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Maximizing Small Biopsy Patient Samples: Unified RNA-Seq Platform Assessment of over 120,000 Patient Biopsies. J Pers Med 2022; 13:jpm13010024. [PMID: 36675685 PMCID: PMC9866839 DOI: 10.3390/jpm13010024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/06/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
Despite its wide-ranging benefits, whole-transcriptome or RNA exome profiling is challenging to implement in a clinical diagnostic setting. The Unified Assay is a comprehensive workflow wherein exome-enriched RNA-sequencing (RNA-Seq) assays are performed on clinical samples and analyzed by a series of advanced machine learning-based classifiers. Gene expression signatures and rare and/or novel genomic events, including fusions, mitochondrial variants, and loss of heterozygosity were assessed using RNA-Seq data generated from 120,313 clinical samples across three clinical indications (thyroid cancer, lung cancer, and interstitial lung disease). Since its implementation, the data derived from the Unified Assay have allowed significantly more patients to avoid unnecessary diagnostic surgery and have played an important role in guiding follow-up decisions regarding treatment. Collectively, data from the Unified Assay show the utility of RNA-Seq and RNA expression signatures in the clinical laboratory, and their importance to the future of precision medicine.
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Nagy Z, Jeselsohn R. ESR1 fusions and therapeutic resistance in metastatic breast cancer. Front Oncol 2022; 12:1037531. [PMID: 36686845 PMCID: PMC9848494 DOI: 10.3389/fonc.2022.1037531] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 11/22/2022] [Indexed: 01/06/2023] Open
Abstract
Breast cancer is the most frequent female malignant tumor, and the leading cause of cancer death in women worldwide. The most common subtype of breast cancer is hormone receptor positive that expresses the estrogen receptor (ER). Targeting ER with endocrine therapy (ET) is the current standard of care for ER positive (ER+) breast cancer, reducing mortality by up to 40% in early- stage disease. However, resistance to ET represents a major clinical challenge for ER+ breast cancer patients leading to disease recurrence or progression of metastatic disease. Salient drivers of ET resistance are missense mutations in the ER gene (ESR1) leading to constitutive transcriptional activity and reduced ET sensitivity. These mutations are particularly prominent and deleterious in metastatic breast cancer (MBC). In addition to activating ESR1 point mutations, emerging evidence imposes that chromosomal translocation involving the ESR1 gene can also drive ET resistance through the formation of chimeric transcription factors with constitutive transcriptional activity. Although these ESR1 gene fusions are relatively rare, they are enriched in ET resistant metastatic disease. This review discusses the characteristics of ER fusion proteins and their association with clinical outcomes in more aggressive and metastatic breast cancer. The structure and classification of ER fusion proteins based on function and clinical significance are also addressed. Finally, this review summarizes the metastatic phenotypes exhibited by the ER fusion proteins and their role in intrinsic ET resistance.
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Affiliation(s)
- Zsuzsanna Nagy
- Center for Functional Cancer Epigenetics, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, United States
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
- Department of Medicine, Harvard Medical School, Boston, MA, United States
- *Correspondence: Rinath Jeselsohn, ; Zsuzsanna Nagy,
| | - Rinath Jeselsohn
- Center for Functional Cancer Epigenetics, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, United States
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
- Department of Medicine, Harvard Medical School, Boston, MA, United States
- Susan F. Smith Center for Women’s Cancers, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, United States
- *Correspondence: Rinath Jeselsohn, ; Zsuzsanna Nagy,
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Desmeules P, Boudreau DK, Bastien N, Boulanger MC, Bossé Y, Joubert P, Couture C. Performance of an RNA-based Next-Generation Sequencing Assay for Combined Detection of Clinically Actionable Fusions and Hotspot Mutations in Non-Small Cell Lung Cancer. JTO Clin Res Rep 2022; 3:100276. [PMID: 35252895 PMCID: PMC8888203 DOI: 10.1016/j.jtocrr.2022.100276] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/23/2021] [Accepted: 01/04/2022] [Indexed: 12/02/2022] Open
Abstract
Introduction With its expanding list of approved and emerging therapeutic indications, NSCLC is the exemplar tumor type requiring upfront assessment of several biomarkers to guide clinical management. Next-generation sequencing allows identification of different types of molecular alterations, each with specific analytical challenges. Library preparation using parallel DNA and RNA workflows can overcome most of them, but it increases complexity of laboratory operations, turnaround time, and costs. We describe the performance characteristics of a 15-gene RNA panel on the basis of anchored multiplex polymerase chain reaction for combined detection of clinically relevant oncogenic fusion transcripts and hotspot small variants. Methods Formalin-fixed, paraffin-embedded NSCLC clinical samples (N = 58) were used along cell lines and commercial controls to validate the assay’s analytical performance, followed by an exploratory prospective cohort (N = 87). Results The raw assay sensitivity for hotspot mutations and fusions was 83% and 93%, respectively, reaching 100% after filtering for key assay metrics. Those include quantity and quality of input of nucleic acid and sequencing metric from primers on housekeeping genes included in the assay. In the prospective cohort, driver alterations were identified in most cases (≥58%). Conclusions This ultrafocused RNA–next-generation sequencing assay offers an advantageous option with single unified workflow for simultaneous detection of clinically relevant hotspot mutations and fusions in NSCLC, focusing on actionable gene targets.
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Affiliation(s)
- Patrice Desmeules
- Service of Anatomic Pathology and Cytology, Institut Universitaire de Cardiologie et de Pneumologie de Québec—Université Laval, Québec City, Québec, Canada
- Research Center, Institut Universitaire de Cardiologie et de Pneumologie de Québec—Université Laval, Québec City, Québec, Canada
- Corresponding author. Address for correspondence: Patrice Desmeules, MD, MSc, Service of Anatomic Pathology and Cytology, Institut Universitaire de Cardiologie et de Pneumologie de Québec—Université Laval, Quebec City, QC G1V 4G5, Canada.
| | - Dominique K. Boudreau
- Research Center, Institut Universitaire de Cardiologie et de Pneumologie de Québec—Université Laval, Québec City, Québec, Canada
| | - Nathalie Bastien
- Service of Anatomic Pathology and Cytology, Institut Universitaire de Cardiologie et de Pneumologie de Québec—Université Laval, Québec City, Québec, Canada
- Research Center, Institut Universitaire de Cardiologie et de Pneumologie de Québec—Université Laval, Québec City, Québec, Canada
| | - Marie-Chloé Boulanger
- Research Center, Institut Universitaire de Cardiologie et de Pneumologie de Québec—Université Laval, Québec City, Québec, Canada
| | - Yohan Bossé
- Research Center, Institut Universitaire de Cardiologie et de Pneumologie de Québec—Université Laval, Québec City, Québec, Canada
| | - Philippe Joubert
- Service of Anatomic Pathology and Cytology, Institut Universitaire de Cardiologie et de Pneumologie de Québec—Université Laval, Québec City, Québec, Canada
- Research Center, Institut Universitaire de Cardiologie et de Pneumologie de Québec—Université Laval, Québec City, Québec, Canada
| | - Christian Couture
- Service of Anatomic Pathology and Cytology, Institut Universitaire de Cardiologie et de Pneumologie de Québec—Université Laval, Québec City, Québec, Canada
- Research Center, Institut Universitaire de Cardiologie et de Pneumologie de Québec—Université Laval, Québec City, Québec, Canada
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Shastry A, Aravind S, Sunil M, Ramesh K, Ashley B, T. N, Ramprasad VL, Gupta R, Seshagiri S, Nongthomba U, Phalke S. Matrilineal analysis of mutations in the DMD gene in a multigenerational South Indian cohort using DMD gene panel sequencing. Mol Genet Genomic Med 2021; 9:e1633. [PMID: 33960727 PMCID: PMC8172192 DOI: 10.1002/mgg3.1633] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 01/28/2021] [Accepted: 02/09/2021] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Duchenne muscular dystrophy (DMD) is an X-linked recessive neuromuscular disorder characterised by progressive irreversible muscle weakness, primarily of the skeletal and the cardiac muscles. DMD is characterised by mutations in the dystrophin gene, resulting in the absence or sparse quantities of dystrophin protein. A precise and timely molecular detection of DMD mutations encourages interventions such as carrier genetic counselling and in undertaking therapeutic measures for the DMD patients. RESULTS In this study, we developed a 2.1 Mb custom DMD gene panel that spans the entire DMD gene, including the exons and introns. The panel also includes the probes against 80 additional genes known to be mutated in other muscular dystrophies. This custom DMD gene panel was used to identify single nucleotide variants (SNVs) and large deletions with precise breakpoints in 77 samples that included 24 DMD patients and their matrilineage across four generations. We used this panel to evaluate the inheritance pattern of DMD mutations in maternal subjects representing 24 DMD patients. CONCLUSION Here we report our observations on the inheritance pattern of DMD gene mutations in matrilineage samples across four generations. Additionally, our data suggest that the DMD gene panel designed by us can be routinely used as a single genetic test to identify all DMD gene variants in DMD patients and the carrier mothers.
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Affiliation(s)
- Arun Shastry
- Dystrophy Annihilation Research Trust (DART)BangaloreIndia
| | - Sankaramoorthy Aravind
- Dystrophy Annihilation Research Trust (DART)BangaloreIndia
- Indian Institute of Science (IISc)BangaloreIndia
| | | | - Keerthi Ramesh
- Dystrophy Annihilation Research Trust (DART)BangaloreIndia
| | - Berty Ashley
- Dystrophy Annihilation Research Trust (DART)BangaloreIndia
| | | | | | | | | | | | - Sameer Phalke
- MedGenome LabsBangaloreIndia
- SciGenom Labs Pvt LtdCochinIndia
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Bruno R, Fontanini G. Next Generation Sequencing for Gene Fusion Analysis in Lung Cancer: A Literature Review. Diagnostics (Basel) 2020; 10:E521. [PMID: 32726941 PMCID: PMC7460167 DOI: 10.3390/diagnostics10080521] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/16/2020] [Accepted: 07/18/2020] [Indexed: 02/07/2023] Open
Abstract
Gene fusions have a pivotal role in non-small cell lung cancer (NSCLC) precision medicine. Several techniques can be used, from fluorescence in situ hybridization and immunohistochemistry to next generation sequencing (NGS). Although several NGS panels are available, gene fusion testing presents more technical challenges than other variants. This is a PubMed-based narrative review aiming to summarize NGS approaches for gene fusion analysis and their performance on NSCLC clinical samples. The analysis can be performed at DNA or RNA levels, using different target enrichment (hybrid-capture or amplicon-based) and sequencing chemistries, with both custom and commercially available panels. DNA sequencing evaluates different alteration types simultaneously, but large introns and repetitive sequences can impact on the performance and it does not discriminate between expressed and unexpressed gene fusions. RNA-based targeted approach analyses and quantifies directly fusion transcripts and is more accurate than DNA panels on tumor tissue, but it can be limited by RNA quality and quantity. On liquid biopsy, satisfying data have been published on circulating tumor DNA hybrid-capture panels. There is not a perfect method for gene fusion analysis, but NGS approaches, though still needing a complete standardization and optimization, present several advantages for the clinical practice.
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Affiliation(s)
- Rossella Bruno
- Unit of Pathological Anatomy, University Hospital of Pisa, Via Roma 67, 56126 Pisa, Italy;
| | - Gabriella Fontanini
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, Via Savi 10, 56126 Pisa, Italy
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