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Gould C, McBean M, Thompson E, Lickiss J, Tiong IS, Westerman D, Blombery P. Observations from a national sample exchange program for molecular haematology testing. Pathology 2024; 56:540-547. [PMID: 38413254 DOI: 10.1016/j.pathol.2023.12.413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 11/27/2023] [Accepted: 12/07/2023] [Indexed: 02/29/2024]
Abstract
External quality assessment programs (EQAP) for molecular haematology generally only assess the analytical phase of laboratory testing or provide limited evaluation of post-analytical components. We incorporated comprehensive post-analytical evaluation into an existing national inter-laboratory sample exchange program for molecular haematology due to the increasing complexity of diagnostic molecular testing and interpretation. We report key findings from four years of longitudinal data using this approach. Eighteen participating laboratories enrolled in an annual reciprocal sample exchange program from 2019-2022, which covered conventional and next-generation sequencing (NGS) assays. Participants submitted results on their laboratory information system-generated reports which then underwent central review. Reports were assessed according to consensus values and relevant national and international reporting standards and guidelines. A total of 680 reports were received. Laboratories had high concordance in the analytical phase of testing, with incorrect variant detection observed in a total of six of 680 (0.9%) reports. In contrast, post-analytical concordance was much lower, with at least one discordance observed in 28.9-57.6% of all conventional reports and 33.3-100% NGS reports. The most frequent post-analytical discordances were: (1) not including key technical information on reports (total 41.9% conventional, 47.2% NGS); (2) not using standard gene and variant nomenclature (total 28.2% conventional, 25.6% NGS). NGS reports also demonstrated discrepancies in variant classification (total 20.4%) and interpretation (total 10.2%). The rate of discrepancies generally improved year-on-year. Inter-laboratory concordance for molecular haematology testing is high in the analytical phase, however opportunities exist for improvement in the post-analytical phase. Given that result interpretation is crucial for clinical decision-making and that molecular testing is a complex and evolving field, we suggest that EQAPs should comprehensively evaluate both analytical and post-analytical components of laboratory performance in order to harmonise reporting and to support the accurate interpretation of molecular haematology tests.
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Affiliation(s)
- Clare Gould
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia.
| | - Michelle McBean
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
| | - Ella Thompson
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
| | - Jennifer Lickiss
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
| | - Ing Soo Tiong
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia
| | - David Westerman
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Vic, Australia
| | - Piers Blombery
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Vic, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Vic, Australia
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Krishnamurthy K, Chai J, Liu X, Wang Y, Naeem R, Goldstein DY. Clinical validation of the Ion Torrent Oncomine Myeloid Assay GX v2 on the Genexus Integrated Sequencer as a stand-alone assay for single-nucleotide variants, insertions/deletions, and fusion genes: Challenges, performance, and perspectives. Am J Clin Pathol 2024:aqae063. [PMID: 38823030 DOI: 10.1093/ajcp/aqae063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Accepted: 04/26/2024] [Indexed: 06/03/2024] Open
Abstract
OBJECTIVES Myeloid neoplasms require comprehensive characterization of genetic abnormalities, including single-nucleotide variants, small insertions and deletions, and fusions and translocations for management. The Oncomine Myeloid Assay GX v2 (Thermo Fisher Scientific) analyzes 17 full genes, 28 hotspot genes, 30 fusion driver genes, and 5 expression genes. METHODS The validation set included 192 DNA samples, 28 RNA samples, and 9 cell lines and contrived controls. The DNA and RNA were extracted from both peripheral blood and bone marrow. Library preparation, templating, and sequencing was performed on the fully automated Genexus Integrated Sequencer (Thermo Fisher Scientific). The sequencing data were analyzed by manual curation, default Oncomine filters and the Oncomine Reporter (Thermo Fisher Scientific). RESULTS Of the 600 reference pathogenic DNA variants targeted by the assay, concordance was seen in 98.3% of unfiltered variant call format files. Precision and reproducibility were 100%, and the lower limit of detection was 2% variant allele frequency for DNA. Inability to detect variants in long homopolymer regions intrinsic to the Ion Torrent chemistry led to 7 missed variants; 100% concordance was seen with reference RNA samples. CONCLUSIONS This extensive clinical validation of the Oncomine Myeloid Assay GX v2 on the Genexus Integrated Sequencer with its built-in bioinformatics pipeline and Ion Torrent Oncomine Reporter shows robust performance in terms of variant calling accuracy, precision, and reproducibility, with the advantage of a rapid turnaround time of 2 days. The greatest limitation is the inability to detect variants in long homopolymer regions.
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Affiliation(s)
| | - Jiani Chai
- Department of Pathology, Montefiore Medical Center, Bronx, New York, US
| | - Xiaowei Liu
- Department of Pathology, Montefiore Medical Center, Bronx, New York, US
| | - Yanhua Wang
- Department of Pathology, Montefiore Medical Center, Bronx, New York, US
- Albert Einstein College of Medicine, Bronx, New York, US
| | - Rizwan Naeem
- Department of Pathology, Montefiore Medical Center, Bronx, New York, US
- Albert Einstein College of Medicine, Bronx, New York, US
| | - D Yitzchak Goldstein
- Department of Pathology, Montefiore Medical Center, Bronx, New York, US
- Albert Einstein College of Medicine, Bronx, New York, US
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Johnson SM, Haberberger J, Galeotti J, Ramkissoon L, Coombs CC, Richardson DR, Foster MC, Duncan D, Montgomery ND, Ferguson NL, Zeidner JF. Comprehensive genomic profiling reveals molecular subsets of ASXL1-mutated myeloid neoplasms. Leuk Lymphoma 2024; 65:209-218. [PMID: 37921062 DOI: 10.1080/10428194.2023.2277672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 10/24/2023] [Indexed: 11/04/2023]
Abstract
A large-scale genomic analysis of patients with ASXL1-mutated myeloid disease has not been performed to date. We reviewed comprehensive genomic profiling results from 6043 adults to characterize clinicopathologic features and co-mutation patterns by ASXL1 mutation status. ASXL1 mutations occurred in 1414 patients (23%). Mutation co-occurrence testing revealed strong co-occurrence (p < 0.01) between mutations in ASXL1 and nine genes (SRSF2, U2AF1, RUNX1, SETBP1, EZH2, STAG2, CUX1, CSF3R, CBL). Further analysis of patients with these co-mutations yielded several novel findings. Co-mutation patterns supported that ASXL1/SF3B1 co-mutation may be biologically distinct from ASXL1/non-SF3B1 spliceosome co-mutation. In AML, ASXL1/SRSF2 co-mutated patients frequently harbored STAG2 mutations (42%), which were dependent on the presence of both ASXL1 and SRSF2 mutation (p < 0.05). STAG2 and SETBP1 mutations were also exclusive in ASXL1/SRSF2 co-mutated patients and associated with divergent chronic myeloid phenotypes. Our findings support that certain multi-mutant genotypes may be biologically relevant in ASXL1-mutated myeloid disease.
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Affiliation(s)
- Steven M Johnson
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | | | - Jonathan Galeotti
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Lori Ramkissoon
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Catherine C Coombs
- Division of Hematology, Department of Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
- UC Irvine, Irvine, CA, USA
| | - Daniel R Richardson
- Division of Hematology, Department of Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Matthew C Foster
- Division of Hematology, Department of Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
- Novartis Pharmaceuticals, Cambridge, MA, USA
| | - Daniel Duncan
- Foundation Medicine, Inc, Cambridge, MA, USA
- GRAIL, Inc, Durham, NC, USA
| | - Nathan D Montgomery
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- NeoGenomics Laboratories, Aliso Viejo, CA, USA
| | | | - Joshua F Zeidner
- Division of Hematology, Department of Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
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4
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Cross NCP, Ernst T, Branford S, Cayuela JM, Deininger M, Fabarius A, Kim DDH, Machova Polakova K, Radich JP, Hehlmann R, Hochhaus A, Apperley JF, Soverini S. European LeukemiaNet laboratory recommendations for the diagnosis and management of chronic myeloid leukemia. Leukemia 2023; 37:2150-2167. [PMID: 37794101 PMCID: PMC10624636 DOI: 10.1038/s41375-023-02048-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/13/2023] [Accepted: 09/20/2023] [Indexed: 10/06/2023]
Abstract
From the laboratory perspective, effective management of patients with chronic myeloid leukemia (CML) requires accurate diagnosis, assessment of prognostic markers, sequential assessment of levels of residual disease and investigation of possible reasons for resistance, relapse or progression. Our scientific and clinical knowledge underpinning these requirements continues to evolve, as do laboratory methods and technologies. The European LeukemiaNet convened an expert panel to critically consider the current status of genetic laboratory approaches to help diagnose and manage CML patients. Our recommendations focus on current best practice and highlight the strengths and pitfalls of commonly used laboratory tests.
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Affiliation(s)
| | - Thomas Ernst
- Klinik für Innere Medizin II, Universitätsklinikum Jena, Jena, Germany
| | - Susan Branford
- Centre for Cancer Biology and SA Pathology, Adelaide, SA, Australia
| | - Jean-Michel Cayuela
- Laboratory of Hematology, University Hospital Saint-Louis, AP-HP and EA3518, Université Paris Cité, Paris, France
| | | | - Alice Fabarius
- III. Medizinische Klinik, Medizinische Fakultät Mannheim, Universität Heidelberg, Mannheim, Germany
| | - Dennis Dong Hwan Kim
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Canada
| | | | | | - Rüdiger Hehlmann
- III. Medizinische Klinik, Medizinische Fakultät Mannheim, Universität Heidelberg, Mannheim, Germany
- ELN Foundation, Weinheim, Germany
| | - Andreas Hochhaus
- Klinik für Innere Medizin II, Universitätsklinikum Jena, Jena, Germany
| | - Jane F Apperley
- Centre for Haematology, Imperial College London, London, UK
- Department of Clinical Haematology, Imperial College Healthcare NHS Trust, London, UK
| | - Simona Soverini
- Department of Medical and Surgical Sciences, Institute of Hematology "Lorenzo e Ariosto Seràgnoli", University of Bologna, Bologna, Italy
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5
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Kim JJ, Jang JE, Lee HA, Park MR, Kook HW, Lee ST, Choi JR, Min YH, Shin S, Cheong JW. Development of a Next-generation Sequencing-based Gene Panel Test to Detect Measurable Residual Disease in Acute Myeloid Leukemia. Ann Lab Med 2023; 43:328-336. [PMID: 36843401 PMCID: PMC9989530 DOI: 10.3343/alm.2023.43.4.328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 12/04/2022] [Accepted: 01/27/2023] [Indexed: 02/28/2023] Open
Abstract
Background AML is a heterogeneous disease, and despite intensive therapy, recurrence is still high in AML patients who achieve the criterion for cytomorphologic remission (residual tumor burden [measurable residual disease, MRD]<5%). This study aimed to develop a targeted next-generation sequencing (NGS) panel to detect MRD in AML patients and validate its performance. Methods We designed an error-corrected, targeted MRD-NGS panel without using physical molecular barcodes, including 24 genes. Fifty-four bone marrow and peripheral blood samples from 23 AML patients were sequenced using the panel. The panel design was validated using reference material, and accuracy was assessed using droplet digital PCR. Results Dilution tests showed excellent linearity and a strong correlation between expected and observed clonal frequencies (R>0.99). The test reproducibly detected MRD in three dilution series samples, with a sensitivity of 0.25% for single-nucleotide variants. More than half of samples from patients with morphologic remission after one month of chemotherapy had detectable mutations. NGS-MRD positivity for samples collected after one month of chemotherapy tended to be associated with poor overall survival and progression-free survival. Conclusions Our highly sensitive and accurate NGS-MRD panel can be readily used to monitor most AML patients in clinical practice, including patients without gene rearrangement. In addition, this NGS-MRD panel may allow the detection of newly emerging clones during clinical relapse, leading to more reliable prognoses of AML.
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Affiliation(s)
- Jin Ju Kim
- Department of Laboratory Medicine, Yonsei University College of Medicine, Severance Hospital, Seoul, Korea
| | - Ji Eun Jang
- Division of Hematology, Department of Internal Medicine, Yonsei University College of Medicine, Severance Hospital, Seoul, Korea
| | - Hyeon Ah Lee
- Department of Laboratory Medicine, Graduate School of Medical Science, Brain Korea 21 PLUS Project, Yonsei University College of Medicine, Seoul, Korea
| | - Mi Ri Park
- Department of Laboratory Medicine, Yonsei University College of Medicine, Severance Hospital, Seoul, Korea
| | - Hye Won Kook
- Division of Hematology, Department of Internal Medicine, Yonsei University College of Medicine, Severance Hospital, Seoul, Korea
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Severance Hospital, Seoul, Korea.,Dxome Co. Ltd., Seongnam, Korea
| | - Jong Rak Choi
- Department of Laboratory Medicine, Yonsei University College of Medicine, Severance Hospital, Seoul, Korea.,Dxome Co. Ltd., Seongnam, Korea
| | - Yoo Hong Min
- Division of Hematology, Department of Internal Medicine, Yonsei University College of Medicine, Severance Hospital, Seoul, Korea
| | - Saeam Shin
- Department of Laboratory Medicine, Yonsei University College of Medicine, Severance Hospital, Seoul, Korea
| | - June-Won Cheong
- Division of Hematology, Department of Internal Medicine, Yonsei University College of Medicine, Severance Hospital, Seoul, Korea
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Johnson SM, Haberberger J, Galeotti J, Ramkissoon L, Coombs CC, Richardson DR, Foster MC, Duncan D, Zeidner JF, Ferguson NL, Montgomery ND. A reappraisal of ASXL1 mutation sites and the cohesin-binding motif in myeloid disease. Blood Cancer J 2023; 13:96. [PMID: 37365170 DOI: 10.1038/s41408-023-00876-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/31/2023] [Accepted: 06/15/2023] [Indexed: 06/28/2023] Open
Affiliation(s)
- Steven M Johnson
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
| | | | - Jonathan Galeotti
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Lori Ramkissoon
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - Catherine C Coombs
- Division of Hematology, Department of Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
- UC Irvine, 1001 Health Sciences Road, Irvine, CA, 92697, USA
| | - Daniel R Richardson
- Division of Hematology, Department of Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Matthew C Foster
- Division of Hematology, Department of Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
- Novartis Pharmaceuticals, Cambridge, MA, 02139, USA
| | - Daniel Duncan
- Foundation Medicine, Inc, Cambridge, MA, USA
- GRAIL, Inc., 4001 E NC 54 Hwy Assembly Suite 1100, Durham, NC, 27709, USA
| | - Joshua F Zeidner
- Division of Hematology, Department of Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | | | - Nathan D Montgomery
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Tempus Labs, Inc., 25 Alexandria Way, Durham, NC, 27703, USA
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7
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Yin CC, Pemmaraju N, You MJ, Li S, Xu J, Wang W, Tang Z, Alswailmi O, Bhalla KN, Qazilbash MH, Konopleva M, Khoury JD. Integrated Clinical Genotype-Phenotype Characteristics of Blastic Plasmacytoid Dendritic Cell Neoplasm. Cancers (Basel) 2021; 13:cancers13235888. [PMID: 34884997 PMCID: PMC8656770 DOI: 10.3390/cancers13235888] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/17/2021] [Accepted: 11/18/2021] [Indexed: 11/16/2022] Open
Abstract
Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is a rare, aggressive neoplasm derived from plasmacytoid dendritic cells. While advances in understanding the pathophysiology of the disease have been made, integrated systematic analyses of the spectrum of immunophenotypic and molecular alterations in real-world clinical cases remain limited. We performed mutation profiling of 50 BPDCN cases and assessed our findings in the context of disease immunophenotype, cytogenetics, and clinical characteristics. Patients included 42 men and 8 women, with a median age of 68 years (range, 14-84) at diagnosis. Forty-two (84%) patients had at least one mutation, and 23 (46%) patients had ≥3 mutations. The most common mutations involved TET2 and ASXL1, detected in 28 (56%) and 23 (46%) patients, respectively. Co-existing TET2 and ASXL1 mutations were present in 17 (34%) patients. Other recurrent mutations included ZRSR2 (16%), ETV6 (13%), DNMT3A (10%), NRAS (10%), IKZF1 (9%), SRSF2 (9%), IDH2 (8%), JAK2 (6%), KRAS (4%), NOTCH1 (4%), and TP53 (4%). We also identified mutations that have not been reported previously, including ETNK1, HNRNPK, HRAS, KDM6A, RAD21, SF3A1, and SH2B3. All patients received chemotherapy, and 20 patients additionally received stem cell transplantation. With a median follow-up of 10.5 months (range, 1-71), 21 patients achieved complete remission, 4 had persistent disease, and 24 died. Patients younger than 65 years had longer overall survival compared to those who were ≥65 years (p = 0.0022). Patients who had ≥3 mutations or mutations in the DNA methylation pathway genes had shorter overall survival (p = 0.0119 and p = 0.0126, respectively). Stem cell transplantation significantly prolonged overall survival regardless of mutation status. In conclusion, the majority of patients with BPDCN have somatic mutations involving epigenetic regulators and RNA splicing factors, in addition to ETV6 and IKZF1, which are also frequently mutated. Older age, multiple mutations, and mutations in the DNA methylation pathway are poor prognostic factors.
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Affiliation(s)
- C. Cameron Yin
- Department of Hematopathology, The University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA; (M.J.Y.); (S.L.); (J.X.); (W.W.); (Z.T.); (O.A.)
- Correspondence: (C.C.Y.); (J.D.K.); Tel.: +1-(713)-745-6134 (C.C.Y.); +1-(713)-745-6452 (J.D.K.)
| | - Naveen Pemmaraju
- Department of Leukemia, The University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA; (N.P.); (K.N.B.); (M.K.)
| | - M. James You
- Department of Hematopathology, The University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA; (M.J.Y.); (S.L.); (J.X.); (W.W.); (Z.T.); (O.A.)
| | - Shaoying Li
- Department of Hematopathology, The University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA; (M.J.Y.); (S.L.); (J.X.); (W.W.); (Z.T.); (O.A.)
| | - Jie Xu
- Department of Hematopathology, The University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA; (M.J.Y.); (S.L.); (J.X.); (W.W.); (Z.T.); (O.A.)
| | - Wei Wang
- Department of Hematopathology, The University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA; (M.J.Y.); (S.L.); (J.X.); (W.W.); (Z.T.); (O.A.)
| | - Zhenya Tang
- Department of Hematopathology, The University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA; (M.J.Y.); (S.L.); (J.X.); (W.W.); (Z.T.); (O.A.)
| | - Omar Alswailmi
- Department of Hematopathology, The University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA; (M.J.Y.); (S.L.); (J.X.); (W.W.); (Z.T.); (O.A.)
| | - Kapil N. Bhalla
- Department of Leukemia, The University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA; (N.P.); (K.N.B.); (M.K.)
| | - Muzaffar H. Qazilbash
- Department of Stem Cell Transplantation, The University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Marina Konopleva
- Department of Leukemia, The University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA; (N.P.); (K.N.B.); (M.K.)
| | - Joseph D. Khoury
- Department of Hematopathology, The University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA; (M.J.Y.); (S.L.); (J.X.); (W.W.); (Z.T.); (O.A.)
- Correspondence: (C.C.Y.); (J.D.K.); Tel.: +1-(713)-745-6134 (C.C.Y.); +1-(713)-745-6452 (J.D.K.)
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ASXL1 mutations are associated with distinct epigenomic alterations that lead to sensitivity to venetoclax and azacytidine. Blood Cancer J 2021; 11:157. [PMID: 34548471 PMCID: PMC8455571 DOI: 10.1038/s41408-021-00541-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 02/23/2021] [Accepted: 03/16/2021] [Indexed: 11/24/2022] Open
Abstract
The BCL2-inhibitor, Venetoclax (VEN), has shown significant anti-leukemic efficacy in combination with the DNMT-inhibitor, Azacytidine (AZA). To explore the mechanisms underlying the selective sensitivity of mutant leukemia cells to VEN and AZA, we used cell-based isogenic models containing a common leukemia-associated mutation in the epigenetic regulator ASXL1. KBM5 cells with CRISPR/Cas9-mediated correction of the ASXL1G710X mutation showed reduced leukemic growth, increased myeloid differentiation, and decreased HOXA and BCL2 gene expression in vitro compared to uncorrected KBM5 cells. Increased expression of the anti-apoptotic gene, BCL2, was also observed in bone marrow CD34+ cells from ASXL1 mutant MDS patients compared to CD34+ cells from wild-type MDS cases. ATAC-sequencing demonstrated open chromatin at the BCL2 promoter in the ASXL1 mutant KBM5 cells. BH3 profiling demonstrated increased dependence of mutant cells on BCL2. Upon treatment with VEN, mutant cells demonstrated increased growth inhibition. In addition, genome-wide methylome analysis of primary MDS samples and isogenic cell lines demonstrated increased gene-body methylation in ASXL1 mutant cells, with consequently increased sensitivity to AZA. These data mechanistically link the common leukemia-associated mutation ASXL1 to enhanced sensitivity to VEN and AZA via epigenetic upregulation of BCL2 expression and widespread alterations in DNA methylation.
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9
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Ebian HF, Elshorbagy S, Mohamed H, Embaby A, Khamis T, Sameh R, Sabbah NA, Hussein S. Clinical implication and prognostic significance of FLT3-ITD and ASXL1 mutations in Egyptian AML patients: A single-center study. Cancer Biomark 2021; 32:379-389. [PMID: 34487021 DOI: 10.3233/cbm-210024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND Both Fms-like tyrosine kinase 3-internal tandem duplication (FLT3-ITD) and Additional Sex Comb-like 1 (ASXL1) mutations are frequent and early genetic alteration events in acute myeloid leukemia (AML) patients. These genetic alterations may be associated with an unfavorable prognosis. OBJECTIVE Up to our knowledge, this is the first study performed to evaluate the clinical implication and prognostic significance of FLT3-ITD and ASXL1 mutations and their coexistence on the outcome of Egyptian AML patients. METHODS Our study included 83 patients with AML who were subjected to immunophenotyping and detection of FLT3-ITD and ASXL1 gene mutation by polymerase chain reaction (PCR) and real-time PCR, respectively. RESULTS FLT3-ITD and ASXL1 mutations were detected in 20.5% and 18.1% of AML patients respectively. Seven patients (8.4%) had co-expression of both genes' mutations. FLT3-ITD mutation was significantly higher in younger age, higher WBCs count and poor cytogenetic risk patients (P= 0.01, < 0.001 and 0.008 respectively). ASXL1 mutation was significantly higher in intermediate cytogenetic risk patients (P= 0.2). The mean period of survival and relapse-free survival (RFS) were significantly reduced in FLT3-ITD and ASXL1 mutations compared with their non-mutant types (P= 0.01 and 0.03 respectively). Both mutations were independent risk factors for overall survival (OS) and (RFS) in univariate and multivariate analysis in AML patients. CONCLUSION FLT3-ITD and ASXL1 gene mutations or their coexistence can predict a poor prognosis in AML patients.
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Affiliation(s)
- Huda F Ebian
- Clinical Pathology Department, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Sherin Elshorbagy
- Oncology Department, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Haitham Mohamed
- Hematology Oncology Unit/Internal Medicine Department, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Ahmad Embaby
- Hematology Oncology Unit/Internal Medicine Department, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Tarek Khamis
- Pharmacology Department, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Reham Sameh
- Pathology Department, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Norhan A Sabbah
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Samia Hussein
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Zagazig University, Zagazig, Egypt
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10
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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: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [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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11
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HIV is associated with an increased risk of age-related clonal hematopoiesis among older adults. Nat Med 2021; 27:1006-1011. [PMID: 34099923 DOI: 10.1038/s41591-021-01357-y] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 04/19/2021] [Indexed: 12/13/2022]
Abstract
People with human immunodeficiency virus (HIV) have higher rates of certain comorbidities, particularly cardiovascular disease and cancer, than people without HIV1-5. In view of observations that somatic mutations associated with age-related clonal hematopoiesis (CH) are linked to similar comorbidities in the general population6-10, we hypothesized that CH may be more prevalent in people with HIV. To address this issue, we established a prospective cohort study, the ARCHIVE study (NCT04641013), in which 220 HIV-positive and 226 HIV-negative participants aged 55 years or older were recruited in Australia. Demographic characteristics, clinical data and peripheral blood were collected to assess the presence of CH mutations and to identify potential risk factors for and clinical sequelae of CH. In total, 135 CH mutations were identified in 100 (22.4%) of 446 participants. CH was more prevalent in HIV-positive participants than in HIV-negative participants (28.2% versus 16.8%, P = 0.004), overall and across all age groups; the adjusted odds ratio for having CH in those with HIV was 2.16 (95% confidence interval 1.34-3.48, P = 0.002). The most common genes mutated overall were DNMT3A (47.4%), TET2 (20.0%) and ASXL1 (13.3%). CH and HIV infection were independently associated with increases in blood parameters and biomarkers associated with inflammation. These data suggest a selective advantage for the emergence of CH in the context of chronic infection and inflammation related to HIV infection.
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12
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Richardson DR, Swoboda DM, Moore DT, Johnson SM, Chan O, Galeotti J, Esparza S, Hussaini MO, Van Deventer H, Foster MC, Coombs CC, Montgomery ND, Sallman DA, Zeidner JF. Genomic characteristics and prognostic significance of co-mutated ASXL1/SRSF2 acute myeloid leukemia. Am J Hematol 2021; 96:462-470. [PMID: 33502020 DOI: 10.1002/ajh.26110] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 01/12/2021] [Accepted: 01/17/2021] [Indexed: 12/24/2022]
Abstract
The ASXL1 and SRSF2 mutations in AML are frequently found in patients with preexisting myeloid malignancies and are individually associated with poor outcomes. In this multi-institutional retrospective analysis, we assessed the genetic features and clinical outcomes of 43 patients with ASXL1mut SRSF2mut AML and compared outcomes to patients with either ASXL1 (n = 57) or SRSF2 (n = 70) mutations. Twenty-six (60%) had secondary-AML (s-AML). Variant allele fractions suggested that SRSF2 mutations preceded ASXL1 mutational events. Median overall survival (OS) was 7.0 months (95% CI:3.8,15.3) and was significantly longer in patients with de novo vs s-AML (15.3 vs 6.4 months, respectively; P = .04 on adjusted analysis). Compared to ASXL1mut SRSF2wt and ASXL1wt SRSF2mut , co-mutated patients had a 1.4 and 1.6 times increase in the probability of death, respectively (P = .049), with a trend towards inferior OS (median OS = 7.0 vs 11.5 vs 10.9 months, respectively; P = .10). Multivariable analysis suggests this difference in OS is attributable to the high proportion of s-AML patients in the co-mutated cohort (60% vs 32% and 23%, respectively). Although this study is limited by the retrospective data collection and the relatively small sample size, these data suggest that ASXL1mut SRSF2mut AML is a distinct subgroup of AML frequently associated with s-AML and differs from ASXL1mut SRSF2wt /ASXL1wt SRSF2mut with respect to etiology and leukemogenesis.
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Affiliation(s)
- Daniel R. Richardson
- Lineberger Comprehensive Cancer Center The University of North Carolina School of Medicine Chapel Hill North Carolina USA
- Division of Hematology, Department of Medicine The University of North Carolina School of Medicine Chapel Hill North Carolina USA
- The Cecil G. Sheps Center for Health Services Research University of North Carolina at Chapel Hill Chapel Hill North Carolina USA
| | - David M. Swoboda
- Department of Malignant Hematology H. Lee Moffitt Cancer Center and Research Institute Tampa Florida USA
| | - Dominic T. Moore
- Lineberger Comprehensive Cancer Center The University of North Carolina School of Medicine Chapel Hill North Carolina USA
| | - Steven M. Johnson
- Department of Pathology and Laboratory Medicine The University of North Carolina School of Medicine Chapel Hill North Carolina USA
| | - Onyee Chan
- Department of Malignant Hematology H. Lee Moffitt Cancer Center and Research Institute Tampa Florida USA
| | - Jonathan Galeotti
- Department of Pathology and Laboratory Medicine The University of North Carolina School of Medicine Chapel Hill North Carolina USA
| | - Sonia Esparza
- Lineberger Comprehensive Cancer Center The University of North Carolina School of Medicine Chapel Hill North Carolina USA
- Division of Hematology, Department of Medicine The University of North Carolina School of Medicine Chapel Hill North Carolina USA
| | - Mohammad O. Hussaini
- Department of Malignant Hematology H. Lee Moffitt Cancer Center and Research Institute Tampa Florida USA
| | - Hendrick Van Deventer
- Lineberger Comprehensive Cancer Center The University of North Carolina School of Medicine Chapel Hill North Carolina USA
- Division of Hematology, Department of Medicine The University of North Carolina School of Medicine Chapel Hill North Carolina USA
| | - Matthew C. Foster
- Lineberger Comprehensive Cancer Center The University of North Carolina School of Medicine Chapel Hill North Carolina USA
- Division of Hematology, Department of Medicine The University of North Carolina School of Medicine Chapel Hill North Carolina USA
| | - Catherine C. Coombs
- Lineberger Comprehensive Cancer Center The University of North Carolina School of Medicine Chapel Hill North Carolina USA
- Division of Hematology, Department of Medicine The University of North Carolina School of Medicine Chapel Hill North Carolina USA
| | - Nathan D. Montgomery
- Lineberger Comprehensive Cancer Center The University of North Carolina School of Medicine Chapel Hill North Carolina USA
- Department of Pathology and Laboratory Medicine The University of North Carolina School of Medicine Chapel Hill North Carolina USA
| | - David A. Sallman
- Department of Malignant Hematology H. Lee Moffitt Cancer Center and Research Institute Tampa Florida USA
| | - Joshua F. Zeidner
- Lineberger Comprehensive Cancer Center The University of North Carolina School of Medicine Chapel Hill North Carolina USA
- Division of Hematology, Department of Medicine The University of North Carolina School of Medicine Chapel Hill North Carolina USA
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13
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Schejbel L, Novotny GW, Breinholt MF, El Fassi D, Schöllkopf C, Hogdall E, Nørgaard P. Improved Variant Detection in Clinical Myeloid NGS Testing by Supplementing a Commercial Myeloid NGS Assay with Custom or Extended Data Filtering and Accessory Fragment Analysis. Mol Diagn Ther 2021; 25:251-266. [PMID: 33687704 DOI: 10.1007/s40291-021-00519-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/15/2021] [Indexed: 12/20/2022]
Abstract
BACKGROUND Commercial myeloid next-generation sequencing (NGS) panels may facilitate uniform generation of raw data between laboratories. However, different strategies for data filtering and variant annotation may contribute to differences in variant detection and reporting. Here, we present how custom data filtering or the use of Oncomine extended data filtering improve detection of clinically relevant mutations with the Oncomine Myeloid Research Assay. METHODS The study included all patient samples (n = 264) analyzed during the first-year, single-site, clinical use of the Ion Torrent Oncomine Myeloid Research Assay. In data analysis, the default analysis filter was supplemented with our own data filtering algorithm in order to detect additional clinically relevant mutations. In addition, we developed a sensitive supplementary test for the ASXL1 c.1934dupG p.Gly646fs mutation by fragment analysis. RESULTS Using our custom filter chain, we found 96 different reportable variants that were not detected by the default filter chain. Twenty-six of these were classified as variants of strong or potential clinical significance (tier I/tier II variants), and the custom filtering discovered otherwise undetected tier I/tier II variants in 25 of 132 patients with clinically relevant mutations (19%). The remaining 70 variants not detected by the default filter chain were classified as variants of unknown significance. Among these were several unique variants with possible pathogenic potential judged by bioinformatic predictions. The recently launched Oncomine 5.14 extended filter algorithm detects most but not all of the tier I/tier II variants that were not detected by the default filter. The supplementary fragment analysis for the ASXL1 c.1934dupG p.Gly646fs confidently detected a variant allele frequency of down to 4.8% (SD 0.83%). The assay also detected the ASXL1 c.1900_1922del23 mutation. CONCLUSION Detection of clinically relevant variants with the Oncomine Myeloid Research NGS assay can be significantly improved by supplementing the default filter chain with custom data filtering or the recently launched Oncomine 5.14 extended filter algorithm. Our accessory fragment analysis facilitates easy testing for frequent ASXL1 mutations that are poorly or not covered by the NGS assay.
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Affiliation(s)
- Lone Schejbel
- Department of Pathology, Herlev and Gentofte Hospital, Borgmester Ib Juuls Vej 73, 2730, Herlev, Denmark.
| | - Guy Wayne Novotny
- Department of Pathology, Herlev and Gentofte Hospital, Borgmester Ib Juuls Vej 73, 2730, Herlev, Denmark
| | - Marie Fredslund Breinholt
- Department of Pathology, Herlev and Gentofte Hospital, Borgmester Ib Juuls Vej 73, 2730, Herlev, Denmark
| | - Daniel El Fassi
- Department of Hematology, Herlev and Gentofte Hospital, Herlev, Denmark
| | | | - Estrid Hogdall
- Department of Pathology, Herlev and Gentofte Hospital, Borgmester Ib Juuls Vej 73, 2730, Herlev, Denmark
| | - Peter Nørgaard
- Department of Pathology, Herlev and Gentofte Hospital, Borgmester Ib Juuls Vej 73, 2730, Herlev, Denmark
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14
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Thompson ER, Nguyen T, Kankanige Y, Yeh P, Ingbritsen M, McBean M, Semple T, Mir Arnau G, Burbury K, Lee N, Khot A, Westerman D, Blombery P. Clonal independence of JAK2 and CALR or MPL mutations in comutated myeloproliferative neoplasms demonstrated by single cell DNA sequencing. Haematologica 2021; 106:313-315. [PMID: 32817290 PMCID: PMC7776355 DOI: 10.3324/haematol.2020.260448] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Ella R Thompson
- Pathology and Oncology Department, Peter MacCallum Cancer Centre, Melbourne
| | - Tamia Nguyen
- Pathology Department, Peter MacCallum Cancer Centre, Melbourne
| | - Yamuna Kankanige
- Pathology and Oncology Department, Peter MacCallum Cancer Centre, Melbourne
| | - Paul Yeh
- Peter MacCallum Cancer Centre, Melbourne
| | | | - Michelle McBean
- Pathology Department, Peter MacCallum Cancer Centre, Melbourne
| | - Timothy Semple
- Research Division, Peter MacCallum Cancer Centre, Melbourne
| | - Gisela Mir Arnau
- Department of Oncology, Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Kate Burbury
- Clinical Haematology, Peter MacCallum Cancer Centre/Royal Melbourne Hospital, Melbourne
| | - Nora Lee
- Clinical Haematology, Peter MacCallum Cancer Centre/Royal Melbourne Hospital, Melbourne
| | - Amit Khot
- Clinical Haematology, Peter MacCallum Cancer Centre/Royal Melbourne Hospital, Melbourne
| | - David Westerman
- Pathology, Oncology and Clinical Hematology, Peter MacCallum Cancer Centre, Melbourne
| | - Piers Blombery
- Pathology, Oncology and Clinical Haematology, Peter MacCallum Cancer Centre, Melbourne
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15
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Sapienza MR, Pileri S. Molecular Features of Blastic Plasmacytoid Dendritic Cell Neoplasm: DNA Mutations and Epigenetics. Hematol Oncol Clin North Am 2020; 34:511-521. [PMID: 32336416 DOI: 10.1016/j.hoc.2020.01.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is a rare hematologic neoplasm with a dismal prognosis and no standard therapy. In the past, its cellular ontogenesis was obscure, and BPDCN had been erroneously named CD56+/TdT+ blastic NK cell tumor and CD4+/CD56+ hematodermic neoplasm. Finally, in 2008, the BPDCN was correctly recognized as a neoplasm deriving from the malignant transformation of plasmacytoid dendritic cell precursors and classified among the myeloid neoplasms. Since then, the understanding of BPDCN biology has improved rapidly: the DNA mutational status of BPDCN has been extensively investigated revealing a spectrum perfectly resembling its myeloid lineage derivation.
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Affiliation(s)
- Maria Rosaria Sapienza
- Division of Diagnostic Haematopathology, European Institute of Oncology, IRCCS, Via Ripamonti 435, Milan 20141, Italy.
| | - Stefano Pileri
- Division of Diagnostic Haematopathology, European Institute of Oncology, IRCCS, Via Ripamonti 435, Milan 20141, Italy
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16
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Discriminating a common somatic ASXL1 mutation (c.1934dup; p.G646Wfs*12) from artifact in myeloid malignancies using NGS. Leukemia 2018; 32:1874-1878. [PMID: 29959414 DOI: 10.1038/s41375-018-0193-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Revised: 05/31/2018] [Accepted: 06/07/2018] [Indexed: 12/11/2022]
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