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Szpechcinski A, Moes-Sosnowska J, Skronska P, Lechowicz U, Pelc M, Szolkowska M, Rudzinski P, Wojda E, Maszkowska-Kopij K, Langfort R, Orlowski T, Sliwinski P, Polaczek M, Chorostowska-Wynimko J. The Advantage of Targeted Next-Generation Sequencing over qPCR in Testing for Druggable EGFR Variants in Non-Small-Cell Lung Cancer. Int J Mol Sci 2024; 25:7908. [PMID: 39063150 PMCID: PMC11277480 DOI: 10.3390/ijms25147908] [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: 06/27/2024] [Revised: 07/09/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
The emergence of targeted therapies in non-small-cell lung cancer (NSCLC), including inhibitors of epidermal growth factor receptor (EGFR) tyrosine kinase, has increased the need for robust companion diagnostic tests. Nowadays, detection of actionable variants in exons 18-21 of the EGFR gene by qPCR and direct DNA sequencing is often replaced by next-generation sequencing (NGS). In this study, we evaluated the diagnostic usefulness of targeted NGS for druggable EGFR variants testing in clinical NSCLC material previously analyzed by the IVD-certified qPCR test with respect to DNA reference material. We tested 59 NSCLC tissue and cytology specimens for EGFR variants using the NGS 'TruSight Tumor 15' assay (Illumina) and the qPCR 'cobas EGFR mutation test v2' (Roche Diagnostics). The sensitivity and specificity of targeted NGS assay were evaluated using the biosynthetic and biological DNA reference material with known allelic frequencies (VAF) of EGFR variants. NGS demonstrated a sufficient lower detection limit for diagnostic applications (VAF < 5%) in DNA reference material; all EGFR variants were correctly identified. NGS showed high repeatability of VAF assessment between runs (CV% from 0.02 to 3.98). In clinical material, the overall concordance between NGS and qPCR was 76.14% (Cohen's Kappa = 0.5933). The majority of discordant results concerned false-positive detection of EGFR exon 20 insertions by qPCR. A total of 9 out of 59 (15%) clinical samples showed discordant results for one or more EGFR variants in both assays. Additionally, we observed TP53 to be a frequently co-mutated gene in EGFR-positive NSCLC patients. In conclusion, targeted NGS showed a number of superior features over qPCR in EGFR variant detection (exact identification of variants, calculation of allelic frequency, high analytical sensitivity), which might enhance the basic diagnostic report.
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Affiliation(s)
- Adam Szpechcinski
- Department of Genetics and Clinical Immunology, The Institute of Tuberculosis and Lung Diseases, 01-138 Warsaw, Poland; (J.M.-S.); (P.S.); (U.L.); (M.P.); (J.C.-W.)
| | - Joanna Moes-Sosnowska
- Department of Genetics and Clinical Immunology, The Institute of Tuberculosis and Lung Diseases, 01-138 Warsaw, Poland; (J.M.-S.); (P.S.); (U.L.); (M.P.); (J.C.-W.)
| | - Paulina Skronska
- Department of Genetics and Clinical Immunology, The Institute of Tuberculosis and Lung Diseases, 01-138 Warsaw, Poland; (J.M.-S.); (P.S.); (U.L.); (M.P.); (J.C.-W.)
| | - Urszula Lechowicz
- Department of Genetics and Clinical Immunology, The Institute of Tuberculosis and Lung Diseases, 01-138 Warsaw, Poland; (J.M.-S.); (P.S.); (U.L.); (M.P.); (J.C.-W.)
| | - Magdalena Pelc
- Department of Genetics and Clinical Immunology, The Institute of Tuberculosis and Lung Diseases, 01-138 Warsaw, Poland; (J.M.-S.); (P.S.); (U.L.); (M.P.); (J.C.-W.)
| | - Malgorzata Szolkowska
- Department of Pathology, The Institute of Tuberculosis and Lung Diseases, 01-138 Warsaw, Poland; (M.S.); (R.L.)
| | - Piotr Rudzinski
- Clinics of Thoracic Surgery, The Institute of Tuberculosis and Lung Diseases, 01-138 Warsaw, Poland; (P.R.); (T.O.)
| | - Emil Wojda
- III Department of Lung Diseases and Oncology, The Institute of Tuberculosis and Lung Diseases, 01-138 Warsaw, Poland; (E.W.); (M.P.)
- II Department of Lung Diseases, The Institute of Tuberculosis and Lung Diseases, 01-138 Warsaw, Poland;
| | | | - Renata Langfort
- Department of Pathology, The Institute of Tuberculosis and Lung Diseases, 01-138 Warsaw, Poland; (M.S.); (R.L.)
| | - Tadeusz Orlowski
- Clinics of Thoracic Surgery, The Institute of Tuberculosis and Lung Diseases, 01-138 Warsaw, Poland; (P.R.); (T.O.)
| | - Pawel Sliwinski
- II Department of Lung Diseases, The Institute of Tuberculosis and Lung Diseases, 01-138 Warsaw, Poland;
| | - Mateusz Polaczek
- III Department of Lung Diseases and Oncology, The Institute of Tuberculosis and Lung Diseases, 01-138 Warsaw, Poland; (E.W.); (M.P.)
| | - Joanna Chorostowska-Wynimko
- Department of Genetics and Clinical Immunology, The Institute of Tuberculosis and Lung Diseases, 01-138 Warsaw, Poland; (J.M.-S.); (P.S.); (U.L.); (M.P.); (J.C.-W.)
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Christopoulos P, Herster F, Hoffknecht P, Falk M, Tiemann M, Kopp HG, Althoff A, Stammberger A, Laack E. Activity of afatinib in patients with NSCLC harboring novel uncommon EGFR mutations with or without co-mutations: a case report. Front Oncol 2024; 14:1347742. [PMID: 38769948 PMCID: PMC11103604 DOI: 10.3389/fonc.2024.1347742] [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: 12/01/2023] [Accepted: 04/18/2024] [Indexed: 05/22/2024] Open
Abstract
Epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) represent first-line standard of care in unresectable EGFR mutation-positive (EGFRm+) non-small cell lung cancer (NSCLC). However, 10-20% of patients with EGFRm+ NSCLC have uncommon EGFR variants, defined as mutations other than L858R substitutions or exon 19 deletions. NSCLC harboring uncommon EGFR mutations may demonstrate lower sensitivity to targeted agents than NSCLC with L858R or exon 19 deletion mutations. Prospective clinical trial data in patients with NSCLC uncommon EGFR mutations are lacking. Afatinib is a second-generation TKI and the only Food and Drug Administration-approved drug for some of the more prevalent uncommon EGFR mutations. We present a series of seven case reports describing clinical outcomes in afatinib-treated patients with NSCLC harboring a diverse range of extremely rare mutations with or without co-mutations affecting other genes. EGFR alterations included compound mutations, P-loop αC-helix compressing mutations, and novel substitution mutations. We also present a case with NSCLC harboring a novel EGFR::CCDC6 gene fusion. Overall, the patients responded well to afatinib, including radiologic partial responses in six patients during treatment. Responses were durable for three patients. The cases presented are in line with a growing body of clinical and preclinical evidence that indicating that NSCLC with various uncommon EGFR mutations, with or without co-mutations, may be sensitive to afatinib.
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Affiliation(s)
- Petros Christopoulos
- Department of Oncology, Thoraxklinik and National Center for Tumor Diseases at Heidelberg University Hospital, Heidelberg, Germany
- Thoracic Oncology, Translational Lung Research Heidelberg, Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Franziska Herster
- Robert Bosch Center for Tumor Diseases (RBCT), Robert Bosch Hospital, Stuttgart, Germany
| | - Petra Hoffknecht
- Lungenzentrum Osnabrueck, Franziskus-Hospital Harderberg, Georgsmarienhütte, Germany
| | - Markus Falk
- Lung Cancer Network NOWEL.org, Oldenburg, Germany
- Molecular Pathology, Institute of Hematopathology Hamburg, Hamburg, Germany
| | - Markus Tiemann
- Lung Cancer Network NOWEL.org, Oldenburg, Germany
- Molecular Pathology, Institute of Hematopathology Hamburg, Hamburg, Germany
| | - Hans-Georg Kopp
- Robert Bosch Center for Tumor Diseases (RBCT), Robert Bosch Hospital, Stuttgart, Germany
| | - Andre Althoff
- Department of Pulmonology, Thoraxzentrum Offenbach, Sana Klinikum Offenbach, Offenbach, Germany
| | - Anja Stammberger
- Oncology, Boehringer Ingelheim Pharma GmbH & Co. KG, Ingelheim, Germany
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Nindra U, Pal A, Bray V, Yip PY, Tognela A, Roberts TL, Becker TM, Williamson J, Farzin M, Li JJ, Lea V, Hagelamin A, Ng W, Wang B, Lee CS, Chua W. Utility of multigene panel next-generation sequencing in routine clinical practice for identifying genomic alterations in newly diagnosed metastatic nonsmall cell lung cancer. Intern Med J 2024; 54:596-601. [PMID: 37713593 DOI: 10.1111/imj.16224] [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: 01/19/2023] [Accepted: 08/17/2023] [Indexed: 09/17/2023]
Abstract
BACKGROUND The standard of care in newly diagnosed metastatic non-small cell lung cancer (NSCLC) is to test for aberrations in three genes for driver mutations - ALK, ROS1 and epidermal growth factor receptor (EGFR) - and also for immunohistochemistry to be performed for programmed death-ligand 1 expression level. Next-generation sequencing (NGS), with or without RNA fusion testing, is increasingly used in standard clinical practice to identify patients with potentially actionable mutations. Stratification of NGS mutation tiers is currently based on the European Society of Medical Oncology Scale for Clinical Actionability of Molecular Targets (ESCAT) Tiers I-V and X. AIM Our aim was to analyse NSCLC tumour samples for the prevalence of Tiers I-V mutations to establish guidance for current and novel treatments in patients with metastatic disease. METHODS NGS was performed employing the Oncomine Precision Assay (without RNA fusion testing) that interrogates DNA hotspot variants across 45 genes to screen 210 NSCLC tissue samples obtained across six Sydney hospitals between June 2021 and March 2022. RESULTS In our cohort, 161 of 210 (77%) had at least one gene mutation identified, with 41 of 210 (20%) having two or more concurrent mutations. Tier I mutations included 42 of 210 (20%) EGFR mutations (EIA) and five of 210 (3%) MET exon 14 skipping mutations (EIB). Non-Tier I variants included 22 of 210 (11%) KRAS G12C hotspot mutations (EIIB), with a further 47 of 210 (22%) having non-G12C KRAS (EX) mutations. NGS testing revealed an additional 15% of cases with Tier II ESCAT mutations in NSCLC. Forty-six percent of patients also demonstrated potential Tier III and IV mutations that are currently under investigation in early-phase clinical trials. CONCLUSIONS In addition to identifying patients with genomic alterations suitable for clinically proven standard-of-care therapeutic options, the 45-gene NGS panel has significant potential in identifying potentially actionable non-Tier 1 mutations that may become future standard clinical practice in NSCLC.
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Affiliation(s)
- Udit Nindra
- Department of Medical Oncology, Liverpool Hospital, Sydney, New South Wales, Australia
- Department of Medical Oncology, Macarthur Cancer Therapy Centre, Campbelltown Hospital, Sydney, New South Wales, Australia
- Department of Medical Oncology, Bankstown-Lidcombe Hospital, Sydney, New South Wales, Australia
- Ingham Institute for Applied Medical Research, Sydney, New South Wales, Australia
| | - Abhijit Pal
- Department of Medical Oncology, Liverpool Hospital, Sydney, New South Wales, Australia
- Department of Medical Oncology, Bankstown-Lidcombe Hospital, Sydney, New South Wales, Australia
| | - Victoria Bray
- Department of Medical Oncology, Liverpool Hospital, Sydney, New South Wales, Australia
| | - Po Y Yip
- Department of Medical Oncology, Macarthur Cancer Therapy Centre, Campbelltown Hospital, Sydney, New South Wales, Australia
- Department of Medical Oncology, Bankstown-Lidcombe Hospital, Sydney, New South Wales, Australia
- Discipline of Pathology, School of Medicine, Western Sydney University, Sydney, New South Wales, Australia
| | - Annette Tognela
- Department of Medical Oncology, Macarthur Cancer Therapy Centre, Campbelltown Hospital, Sydney, New South Wales, Australia
| | - Tara L Roberts
- Department of Medical Oncology, Bankstown-Lidcombe Hospital, Sydney, New South Wales, Australia
- Discipline of Pathology, School of Medicine, Western Sydney University, Sydney, New South Wales, Australia
- South Western Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Therese M Becker
- Department of Medical Oncology, Bankstown-Lidcombe Hospital, Sydney, New South Wales, Australia
- Discipline of Pathology, School of Medicine, Western Sydney University, Sydney, New South Wales, Australia
- South Western Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Jonathon Williamson
- Department of Respiratory Medicine, Liverpool Hospital, Sydney, New South Wales, Australia
| | - Mahtab Farzin
- Department of Anatomical Pathology, Liverpool Hospital, Sydney, New South Wales, Australia
| | - Jing J Li
- Department of Anatomical Pathology, Liverpool Hospital, Sydney, New South Wales, Australia
| | - Vivienne Lea
- Department of Anatomical Pathology, Liverpool Hospital, Sydney, New South Wales, Australia
| | - Abeer Hagelamin
- Department of Anatomical Pathology, Liverpool Hospital, Sydney, New South Wales, Australia
| | - Weng Ng
- Department of Medical Oncology, Liverpool Hospital, Sydney, New South Wales, Australia
- Ingham Institute for Applied Medical Research, Sydney, New South Wales, Australia
- Discipline of Pathology, School of Medicine, Western Sydney University, Sydney, New South Wales, Australia
- South Western Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Bin Wang
- Department of Anatomical Pathology, Liverpool Hospital, Sydney, New South Wales, Australia
| | - C Soon Lee
- Ingham Institute for Applied Medical Research, Sydney, New South Wales, Australia
- Discipline of Pathology, School of Medicine, Western Sydney University, Sydney, New South Wales, Australia
- South Western Clinical School, University of New South Wales, Sydney, New South Wales, Australia
- Department of Anatomical Pathology, Liverpool Hospital, Sydney, New South Wales, Australia
| | - Wei Chua
- Department of Medical Oncology, Liverpool Hospital, Sydney, New South Wales, Australia
- Ingham Institute for Applied Medical Research, Sydney, New South Wales, Australia
- Discipline of Pathology, School of Medicine, Western Sydney University, Sydney, New South Wales, Australia
- South Western Clinical School, University of New South Wales, Sydney, New South Wales, Australia
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Galant N, Nicoś M, Kuźnar-Kamińska B, Krawczyk P. Variant Allele Frequency Analysis of Circulating Tumor DNA as a Promising Tool in Assessing the Effectiveness of Treatment in Non-Small Cell Lung Carcinoma Patients. Cancers (Basel) 2024; 16:782. [PMID: 38398173 PMCID: PMC10887123 DOI: 10.3390/cancers16040782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/06/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Despite the different possible paths of treatment, lung cancer remains one of the leading causes of death in oncological patients. New tools guiding the therapeutic process are under scientific investigation, and one of the promising indicators of the effectiveness of therapy in patients with NSCLC is variant allele frequency (VAF) analysis. VAF is a metric characterized as the measurement of the specific variant allele proportion within a genomic locus, and it can be determined using methods based on NGS or PCR. It can be assessed using not only tissue samples but also ctDNA (circulating tumor DNA) isolated from liquid biopsy. The non-invasive characteristic of liquid biopsy enables a more frequent collection of material and increases the potential of VAF analysis in monitoring therapy. Several studies have been performed on patients with NSCLC to evaluate the possibility of VAF usage. The research carried out so far demonstrates that the evaluation of VAF dynamics may be useful in monitoring tumor progression, remission, and recurrence during or after treatment. Moreover, the use of VAF analysis appears to be beneficial in making treatment decisions. However, several issues require better understanding and standardization before VAF testing can be implemented in clinical practice. In this review, we discuss the difficulties in the application of ctDNA VAF analysis in clinical routine, discussing the diagnostic and methodological challenges in VAF measurement in liquid biopsy. We highlight the possible applications of VAF-based measurements that are under consideration in clinical trials in the monitoring of personalized treatments for patients with NSCLC.
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Affiliation(s)
- Natalia Galant
- Department of Pneumonology, Oncology and Allergology, Medical University of Lublin, 20-059 Lublin, Poland
| | - Marcin Nicoś
- Department of Pneumonology, Oncology and Allergology, Medical University of Lublin, 20-059 Lublin, Poland
| | - Barbara Kuźnar-Kamińska
- Department of Pulmonology, Allergology and Respiratory Oncology, Poznan University of Medical Sciences, 61-710 Poznan, Poland;
| | - Paweł Krawczyk
- Department of Pneumonology, Oncology and Allergology, Medical University of Lublin, 20-059 Lublin, Poland
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Incorvaia L, De Biase D, Nannini M, Fumagalli E, Vincenzi B, De Luca I, Brando C, Perez A, Pantaleo MA, Gasperoni S, D’Ambrosio L, Grignani G, Maloberti T, Pedone E, Bazan Russo TD, Mazzocca A, Algeri L, Dimino A, Barraco N, Serino R, Gristina V, Galvano A, Bazan V, Russo A, Badalamenti G. KIT/PDGFRA Variant Allele Frequency as Prognostic Factor in Gastrointestinal Stromal Tumors (GISTs): Results From a Multi-Institutional Cohort Study. Oncologist 2024; 29:e141-e151. [PMID: 37463014 PMCID: PMC10769785 DOI: 10.1093/oncolo/oyad206] [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: 04/04/2023] [Accepted: 06/09/2023] [Indexed: 01/07/2024] Open
Abstract
BACKGROUND The patient selection for optimal adjuvant therapy in gastrointestinal stromal tumors (GISTs) is provided by nomogram based on tumor size, mitotic index, tumor location, and tumor rupture. Although mutational status is not currently used to risk assessment, tumor genotype showed a prognostic influence on natural history and tumor relapse. Innovative measures, such as KIT/PDGFRA-mutant-specific variant allele frequency (VAF) levels detection from next-generation sequencing (NGS), may act as a surrogate of tumor burden and correlate with prognosis and overall survival of patients with GIST, helping the choice for adjuvant treatment. PATIENTS AND METHODS This was a multicenter, hospital-based, retrospective/prospective cohort study to investigate the prognostic role of KIT or PDGFRA-VAF of GIST in patients with radically resected localized disease. In the current manuscript, we present the results from the retrospective phase of the study. RESULTS Two-hundred (200) patients with GIST between 2015 and 2022 afferent to 6 Italian Oncologic Centers in the EURACAN Network were included in the study. The receiver operating characteristic (ROC) curves analysis was used to classify "low" vs. "high" VAF values, further normalized on neoplastic cellularity (nVAF). When RFS between the low and high nVAF groups were compared, patients with GIST with KIT/PDGFRA nVAF > 50% showed less favorable RFS than patients in the group of nVAF ≤ 50% (2-year RFS, 72.6% vs. 93%, respectively; P = .003). The multivariable Cox regression model confirmed these results. In the homogeneous sub-population of intermediate-risk, patients with KIT-mutated GIST, the presence of nVAF >50% was statistically associated with higher disease recurrence. CONCLUSION In our study, we demonstrated that higher nVAF levels were independent predictors of GIST prognosis and survival in localized GIST patients with tumors harboring KIT or PDGFRA mutations. In the cohort of intermediate-risk patients, nVAF could be helpful to improve prognostication and the use of adjuvant imatinib.
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Affiliation(s)
- Lorena Incorvaia
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, Palermo, Italy
| | - Dario De Biase
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
- Solid Tumor Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Margherita Nannini
- Department of Experimental, Diagnostic and Specialized Medicine, S. Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Elena Fumagalli
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Bruno Vincenzi
- Department of Medical Oncology, Campus Biomedico University of Rome, Rome, Italy
| | - Ida De Luca
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, Palermo, Italy
| | - Chiara Brando
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, Palermo, Italy
| | - Alessandro Perez
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, Palermo, Italy
| | - Maria A Pantaleo
- Department of Experimental, Diagnostic and Specialized Medicine, S. Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Silvia Gasperoni
- Department of Oncology and Robotic Surgery, Translational Oncology Unit, University Hospital Careggi, Firenze, Italy
| | - Lorenzo D’Ambrosio
- Division of Medical Oncology, Candiolo Cancer Institute, FPO - IRCCS, Candiolo, TO, Italy
| | - Giovanni Grignani
- Division of Medical Oncology, Candiolo Cancer Institute, FPO - IRCCS, Candiolo, TO, Italy
| | - Thais Maloberti
- Solid Tumor Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - Erika Pedone
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, Palermo, Italy
| | - Tancredi Didier Bazan Russo
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, Palermo, Italy
| | - Alessandro Mazzocca
- Department of Medical Oncology, Campus Biomedico University of Rome, Rome, Italy
| | - Laura Algeri
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, Palermo, Italy
| | - Alessandra Dimino
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, Palermo, Italy
| | - Nadia Barraco
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, Palermo, Italy
| | - Roberta Serino
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Valerio Gristina
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, Palermo, Italy
| | - Antonio Galvano
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, Palermo, Italy
| | - Viviana Bazan
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (BIND), Section of Medical Oncology, University of Palermo, Palermo, Italy
| | - Antonio Russo
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, Palermo, Italy
| | - Giuseppe Badalamenti
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, Palermo, Italy
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Hu J, Alami V, Zhuang Y, Alzofon N, Jimeno A, Gao D. Integrated variant allele frequency analysis pipeline and R package: easyVAF. Mol Carcinog 2023; 62:1877-1887. [PMID: 37606183 PMCID: PMC10843735 DOI: 10.1002/mc.23621] [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: 05/12/2023] [Revised: 07/25/2023] [Accepted: 08/02/2023] [Indexed: 08/23/2023]
Abstract
Somatic sequence variants are associated with cancer diagnosis, prognostic stratification, and treatment response. Variant allele frequency (VAF), the percentage of sequence reads with a specific DNA variant over the read depth at that locus, has been used as a metric to quantify mutation rates in these applications. VAF has the potential for feature detection by reflecting changes in tumor clonal composition across treatments or time points. Although there are several packages, including Genome Analysis Toolkit and VarScan, designed for variant calling and rare mutation identification, there is no readily available package for comparing VAFs among and between groups to identify loci of interest. To this end, we have developed the R package easyVAF, which includes parametric and nonparametric tests to compare VAFs among multiple groups. It is accompanied by an interactive R Shiny app. With easyVAF, the investigator has the option between three statistical tests to maximize power while maintaining an acceptable type I error rate. This paper presents our proposed pipeline for VAF analysis, from quality checking to group comparison. We evaluate our method in a wide range of simulated scenarios and show that choosing the appropriate test to limit the type I error rate is critical. For situations where data is sparse, we recommend comparing VAFs with the beta-binomial likelihood ratio test over Fisher's exact test and Pearson's χ2 test.
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Affiliation(s)
- Junxiao Hu
- Biostatistics Shared Resource, University of Colorado Cancer Center, University of Colorado Anschutz Medical Campus, CO, USA
- Department of Pediatrics, School of Medicine, University of Colorado Anschutz Medical Campus, CO, USA
| | - Vida Alami
- Biostatistics Shared Resource, University of Colorado Cancer Center, University of Colorado Anschutz Medical Campus, CO, USA
| | - Yonghua Zhuang
- Biostatistics Shared Resource, University of Colorado Cancer Center, University of Colorado Anschutz Medical Campus, CO, USA
- Department of Pediatrics, School of Medicine, University of Colorado Anschutz Medical Campus, CO, USA
| | - Nathaniel Alzofon
- Division of Medical Oncology, School of Medicine, University of Colorado Anschutz Medical Campus, CO, USA
| | - Antonio Jimeno
- Division of Medical Oncology, School of Medicine, University of Colorado Anschutz Medical Campus, CO, USA
| | - Dexiang Gao
- Biostatistics Shared Resource, University of Colorado Cancer Center, University of Colorado Anschutz Medical Campus, CO, USA
- Department of Pediatrics, School of Medicine, University of Colorado Anschutz Medical Campus, CO, USA
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Nindra U, Pal A, Lea V, Lim SHS, Wilkinson K, Asghari R, Roberts TL, Becker TM, Farzin M, Rutland T, Lee M, MacKenzie S, Ng W, Wang B, Lee CS, Chua W. Multigene panel next generation sequencing in metastatic colorectal cancer in an Australian population. PLoS One 2023; 18:e0292087. [PMID: 37796807 PMCID: PMC10553362 DOI: 10.1371/journal.pone.0292087] [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: 05/21/2023] [Accepted: 09/12/2023] [Indexed: 10/07/2023] Open
Abstract
BACKGROUND Next generation sequencing (NGS) is increasingly used in standard clinical practice to identify patients with potentially actionable mutations. Stratification of NGS mutation tiers is currently based on the European Society of Medical Oncology (ESMO) Scale for Clinical Actionability of Molecular Targets (ESCAT[E]) Tier I-V & X. Allele frequency is also increasingly recognised as an important prognostic tool in advanced cancer. The aim of this study was to determine the genomic mutations in metastatic colorectal cancer (CRC) in an Australian multicultural population and their influence on survival outcomes. METHODS Next generation sequencing with the 50-gene panel Oncomine Precision Assay™ was used on 180 CRC tissue samples obtained across six Sydney hospitals between June 2021 and March 2022. RESULTS From 180 samples, 147 (82%) had at least one gene mutation identified with 68 (38%) having two or more concurrent mutations. Tier I variants included RAS wild-type [EI] in 73 (41%) and BRAF V600E [EIA] in 27 (15%). Non-tier I variants include 2 (1%) ERBB2 amplification [EIIB], 26 (15%) PIK3CA hotspot mutations [EIIIA] and 9 (5%) MET focal amplifications [EIIIA]. NGS testing revealed an additional 22% of cases with Tier II & III mutations. 43% of patients also presented with potentially actionable Tier III & IV mutations. Patients with concurrent TP53 and RAS mutations had significantly reduced overall survival (6.1 months versus 21.1 months, p <0.01). High KRAS allele frequency, as defined by those with over 20% variant allele frequency (VAF), also demonstrated reduced overall survival (12.1 months versus 42.9 months, p = 0.04). CONCLUSIONS In addition to identifying patients with genomic alterations suitable for clinically proven standard of care therapeutic options, the 50 gene NGS panel has significant potential in identifying potentially actionable non-tier 1 mutations and therefore may become future standard clinical practice.
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Affiliation(s)
- Udit Nindra
- Department of Medical Oncology, Liverpool Hospital, Liverpool, New South Wales, Australia
- Department of Medical Oncology, Macarthur Cancer Therapy Centre, Campbelltown Hospital, Campbelltown, New South Wales, Australia
- Department of Medical Oncology, Bankstown-Lidcombe Hospital, Bankstown, New South Wales, Australia
- Ingham Institute for Applied Medical Research, Liverpool, Australia
- School of Medicine, Western Sydney University, Sydney, Australia
| | - Abhijit Pal
- Department of Medical Oncology, Liverpool Hospital, Liverpool, New South Wales, Australia
- Department of Medical Oncology, Bankstown-Lidcombe Hospital, Bankstown, New South Wales, Australia
- Ingham Institute for Applied Medical Research, Liverpool, Australia
| | - Vivienne Lea
- Department of Anatomical Pathology, Liverpool Hospital, Liverpool, Sydney, Australia
| | - Stephanie Hui-Su Lim
- Department of Medical Oncology, Macarthur Cancer Therapy Centre, Campbelltown Hospital, Campbelltown, New South Wales, Australia
- Ingham Institute for Applied Medical Research, Liverpool, Australia
- School of Medicine, Western Sydney University, Sydney, Australia
| | - Kate Wilkinson
- Department of Medical Oncology, Liverpool Hospital, Liverpool, New South Wales, Australia
| | - Ray Asghari
- Department of Medical Oncology, Bankstown-Lidcombe Hospital, Bankstown, New South Wales, Australia
| | - Tara L. Roberts
- Ingham Institute for Applied Medical Research, Liverpool, Australia
- School of Medicine, Western Sydney University, Sydney, Australia
- South Western Clinical School, University of New South Wales, Sydney, Australia
| | - Therese M. Becker
- Ingham Institute for Applied Medical Research, Liverpool, Australia
- School of Medicine, Western Sydney University, Sydney, Australia
- South Western Clinical School, University of New South Wales, Sydney, Australia
| | - Mahtab Farzin
- Department of Anatomical Pathology, Liverpool Hospital, Liverpool, Sydney, Australia
| | - Tristan Rutland
- School of Medicine, Western Sydney University, Sydney, Australia
- Department of Anatomical Pathology, Liverpool Hospital, Liverpool, Sydney, Australia
| | - Mark Lee
- South Western Clinical School, University of New South Wales, Sydney, Australia
| | - Scott MacKenzie
- School of Medicine, Western Sydney University, Sydney, Australia
| | - Weng Ng
- Department of Medical Oncology, Liverpool Hospital, Liverpool, New South Wales, Australia
- Ingham Institute for Applied Medical Research, Liverpool, Australia
- School of Medicine, Western Sydney University, Sydney, Australia
- South Western Clinical School, University of New South Wales, Sydney, Australia
| | - Bin Wang
- Department of Anatomical Pathology, Liverpool Hospital, Liverpool, Sydney, Australia
| | - C. Soon Lee
- Department of Medical Oncology, Bankstown-Lidcombe Hospital, Bankstown, New South Wales, Australia
- School of Medicine, Western Sydney University, Sydney, Australia
- Department of Anatomical Pathology, Liverpool Hospital, Liverpool, Sydney, Australia
- South Western Clinical School, University of New South Wales, Sydney, Australia
| | - Wei Chua
- Department of Medical Oncology, Liverpool Hospital, Liverpool, New South Wales, Australia
- Ingham Institute for Applied Medical Research, Liverpool, Australia
- School of Medicine, Western Sydney University, Sydney, Australia
- South Western Clinical School, University of New South Wales, Sydney, Australia
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8
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Garon EB, Reck M, Nishio K, Heymach JV, Nishio M, Novello S, Paz-Ares L, Popat S, Aix SP, Graham H, Butts BD, Visseren-Grul C, Nakagawa K. Ramucirumab plus erlotinib versus placebo plus erlotinib in previously untreated EGFR-mutated metastatic non-small-cell lung cancer (RELAY): exploratory analysis of next-generation sequencing results. ESMO Open 2023; 8:101580. [PMID: 37390764 PMCID: PMC10485403 DOI: 10.1016/j.esmoop.2023.101580] [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: 02/21/2023] [Revised: 04/12/2023] [Accepted: 05/08/2023] [Indexed: 07/02/2023] Open
Abstract
BACKGROUND Ramucirumab plus erlotinib (RAM + ERL) demonstrated superior progression-free survival (PFS) over placebo + ERL (PBO + ERL) in the phase III RELAY study of patients with epidermal growth factor receptor (EGFR)-mutated metastatic non-small-cell lung cancer (EGFR+ mNSCLC; NCT02411448). Next-generation sequencing (NGS) was used to identify clinically relevant alterations in circulating tumor DNA (ctDNA) and explore their impact on treatment outcomes. PATIENTS AND METHODS Eligible patients with EGFR+ mNSCLC were randomized 1 : 1 to ERL (150 mg/day) plus RAM (10 mg/kg)/PBO every 2 weeks. Liquid biopsies were to be prospectively collected at baseline, cycle 4 (C4), and postdiscontinuation follow-up. EGFR and co-occurring/treatment-emergent (TE) genomic alterations in ctDNA were analyzed using Guardant360 NGS platform. RESULTS In those with valid baseline samples, detectable activating EGFR alterations in ctDNA (aEGFR+) were associated with shorter PFS [aEGFR+: 12.7 months (n = 255) versus aEGFR-: 22.0 months (n = 131); hazard ratio (HR) = 1.87, 95% confidence interval (CI) 1.42-2.51]. Irrespective of detectable/undetectable baseline aEGFR, RAM + ERL was associated with longer PFS versus PBO + ERL [aEGFR+: median PFS (mPFS) = 15.2 versus 11.1 months, HR = 0.63, 95% CI 0.46-0.85; aEGFR-: mPFS = 22.1 versus 19.2 months, HR = 0.80, 95% CI 0.49-1.30]. Baseline alterations co-occurring with aEGFR were identified in 69 genes, most commonly TP53 (43%), EGFR (other than aEGFR; 25%), and PIK3CA (10%). PFS was longer in RAM + ERL, irrespective of baseline co-occurring alterations. Clearance of baseline aEGFR by C4 was associated with longer PFS (mPFS = 14.1 versus 7.0 months, HR = 0.481, 95% CI 0.33-0.71). RAM + ERL improved PFS outcomes, irrespective of aEGFR mutation clearance. TE gene alterations were most commonly in EGFR [T790M (29%), other (19%)] and TP53 (16%). CONCLUSIONS Baseline aEGFR alterations in ctDNA were associated with shorter mPFS. RAM + ERL was associated with improved PFS outcomes, irrespective of detectable/undetectable aEGFR, co-occurring baseline alterations, or aEGFR+ clearance by C4. aEGFR+ clearance by C4 was associated with improved PFS outcomes. Monitoring co-occurring alterations and aEGFR+ clearance may provide insights into mechanisms of EGFR tyrosine kinase inhibitor resistance and the patients who may benefit from intensified treatment schedules.
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Affiliation(s)
- E B Garon
- David Geffen School of Medicine at University of California Los Angeles/TRIO-US Network, Los Angeles, USA.
| | - M Reck
- LungenClinic, Airway Research Center North (ARCN), German Center for Lung Research (DZL), Grosshansdorf, Germany
| | - K Nishio
- Department of Medical Oncology, Kindai University, Osaka, Japan
| | - J V Heymach
- Department of Thoracic/Head & Neck Medical Oncology, University of Texas, MD Anderson Cancer Center, Houston, USA; Department of Cancer Biology, University of Texas, MD Anderson Cancer Center, Houston, USA
| | - M Nishio
- Department of Thoracic Medical Oncology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - S Novello
- Department of Oncology, AOU San Luigi, University of Turin, Turin, Italy
| | - L Paz-Ares
- Medical Oncology Department, Hospital Universitario Doce de Octubre, Madrid, Spain
| | - S Popat
- Royal Marsden NHS Trust, London, UK
| | - S Ponce Aix
- Hospital Universitario 12 de Octubre, Madrid, Spain
| | - H Graham
- Eli Lilly and Company, Indianapolis, USA
| | - B D Butts
- Eli Lilly and Company, Indianapolis, USA
| | | | - K Nakagawa
- Department of Medical Oncology, Kindai University Faculty of Medicine, Osaka, Japan
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9
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Rao W, Liu Y, Li Y, Guo L, Qiu T, Dong L, Ying J, Li W. Potential unreliability of ALK variant allele frequency in the efficacy prediction of targeted therapy in NSCLC. Front Med 2023; 17:493-502. [PMID: 37010729 DOI: 10.1007/s11684-022-0946-x] [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: 04/05/2022] [Accepted: 06/28/2022] [Indexed: 04/04/2023]
Abstract
Anaplastic lymphoma kinase (ALK) is the most common fusion gene involved in non-small cell lung cancer (NSCLC), and remarkable response has been achieved with the use of ALK tyrosine kinase inhibitors (ALK-TKIs). However, the clinical efficacy is highly variable. Pre-existing intratumoral heterogeneity (ITH) has been proven to contribute to the poor treatment response and the resistance to targeted therapies. In this work, we investigated whether the variant allele frequencies (VAFs) of ALK fusions can help assess ITH and predict targeted therapy efficacy. Through the application of next-generation sequencing (NGS), 7.2% (326/4548) of patients were detected to be ALK positive. On the basis of the adjusted VAF (adjVAF, VAF normalization for tumor purity) of four different threshold values (adjVAF < 50%, 40%, 30%, or 20%), the association of ALK subclonality with crizotinib efficacy was assessed. Nonetheless, no statistical association was observed between median progression-free survival (PFS) and ALK subclonality assessed by adjVAF, and a poor correlation of adjVAF with PFS was found among the 85 patients who received first-line crizotinib. Results suggest that the ALK VAF determined by hybrid capture-based NGS is probably unreliable for ITH assessment and targeted therapy efficacy prediction in NSCLC.
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Affiliation(s)
- Wei Rao
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yutao Liu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yan Li
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Lei Guo
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Tian Qiu
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Lin Dong
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jianming Ying
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Weihua Li
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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10
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Pezzuto F, Hofman V, Bontoux C, Fortarezza F, Lunardi F, Calabrese F, Hofman P. The significance of co-mutations in EGFR-mutated non-small cell lung cancer: Optimizing the efficacy of targeted therapies? Lung Cancer 2023; 181:107249. [PMID: 37244040 DOI: 10.1016/j.lungcan.2023.107249] [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: 02/27/2023] [Revised: 05/03/2023] [Accepted: 05/11/2023] [Indexed: 05/29/2023]
Abstract
Non-small cell lung cancer (NSCLC) is the most common cause of cancer death worldwide. In non-squamous NSCLC, the identification of oncogenic drivers and the development of target-specific molecules led to remarkable progress in therapeutic strategies and overall survival over the last decade. Nevertheless, responses are limited by systematically acquired mechanisms of resistance early on after starting a targeted therapy. Moreover, mounting evidence has demonstrated that each oncogenic-driven cluster is actually heterogeneous in terms of molecular features, clinical behaviour, and sensitivity to targeted therapy. In this review, we aimed to examine the prognostic and predictive significance of oncogene-driven co-mutations, focusing mainly on EGFR and TP53. A narrative review was performed by searching MEDLINE databases for English articles published over the last decade (from January 2012 until November 2022). The bibliographies of key references were manually reviewed to select those eligible for the topic. The genetic landscape of EGFR-mutated NSCLC is more complicated than what is known so far. In particular, the occurrence of TP53 co-mutations stratify patients carrying EGFR mutations in terms of treatment response. The study provides a deeper understanding of the mechanisms underlying the variability of the genetic landscape of EGFR-mutated NSCLC and summarizes notably the clinical importance of TP53 co-mutations for an open avenue to more properly addressing the clinical decision-making in the near future.
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Affiliation(s)
- Federica Pezzuto
- University Côte d'Azur, Laboratory of Clinical and Experimental Pathology, FHU OncoAge, BB-0033-00025, Pasteur Hospital, 30 voie romaine, 06001 Nice, France; Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova Medical School, Via A. Gabelli 61, 35121 Padova, Italy.
| | - Véronique Hofman
- University Côte d'Azur, Laboratory of Clinical and Experimental Pathology, FHU OncoAge, BB-0033-00025, Pasteur Hospital, 30 voie romaine, 06001 Nice, France
| | - Christophe Bontoux
- University Côte d'Azur, Laboratory of Clinical and Experimental Pathology, FHU OncoAge, BB-0033-00025, Pasteur Hospital, 30 voie romaine, 06001 Nice, France
| | - Francesco Fortarezza
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova Medical School, Via A. Gabelli 61, 35121 Padova, Italy
| | - Francesca Lunardi
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova Medical School, Via A. Gabelli 61, 35121 Padova, Italy
| | - Fiorella Calabrese
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova Medical School, Via A. Gabelli 61, 35121 Padova, Italy
| | - Paul Hofman
- University Côte d'Azur, Laboratory of Clinical and Experimental Pathology, FHU OncoAge, BB-0033-00025, Pasteur Hospital, 30 voie romaine, 06001 Nice, France.
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11
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Corrected Allele Frequency of BRCA1/2 Mutations Is an Independent Prognostic Factor for Treatment Response to PARP-Inhibitors in Ovarian Cancer Patients. J Pers Med 2022; 12:jpm12091467. [PMID: 36143252 PMCID: PMC9504000 DOI: 10.3390/jpm12091467] [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: 08/10/2022] [Revised: 08/29/2022] [Accepted: 09/02/2022] [Indexed: 11/17/2022] Open
Abstract
PARP inhibitors (PARPi) have increased treatment options in ovarian cancer, particularly in patients with BRCA1/2 mutations, although there are still marked differences in the duration of patients’ response to this targeted therapy. BRCA testing is routinely performed in tumor tissue of ovarian cancer patients. The resulting molecular pathological findings include the genetic nomenclature of the mutation, the frequency of the mutated allele (variant allele frequency, VAF), and the tumor cell content. VAF measures the percentage of mutated alleles from the total alleles in the cells of the examined tissue. The aim of this study was to investigate the significance of VAF on the therapeutic response to PARPis in ovarian cancer patients. Epithelial ovarian cancer patients harboring BRCA1/2 tumor mutations, who underwent germline testing and received PARPi therapy at the Medical University of Vienna (n = 41) were included in the study. Corrected VAF (cVAF) was calculated based on VAF, tumor cell content, and germline mutation. Patients were divided into two groups based on their cVAF. Median PFS under PARPi in patients with low cVAF was 13.0 months (IQR [10.3-not reached]) and was not reached in the high cVAF group. High cVAF was significantly associated with longer PFS in the multivariate analysis (HR = 0.07; 95% CI [0.01–0.63]; p = 0.017). In conclusion, high cVAF was associated with a significantly better response to PARPi in this study population.
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12
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Long Q, Yuan Y, Li M. RNA-SSNV: A Reliable Somatic Single Nucleotide Variant Identification Framework for Bulk RNA-Seq Data. Front Genet 2022; 13:865313. [PMID: 35846154 PMCID: PMC9279659 DOI: 10.3389/fgene.2022.865313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 05/17/2022] [Indexed: 11/13/2022] Open
Abstract
The usage of expressed somatic mutations may have a unique advantage in identifying active cancer driver mutations. However, accurately calling mutations from RNA-seq data is difficult due to confounding factors such as RNA-editing, reverse transcription, and gap alignment. In the present study, we proposed a framework (named RNA-SSNV, https://github.com/pmglab/RNA-SSNV) to call somatic single nucleotide variants (SSNV) from tumor bulk RNA-seq data. Based on a comprehensive multi-filtering strategy and a machine-learning classification model trained with comprehensively curated features, RNA-SSNV achieved the best precision–recall rate (0.880–0.884) in a testing dataset and robustly retained 0.94 AUC for the precision–recall curve in three validation adult-based TCGA (The Cancer Genome Atlas) datasets. We further showed that the somatic mutations called by RNA-SSNV tended to have a higher functional impact and therapeutic power in known driver genes. Furthermore, VAF (variant allele fraction) analysis revealed that subclonal harboring expressed mutations had evolutional selection advantage and RNA had higher detection power to rescue DNA-omitted mutations. In sum, RNA-SSNV will be a useful approach to accurately call expressed somatic mutations for a more insightful analysis of cancer drive genes and carcinogenic mechanisms.
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Affiliation(s)
- Qihan Long
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Center for Precision Medicine, Sun Yat-Sen University, Guangzhou, China
- Center for Disease Genome Research, Sun Yat-Sen University, Guangzhou, China
| | - Yangyang Yuan
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Center for Precision Medicine, Sun Yat-Sen University, Guangzhou, China
- Center for Disease Genome Research, Sun Yat-Sen University, Guangzhou, China
| | - Miaoxin Li
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Center for Precision Medicine, Sun Yat-Sen University, Guangzhou, China
- Center for Disease Genome Research, Sun Yat-Sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, China
- Key Laboratory of Tropical Disease Control (SYSU), Ministry of Education, Guangzhou, China
- *Correspondence: Miaoxin Li,
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13
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Barzilai O, Martin A, Reiner AS, Laufer I, Schmitt A, Bilsky MH. Clinical reliability of genomic data obtained from spinal metastatic tumor samples. Neuro Oncol 2022; 24:1090-1100. [PMID: 34999837 PMCID: PMC9248391 DOI: 10.1093/neuonc/noac009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND The role of tumor genomic profiling is rapidly growing as it results in targeted, personalized, cancer therapy. Though routinely used in clinical practice, there are no data exploring the reliability of genomic data obtained from spine metastases samples often leading to multiple biopsies in clinical practice. This study compares the genomic tumor landscape between spinal metastases and the corresponding primary tumors as well as between spinal metastases and visceral metastases. METHODS Spine tumor samples, obtained for routine clinical care from 2013 to 2019, were analyzed using MSK-IMPACT, a next-generation sequencing assay. These samples were matched to primary or metastatic tumors from the corresponding patients. A concordance rate for genomic alterations was calculated for matching sample pairs within patients for the primary and spinal metastatic tumor samples as well as for the matching sample pairs within patients for the spinal and visceral metastases. For a more robust and clinically relevant estimate of concordance, subgroup analyses of previously established driver mutations specific to the main primary tumor histologies were performed. RESULTS Eighty-four patients contributed next-generation sequencing data from a spinal metastasis and at least one other site of disease: 54 from the primary tumor, 39 had genomic tumor data from another, nonspinal metastasis, 12 patients participated in both subsets. For the cohort of matched primary tumors and spinal metastases (n = 54) comprised of mixed histologies, we found an average concordance rate of 96.97% for all genetic events, 97.17% for mutations, 100% for fusions, 89.81% for deletions, and 97.01% for amplifications across all matched samples. Notably, >25% of patients harbored at least one genetic variant between samples tested, though not specifically for known driver mutations. The average concordance rate of driver mutations was 96.99% for prostate cancer, 95.69% (P = .0004513) for lung cancer, and 96.43% for breast cancer. An average concordance of 99.02% was calculated for all genetic events between spine metastases and non-spinal metastases (n = 41) and, more specifically, a concordance rate of 98.91% was calculated between spine metastases and liver metastases (n = 12) which was the largest represented group of nonspine metastases. CONCLUSION Sequencing data performed on spine tumor samples demonstrate a high concordance rate for genetic alterations between the primary tumor and spinal metastasis as well as between spinal metastases and other, visceral metastases, particularly for driver mutations. Spine tumor samples may be reliably used for genomic-based decision making in cancer care, particularly for prostate, NSCLC, and breast cancer.
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Affiliation(s)
- Ori Barzilai
- Corresponding Author: Ori Barzilai, MD, Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA ()
| | - Axel Martin
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | - Anne S Reiner
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | - Ilya Laufer
- Department of Neurosurgery, New York University School of Medicine, New York, New York, USA
| | - Adam Schmitt
- Department of Radiation Oncology, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | - Mark H Bilsky
- Department of Neurosurgery, Memorial Sloan-Kettering Cancer Center, New York, New York, USA,Department of Neurological Surgery, Weill Cornell Medical College, New York, New York, USA
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14
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Passaro A, de Marinis F, Tu HY, Laktionov KK, Feng J, Poltoratskiy A, Zhao J, Tan EH, Gottfried M, Lee V, Kowalski D, Yang CT, Srinivasa BJ, Clementi L, Jalikop T, Huang DCL, Cseh A, Park K, Wu YL. Afatinib in EGFR TKI-Naïve Patients with Locally Advanced or Metastatic EGFR Mutation-Positive Non-Small Cell Lung Cancer: A Pooled Analysis of Three Phase IIIb Studies. Front Oncol 2021; 11:709877. [PMID: 34307179 PMCID: PMC8298067 DOI: 10.3389/fonc.2021.709877] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 06/21/2021] [Indexed: 01/26/2023] Open
Abstract
Background Afatinib is approved for first-line treatment of patients with epidermal growth factor receptor mutation-positive (EGFRm+) non-small-cell lung cancer (NSCLC). Here, we report findings from a combined analysis of three phase IIIb studies of afatinib in EGFR tyrosine kinase inhibitor (TKI)-naïve patients. Methods EGFR-TKI-naïve patients with EGFRm+ NSCLC received afatinib 40 mg/day. Dose reductions were permitted for adverse events (AEs). Efficacy endpoints included progression-free survival (PFS), time to symptomatic progression (TTSP), and tumor response. Subgroup analyses were performed by Eastern Cooperative Oncology Group performance status (ECOG PS), presence of brain metastasis, age and common/uncommon EGFR mutations (plus other factors). Results 1108 patients were treated. Median age was 61 years (range, 25-89); 19.2% had baseline brain metastases, 4.4% had ECOG PS ≥2, and 17.9% had tumors harboring uncommon mutations. Treatment-related AEs (TRAEs) were reported in 97.2%, most commonly diarrhea and rash. 41.6% had AEs leading to dose reduction. Median PFS was 13.0 months [95% confidence interval (CI): 12.0-13.8]; median TTSP was 14.8 months (95% CI: 13.9-16.1). Objective response rate (ORR) was 55.0%. Age, presence of baseline brain metastases, major (G719X, L861Q, S768I) or compound uncommon mutations had little/no effect on PFS, TTSP, or ORR, while outcomes were poorer in patients with ECOG PS 2 or exon 20 insertion/T790M mutations. Conclusions Afatinib was tolerable with no new safety signals. Afatinib demonstrated encouraging efficacy in a broad patient population, including those with brain metastases or uncommon EGFR mutations.
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Affiliation(s)
- Antonio Passaro
- Division of Thoracic Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Filippo de Marinis
- Division of Thoracic Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Hai-Yan Tu
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | | | - Jifeng Feng
- Jiangsu Provincial Tumor Hospital, Nanjing, China
| | | | - Jun Zhao
- Peking University Cancer Hospital & Institute, Beijing, China
| | | | | | - Victor Lee
- Department of Clinical Oncology, Queen Mary Hospital, The University of Hong Kong, Hong Kong, China
| | - Dariusz Kowalski
- Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Cheng Ta Yang
- Chang Gung Memorial Hospital, Guishan, Taoyuan, Taiwan
| | | | | | | | | | - Agnieszka Cseh
- Boehringer Ingelheim International GmbH, Ingelheim am Rhein, Germany
| | - Keunchil Park
- Division of Hematology Oncology, Samsung Medical Center Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Yi-Long Wu
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
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15
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Crombet Ramos T, Santos Morales O, Dy GK, León Monzón K, Lage Dávila A. The Position of EGF Deprivation in the Management of Advanced Non-Small Cell Lung Cancer. Front Oncol 2021; 11:639745. [PMID: 34211836 PMCID: PMC8240591 DOI: 10.3389/fonc.2021.639745] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 05/17/2021] [Indexed: 12/22/2022] Open
Abstract
Advanced non-small cell lung cancer (NSCLC) has faced a therapeutic revolution with the advent of tyrosine kinase inhibitors (TKIs) and immune checkpoints inhibitors (ICIs) approved for first and subsequent therapies. CIMAvax-EGF is a chemical conjugate between human-recombinant EGF and P64, a recombinant protein from Neisseria meningitides, which induces neutralizing antibodies against EGF. In the last 15 years, it has been extensively evaluated in advanced NSCLC patients. CIMAvax-EGF is safe, even after extended use, and able to keep EGF serum concentration below detectable levels. In a randomized phase III study, CIMAvax-EGF increased median overall survival of advanced NSCLC patients with at least stable disease after front-line chemotherapy. Patients bearing squamous-cell or adenocarcinomas and serum EGF concentration above 870 pg/ml had better survival compared to control patients treated with best supportive care as maintenance, confirming tumors’ sensitivity to the EGF depletion. This manuscript reviews the state-of-the-art NSCLC therapy and proposes the most promising scenarios for evaluating CIMAvax-EGF, particularly in combination with TKIs or ICIs. We hypothesize that the optimal combination of CIMAvax-EGF with established therapies can further contribute to transform advanced cancer into a manageable chronic disease, compatible with years of good quality of life.
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Affiliation(s)
| | | | - Grace K Dy
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
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