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Fernandez SV, Tan YF, Rao S, Fittipaldi P, Sheriff F, Borghaei H, Dotan E, Winn JS, Edelman MJ, Treat J, Judd J, Alpaugh RK, Wang YL, Yu JQ, Wasik M, Baldwin DA. Validation of a Molecular Diagnostic Test for Circulating Tumor DNA by Next-Gen Sequencing. Int J Mol Sci 2023; 24:15779. [PMID: 37958763 PMCID: PMC10648112 DOI: 10.3390/ijms242115779] [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: 10/09/2023] [Revised: 10/26/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023] Open
Abstract
A modified version of the PGDx elioTM Plasma Resolve assay was validated as a laboratory-developed test (LDT) for clinical use in the Molecular Diagnostics Laboratory at Fox Chase Cancer Center. The test detects single nucleotide variants (SNVs) and small insertions and deletions (indels) in 33 target genes using fragmented genomic DNA extracted from plasma. The analytical performance of this assay was assessed with reference standard DNA and 29 samples from cancer patients and detected 66 SNVs and 23 indels. Using 50 ng of input DNA, the sensitivity was 95.5% to detect SNVs at 0.5% allele frequency, and the specificity was 92.3%. The sensitivity to detect indels at 1% allele frequency was 70.4%. A cutoff of 0.25% variant allele frequency (VAF) was set up for diagnostic reporting. An inter-laboratory study of concordance with an orthologous test resulted in a positive percent agreement (PPA) of 91.7%.
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Affiliation(s)
- Sandra V. Fernandez
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; (Y.F.T.); (S.R.); (Y.L.W.); (M.W.)
| | - Yin Fei Tan
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; (Y.F.T.); (S.R.); (Y.L.W.); (M.W.)
| | - Shilpa Rao
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; (Y.F.T.); (S.R.); (Y.L.W.); (M.W.)
| | - Patricia Fittipaldi
- Protocol Support Laboratory, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; (P.F.); (R.K.A.)
| | - Fathima Sheriff
- Office of Clinical Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA;
| | - Hossein Borghaei
- Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; (H.B.); (E.D.); (J.S.W.); (M.J.E.); (J.T.); (J.J.)
| | - Efrat Dotan
- Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; (H.B.); (E.D.); (J.S.W.); (M.J.E.); (J.T.); (J.J.)
| | - Jennifer S. Winn
- Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; (H.B.); (E.D.); (J.S.W.); (M.J.E.); (J.T.); (J.J.)
| | - Martin J. Edelman
- Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; (H.B.); (E.D.); (J.S.W.); (M.J.E.); (J.T.); (J.J.)
| | - Joseph Treat
- Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; (H.B.); (E.D.); (J.S.W.); (M.J.E.); (J.T.); (J.J.)
| | - Julia Judd
- Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; (H.B.); (E.D.); (J.S.W.); (M.J.E.); (J.T.); (J.J.)
| | - R. Katherine Alpaugh
- Protocol Support Laboratory, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; (P.F.); (R.K.A.)
| | - Y. Lynn Wang
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; (Y.F.T.); (S.R.); (Y.L.W.); (M.W.)
| | - Jian Q. Yu
- Department of Radiology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA;
| | - Mariusz Wasik
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; (Y.F.T.); (S.R.); (Y.L.W.); (M.W.)
| | - Don A. Baldwin
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA 19111, USA; (Y.F.T.); (S.R.); (Y.L.W.); (M.W.)
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Mondelo-Macía P, Lago-Lestón RM, Rodríguez-Casanova A, Abalo A, Díaz-Lagares Á, García-González J, León-Mateos L, Díaz-Peña R, Muinelo-Romay L. Rapid Idylla mutational testing to detect EGFR mutations in plasma samples and to monitor therapy in advanced non-small cell lung cancer patients. Pathology 2023; 55:698-703. [PMID: 37037720 DOI: 10.1016/j.pathol.2023.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 12/09/2022] [Accepted: 01/06/2023] [Indexed: 03/17/2023]
Affiliation(s)
- Patricia Mondelo-Macía
- Liquid Biopsy Analysis Unit, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain; Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain; Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
| | - Ramón Manuel Lago-Lestón
- Liquid Biopsy Analysis Unit, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain
| | - Aitor Rodríguez-Casanova
- Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain; Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain; Epigenomics Unit, Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain; Roche-CHUS Joint Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), 15706 Santiago de Compostela, Spain
| | - Alicia Abalo
- Liquid Biopsy Analysis Unit, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain
| | - Ángel Díaz-Lagares
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain; Epigenomics Unit, Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Santiago de Compostela, Spain
| | - Jorge García-González
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Santiago de Compostela, Spain; Department of Medical Oncology, Complexo Hospitalario Universitario de Santiago de Compostela (SERGAS), Santiago de Compostela, Spain; Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain
| | - Luis León-Mateos
- Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain; Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Santiago de Compostela, Spain; Department of Medical Oncology, Complexo Hospitalario Universitario de Santiago de Compostela (SERGAS), Santiago de Compostela, Spain; Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain
| | - Roberto Díaz-Peña
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain; Fundación Pública Galega de Medicina Xenómica, SERGAS; Grupo de Medicina Xenomica-USC, Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain.
| | - Laura Muinelo-Romay
- Liquid Biopsy Analysis Unit, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain; Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Santiago de Compostela, Spain.
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Qiu T, Zhi X, Ren S. Recent advance of next-generation sequencing in patients with lung cancer. Expert Rev Mol Diagn 2023; 23:959-970. [PMID: 37750512 DOI: 10.1080/14737159.2023.2260755] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 09/15/2023] [Indexed: 09/27/2023]
Abstract
INTRODUCTION Precision medicine based on the driver genes mutation status is the current systemic therapeutic paradigm in patients with lung cancer. Next-generation sequencing (NGS) has emerged as a powerful platform for molecular diagnosis by virtue of high-throughput and massively parallel sequencing. Liquid biopsy also enabled the dynamic monitoring and comprehensive profiling of lung cancer in a noninvasive manner. However, challenges remain in the field of technology and clinical applications, especially in the era of immunotherapy. AREAS COVERED Here, we update the role of NGS in the context of lung cancer screening, molecular diagnosis, predictive and prognostic biomarkers, and guiding personalized treatment. EXPERT OPINION The NGS application for actable genomic alternation has greatly changed the therapeutic landscape in patients with lung cancer including perioperative setting and advanced stage. Meanwhile, emerging evidence has shown the potential of other applications such as early screening and detection, and MRD. However, challenges remain such as the lack of standardized protocols across different platforms and bioinformatics analysis pipelines, and the complexity of interpreting and leveraging numerous genomic mutation messages for therapy selection. Future research is needed to overcome these challenges and expand the applications of NGS to other aspects such as immunotherapy.
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Affiliation(s)
- Tianyu Qiu
- Department of Medical Oncology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xinxin Zhi
- Department of Medical Oncology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Shengxiang Ren
- Department of Medical Oncology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
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Zulato E, Del Bianco P, Nardo G, Attili I, Pavan A, Boscolo Bragadin A, Marra L, Pasello G, Fassan M, Calabrese F, Guarneri V, Conte PF, Indraccolo S, Bonanno L. Longitudinal liquid biopsy anticipates hyperprogression and early death in advanced non-small cell lung cancer patients treated with immune checkpoint inhibitors. Br J Cancer 2022; 127:2034-2042. [PMID: 36175621 PMCID: PMC9681746 DOI: 10.1038/s41416-022-01978-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 08/24/2022] [Accepted: 08/31/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Immune checkpoint inhibitors (ICIs) have revolutionised treatment of advanced non-small cell lung cancer (aNSCLC), but a proportion of patients had no clinical benefit and even experienced detrimental effects. This study aims to characterise patients experiencing hyperprogression (HPD) and early death (ED) by longitudinal liquid biopsy. METHODS aNSCLC receiving ICIs were prospectively enrolled. Plasma was collected at baseline (T1) and after 3/4 weeks of treatment, according to the treatment schedule (T2). Cell-free DNA (cfDNA) was quantified and analysed by NGS. cfDNA quantification and variant allele fraction (VAF) of tumour-associated genetic alterations were evaluated for their potential impact on outcome. The genetic alteration with the highest VAF (maxVAF) at baseline was considered as a reference. RESULTS From March 2017 to August 2019, 171 patients were enrolled. Five cases matched criteria for HPD and 31 ED were recorded; one overlapped. Quantification of cfDNA at T2 and its absolute and relative variation (T2-T1) were significantly associated with the risk of ED (P = 0.012, P = 0.005, P = 0.009). MaxVAF relative change (T2-T1/T1) was significantly associated with the risk of HPD (P = 0.02). After identifying optimal cut-off values, a two-step risk assessment model was proposed. DISCUSSION Liquid biopsy performed early during treatment has the potential to identify patients at high risk of ED and HPD.
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Affiliation(s)
- Elisabetta Zulato
- grid.419546.b0000 0004 1808 1697Basic and Translational Oncology Unit, Istituto Oncologico Veneto IOV IRCCS, Padova, Italy
| | - Paola Del Bianco
- grid.419546.b0000 0004 1808 1697Clinical Research Unit, Istituto Oncologico Veneto IOV IRCCS, Padova, Italy
| | - Giorgia Nardo
- grid.419546.b0000 0004 1808 1697Basic and Translational Oncology Unit, Istituto Oncologico Veneto IOV IRCCS, Padova, Italy
| | - Ilaria Attili
- grid.5608.b0000 0004 1757 3470Department of Surgery, Oncology and Gastroeneterology, Università degli Studi di Padova, Padova, Italy
| | - Alberto Pavan
- grid.5608.b0000 0004 1757 3470Department of Surgery, Oncology and Gastroeneterology, Università degli Studi di Padova, Padova, Italy
| | - Andrea Boscolo Bragadin
- grid.419546.b0000 0004 1808 1697Immunology and Molecular Oncology Diagnostics Unit, Istituto Oncologico Veneto IOV IRCCS, Padova, Italy
| | - Ludovica Marra
- grid.419546.b0000 0004 1808 1697Immunology and Molecular Oncology Diagnostics Unit, Istituto Oncologico Veneto IOV IRCCS, Padova, Italy
| | - Giulia Pasello
- grid.5608.b0000 0004 1757 3470Department of Surgery, Oncology and Gastroeneterology, Università degli Studi di Padova, Padova, Italy ,grid.419546.b0000 0004 1808 1697Medical Oncology 2, Istituto Oncologico Veneto IOV IRCSS, Padova, Italy
| | - Matteo Fassan
- grid.5608.b0000 0004 1757 3470Surgical Pathology Unit, Department of Medicine, Università degli Studi di Padova, Padova, Italy
| | - Fiorella Calabrese
- grid.5608.b0000 0004 1757 3470Surgical Pathology Unit, Department of Medicine, Università degli Studi di Padova, Padova, Italy
| | - Valentina Guarneri
- grid.5608.b0000 0004 1757 3470Department of Surgery, Oncology and Gastroeneterology, Università degli Studi di Padova, Padova, Italy ,grid.419546.b0000 0004 1808 1697Medical Oncology 2, Istituto Oncologico Veneto IOV IRCSS, Padova, Italy
| | - Pier Franco Conte
- grid.5608.b0000 0004 1757 3470Department of Surgery, Oncology and Gastroeneterology, Università degli Studi di Padova, Padova, Italy ,grid.419546.b0000 0004 1808 1697Medical Oncology 2, Istituto Oncologico Veneto IOV IRCSS, Padova, Italy
| | - Stefano Indraccolo
- grid.419546.b0000 0004 1808 1697Basic and Translational Oncology Unit, Istituto Oncologico Veneto IOV IRCCS, Padova, Italy ,grid.5608.b0000 0004 1757 3470Department of Surgery, Oncology and Gastroeneterology, Università degli Studi di Padova, Padova, Italy
| | - Laura Bonanno
- Medical Oncology 2, Istituto Oncologico Veneto IOV IRCSS, Padova, Italy.
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Special Issue: Next-Generation Sequencing in Tumor Diagnosis and Treatment II. Diagnostics (Basel) 2022; 12:diagnostics12082017. [PMID: 36010367 PMCID: PMC9407571 DOI: 10.3390/diagnostics12082017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 11/17/2022] Open
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Werner TV, Kock S, Weber I, Kayser G, Werner M, Lassmann S. Validation of a DNA-Based Next-Generation Sequencing Test for Molecular Diagnostic Variant and Fusion Detection in Formalin-Fixed, Paraffin-Embedded Tissue Specimens and Liquid Biopsy Plasma/Cell-Free DNA Samples. J Mol Diagn 2022; 24:784-802. [PMID: 35787794 DOI: 10.1016/j.jmoldx.2022.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 03/26/2022] [Accepted: 04/06/2022] [Indexed: 11/26/2022] Open
Abstract
This study evaluated two DNA-based next-generation sequencing approaches for detection of single-nucleotide variants (SNVs) and fusions in formalin-fixed, paraffin-embedded (FFPE) tissue specimens and liquid biopsies (AVENIO Targeted and Surveillance Panels). Reference standards (n = 7 with SNVs and structural variants) and real-world FFPE tissue specimens (n = 26 lung, colorectal, pancreas, ovary, breast, prostate, melanoma, and soft tissue cancer cases with n = 27 samples), liquid biopsies [n = 29 cases with n = 40 plasma/cell-free DNA (cfDNA) samples], and one pleural effusion (lung cancer) were analyzed by the AVENIO workflow for known SNVs (BRAF, BRCA1/2, CTNNB1, EGFR, KRAS, MET exon 14 skipping, NRAS, PIK3CA, and TP53), insertions and deletions (ERBB2 and KIT), and fusions (ALK and ROS1). Detection of SNVs, insertions and deletions, and fusions was reliable in 24 of 26 FFPE tissue specimen cases and at 1% allele frequency in 5 of 5 cfDNA reference standards and 37 of 40 plasma/cfDNA samples. Pitfalls were identified for the AVENIO workflow in calling and listing of clinically relevant variants, requiring additional manual inspection. Moreover, laboratory workflows are distinct for FFPE tissue specimens and liquid biopsies as well as time-consuming for sample quality control assays. In summary, the DNA-based next-generation sequencing approaches may be suitable for routine molecular pathology diagnostics on careful data interpretation and further optimization of the technical and laboratory workflows.
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Affiliation(s)
- Tamara V Werner
- Institute for Surgical Pathology, Medical Center, Medical Faculty, University of Freiburg, Freiburg im Breisgau, Germany; German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg, Germany
| | - Sylvia Kock
- Institute for Surgical Pathology, Medical Center, Medical Faculty, University of Freiburg, Freiburg im Breisgau, Germany
| | - Isabel Weber
- Institute for Surgical Pathology, Medical Center, Medical Faculty, University of Freiburg, Freiburg im Breisgau, Germany
| | - Gian Kayser
- Institute for Surgical Pathology, Medical Center, Medical Faculty, University of Freiburg, Freiburg im Breisgau, Germany
| | - Martin Werner
- Institute for Surgical Pathology, Medical Center, Medical Faculty, University of Freiburg, Freiburg im Breisgau, Germany; German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg, Germany
| | - Silke Lassmann
- Institute for Surgical Pathology, Medical Center, Medical Faculty, University of Freiburg, Freiburg im Breisgau, Germany; German Cancer Consortium, partner site Freiburg, and German Cancer Research Center, Heidelberg, Germany.
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