy/Air Force, Department of Defense, or US government. The other authors have no relevant financial interest in the products or companies described in this article
| | - Angela N Bartley
- From the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, St Joseph Mercy Hospital, Ypsilanti, Michigan (Dr Bartley); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); the Department of Pathology, University Health Network, University of Toronto, Toronto, Ontario, Canada (Dr Kamel-Reid); the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Lazar); the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Lindeman and Kim); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), College of American Pathologists, Northfield, Illinois; the Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill (Dr Merker); the Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York (Dr Rai); the Department of Pathology, Yale University School of Medicine, New Haven, Connecticut (Dr Rimm); and the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center and Pathology and Laboratory Medicine, Molecular Diagnostic Laboratory, Rochester, New York (Dr Rothberg). Dr Moncur is employed by the US Army. The identification of specific products or scientific instrumentation is considered an integral part of the scientific endeavor and does not constitute endorsement or implied endorsement on the part of the authors, the Department of Defense, or any component agency. The views expressed in this article are those of the authors and do not reflect the official policy of the Department of Army/Navy/Air Force, Department of Defense, or US government. The other authors have no relevant financial interest in the products or companies described in this article
| | - Julia A Bridge
- From the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, St Joseph Mercy Hospital, Ypsilanti, Michigan (Dr Bartley); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); the Department of Pathology, University Health Network, University of Toronto, Toronto, Ontario, Canada (Dr Kamel-Reid); the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Lazar); the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Lindeman and Kim); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), College of American Pathologists, Northfield, Illinois; the Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill (Dr Merker); the Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York (Dr Rai); the Department of Pathology, Yale University School of Medicine, New Haven, Connecticut (Dr Rimm); and the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center and Pathology and Laboratory Medicine, Molecular Diagnostic Laboratory, Rochester, New York (Dr Rothberg). Dr Moncur is employed by the US Army. The identification of specific products or scientific instrumentation is considered an integral part of the scientific endeavor and does not constitute endorsement or implied endorsement on the part of the authors, the Department of Defense, or any component agency. The views expressed in this article are those of the authors and do not reflect the official policy of the Department of Army/Navy/Air Force, Department of Defense, or US government. The other authors have no relevant financial interest in the products or companies described in this article
| | - Suzanne Kamel-Reid
- From the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, St Joseph Mercy Hospital, Ypsilanti, Michigan (Dr Bartley); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); the Department of Pathology, University Health Network, University of Toronto, Toronto, Ontario, Canada (Dr Kamel-Reid); the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Lazar); the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Lindeman and Kim); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), College of American Pathologists, Northfield, Illinois; the Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill (Dr Merker); the Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York (Dr Rai); the Department of Pathology, Yale University School of Medicine, New Haven, Connecticut (Dr Rimm); and the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center and Pathology and Laboratory Medicine, Molecular Diagnostic Laboratory, Rochester, New York (Dr Rothberg). Dr Moncur is employed by the US Army. The identification of specific products or scientific instrumentation is considered an integral part of the scientific endeavor and does not constitute endorsement or implied endorsement on the part of the authors, the Department of Defense, or any component agency. The views expressed in this article are those of the authors and do not reflect the official policy of the Department of Army/Navy/Air Force, Department of Defense, or US government. The other authors have no relevant financial interest in the products or companies described in this article
| | - Alexander J Lazar
- From the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, St Joseph Mercy Hospital, Ypsilanti, Michigan (Dr Bartley); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); the Department of Pathology, University Health Network, University of Toronto, Toronto, Ontario, Canada (Dr Kamel-Reid); the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Lazar); the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Lindeman and Kim); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), College of American Pathologists, Northfield, Illinois; the Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill (Dr Merker); the Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York (Dr Rai); the Department of Pathology, Yale University School of Medicine, New Haven, Connecticut (Dr Rimm); and the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center and Pathology and Laboratory Medicine, Molecular Diagnostic Laboratory, Rochester, New York (Dr Rothberg). Dr Moncur is employed by the US Army. The identification of specific products or scientific instrumentation is considered an integral part of the scientific endeavor and does not constitute endorsement or implied endorsement on the part of the authors, the Department of Defense, or any component agency. The views expressed in this article are those of the authors and do not reflect the official policy of the Department of Army/Navy/Air Force, Department of Defense, or US government. The other authors have no relevant financial interest in the products or companies described in this article
| | - Neal I Lindeman
- From the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, St Joseph Mercy Hospital, Ypsilanti, Michigan (Dr Bartley); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); the Department of Pathology, University Health Network, University of Toronto, Toronto, Ontario, Canada (Dr Kamel-Reid); the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Lazar); the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Lindeman and Kim); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), College of American Pathologists, Northfield, Illinois; the Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill (Dr Merker); the Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York (Dr Rai); the Department of Pathology, Yale University School of Medicine, New Haven, Connecticut (Dr Rimm); and the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center and Pathology and Laboratory Medicine, Molecular Diagnostic Laboratory, Rochester, New York (Dr Rothberg). Dr Moncur is employed by the US Army. The identification of specific products or scientific instrumentation is considered an integral part of the scientific endeavor and does not constitute endorsement or implied endorsement on the part of the authors, the Department of Defense, or any component agency. The views expressed in this article are those of the authors and do not reflect the official policy of the Department of Army/Navy/Air Force, Department of Defense, or US government. The other authors have no relevant financial interest in the products or companies described in this article
| | - Thomas A Long
- From the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, St Joseph Mercy Hospital, Ypsilanti, Michigan (Dr Bartley); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); the Department of Pathology, University Health Network, University of Toronto, Toronto, Ontario, Canada (Dr Kamel-Reid); the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Lazar); the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Lindeman and Kim); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), College of American Pathologists, Northfield, Illinois; the Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill (Dr Merker); the Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York (Dr Rai); the Department of Pathology, Yale University School of Medicine, New Haven, Connecticut (Dr Rimm); and the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center and Pathology and Laboratory Medicine, Molecular Diagnostic Laboratory, Rochester, New York (Dr Rothberg). Dr Moncur is employed by the US Army. The identification of specific products or scientific instrumentation is considered an integral part of the scientific endeavor and does not constitute endorsement or implied endorsement on the part of the authors, the Department of Defense, or any component agency. The views expressed in this article are those of the authors and do not reflect the official policy of the Department of Army/Navy/Air Force, Department of Defense, or US government. The other authors have no relevant financial interest in the products or companies described in this article
| | - Jason D Merker
- From the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, St Joseph Mercy Hospital, Ypsilanti, Michigan (Dr Bartley); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); the Department of Pathology, University Health Network, University of Toronto, Toronto, Ontario, Canada (Dr Kamel-Reid); the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Lazar); the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Lindeman and Kim); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), College of American Pathologists, Northfield, Illinois; the Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill (Dr Merker); the Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York (Dr Rai); the Department of Pathology, Yale University School of Medicine, New Haven, Connecticut (Dr Rimm); and the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center and Pathology and Laboratory Medicine, Molecular Diagnostic Laboratory, Rochester, New York (Dr Rothberg). Dr Moncur is employed by the US Army. The identification of specific products or scientific instrumentation is considered an integral part of the scientific endeavor and does not constitute endorsement or implied endorsement on the part of the authors, the Department of Defense, or any component agency. The views expressed in this article are those of the authors and do not reflect the official policy of the Department of Army/Navy/Air Force, Department of Defense, or US government. The other authors have no relevant financial interest in the products or companies described in this article
| | - Alex J Rai
- From the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, St Joseph Mercy Hospital, Ypsilanti, Michigan (Dr Bartley); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); the Department of Pathology, University Health Network, University of Toronto, Toronto, Ontario, Canada (Dr Kamel-Reid); the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Lazar); the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Lindeman and Kim); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), College of American Pathologists, Northfield, Illinois; the Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill (Dr Merker); the Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York (Dr Rai); the Department of Pathology, Yale University School of Medicine, New Haven, Connecticut (Dr Rimm); and the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center and Pathology and Laboratory Medicine, Molecular Diagnostic Laboratory, Rochester, New York (Dr Rothberg). Dr Moncur is employed by the US Army. The identification of specific products or scientific instrumentation is considered an integral part of the scientific endeavor and does not constitute endorsement or implied endorsement on the part of the authors, the Department of Defense, or any component agency. The views expressed in this article are those of the authors and do not reflect the official policy of the Department of Army/Navy/Air Force, Department of Defense, or US government. The other authors have no relevant financial interest in the products or companies described in this article
| | - David L Rimm
- From the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, St Joseph Mercy Hospital, Ypsilanti, Michigan (Dr Bartley); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); the Department of Pathology, University Health Network, University of Toronto, Toronto, Ontario, Canada (Dr Kamel-Reid); the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Lazar); the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Lindeman and Kim); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), College of American Pathologists, Northfield, Illinois; the Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill (Dr Merker); the Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York (Dr Rai); the Department of Pathology, Yale University School of Medicine, New Haven, Connecticut (Dr Rimm); and the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center and Pathology and Laboratory Medicine, Molecular Diagnostic Laboratory, Rochester, New York (Dr Rothberg). Dr Moncur is employed by the US Army. The identification of specific products or scientific instrumentation is considered an integral part of the scientific endeavor and does not constitute endorsement or implied endorsement on the part of the authors, the Department of Defense, or any component agency. The views expressed in this article are those of the authors and do not reflect the official policy of the Department of Army/Navy/Air Force, Department of Defense, or US government. The other authors have no relevant financial interest in the products or companies described in this article
| | - Paul G Rothberg
- From the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, St Joseph Mercy Hospital, Ypsilanti, Michigan (Dr Bartley); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); the Department of Pathology, University Health Network, University of Toronto, Toronto, Ontario, Canada (Dr Kamel-Reid); the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Lazar); the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Lindeman and Kim); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), College of American Pathologists, Northfield, Illinois; the Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill (Dr Merker); the Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York (Dr Rai); the Department of Pathology, Yale University School of Medicine, New Haven, Connecticut (Dr Rimm); and the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center and Pathology and Laboratory Medicine, Molecular Diagnostic Laboratory, Rochester, New York (Dr Rothberg). Dr Moncur is employed by the US Army. The identification of specific products or scientific instrumentation is considered an integral part of the scientific endeavor and does not constitute endorsement or implied endorsement on the part of the authors, the Department of Defense, or any component agency. The views expressed in this article are those of the authors and do not reflect the official policy of the Department of Army/Navy/Air Force, Department of Defense, or US government. The other authors have no relevant financial interest in the products or companies described in this article
| | - Patricia Vasalos
- From the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, St Joseph Mercy Hospital, Ypsilanti, Michigan (Dr Bartley); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); the Department of Pathology, University Health Network, University of Toronto, Toronto, Ontario, Canada (Dr Kamel-Reid); the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Lazar); the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Lindeman and Kim); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), College of American Pathologists, Northfield, Illinois; the Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill (Dr Merker); the Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York (Dr Rai); the Department of Pathology, Yale University School of Medicine, New Haven, Connecticut (Dr Rimm); and the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center and Pathology and Laboratory Medicine, Molecular Diagnostic Laboratory, Rochester, New York (Dr Rothberg). Dr Moncur is employed by the US Army. The identification of specific products or scientific instrumentation is considered an integral part of the scientific endeavor and does not constitute endorsement or implied endorsement on the part of the authors, the Department of Defense, or any component agency. The views expressed in this article are those of the authors and do not reflect the official policy of the Department of Army/Navy/Air Force, Department of Defense, or US government. The other authors have no relevant financial interest in the products or companies described in this article
| | - Annette S Kim
- From the Office of the Director, The Joint Pathology Center, Silver Spring, Maryland (Dr Moncur); the Department of Pathology, St Joseph Mercy Hospital, Ypsilanti, Michigan (Dr Bartley); the Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha (Dr Bridge); the Department of Pathology, University Health Network, University of Toronto, Toronto, Ontario, Canada (Dr Kamel-Reid); the Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston (Dr Lazar); the Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts (Drs Lindeman and Kim); Biostatistics (Mr Long) and Proficiency Testing (Ms Vasalos), College of American Pathologists, Northfield, Illinois; the Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill (Dr Merker); the Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York (Dr Rai); the Department of Pathology, Yale University School of Medicine, New Haven, Connecticut (Dr Rimm); and the Department of Pathology and Laboratory Medicine, Strong Memorial Hospital, University of Rochester Medical Center and Pathology and Laboratory Medicine, Molecular Diagnostic Laboratory, Rochester, New York (Dr Rothberg). Dr Moncur is employed by the US Army. The identification of specific products or scientific instrumentation is considered an integral part of the scientific endeavor and does not constitute endorsement or implied endorsement on the part of the authors, the Department of Defense, or any component agency. The views expressed in this article are those of the authors and do not reflect the official policy of the Department of Army/Navy/Air Force, Department of Defense, or US government. The other authors have no relevant financial interest in the products or companies described in this article
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Kim AS, Bartley AN, Bridge JA, Devereaux K, Iafrate AJ, Jennings L, Kamel-Reid S, Keegan A, Lazar AJ, Lindeman NI, Long TA, Merker JD, Moncur JT, Montgomery N, Montgomery SB, Nagarajan R, Oakley FD, Portier BP, Rai AJ, Rimm DL, Rothberg PG, Smail C, Surrey LF, Vasalos P, Xian R. 31. The PT alphabet soup: LDT, FDA, NGS, non-NGS, @#$!%. Cancer Genet 2019. [DOI: 10.1016/j.cancergen.2019.04.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Merker JD, Devereaux K, Iafrate AJ, Kamel-Reid S, Kim AS, Moncur JT, Montgomery SB, Nagarajan R, Portier BP, Routbort MJ, Smail C, Surrey LF, Vasalos P, Lazar AJ, Lindeman NI. Proficiency Testing of Standardized Samples Shows Very High Interlaboratory Agreement for Clinical Next-Generation Sequencing-Based Oncology Assays. Arch Pathol Lab Med 2019; 143:463-471. [PMID: 30376374 PMCID: PMC6910717 DOI: 10.5858/arpa.2018-0336-cp] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [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] [Indexed: 11/06/2022]
Abstract
CONTEXT.— Next-generation sequencing-based assays are being increasingly used in the clinical setting for the detection of somatic variants in solid tumors, but limited data are available regarding the interlaboratory performance of these assays. OBJECTIVE.— To examine proficiency testing data from the initial College of American Pathologists (CAP) Next-Generation Sequencing Solid Tumor survey to report on laboratory performance. DESIGN.— CAP proficiency testing results from 111 laboratories were analyzed for accuracy and associated assay performance characteristics. RESULTS.— The overall accuracy observed for all variants was 98.3%. Rare false-negative results could not be attributed to sequencing platform, selection method, or other assay characteristics. The median and average of the variant allele fractions reported by the laboratories were within 10% of those orthogonally determined by digital polymerase chain reaction for each variant. The median coverage reported at the variant sites ranged from 1922 to 3297. CONCLUSIONS.— Laboratories demonstrated an overall accuracy of greater than 98% with high specificity when examining 10 clinically relevant somatic single-nucleotide variants with a variant allele fraction of 15% or greater. These initial data suggest excellent performance, but further ongoing studies are needed to evaluate the performance of lower variant allele fractions and additional variant types.
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Affiliation(s)
- Jason D. Merker
- Departments of Pathology & Laboratory Medicine and Genetics, Lineberger Comprehensive Cancer Center,
University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Kelly Devereaux
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - A. John Iafrate
- Department of Pathology, Massachusetts General Hospital, Harvard University, Boston, MA, USA
| | - Suzanne Kamel-Reid
- Departments of Pathology and Clinical Laboratory Genetics, The University Health Network and the University
of Toronto, Toronto, Ontario, Canada
| | - Annette S. Kim
- Department of Pathology, Brigham and Women’s Hospital, Harvard University, Boston, MA, USA
| | - Joel T. Moncur
- Department of Pathology, Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Stephen B Montgomery
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | | | | | - Mark J. Routbort
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Craig Smail
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Biomedical Informatics Program, Stanford University, Stanford, CA, USA
| | - Lea F. Surrey
- Department of Pathology, Children’s Hospital of Philadelphia, University of Pennsylvania,
Philadelphia, PA
| | - Patricia Vasalos
- Proficiency Testing, College of American Pathologists, Northfield, IL, USA
| | - Alexander J. Lazar
- Departments of Pathology, Genomic Medicine, and Translational Molecular Pathology, The University of Texas
MD Anderson Cancer Center, Houston, TX, USA
| | - Neal I. Lindeman
- Department of Pathology, Brigham and Women’s Hospital, Harvard University, Boston, MA, USA
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