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van der Leest P, Schuuring E. Critical Factors in the Analytical Work Flow of Circulating Tumor DNA-Based Molecular Profiling. Clin Chem 2024; 70:220-233. [PMID: 38175597 DOI: 10.1093/clinchem/hvad194] [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: 07/29/2023] [Accepted: 10/30/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND Liquid biopsy testing, especially molecular tumor profiling of circulating tumor DNA (ctDNA) in cell-free plasma, has received increasing interest in recent years as it serves as a reliable alternative for the detection of tumor-specific aberrations to guide treatment decision-making in oncology. Many (commercially available) applications have been developed, however, broad divergences in (pre)analytical work flows and lack of universally applied guidelines impede routine clinical implementation. In this review, critical factors in the blood-based ctDNA liquid biopsy work flow are evaluated. CONTENT In the preanalytical phase, several aspects (e.g., blood collection tubes [BCTs], plasma processing, and extraction method) affect the quantity and quality of the circulating cell-free DNA (ccfDNA) applicable for subsequent molecular analyses and should meet certain standards to be applied in diagnostic work flows. Analytical considerations, such as analytical input and choice of assay, might vary based on the clinical application (i.e., screening, primary diagnosis, minimal residual disease [MRD], response monitoring, and resistance identification). In addition to practical procedures, variant interpretation and reporting ctDNA results should be harmonized. Collaborative efforts in (inter)national consortia and societies are essential for the establishment of standard operating procedures (SOPs) in attempts to standardize the plasma-based ctDNA analysis work flow. SUMMARY Development of universally applicable guidelines regarding the critical factors in liquid biopsy testing are necessary to pave the way to clinical implementation for routine diagnostics.
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Affiliation(s)
- Paul van der Leest
- Department of Pathology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Laboratory Medicine, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Ed Schuuring
- Department of Pathology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
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Gimeno-Valiente F, Martín-Arana J, Tébar-Martínez R, Gambardella V, Martínez-Ciarpaglini C, García-Micó B, Martínez-Castedo B, Palomar B, García-Bartolomé M, Seguí V, Huerta M, Moro-Valdezate D, Pla-Martí V, Pérez-Santiago L, Roselló S, Roda D, Cervantes A, Tarazona N. Sequencing paired tumor DNA and white blood cells improves circulating tumor DNA tracking and detects pathogenic germline variants in localized colon cancer. ESMO Open 2023; 8:102051. [PMID: 37951129 PMCID: PMC10774972 DOI: 10.1016/j.esmoop.2023.102051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 09/22/2023] [Indexed: 11/13/2023] Open
Abstract
BACKGROUND In the setting of localized colon cancer (CC), circulating tumor DNA (ctDNA) monitoring in plasma has shown potential for detecting minimal residual disease (MRD) and predicting a higher risk of recurrence. With the tumor-only sequencing approach, however, germline variants may be misidentified as somatic variations, precluding the possibility of tracking in up to 11% of patients due to a lack of known somatic mutations. In this study, we assess the potential value of adding white blood cells (WBCs) to tumor tissue sequencing to enhance the accuracy of sequencing results. PATIENTS AND METHODS A total of 148 patients diagnosed with localized CC were prospectively recruited at the Hospital Clínico Universitario in Valencia (Spain). Employing a custom 29-gene panel, sequencing was conducted on tumor tissue, plasma and corresponding WBCs. Droplet digital PCR and amplicon-based NGS were performed on plasma samples post-surgery to track MRD. Oncogenic somatic variants were identified by annotating with COSMIC, OncoKB and an internal repository of pathogenic mutations database. A variant prioritization analysis, mainly characterized by the match of oncogenic mutations with the evidence levels defined in OncoKB, was carried out to select specific targeted therapies. RESULTS Utilizing paired tumor and WBCs sequencing, we identified somatic mutations in all patients (100%) within our cohort, compared to 89% using only tumor tissue. Consequently, the top 10 most frequently mutated genes for plasma monitoring were altered. The sequencing of WBCs identified 9% of patients with pathogenic mutations in the germline, with APC and TP53 being the most frequently mutated genes. Additionally, mutations in genes related to clonal hematopoiesis of indeterminate potential were detected in 27% of the cohort, with TP53, KRAS, and KMT2C being the most frequently altered genes. There were no observed differences in the sensitivity of monitoring MRD using ddPCR or amplicon-based NGS (p = 1). Ultimately, 41% of the patients harbored potentially targetable alterations at diagnosis. CONCLUSION The germline testing method not only enhanced sequencing results and raised the proportion of patients eligible for plasma monitoring, but also uncovered the existence of pathogenic germline variations, thereby aiding in the identification of patients at a higher risk of hereditary cancer syndromes.
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Affiliation(s)
- F Gimeno-Valiente
- Cancer Evolution and Genome Instability Laboratory, University College London Cancer Institute, London, UK
| | - J Martín-Arana
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia; CIBERONC, Instituto de Salud Carlos III, Madrid
| | - R Tébar-Martínez
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia
| | - V Gambardella
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia
| | - C Martínez-Ciarpaglini
- CIBERONC, Instituto de Salud Carlos III, Madrid; Department of Pathology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia
| | - B García-Micó
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia; CIBERONC, Instituto de Salud Carlos III, Madrid
| | - B Martínez-Castedo
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia; CIBERONC, Instituto de Salud Carlos III, Madrid
| | - B Palomar
- Department of Pathology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia
| | - M García-Bartolomé
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia
| | - V Seguí
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia
| | - M Huerta
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia
| | - D Moro-Valdezate
- Colorectal Surgery Unit, INCLIVA Biomedical Research Institute, Hospital Clínico Universitario de Valencia, Department of Surgery, University of Valencia, Valencia, Spain
| | - V Pla-Martí
- Colorectal Surgery Unit, INCLIVA Biomedical Research Institute, Hospital Clínico Universitario de Valencia, Department of Surgery, University of Valencia, Valencia, Spain
| | - L Pérez-Santiago
- Colorectal Surgery Unit, INCLIVA Biomedical Research Institute, Hospital Clínico Universitario de Valencia, Department of Surgery, University of Valencia, Valencia, Spain
| | - S Roselló
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia; CIBERONC, Instituto de Salud Carlos III, Madrid
| | - D Roda
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia; CIBERONC, Instituto de Salud Carlos III, Madrid
| | - A Cervantes
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia; CIBERONC, Instituto de Salud Carlos III, Madrid.
| | - N Tarazona
- Department of Medical Oncology, INCLIVA Biomedical Research Institute, University of Valencia, Valencia; CIBERONC, Instituto de Salud Carlos III, Madrid.
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Haselmann V, Hedtke M, Neumaier M. Liquid Profiling for Cancer Patient Stratification in Precision Medicine—Current Status and Challenges for Successful Implementation in Standard Care. Diagnostics (Basel) 2022; 12:diagnostics12030748. [PMID: 35328301 PMCID: PMC8947441 DOI: 10.3390/diagnostics12030748] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/09/2022] [Accepted: 03/11/2022] [Indexed: 12/13/2022] Open
Abstract
Circulating tumor DNA (ctDNA), accurately described by the term liquid profiling (LP), enables real-time assessment of the tumor mutational profile as a minimally invasive test and has therefore rapidly gained traction, particular for the management of cancer patients. By LP, tumor-specific genetic alterations can be determined as part of companion diagnostics to guide selection of appropriate targeted therapeutics. Because LP facilitates longitudinal monitoring of cancer patients, it can be used to detect acquired resistant mechanisms or as a personalized biomarker for earlier detection of disease recurrence, among other applications. However, LP is not yet integrated into routine care to the extent that might be expected. This is due to the lack of harmonization and standardization of preanalytical and analytical workflows, the lack of proper quality controls, limited evidence of its clinical utility, heterogeneous study results, the uncertainty of clinicians regarding the value and appropriate indications for LP and its interpretation, and finally, the lack of reimbursement for most LP tests. In this review, the value proposition of LP for cancer patient management and treatment optimization, the current status of implementation in standard care, and the main challenges that need to be overcome are discussed in detail.
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van der Leest P, Hiddinga B, Miedema A, Aguirre Azpurua ML, Rifaela N, ter Elst A, Timens W, Groen HJM, van Kempen LC, Hiltermann TJN, Schuuring E. Circulating tumor DNA as a biomarker for monitoring early treatment responses of patients with advanced lung adenocarcinoma receiving immune checkpoint inhibitors. Mol Oncol 2021; 15:2910-2922. [PMID: 34449963 PMCID: PMC8564646 DOI: 10.1002/1878-0261.13090] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 07/27/2021] [Accepted: 08/25/2021] [Indexed: 11/07/2022] Open
Abstract
Immunotherapy for metastasized non-small-cell lung cancer (NSCLC) can show long-lasting clinical responses. Selection of patients based on programmed death-ligand 1 (PD-L1) expression shows limited predictive value for durable clinical benefit (DCB). We investigated whether early treatment effects as measured by a change in circulating tumor DNA (ctDNA) level is a proxy of early tumor response to immunotherapy according to response evaluation criteria in solid tumors v1.1 criteria, progression-free survival (PFS), DCB, and overall survival (OS). To this aim, blood tubes were collected from advanced-stage lung adenocarcinoma patients (n = 100) receiving immune checkpoint inhibitors (ICI) at baseline (t0 ) and prior to first treatment evaluation (4-6 weeks; t1 ). Nontargetable (driver) mutations detected in the pretreatment tumor biopsy were used to quantify tumor-specific ctDNA levels using droplet digital PCR. We found that changes in ctDNA levels were strongly associated with tumor response. A > 30% decrease in ctDNA at t1 correlated with a longer PFS and OS. In total, 80% of patients with a DCB of ≥ 26 weeks displayed a > 30% decrease in ctDNA levels. For patients with a PD-L1 tumor proportion score of ≥ 1%, decreasing ctDNA levels were associated with a higher frequency a DCB (80%) and a prolonged median PFS (85 weeks) and OS (101 weeks) compared with patients with no decrease in ctDNA (34%; 11 and 39 weeks, respectively). This study shows that monitoring of ctDNA dynamics is an easy-to-use and promising tool for assessing PFS, DCB, and OS for ICI-treated NSCLC patients.
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Affiliation(s)
- Paul van der Leest
- Department of PathologyUniversity of GroningenUniversity Medical Center GroningenThe Netherlands
| | - Birgitta Hiddinga
- Department of Pulmonary DiseasesUniversity of GroningenUniversity Medical Center GroningenThe Netherlands
| | - Anneke Miedema
- Department of PathologyUniversity of GroningenUniversity Medical Center GroningenThe Netherlands
| | - Maria L. Aguirre Azpurua
- Department of PathologyUniversity of GroningenUniversity Medical Center GroningenThe Netherlands
| | - Naomi Rifaela
- Department of PathologyUniversity of GroningenUniversity Medical Center GroningenThe Netherlands
| | - Arja ter Elst
- Department of PathologyUniversity of GroningenUniversity Medical Center GroningenThe Netherlands
| | - Wim Timens
- Department of PathologyUniversity of GroningenUniversity Medical Center GroningenThe Netherlands
| | - Harry J. M. Groen
- Department of Pulmonary DiseasesUniversity of GroningenUniversity Medical Center GroningenThe Netherlands
| | - Léon C. van Kempen
- Department of PathologyUniversity of GroningenUniversity Medical Center GroningenThe Netherlands
| | - T. Jeroen N. Hiltermann
- Department of Pulmonary DiseasesUniversity of GroningenUniversity Medical Center GroningenThe Netherlands
| | - Ed Schuuring
- Department of PathologyUniversity of GroningenUniversity Medical Center GroningenThe Netherlands
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5
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Al Zoughbi W, Fox J, Beg S, Papp E, Hissong E, Ohara K, Keefer L, Sigouros M, Kane T, Bockelman D, Nichol D, Patchell E, Bareja R, Karandikar A, Alnajar H, Cerqueira G, Guthrie VB, Verner E, Manohar J, Greco N, Wilkes D, Tagawa S, Malbari MS, Holcomb K, Eng KW, Shah M, Altorki NK, Sboner A, Nanus D, Faltas B, Sternberg CN, Simmons J, Houvras Y, Molina AM, Angiuoli S, Elemento O, Mosquera JM. Validation of a Circulating Tumor DNA-Based Next-Generation Sequencing Assay in a Cohort of Patients with Solid tumors: A Proposed Solution for Decentralized Plasma Testing. Oncologist 2021; 26:e1971-e1981. [PMID: 34286887 PMCID: PMC8571755 DOI: 10.1002/onco.13905] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 07/09/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Characterization of circulating tumor DNA (ctDNA) has been integrated into clinical practice. Although labs have standardized validation procedures to develop single locus tests, the efficacy of on-site plasma-based next-generation sequencing (NGS) assays still needs to be proved. MATERIALS AND METHODS In this retrospective study, we profiled DNA from matched tissue and plasma samples from 75 patients with cancer. We applied an NGS test that detects clinically relevant alterations in 33 genes and microsatellite instability (MSI) to analyze plasma cell-free DNA (cfDNA). RESULTS The concordance between alterations detected in both tissue and plasma samples was higher in patients with metastatic disease. The NGS test detected 77% of sequence alterations, amplifications, and fusions that were found in metastatic samples compared with 45% of those alterations found in the primary tumor samples (p = .00005). There was 87% agreement on MSI status between the NGS test and tumor tissue results. In three patients, MSI-high ctDNA correlated with response to immunotherapy. In addition, the NGS test revealed an FGFR2 amplification that was not detected in tumor tissue from a patient with metastatic gastric cancer, emphasizing the importance of profiling plasma samples in patients with advanced cancer. CONCLUSION Our validation experience of a plasma-based NGS assay advances current knowledge about translating cfDNA testing into clinical practice and supports the application of plasma assays in the management of oncology patients with metastatic disease. With an in-house method that minimizes the need for invasive procedures, on-site cfDNA testing supplements tissue biopsy to guide precision therapy and is entitled to become a routine practice. IMPLICATIONS FOR PRACTICE This study proposes a solution for decentralized liquid biopsy testing based on validation of a next-generation sequencing (NGS) test that detects four classes of genomic alterations in blood: sequence mutations (single nucleotide substitutions or insertions and deletions), fusions, amplifications, and microsatellite instability (MSI). Although there are reference labs that perform single-site comprehensive liquid biopsy testing, the targeted assay this study validated can be established locally in any lab with capacity to offer clinical molecular pathology assays. To the authors' knowledge, this is the first report that validates evaluating an on-site plasma-based NGS test that detects the MSI status along with common sequence alterations encountered in solid tumors.
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Affiliation(s)
- Wael Al Zoughbi
- Department of Pathology and Laboratory Medicine, Weill Cornell MedicineNew YorkNew YorkUSA
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York‐PresbyterianNew YorkNew YorkUSA
| | - Jesse Fox
- Personal Genome Diagnostics Inc.BaltimoreMarylandUSA
| | - Shaham Beg
- Department of Pathology and Laboratory Medicine, Weill Cornell MedicineNew YorkNew YorkUSA
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York‐PresbyterianNew YorkNew YorkUSA
| | - Eniko Papp
- Personal Genome Diagnostics Inc.BaltimoreMarylandUSA
| | - Erika Hissong
- Department of Pathology and Laboratory Medicine, Weill Cornell MedicineNew YorkNew YorkUSA
| | - Kentaro Ohara
- Department of Pathology and Laboratory Medicine, Weill Cornell MedicineNew YorkNew YorkUSA
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York‐PresbyterianNew YorkNew YorkUSA
| | - Laurel Keefer
- Personal Genome Diagnostics Inc.BaltimoreMarylandUSA
| | - Michael Sigouros
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York‐PresbyterianNew YorkNew YorkUSA
| | - Troy Kane
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York‐PresbyterianNew YorkNew YorkUSA
| | - Daniel Bockelman
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York‐PresbyterianNew YorkNew YorkUSA
| | - Donna Nichol
- Personal Genome Diagnostics Inc.BaltimoreMarylandUSA
| | - Emily Patchell
- Department of Pathology and Laboratory Medicine, Weill Cornell MedicineNew YorkNew YorkUSA
| | - Rohan Bareja
- Institute for Computational Biomedicine, Weill Cornell MedicineNew YorkNew YorkUSA
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York‐PresbyterianNew YorkNew YorkUSA
| | | | - Hussein Alnajar
- Department of Pathology and Laboratory Medicine, Weill Cornell MedicineNew YorkNew YorkUSA
| | | | | | - Ellen Verner
- Personal Genome Diagnostics Inc.BaltimoreMarylandUSA
| | - Jyothi Manohar
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York‐PresbyterianNew YorkNew YorkUSA
| | - Noah Greco
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York‐PresbyterianNew YorkNew YorkUSA
| | - David Wilkes
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York‐PresbyterianNew YorkNew YorkUSA
| | - Scott Tagawa
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell MedicineNew YorkNew YorkUSA
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York‐PresbyterianNew YorkNew YorkUSA
| | | | - Kevin Holcomb
- Department of Obstetrics and Gynecology, Weill Cornell MedicineNew YorkNew YorkUSA
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York‐PresbyterianNew YorkNew YorkUSA
| | - Kenneth Wha Eng
- Institute for Computational Biomedicine, Weill Cornell MedicineNew YorkNew YorkUSA
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York‐PresbyterianNew YorkNew YorkUSA
| | - Manish Shah
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell MedicineNew YorkNew YorkUSA
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York‐PresbyterianNew YorkNew YorkUSA
| | - Nasser K. Altorki
- Division of Thoracic Surgery, Weill Cornell MedicineNew YorkNew YorkUSA
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York‐PresbyterianNew YorkNew YorkUSA
| | - Andrea Sboner
- Department of Pathology and Laboratory Medicine, Weill Cornell MedicineNew YorkNew YorkUSA
- Institute for Computational Biomedicine, Weill Cornell MedicineNew YorkNew YorkUSA
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York‐PresbyterianNew YorkNew YorkUSA
| | - David Nanus
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell MedicineNew YorkNew YorkUSA
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York‐PresbyterianNew YorkNew YorkUSA
| | - Bishoy Faltas
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell MedicineNew YorkNew YorkUSA
- Department of Cell and Developmental Biology, Weill Cornell MedicineNew YorkNew YorkUSA
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York‐PresbyterianNew YorkNew YorkUSA
| | - Cora N. Sternberg
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell MedicineNew YorkNew YorkUSA
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York‐PresbyterianNew YorkNew YorkUSA
| | - John Simmons
- Personal Genome Diagnostics Inc.BaltimoreMarylandUSA
| | - Yariv Houvras
- Department of Surgery, Weill Cornell MedicineNew YorkNew YorkUSA
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York‐PresbyterianNew YorkNew YorkUSA
| | - Ana M. Molina
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell MedicineNew YorkNew YorkUSA
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York‐PresbyterianNew YorkNew YorkUSA
| | | | - Olivier Elemento
- Institute for Computational Biomedicine, Weill Cornell MedicineNew YorkNew YorkUSA
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York‐PresbyterianNew YorkNew YorkUSA
| | - Juan Miguel Mosquera
- Department of Pathology and Laboratory Medicine, Weill Cornell MedicineNew YorkNew YorkUSA
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York‐PresbyterianNew YorkNew YorkUSA
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Lamy PJ, van der Leest P, Lozano N, Becht C, Duboeuf F, Groen HJM, Hilgers W, Pourel N, Rifaela N, Schuuring E, Alix-Panabières C. Mass Spectrometry as a Highly Sensitive Method for Specific Circulating Tumor DNA Analysis in NSCLC: A Comparison Study. Cancers (Basel) 2020; 12:cancers12103002. [PMID: 33081150 PMCID: PMC7602843 DOI: 10.3390/cancers12103002] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/14/2020] [Accepted: 10/15/2020] [Indexed: 12/12/2022] Open
Abstract
Simple Summary We compared the UltraSEEK™ Lung Panel on the MassARRAY® System (Agena Bioscience) with the FDA-approved Cobas® EGFR Mutation Test v2 for the detection of EGFR mutations in liquid biopsies of NSCLC patients, accompanied with preanalytical sample assessment using the novel Liquid IQ® Panel. For the detection of relevant predictive mutations using the UltraSEEK™ Lung Panel, an input of over 10 ng showed 100% concordance with Cobas® EGFR Mutation Test v2 and detection of all tissue confirmed mutations. In case of lower ccfDNA input, the risk of missing clinically relevant mutations should be considered. The use of a preanalytical ccfDNA quality control assay such as the Liquid IQ® Panel is recommended to confidently interpret results, avoiding bias induced by non-specific genomic DNA and low input of specific tumoral ccfDNA fragments. Abstract Plasma-based tumor mutational profiling is arising as a reliable approach to detect primary and therapy-induced resistance mutations required for accurate treatment decision making. Here, we compared the FDA-approved Cobas® EGFR Mutation Test v2 with the UltraSEEK™ Lung Panel on the MassARRAY® System on detection of EGFR mutations, accompanied with preanalytical sample assessment using the novel Liquid IQ® Panel. 137 cancer patient-derived cell-free plasma samples were analyzed with the Cobas® and UltraSEEK™ tests. Liquid IQ® analysis was initially validated (n = 84) and used to determine ccfDNA input for all samples. Subsequently, Liquid IQ® results were applied to harmonize ccfDNA input for the Cobas® and UltraSEEK™ tests for 63 NSCLC patients. The overall concordance between the Cobas® and UltraSEEK™ tests was 86%. The Cobas® test detected more EGFR exon19 deletions and L858R mutations, while the UltraSEEK™ test detected more T790M mutations. A 100% concordance in both the clinical (n = 137) and harmonized (n = 63) cohorts was observed when >10 ng of ccfDNA was used as determined by the Liquid IQ® Panel. The Cobas® and UltraSEEK™ tests showed similar sensitivity in EGFR mutation detection, particularly when ccfDNA input was sufficient. It is recommended to preanalytically determine the ccfDNA concentration accurately to ensure sufficient input for reliable interpretation and treatment decision making.
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Affiliation(s)
- Pierre-Jean Lamy
- Biopathologie et Génétique des Cancers, Institute d’Analyse Médicale Imagenome, Inovie, 6 Rue Fontenille, 34000 Montpellier, France;
- Correspondence: ; Tel.: +33-430-053-100
| | - Paul van der Leest
- Department of Pathology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (P.v.d.L.); (N.R.); (E.S.)
| | - Nicolas Lozano
- Biopathologie et Génétique des Cancers, Institute d’Analyse Médicale Imagenome, Inovie, 6 Rue Fontenille, 34000 Montpellier, France;
| | - Catherine Becht
- Oncologie Médicale, Clinique Clémenville, 25 rue Clémenville, 34000 Montpellier, France; (C.B.); (F.D.)
| | - Frédérique Duboeuf
- Oncologie Médicale, Clinique Clémenville, 25 rue Clémenville, 34000 Montpellier, France; (C.B.); (F.D.)
| | - Harry J. M. Groen
- Department of Pulmonary Medicine, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands;
| | - Werner Hilgers
- Oncologie Médicale, Institute Sainte Catherine, 250 Chemin de Baigne Pieds, 84918 Avignon, France; (W.H.); (N.P.)
| | - Nicolas Pourel
- Oncologie Médicale, Institute Sainte Catherine, 250 Chemin de Baigne Pieds, 84918 Avignon, France; (W.H.); (N.P.)
| | - Naomi Rifaela
- Department of Pathology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (P.v.d.L.); (N.R.); (E.S.)
| | - Ed Schuuring
- Department of Pathology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (P.v.d.L.); (N.R.); (E.S.)
| | - Catherine Alix-Panabières
- Laboratoire de Cellules Rares Circulantes, University Medical Center of Montpellier, 641, Avenue du Doyen Gaston GIRAUD, 34093 Montpellier, France;
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7
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Tanos R, Tosato G, Otandault A, Al Amir Dache Z, Pique Lasorsa L, Tousch G, El Messaoudi S, Meddeb R, Diab Assaf M, Ychou M, Du Manoir S, Pezet D, Gagnière J, Colombo P, Jacot W, Assénat E, Dupuy M, Adenis A, Mazard T, Mollevi C, Sayagués JM, Colinge J, Thierry AR. Machine Learning-Assisted Evaluation of Circulating DNA Quantitative Analysis for Cancer Screening. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2000486. [PMID: 32999827 PMCID: PMC7509651 DOI: 10.1002/advs.202000486] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 05/30/2020] [Indexed: 05/24/2023]
Abstract
While the utility of circulating cell-free DNA (cfDNA) in cancer screening and early detection have recently been investigated by testing genetic and epigenetic alterations, here, an original approach by examining cfDNA quantitative and structural features is developed. First, the potential of cfDNA quantitative and structural parameters is independently demonstrated in cell culture, murine, and human plasma models. Subsequently, these variables are evaluated in a large retrospective cohort of 289 healthy individuals and 983 patients with various cancer types; after age resampling, this evaluation is done independently and the variables are combined using a machine learning approach. Implementation of a decision tree prediction model for the detection and classification of healthy and cancer patients shows unprecedented performance for 0, I, and II colorectal cancer stages (specificity, 0.89 and sensitivity, 0.72). Consequently, the methodological proof of concept of using both quantitative and structural biomarkers, and classification with a machine learning method are highlighted, as an efficient strategy for cancer screening. It is foreseen that the classification rate may even be improved by the addition of such biomarkers to fragmentomics, methylation, or the detection of genetic alterations. The optimization of such a multianalyte strategy with this machine learning method is therefore warranted.
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8
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Chan HT, Nagayama S, Chin YM, Otaki M, Hayashi R, Kiyotani K, Fukunaga Y, Ueno M, Nakamura Y, Low S. Clinical significance of clonal hematopoiesis in the interpretation of blood liquid biopsy. Mol Oncol 2020; 14:1719-1730. [PMID: 32449983 PMCID: PMC7400786 DOI: 10.1002/1878-0261.12727] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 05/13/2020] [Accepted: 05/20/2020] [Indexed: 02/06/2023] Open
Abstract
As the use of next-generation sequencing (NGS) for plasma cell-free DNA (cfDNA) continues to expand in clinical settings, accurate identification of circulating tumor DNA mutations is important to validate its use in the clinical management for cancer patients. Here, we aimed to characterize mutations including clonal hematopoiesis (CH)-related mutations in plasma cfDNA and tumor tissues using the same ultradeep NGS assay and evaluate the clinical significance of CH-related mutations on the interpretation of liquid biopsy results. Ultradeep targeted NGS using Oncomine Pan-Cancer Panel was performed on matched surgically resected tumor tissues, peripheral blood cells (PBCs), and 120 plasma cfDNA samples from 38 colorectal cancer patients. The clinical significance of the CH-related mutations in plasma cfDNA was evaluated by longitudinal monitoring of the postoperative plasma samples. Among the 38 patients, 74 nonsynonymous mutations were identified from tumor tissues and 64 mutations from the preoperative plasma samples. Eleven (17%) of the 64 mutations identified in plasma cfDNA were also detected in PBC DNA and were identified to be CH-related mutations. Overall, 11 of 38 (29%) patients in this cohort harbored at least one CH-related mutation in plasma cfDNA. These CH-related mutations were continuously detected in subsequent postoperative plasma samples from three patients which could be misinterpreted as the presence of residual disease or as lack of treatment response. Our results indicated that it is essential to integrate the mutational information of PBCs to differentiate tumor-derived from CH-related mutations in liquid biopsy analysis. This would prevent the misinterpretation of results to avoid misinformed clinical management for cancer patients.
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Affiliation(s)
- Hiu Ting Chan
- Cancer Precision Medicine CenterJapanese Foundation for Cancer ResearchTokyoJapan
| | - Satoshi Nagayama
- Department of Gastroenterological and SurgeryCancer Institute HospitalJapanese Foundation for Cancer ResearchTokyoJapan
| | - Yoon Ming Chin
- Cancer Precision Medicine CenterJapanese Foundation for Cancer ResearchTokyoJapan
- Cancer Precision Medicine, IncKawasakiJapan
| | - Masumi Otaki
- Cancer Precision Medicine CenterJapanese Foundation for Cancer ResearchTokyoJapan
| | - Rie Hayashi
- Cancer Precision Medicine CenterJapanese Foundation for Cancer ResearchTokyoJapan
- Cancer Precision Medicine, IncKawasakiJapan
| | - Kazuma Kiyotani
- Cancer Precision Medicine CenterJapanese Foundation for Cancer ResearchTokyoJapan
| | - Yosuke Fukunaga
- Department of Gastroenterological and SurgeryCancer Institute HospitalJapanese Foundation for Cancer ResearchTokyoJapan
| | - Masashi Ueno
- Department of Gastroenterological and SurgeryCancer Institute HospitalJapanese Foundation for Cancer ResearchTokyoJapan
| | - Yusuke Nakamura
- Cancer Precision Medicine CenterJapanese Foundation for Cancer ResearchTokyoJapan
| | - Siew‐Kee Low
- Cancer Precision Medicine CenterJapanese Foundation for Cancer ResearchTokyoJapan
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9
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Coombs CC, Dickherber T, Crompton BD. Chasing ctDNA in Patients With Sarcoma. Am Soc Clin Oncol Educ Book 2020; 40:e351-e360. [PMID: 32598183 DOI: 10.1200/edbk_280749] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Liquid biopsies are new technologies that allow cancer profiling of tumor fragments found in body fluids, such as peripheral blood, collected noninvasively from patients with malignancies. These assays are increasingly valuable in clinical oncology practice as prognostic biomarkers, as guides for therapy selection, for treatment monitoring, and for early detection of disease progression and relapse. However, application of these assays to rare cancers, such as pediatric and adult sarcomas, have lagged. In this article, we review the technical challenges of applying liquid biopsy technologies to sarcomas, provide an update on progress in the field, describe common pitfalls in interpreting liquid biopsy data, and discuss the intersection of sarcoma clinical care and commercial assays emerging on the horizon.
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Affiliation(s)
| | | | - Brian D Crompton
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA
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10
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van der Leest P, Boonstra PA, ter Elst A, van Kempen LC, Tibbesma M, Koopmans J, Miedema A, Tamminga M, Groen HJM, Reyners AKL, Schuuring E. Comparison of Circulating Cell-Free DNA Extraction Methods for Downstream Analysis in Cancer Patients. Cancers (Basel) 2020; 12:E1222. [PMID: 32414097 PMCID: PMC7281769 DOI: 10.3390/cancers12051222] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/05/2020] [Accepted: 05/08/2020] [Indexed: 12/28/2022] Open
Abstract
Circulating cell-free DNA (ccfDNA) may contain DNA originating from the tumor in plasma of cancer patients (ctDNA) and enables noninvasive cancer diagnosis, treatment predictive testing, and response monitoring. A recent multicenter evaluation of workflows by the CANCER-ID consortium using artificial spiked-in plasma showed significant differences and consequently the importance of carefully selecting ccfDNA extraction methods. Here, the quantity and integrity of extracted ccfDNA from the plasma of cancer patients were assessed. Twenty-one cancer patient-derived cell-free plasma samples were selected to compare the Qiagen CNA, Maxwell RSC ccfDNA plasma, and Zymo manual quick ccfDNA kit. High-volume citrate plasma samples collected by diagnostic leukapheresis from six cancer patients were used to compare the Qiagen CNA (2 mL) and QIAamp MinElute ccfDNA kit (8 mL). This study revealed similar integrity and similar levels of amplified short-sized fragments and tumor-specific mutants comparing the CNA and RSC kits. However, the CNA kit consistently showed the highest yield of ccfDNA and short-sized fragments, while the RSC and ME kits showed higher variant allelic frequencies (VAFs). Our study pinpoints the importance of standardizing preanalytical conditions as well as consensus on defining the input of ccfDNA to accurately detect ctDNA and be able to compare results in a clinical routine practice, within and between clinical studies.
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Affiliation(s)
- Paul van der Leest
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (P.v.d.L.); (A.t.E.); (L.C.v.K.); (M.T.); (J.K.); (A.M.)
| | - Pieter A. Boonstra
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (P.A.B.); (A.K.L.R.)
| | - Arja ter Elst
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (P.v.d.L.); (A.t.E.); (L.C.v.K.); (M.T.); (J.K.); (A.M.)
| | - Léon C. van Kempen
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (P.v.d.L.); (A.t.E.); (L.C.v.K.); (M.T.); (J.K.); (A.M.)
| | - Marco Tibbesma
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (P.v.d.L.); (A.t.E.); (L.C.v.K.); (M.T.); (J.K.); (A.M.)
| | - Jill Koopmans
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (P.v.d.L.); (A.t.E.); (L.C.v.K.); (M.T.); (J.K.); (A.M.)
| | - Anneke Miedema
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (P.v.d.L.); (A.t.E.); (L.C.v.K.); (M.T.); (J.K.); (A.M.)
| | - Menno Tamminga
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (M.T.); (H.J.M.G.)
| | - Harry J. M. Groen
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (M.T.); (H.J.M.G.)
| | - Anna K. L. Reyners
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (P.A.B.); (A.K.L.R.)
| | - Ed Schuuring
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands; (P.v.d.L.); (A.t.E.); (L.C.v.K.); (M.T.); (J.K.); (A.M.)
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