1
|
Orsmark-Pietras C, Lyander A, Ladenvall C, Hallström B, Staffas A, Awier H, Krstic A, Baliakas P, Barbany G, Håkansson CB, Gellerbring A, Hagström A, Hellström-Lindberg E, Juliusson G, Lazarevic V, Munters A, Pandzic T, Wadelius M, Ås J, Fogelstrand L, Wirta V, Rosenquist R, Cavelier L, Fioretos T. Precision Diagnostics in Myeloid Malignancies: Development and Validation of a National Capture-Based Gene Panel. Genes Chromosomes Cancer 2024; 63:e23257. [PMID: 39031442 DOI: 10.1002/gcc.23257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 06/23/2024] [Indexed: 07/22/2024] Open
Abstract
Gene panel sequencing has become a common diagnostic tool for detecting somatically acquired mutations in myeloid neoplasms. However, many panels have restricted content, provide insufficient sensitivity levels, or lack clinically validated workflows. We here describe the development and validation of the Genomic Medicine Sweden myeloid gene panel (GMS-MGP), a capture-based 191 gene panel including mandatory genes in contemporary guidelines as well as emerging candidates. The GMS-MGP displayed uniform coverage across all targets, including recognized difficult GC-rich areas. The validation of 117 previously described somatic variants showed a 100% concordance with a limit-of-detection of a 0.5% variant allele frequency (VAF), achieved by utilizing error correction and filtering against a panel-of-normals. A national interlaboratory comparison investigating 56 somatic variants demonstrated highly concordant results in both detection rate and reported VAFs. In addition, prospective analysis of 323 patients analyzed with the GMS-MGP as part of standard-of-care identified clinically significant genes as well as recurrent mutations in less well-studied genes. In conclusion, the GMS-MGP workflow supports sensitive detection of all clinically relevant genes, facilitates novel findings, and is, based on the capture-based design, easy to update once new guidelines become available. The GMS-MGP provides an important step toward nationally harmonized precision diagnostics of myeloid malignancies.
Collapse
Affiliation(s)
- Christina Orsmark-Pietras
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
- Clinical Genomics Lund, Science for Life Laboratory, Lund University, Lund, Sweden
| | - Anna Lyander
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Clinical Genomics Stockholm, Science Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Microbiology, Tumor and Cell Biology, Clinical Genomics Stockholm, Science Life Laboratory, Karolinska Institutet, Solna, Sweden
| | - Claes Ladenvall
- Department of Immunology, Genetics and Pathology, Clinical Genomics Uppsala, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Björn Hallström
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
| | - Anna Staffas
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Sweden
| | - Hero Awier
- Department of Clinical Genetics, Karolinska University Hospital, Solna, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Aleksandra Krstic
- Department of Clinical Genetics, Karolinska University Hospital, Solna, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Panagiotis Baliakas
- Department of Immunology, Genetics and Pathology, Clinical Genomics Uppsala, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Clinical Genetics, Uppsala University Hospital, Uppsala, Sweden
| | - Gisela Barbany
- Department of Clinical Genetics, Karolinska University Hospital, Solna, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Cecilia Brunhoff Håkansson
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
| | - Anna Gellerbring
- Department of Microbiology, Tumor and Cell Biology, Clinical Genomics Stockholm, Science Life Laboratory, Karolinska Institutet, Solna, Sweden
| | - Anna Hagström
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Eva Hellström-Lindberg
- Department of Medicine Huddinge, Center for Hematology and Regenerative Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Gunnar Juliusson
- Department of Hematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden
| | - Vladimir Lazarevic
- Department of Hematology, Oncology and Radiation Physics, Skåne University Hospital, Lund, Sweden
| | - Arielle Munters
- Department of Immunology, Genetics and Pathology, Clinical Genomics Uppsala, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Tatjana Pandzic
- Department of Immunology, Genetics and Pathology, Clinical Genomics Uppsala, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Clinical Genetics, Uppsala University Hospital, Uppsala, Sweden
| | - Mia Wadelius
- Department of Medical Sciences, Clinical Pharmacogenomics, Uppsala University, Uppsala, Sweden
| | - Joel Ås
- Department of Medical Sciences, Clinical Pharmacogenomics, Uppsala University, Uppsala, Sweden
| | - Linda Fogelstrand
- Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Valtteri Wirta
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Clinical Genomics Stockholm, Science Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Microbiology, Tumor and Cell Biology, Clinical Genomics Stockholm, Science Life Laboratory, Karolinska Institutet, Solna, Sweden
- Genomic Medicine Center Karolinska, Karolinska University Hospital, Stockholm, Sweden
| | - Richard Rosenquist
- Department of Clinical Genetics, Karolinska University Hospital, Solna, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Genomic Medicine Center Karolinska, Karolinska University Hospital, Stockholm, Sweden
| | - Lucia Cavelier
- Department of Immunology, Genetics and Pathology, Clinical Genomics Uppsala, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Solna, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Uppsala University Hospital, Uppsala, Sweden
- Genomic Medicine Center Karolinska, Karolinska University Hospital, Stockholm, Sweden
| | - Thoas Fioretos
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
- Clinical Genomics Lund, Science for Life Laboratory, Lund University, Lund, Sweden
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Zbieranski N, Insuasti-Beltran G. Analytical Validation of an Automated Semiconductor-Based Next-Generation Sequencing Assay for Detection of DNA and RNA Alterations in Myeloid Neoplasms. J Mol Diagn 2024; 26:29-36. [PMID: 37879438 DOI: 10.1016/j.jmoldx.2023.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/23/2023] [Accepted: 09/20/2023] [Indexed: 10/27/2023] Open
Abstract
Myeloid neoplasms are heterogeneous tumors derived from early hematopoietic progenitors. Most international guidelines, including the European LeukemiaNet 2022 update, recommend testing a comprehensive set of genes, most within a 3- to 5-day period for optimal treatment decisions. Next-generation sequencing gene panels are essential for identifying genetic alterations, risk stratification, and determining targeted therapies for myeloid malignancies. This study describes the analytical validation of the Oncomine Myeloid Assay GX v2 (Myeloid GX v2) in combination with the Ion Torrent Genexus System using commercial controls, 16 variant-negative samples, and 130 clinical samples of myeloid neoplasms. The Myeloid GX v2 panel detected single nucleotide variants (SNVs), insertions/deletions (indels) (allele frequency >5%), and gene fusions (minimum 11 fusion copies/μL) in synthetic controls with a sensitivity of 100%. Specificity for detection of SNVs, indels, or fusions in 16 variant-negative samples was 100%. Sensitivity for detection of SNVs, indels, and gene fusions in 130 clinical samples was 99%, 97%, and 100%, respectively. Overall precision was 100% for SNVs, 96% for indels, and 100% for fusions. The average turnaround time from nucleic acid extraction to results was 2 days. The Myeloid GX v2 panel is highly accurate and reproducible for the detection of SNVs, indels, and gene fusions in myeloid neoplasms. The ability to deliver clinically relevant results in a short time is key to providing personalized treatments.
Collapse
Affiliation(s)
- Nora Zbieranski
- Department of Pathology, Wake Forest Baptist Medical Center, Winston-Salem, North Carolina
| | | |
Collapse
|
4
|
Jeon MJ, Yu ES, Kim DS, Choi CW, Kim HN, Ah Kwon J, Yoon SY, Yoon J. Performance evaluation and clinical impact of the Oncomine Myeloid Research Assay for gene expression analysis in myeloid haematologic malignancies. J Clin Pathol 2023; 76:778-783. [PMID: 35999034 DOI: 10.1136/jcp-2022-208425] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/19/2022] [Indexed: 11/04/2022]
Abstract
AIM Gene expression analysis facilitates the detection of diagnostic and prognostic biomarkers for myeloid haematological malignancies. The Oncomine Myeloid Research Assay (OMA; Thermo Fisher Scientific, Massachusetts, USA) provides a comprehensive analysis of gene expression of five target genes, along with gene alteration and fusion. Here, we present the performance of the OMA for gene expression analysis. METHODS In total, 53 RNA samples from patients diagnosed with acute myeloid leukaemia (AML) or myelodysplastic syndrome were included. Of these 53 samples, 3 were evaluated for reproducibility and 50 were evaluated for comparison with RNA-sequencing (RNA-seq). The prognostic impact of the gene expression profile produced by both OMA and RNA-seq in AML was investigated using follow-up data from 33 patients with AML. RESULTS The OMA showed good intrarun and interrun reproducibility. Compared with the RNA-seq results, high correlations were found in BAALC, MECOM and WT1 (all r>0.9), with moderate correlations in MYC (r=0.75, p<0.001) and SMC1A (r=0.42, p=0.002). The agreement between OMA and RNA-seq in classifying the dysregulated expression group was almost perfect, except for SMC1A (κ=0.175). Among these five genes, only BAALC showed a significant clinical impact in patients with AML. Patients with high BAALC expression showed significantly shorter overall survival based on both OMA (p=0.037) and RNA-seq (p=0.003). CONCLUSIONS OMA gene expression analysis offers reproducible and accurate gene expression data for most targeted genes and demonstrates the utility of BAALC expression as a prognostic marker in AML.
Collapse
Affiliation(s)
- Min Ji Jeon
- Division of Hematology-Oncology, Department of Internal Medicine, Korea University Guro Hospital, Seoul, Korea (the Republic of)
| | - Eun Sang Yu
- Division of Hematology-Oncology, Department of Internal Medicine, Korea University Guro Hospital, Seoul, Korea (the Republic of)
| | - Dae Sik Kim
- Division of Hematology-Oncology, Department of Internal Medicine, Korea University Guro Hospital, Seoul, Korea (the Republic of)
| | - Chul Won Choi
- Division of Hematology-Oncology, Department of Internal Medicine, Korea University Guro Hospital, Seoul, Korea (the Republic of)
| | - Ha Nui Kim
- Department of Laboratory Medicine, College of Medicine, Korea University, Seoul, Korea (the Republic of)
| | - Jeong Ah Kwon
- Department of Laboratory Medicine, College of Medicine, Korea University, Seoul, Korea (the Republic of)
| | - Soo-Young Yoon
- Department of Laboratory Medicine, College of Medicine, Korea University, Seoul, Korea (the Republic of)
| | - Jung Yoon
- Department of Laboratory Medicine, College of Medicine, Korea University, Seoul, Korea (the Republic of)
| |
Collapse
|
5
|
Breinholt MF, Schejbel L, Gang AO, Nielsen TH, Pedersen LM, Høgdall E, Nørgaard P. Next generation sequencing in routine diagnostics of mature non-Hodgkin's B-cell lymphomas. Eur J Haematol 2023; 111:583-591. [PMID: 37452559 DOI: 10.1111/ejh.14048] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 07/18/2023]
Abstract
INTRODUCTION Integration of molecular characterization of lymphomas in clinical diagnostics may improve subclassification and risk-stratification, and we implemented a next generation sequencing (NGS) analysis as part of routine diagnostic work-up of all mature B-cell non-Hodgkin's lymphoma (B-NHL). Here, we present data of mutational profiles with potential complementary diagnostic, prognostic, and predictive value detected in our consecutive non-selected cohort of B-NHL patients. METHODS NGS results from 298 patients with both newly diagnosed and relapsed/refractory disease were included as a single center study. NGS was performed as routine analysis together with standard diagnostic work-up using a custom-made amplicon PCR-based multiplex NGS panel covering all coding exons and consensus splice sites in 59 genes. RESULTS Mutations were detected in 94% of the 298 samples. Most lymphomas could be classified definitively, but 24 cases were classified as small B-cell lymphomas without defining characteristics. Of these, 50% (12/24 cases) could retrospectively be assigned a likely diagnostic subtype according to mutational findings. CONCLUSION Implementation of a 59 gene exome sequencing panel added diagnostic value to 50% of unclassified cases and provided in 94% of the cases possible biomarkers for disease monitoring as well as potential diagnostic, prognostic, and predictive markers for future studies.
Collapse
Affiliation(s)
| | - Lone Schejbel
- Department of Pathology, Herlev-Gentofte Hospital, Herlev, Denmark
| | - Anne Ortved Gang
- Department of Hematology, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Torsten Holm Nielsen
- Department of Hematology, Rigshospitalet, Copenhagen, Denmark
- Danish Medicines Agency, Copenhagen, Denmark
| | - Lars Møller Pedersen
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Department of Hematology, Zealand University Hospital, Roskilde, Denmark
| | - Estrid Høgdall
- Department of Pathology, Herlev-Gentofte Hospital, Herlev, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Peter Nørgaard
- Department of Pathology, Herlev-Gentofte Hospital, Herlev, Denmark
- Department of Pathology, Hvidovre Hospital, Hvidovre, Denmark
| |
Collapse
|
6
|
Hersby DS, Schejbel L, Breinholt MF, Høgdall E, Nørgaard P, Dencker D, Nielsen TH, Pedersen LM, Gang AO. Multi-site pre-therapeutic biopsies demonstrate genetic heterogeneity in patients with newly diagnosed diffuse large B-cell lymphoma. Leuk Lymphoma 2023; 64:1527-1535. [PMID: 37328933 DOI: 10.1080/10428194.2023.2220454] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/23/2023] [Accepted: 05/26/2023] [Indexed: 06/18/2023]
Abstract
Diffuse large B-cell lymphoma (DLBCL) is a heterogeneous disease, both regarding clinical presentation, response to treatment and outcome. Recently, subclassification of DLBCL based on mutational profile has been suggested, and next generation sequencing (NGS) analysis may be relevant as part of the diagnostic workflow. This will, however, often be based on analysis of one tumor biopsy. Here, we present a prospective study where multi-site sampling was performed prior to treatment in patients with newly diagnosed DLBCL. Two spatially different biopsies from 16 patients were analyzed using NGS with an in-house 59-gene lymphoma panel. In 8/16 (50%) patients, mutational differences were found between the two biopsy sites, including differences in TP53 mutational status. Our data indicate that a biopsy from the extra-nodal site may represent the most advanced clone, and an extra-nodal biopsy should be preferred for analysis, if safely accessible. This will help ensure a standardized stratification and treatment decision.
Collapse
Affiliation(s)
| | - Lone Schejbel
- Department of Pathology, Herlev Hospital, Copenhagen University Hospital, Herlev, Denmark
| | | | - Estrid Høgdall
- Department of Pathology, Herlev Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Peter Nørgaard
- Department of Pathology, Hvidovre Hospitalet, Hvidovre, Denmark
| | - Ditte Dencker
- Department of Radiology, Rigshospitalet, Copenhagen, Denmark
| | - Torsten Holm Nielsen
- Department of Hematology, Rigshospitalet, Copenhagen, Denmark
- Danish Medicines Agency, Copenhagen, Denmark
| | - Lars Møller Pedersen
- Department of Hematology, Zealand Hospital, Roskilde, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Anne Ortved Gang
- Department of Hematology, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
7
|
Hu W, Yuan L, Zhang X, Ni Y, Hong D, Wang Z, Li X, Ling Y, Zhang C, Deng W, Tian M, Ding R, Song C, Li J, Zhang X. Development and validation of an RNA sequencing panel for gene fusions in soft tissue sarcoma. Cancer Sci 2022; 113:1843-1854. [PMID: 35238118 PMCID: PMC9128172 DOI: 10.1111/cas.15317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 02/08/2022] [Accepted: 02/24/2022] [Indexed: 11/29/2022] Open
Abstract
Gene fusions are one of the most common genomic alterations in soft tissue sarcomas (STS), which contain more than 70 subtypes. In this study, a custom-designed RNA sequencing panel including 67 genes was developed and validated to identify gene fusions in STS. In total, 92 STS samples were analyzed using the RNA panel and 95.7% (88/92) successfully passed all the quality control parameters. Fusion transcripts were detected in 60.2% (53/88) of samples, including three novel fusions (MEG3-PLAG1, SH3BP1-NTRK1, and RPSAP52-HMGA2). The panel demonstrated excellent analytic accuracy, with 93.9% sensitivity and 100% specificity. The intra-assay, inter-assay, and personnel consistencies were all 100.0% in four samples and three replicates. In addition, different variants of ESWR1-FLI, COL1A1-PDGFB, NAB2-STAT6, and SS18-SSX were also identified in the corresponding subtypes of STS. In combination with histological and molecular diagnosis, 14.8% (13/88) patients finally changed preliminary histology-based classification. Collectively, this RNA panel developed in our study shows excellent performance on RNA from formalin-fixed, paraffin-embedded samples and can complement DNA-based assay, thereby facilitating precise diagnosis and novel fusion detection.
Collapse
Affiliation(s)
- Wanming Hu
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineDepartment of PathologySun Yat‐sen University Cancer CenterGuangzhouChina
| | - Li Yuan
- Department of PathologyGuangzhou Women and Children's Medical CenterGuangzhouChina
| | - Xinke Zhang
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineDepartment of PathologySun Yat‐sen University Cancer CenterGuangzhouChina
| | - Yang Ni
- State Key Laboratory of Translational Medicine and Innovative Drug DevelopmentJiangsu Simcere Diagnostics Co., LtdNanjingChina
- Department of MedicineNanjing Simcere Medical Laboratory Science Co., LtdNanjingChina
| | - Dongchun Hong
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineDepartment of Medical Melanoma and SarcomaSun Yat‐sen University Cancer CenterGuangzhouChina
| | - Zhicai Wang
- Department of General SurgeryJiangsu Cancer Hospital & Jiangsu Institute of Cancer Research &The Affiliated Cancer Hospital of Nanjing Medical UniversityNanjingChina
| | - Xiaomin Li
- State Key Laboratory of Translational Medicine and Innovative Drug DevelopmentJiangsu Simcere Diagnostics Co., LtdNanjingChina
| | - Yuan Ling
- State Key Laboratory of Translational Medicine and Innovative Drug DevelopmentJiangsu Simcere Diagnostics Co., LtdNanjingChina
| | - Chao Zhang
- State Key Laboratory of Translational Medicine and Innovative Drug DevelopmentJiangsu Simcere Diagnostics Co., LtdNanjingChina
| | - Wanglong Deng
- State Key Laboratory of Translational Medicine and Innovative Drug DevelopmentJiangsu Simcere Diagnostics Co., LtdNanjingChina
| | - Minqi Tian
- State Key Laboratory of Translational Medicine and Innovative Drug DevelopmentJiangsu Simcere Diagnostics Co., LtdNanjingChina
| | - Ran Ding
- State Key Laboratory of Translational Medicine and Innovative Drug DevelopmentJiangsu Simcere Diagnostics Co., LtdNanjingChina
| | - Chao Song
- State Key Laboratory of Translational Medicine and Innovative Drug DevelopmentJiangsu Simcere Diagnostics Co., LtdNanjingChina
- Department of MedicineNanjing Simcere Medical Laboratory Science Co., LtdNanjingChina
| | - Jianmin Li
- Department of OrthopedicsQilu Hospital of Shandong UniversityJinanChina
| | - Xing Zhang
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineDepartment of Medical Melanoma and SarcomaSun Yat‐sen University Cancer CenterGuangzhouChina
| |
Collapse
|
8
|
Vicente-Garcés C, Esperanza-Cebollada E, Montesdeoca S, Torrebadell M, Rives S, Dapena JL, Català A, Conde N, Camós M, Vega-García N. Technical Validation and Clinical Utility of an NGS Targeted Panel to Improve Molecular Characterization of Pediatric Acute Leukemia. Front Mol Biosci 2022; 9:854098. [PMID: 35463953 PMCID: PMC9021638 DOI: 10.3389/fmolb.2022.854098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 02/18/2022] [Indexed: 12/03/2022] Open
Abstract
Development of next-generation sequencing (NGS) has provided useful genetic information to redefine diagnostic, prognostic, and therapeutic strategies for the management of acute leukemia (AL). However, the application in the clinical setting is still challenging. Our aim was to validate the AmpliSeq™ for Illumina® Childhood Cancer Panel, a pediatric pan-cancer targeted NGS panel that includes the most common genes associated with childhood cancer, and assess its utility in the daily routine of AL diagnostics. In terms of sequencing metrics, the assay reached all the expected values. We obtained a mean read depth greater than 1000×. The panel demonstrated a high sensitivity for DNA (98.5% for variants with 5% variant allele frequency (VAF)) and RNA (94.4%), 100% of specificity and reproducibility for DNA and 89% of reproducibility for RNA. Regarding clinical utility, 49% of mutations and 97% of the fusions identified were demonstrated to have clinical impact. Forty-one percent of mutations refined diagnosis, while 49% of them were considered targetable. Regarding RNA, fusion genes were more clinically impactful in terms of refining diagnostic (97%). Overall, the panel found clinically relevant results in the 43% of patients tested in this cohort. To sum up, we validated a reliable and reproducible method to refine pediatric AL diagnosis, prognosis, and treatment, and demonstrated the feasibility of incorporating a targeted NGS panel into pediatric hematology practice.
Collapse
Affiliation(s)
- Clara Vicente-Garcés
- Hematology Laboratory, Hospital Sant Joan de Déu Barcelona, Esplugues de Llobregat, Barcelona, Spain
- Leukemia and Other Pediatric Hemopathies, Developmental Tumors Biology Group, Institut de Recerca Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Elena Esperanza-Cebollada
- Hematology Laboratory, Hospital Sant Joan de Déu Barcelona, Esplugues de Llobregat, Barcelona, Spain
- Leukemia and Other Pediatric Hemopathies, Developmental Tumors Biology Group, Institut de Recerca Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Sara Montesdeoca
- Hematology Laboratory, Hospital Sant Joan de Déu Barcelona, Esplugues de Llobregat, Barcelona, Spain
- Leukemia and Other Pediatric Hemopathies, Developmental Tumors Biology Group, Institut de Recerca Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Montserrat Torrebadell
- Hematology Laboratory, Hospital Sant Joan de Déu Barcelona, Esplugues de Llobregat, Barcelona, Spain
- Leukemia and Other Pediatric Hemopathies, Developmental Tumors Biology Group, Institut de Recerca Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Susana Rives
- Leukemia and Other Pediatric Hemopathies, Developmental Tumors Biology Group, Institut de Recerca Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Pediatric Hematology and Oncology Department, Hospital Sant Joan de Déu Barcelona, University of Barcelona, Barcelona, Spain
| | - José Luis Dapena
- Leukemia and Other Pediatric Hemopathies, Developmental Tumors Biology Group, Institut de Recerca Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
- Pediatric Hematology and Oncology Department, Hospital Sant Joan de Déu Barcelona, University of Barcelona, Barcelona, Spain
| | - Albert Català
- Leukemia and Other Pediatric Hemopathies, Developmental Tumors Biology Group, Institut de Recerca Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Pediatric Hematology and Oncology Department, Hospital Sant Joan de Déu Barcelona, University of Barcelona, Barcelona, Spain
| | - Nuria Conde
- Leukemia and Other Pediatric Hemopathies, Developmental Tumors Biology Group, Institut de Recerca Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
- Pediatric Hematology and Oncology Department, Hospital Sant Joan de Déu Barcelona, University of Barcelona, Barcelona, Spain
| | - Mireia Camós
- Hematology Laboratory, Hospital Sant Joan de Déu Barcelona, Esplugues de Llobregat, Barcelona, Spain
- Leukemia and Other Pediatric Hemopathies, Developmental Tumors Biology Group, Institut de Recerca Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Nerea Vega-García
- Hematology Laboratory, Hospital Sant Joan de Déu Barcelona, Esplugues de Llobregat, Barcelona, Spain
- Leukemia and Other Pediatric Hemopathies, Developmental Tumors Biology Group, Institut de Recerca Hospital Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
- *Correspondence: Nerea Vega-García,
| |
Collapse
|
9
|
Park J, Kim HS, Lee JM, Jung J, Kang D, Choi H, Lee GD, Son J, Park S, Cho BS, Kim HJ, Kim S, Lee JW, Chung NG, Cho B, Zhang H, Khazanov NA, Choi J, Jung JW, Kim Y, Kim M. Analytical and Potential Clinical Performance of Oncomine Myeloid Research Assay for Myeloid Neoplasms. Mol Diagn Ther 2021; 24:579-592. [PMID: 32676933 DOI: 10.1007/s40291-020-00484-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Next-generation sequencing (NGS) panels have recently been introduced to efficiently detect genetic variations in hematologic malignancies. OBJECTIVES Our aim was to evaluate the performance of the commercialized Oncomine™ myeloid research assay (OMA) for myeloid neoplasms. METHODS Certified reference materials and clinical research samples were used, including 60 genomic DNA and 56 RNA samples. NGS was performed using OMA, which enables the interrogation of 40 target genes, 29 gene fusions, and five expression target genes with five expression control genes by the Ion S5 XL Sequencer. The analyzed data were compared with clinical data using karyotyping, reverse transcription polymerase chain reaction (PCR), fluorescence in situ hybridization, Sanger sequencing, customized NGS panel, and fragment analysis. RESULTS All targets of reference materials were detected except three (two ASXL1 and one CEBPA) mutations, which we had not expected OMA to detect. In clinical search samples, OMA satisfactorily identified DNA variants, including 90 single nucleotide variants (SNVs), 48 small insertions and deletions (indels), and eight FLT3 internal tandem duplications (ITDs) (Kappa agreement 0.938). The variant allele frequencies of SNVs and indels measured by OMA correlated well with clinical data, whereas those of FLT3-ITDs were significantly lower than with fragment analysis (P = 0.008). Together, OMA showed strong ability to identify RNA gene fusions (Kappa agreement 0.961), except one RUNX1-MECOM. The MECOM gene was highly expressed in all five samples with MECOM-associated rearrangements, including inv(3), t(3;3), and t(3;21). CONCLUSION OMA revealed excellent analytical and potential clinical performance and could be a good replacement for conventional molecular tests.
Collapse
Affiliation(s)
- Joonhong Park
- Department of Laboratory Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul, 06591, Republic of Korea
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hoon Seok Kim
- Department of Laboratory Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul, 06591, Republic of Korea
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jong-Mi Lee
- Department of Laboratory Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul, 06591, Republic of Korea
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jin Jung
- Department of Laboratory Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul, 06591, Republic of Korea
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Dain Kang
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hayoung Choi
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Gun Dong Lee
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jungok Son
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Silvia Park
- Division of Acute Leukemia, Department of Hematology, Catholic Hematology Hospital, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Byung-Sik Cho
- Division of Acute Leukemia, Department of Hematology, Catholic Hematology Hospital, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hee-Je Kim
- Division of Acute Leukemia, Department of Hematology, Catholic Hematology Hospital, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Seongkoo Kim
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jae Wook Lee
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Nack-Gyun Chung
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Bin Cho
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hua Zhang
- Thermo Fisher Scientific, Waltham, MA, USA
| | | | - Jongpill Choi
- Thermo Fisher Scientific Solutions, Seoul, Republic of Korea
| | - Jae-Won Jung
- Thermo Fisher Scientific Solutions, Seoul, Republic of Korea
| | - Yonggoo Kim
- Department of Laboratory Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul, 06591, Republic of Korea.
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
| | - Myungshin Kim
- Department of Laboratory Medicine, The Catholic University of Korea, 222 Banpo-daero, Seocho-gu, Seoul, 06591, Republic of Korea.
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
| |
Collapse
|
10
|
Ferrone CK, Wong H, Semenuk L, Werunga B, Snetsinger B, Zhang X, Zhang G, Lui J, Richard-Carpentier G, Crocker S, Good D, Hay AE, Quest G, Carson N, Feilotter HE, Rauh MJ. Validation, Implementation, and Clinical Impact of the Oncomine Myeloid Targeted-Amplicon DNA and RNA Ion Semiconductor Sequencing Assay. J Mol Diagn 2021; 23:1292-1305. [PMID: 34365012 DOI: 10.1016/j.jmoldx.2021.07.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 05/04/2021] [Accepted: 07/07/2021] [Indexed: 12/17/2022] Open
Abstract
The identification of clinically significant genes recurrently mutated in myeloid malignancies necessitates expanding diagnostic testing with higher throughput, such as targeted next-generation sequencing. We present validation of the Thermo Fisher Oncomine Myeloid Next-Generation Sequencing Panel (OMP), targeting 40 genes and 29 fusion drivers recurrently mutated in myeloid malignancies. The study includes data from a sample exchange between two Canadian hospitals demonstrating high concordance for detection of DNA and RNA aberrations. Clinical validation demonstrates high accuracy, sensitivity, and specificity of the OMP, with a lower limit of detection of 5% for single-nucleotide variants and 10% for insertions/deletions. Prospective sequencing was performed for 187 samples from 168 unique patients presenting with suspected or confirmed myeloid malignancy and other hematological conditions to assess clinical impact of identifying variants. Of detected variants, 48% facilitated or clarified diagnoses, 29% affected prognoses, and 25% had the potential to influence clinical management. Of note, OMP was essential to identifying patients with premalignant clonal states likely contributing to cytopenias. We also found that the detection of even a single variant by the OMP assay, versus 0 variants, was predictive of overall survival, independent of age, sex, or diagnosis (P = 0.03). This study demonstrates that molecular profiling of myeloid malignancies with the OMP represents a promising strategy to advance molecular diagnostics.
Collapse
Affiliation(s)
- Christina K Ferrone
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - Henry Wong
- Molecular Genetics Laboratory, Kingston Health Sciences Centre, Kingston, Ontario, Canada
| | - Laura Semenuk
- Molecular Genetics Laboratory, Kingston Health Sciences Centre, Kingston, Ontario, Canada
| | - Barnaba Werunga
- Division of Genetics, Department of Lab Medicine and Pathology, Saint John Regional Hospital, Saint John, New Brunswick, Canada
| | - Brooke Snetsinger
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - Xiao Zhang
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - Grace Zhang
- Division of Hematology, Department of Medicine, Kingston Health Sciences Centre, Kingston, Ontario, Canada
| | - Janet Lui
- Division of Hematology, Department of Medicine, Kingston Health Sciences Centre, Kingston, Ontario, Canada
| | | | - Susan Crocker
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada; Cytogenetics Laboratory, Kingston Health Sciences Centre, Kingston, Ontario, Canada
| | - David Good
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - Annette E Hay
- Division of Hematology, Department of Medicine, Kingston Health Sciences Centre, Kingston, Ontario, Canada
| | - Graeme Quest
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - Nancy Carson
- Division of Genetics, Department of Lab Medicine and Pathology, Saint John Regional Hospital, Saint John, New Brunswick, Canada
| | - Harriet E Feilotter
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada; Molecular Genetics Laboratory, Kingston Health Sciences Centre, Kingston, Ontario, Canada
| | - Michael J Rauh
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada.
| |
Collapse
|
11
|
Rosenthal SH, Gerasimova A, Ma C, Li HR, Grupe A, Chong H, Acab A, Smolgovsky A, Owen R, Elzinga C, Chen R, Sugganth D, Freitas T, Graham J, Champion K, Bhattacharya A, Racke F, Lacbawan F. Analytical validation and performance characteristics of a 48-gene next-generation sequencing panel for detecting potentially actionable genomic alterations in myeloid neoplasms. PLoS One 2021; 16:e0243683. [PMID: 33909614 PMCID: PMC8081174 DOI: 10.1371/journal.pone.0243683] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 04/14/2021] [Indexed: 11/18/2022] Open
Abstract
Identification of genomic mutations by molecular testing plays an important role in diagnosis, prognosis, and treatment of myeloid neoplasms. Next-generation sequencing (NGS) is an efficient method for simultaneous detection of clinically significant genomic mutations with high sensitivity. Various NGS based in-house developed and commercial myeloid neoplasm panels have been integrated into routine clinical practice. However, some genes frequently mutated in myeloid malignancies are particularly difficult to sequence with NGS panels (e.g., CEBPA, CARL, and FLT3). We report development and validation of a 48-gene NGS panel that includes genes that are technically challenging for molecular profiling of myeloid neoplasms including acute myeloid leukemia (AML), myelodysplastic syndrome (MDS), and myeloproliferative neoplasms (MPN). Target regions were captured by hybridization with complementary biotinylated DNA baits, and NGS was performed on an Illumina NextSeq500 instrument. A bioinformatics pipeline that was developed in-house was used to detect single nucleotide variations (SNVs), insertions/deletions (indels), and FLT3 internal tandem duplications (FLT3-ITD). An analytical validation study was performed on 184 unique specimens for variants with allele frequencies ≥5%. Variants identified by the 48-gene panel were compared to those identified by a 35-gene hematologic neoplasms panel using an additional 137 unique specimens. The developed assay was applied to a large cohort (n = 2,053) of patients with suspected myeloid neoplasms. Analytical validation yielded 99.6% sensitivity (95% CI: 98.9-99.9%) and 100% specificity (95% CI: 100%). Concordance of variants detected by the 2 tested panels was 100%. Among patients with suspected myeloid neoplasms (n = 2,053), 54.5% patients harbored at least one clinically significant mutation: 77% in AML patients, 48% in MDS, and 45% in MPN. Together, these findings demonstrate that the assay can identify mutations associated with diagnosis, prognosis, and treatment options of myeloid neoplasms even in technically challenging genes.
Collapse
Affiliation(s)
- Sun Hee Rosenthal
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Anna Gerasimova
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Charles Ma
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Hai-Rong Li
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Andrew Grupe
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Hansook Chong
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Allan Acab
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Alla Smolgovsky
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Renius Owen
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Christopher Elzinga
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Rebecca Chen
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Daniel Sugganth
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Tracey Freitas
- Department of Molecular Oncology, Med Fusion, Lewisville, TX, United States of America
| | - Jennifer Graham
- Department of Molecular Oncology, Med Fusion, Lewisville, TX, United States of America
| | - Kristen Champion
- Department of Molecular Oncology, Med Fusion, Lewisville, TX, United States of America
| | - Anindya Bhattacharya
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Frederick Racke
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| | - Felicitas Lacbawan
- Department of Advanced Diagnostics, Quest Diagnostics, San Juan Capistrano, CA, United States of America
| |
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
Impact of Integrated Genetic Information on Diagnosis and Prognostication for Myeloproliferative Neoplasms in the Next-Generation Sequencing Era. J Clin Med 2021; 10:jcm10051033. [PMID: 33802367 PMCID: PMC7959293 DOI: 10.3390/jcm10051033] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/15/2021] [Accepted: 02/18/2021] [Indexed: 12/19/2022] Open
Abstract
Since next-generation sequencing has been widely used in clinical laboratories, the diagnosis and risk stratification of hematologic malignancies are greatly dependent on genetic aberrations. In this study, we analyzed the genomic landscapes of 200 patients with myeloproliferative neoplasms (MPNs) and evaluated the impact of the genomic landscape on diagnosis and risk stratification. Mutations in JAK2, CALR and MPL were detected in 76.4% of MPNs. The proportion of patients with clonal genetic markers increased up to 86.4% when all detectable genetic aberrations were included. Significant co-occurring genetic aberrations potentially associated with phenotype and/or disease progression, including those in JAK2/SF3B1 and TP53/del(13q), del(5q), −7/del(7q) and complex karyotypes, were detected. We also identified genetic aberrations associated with patient outcomes: TP53 and −7/del(7q) were associated with an inferior chance of survival, RUNX1, TP53 and IDH1/2 were associated with leukemic transformation and SF3B1, IDH1/2, ASXL1 and del(20q) were associated with fibrotic progression. We compared risk stratification systems and found that mutation-enhanced prognostic scoring systems could identify lower risk polycythemia vera, essential thrombocythemia and higher risk primary myelofibrosis. Furthermore, the new risk stratification systems showed a better predictive capacity for patient outcome. These results collectively indicate that integrated genetic information can enhance diagnosis and prognostication in patients with myeloproliferative neoplasms.
Collapse
|
14
|
Jiang L, Pallavajjala A, Huang J, Haley L, Morsberger L, Stinnett V, Hardy M, Park R, Ament C, Finch A, Shane A, Parish R, Nozari A, Long P, Adams E, Smith K, Parimi V, Dougaparsad S, Long L, Gocke CD, Zou YS. Clinical Utility of Targeted Next-Generation Sequencing Assay to Detect Copy Number Variants Associated with Myelodysplastic Syndrome in Myeloid Malignancies. J Mol Diagn 2021; 23:467-483. [PMID: 33577993 DOI: 10.1016/j.jmoldx.2021.01.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 12/17/2020] [Accepted: 01/05/2021] [Indexed: 12/11/2022] Open
Abstract
Copy number variants (CNVs) and gene mutations are important for diagnosis and treatment of myeloid malignancies. In a routine clinical setting, somatic gene mutations are detected by targeted next-generation sequencing (NGS) assay, but CNVs are commonly detected by conventional chromosome analysis and fluorescence in situ hybridization (FISH). The aim of this proof-of-principle study was to investigate the feasibility of using targeted NGS to simultaneously detect both somatic mutations and CNVs. Herein, we sequenced 406 consecutive patients with myeloid malignancies by targeted NGS and performed a head-to-head comparison with the results from a myelodysplastic syndrome (MDS) FISH and conventional chromosome analysis to detect CNVs. Among 91 patients with abnormal MDS FISH results, the targeted NGS revealed all 120 CNVs detected by MDS FISH (including -5/5q-, -7/7q-, +8, and 20q-) and 193 extra CNVs detected by conventional chromosome analysis. The targeted NGS achieved 100% concordance with the MDS FISH. The lower limit of detection of MDS CNVs by the targeted NGS was generally 5% variant allele fraction for DNA, based on the lowest percentages of abnormal cells detected by MDS FISH in this study. This proof-of-principle study demonstrated that the targeted NGS assay can simultaneously detect both MDS CNVs and somatic mutations, which can provide a more comprehensive genetic profiling for patients with myeloid malignancies using a single assay in a clinical setting.
Collapse
Affiliation(s)
- Liqun Jiang
- Johns Hopkins Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Aparna Pallavajjala
- Johns Hopkins Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jialing Huang
- Johns Hopkins Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Pathology, Thomas Jefferson University, Philadelphia, Pennsylvania; BioDiscovery Inc., El Segundo, California
| | - Lisa Haley
- Johns Hopkins Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Laura Morsberger
- Clinical Cytogenetics Laboratory, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Victoria Stinnett
- Clinical Cytogenetics Laboratory, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Melanie Hardy
- Clinical Cytogenetics Laboratory, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Rebecca Park
- Clinical Cytogenetics Laboratory, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Candice Ament
- Clinical Cytogenetics Laboratory, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Alexandra Finch
- Clinical Cytogenetics Laboratory, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Alison Shane
- Clinical Cytogenetics Laboratory, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Rebecca Parish
- Clinical Cytogenetics Laboratory, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Azin Nozari
- Clinical Cytogenetics Laboratory, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Patty Long
- Clinical Cytogenetics Laboratory, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Emily Adams
- Johns Hopkins Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kirstin Smith
- Johns Hopkins Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Vamsi Parimi
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Lori Long
- MacroGenics Inc., Rockville, Maryland
| | - Christopher D Gocke
- Johns Hopkins Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ying S Zou
- Johns Hopkins Genomics, Johns Hopkins University School of Medicine, Baltimore, Maryland; Clinical Cytogenetics Laboratory, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| |
Collapse
|
15
|
Establishment of a High-risk MDS/AML Cell Line YCU-AML1 and its Xenograft Model Harboring t(3;3) and Monosomy 7. Hemasphere 2020; 4:e469. [PMID: 33163905 PMCID: PMC7643909 DOI: 10.1097/hs9.0000000000000469] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 07/20/2020] [Indexed: 11/27/2022] Open
Abstract
Acute myeloid leukemia (AML) or myelodysplastic syndromes (MDS) with both inv(3)(q21q26.2)/t(3;3)(q21;q26.2) and monosomy 7 defines an extremely aggressive myeloid cancer whose molecular pathogenesis and optimal therapeutic strategy still remain unclear. We established a new MDS/AML cell line, YCU-AML1, and its patient-derived xenograft (PDX) model from a high-risk MDS patient who later transformed into AML harboring both t(3;3)(q21;q26.2) and monosomy 7. YCU-AML1 cells propagated in co-culture system with stromal cells in granulocyte macrophage colony-stimulating factor (GM-CSF)-dependent manner. CD34+ bone marrow cells derived from our PDX model showed high EVI1 and low GATA2 expression. Moreover, mutational profile of our MDS/AML model was consistent with recently published mutational spectrum of myeloid malignancies with inv(3)/t(3;3). These data suggest that YCU-AML1 cells and its MDS/AML model strongly mimics a high-risk human myeloid cancer with inv(3)(q21q26.2)/t(3;3)(q21;q26.2) and monosomy 7 in terms of both clinical phenotype and molecular basis. We believe our model can be used as a feasible tool to further explore molecular pathogenesis and novel treatment strategy of high-risk MDS/AML with t(3;3)(q21;q26.2) and monosomy 7.
Collapse
|
16
|
Bond DR, Uddipto K, Enjeti AK, Lee HJ. Single-cell epigenomics in cancer: charting a course to clinical impact. Epigenomics 2020; 12:1139-1151. [PMID: 32790506 DOI: 10.2217/epi-2020-0046] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Cancer is a disease of global epigenetic dysregulation. Mutations in epigenetic regulators are common events in multiple cancer types and epigenetic therapies are emerging as a treatment option in several malignancies. A major challenge for the clinical management of cancer is the heterogeneous nature of this disease. Cancers are composed of numerous cell types and evolve over time. This heterogeneity confounds decisions regarding treatment and promotes disease relapse. The emergence of single-cell epigenomic technologies has introduced the exciting possibility of linking genetic and transcriptional heterogeneity in the context of cancer biology. The next challenge is to leverage these tools for improved patient outcomes. Here we consider how single-cell epigenomic technologies may address the current challenges faced by cancer clinicians.
Collapse
Affiliation(s)
- Danielle R Bond
- School of Biomedical Sciences & Pharmacy, Faculty of Health & Medicine, University of Newcastle, Callaghan 2308, New South Wales, Australia
| | - Kumar Uddipto
- School of Biomedical Sciences & Pharmacy, Faculty of Health & Medicine, University of Newcastle, Callaghan 2308, New South Wales, Australia
| | - Anoop K Enjeti
- Department of Haematology, Calvary Mater Newcastle, Waratah 2298, New South Wales, Australia.,School of Medicine & Public Health, Faculty of Health & Medicine, University of Newcastle, Callaghan 2308, New South Wales, Australia.,NSW Health Pathology - Hunter, New Lambton Heights 2305, New South Wales, Australia
| | - Heather J Lee
- School of Biomedical Sciences & Pharmacy, Faculty of Health & Medicine, University of Newcastle, Callaghan 2308, New South Wales, Australia
| |
Collapse
|
17
|
Zhao J, Yang L. Broad-spectrum next-generation sequencing-based diagnosis of a case of Nager syndrome. J Clin Lab Anal 2020; 34:e23426. [PMID: 32537850 PMCID: PMC7521291 DOI: 10.1002/jcla.23426] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Nager syndrome is a rare genetic syndrome characterized by craniofacial and preaxial limb anomalies. Haploinsufficiency of the SF3B4 gene has been identified as a significant reason for Nager syndrome. Treacher Collins syndrome (TCS) has similar facial features; however, the TCOF1, POLR1D, and POLR1C genes have been reported as the critical disease-causing genes. Similar phenotypes make it easy to misdiagnose. CASE REPORT In this report, we have presented a case of one newborn with acrofacial dysostosis, who was first diagnosed with TCS. Expanded next-generation sequencing eventually detected a (c.1A>G) heterozygous mutation in the SF3B4 gene at chr1:149899651 that was confirmed by Sanger sequencing. Combined with his preaxial limb anomalies discovered after his death, a diagnosis of Nager syndrome was made. CONCLUSIONS This report presents one patient with Nager syndrome who was initially misdiagnosed with TCS. Correct genetic testing will be beneficial to future prenatal diagnosis.
Collapse
Affiliation(s)
- Jue Zhao
- Department of Obstetrics, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Liwei Yang
- Department of Obstetrics, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
| |
Collapse
|