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Thiery J, Fahrner M. Integration of proteomics in the molecular tumor board. Proteomics 2024; 24:e2300002. [PMID: 38143279 DOI: 10.1002/pmic.202300002] [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: 07/24/2023] [Revised: 12/03/2023] [Accepted: 12/05/2023] [Indexed: 12/26/2023]
Abstract
Cancer remains one of the most complex and challenging diseases in mankind. To address the need for a personalized treatment approach for particularly complex tumor cases, molecular tumor boards (MTBs) have been initiated. MTBs are interdisciplinary teams that perform in-depth molecular diagnostics to cooperatively and interdisciplinarily advise on the best therapeutic strategy. Current molecular diagnostics are routinely performed on the transcriptomic and genomic levels, aiming to identify tumor-driving mutations. However, these approaches can only partially capture the actual phenotype and the molecular key players of tumor growth and progression. Thus, direct investigation of the expressed proteins and activated signaling pathways provide valuable complementary information on the tumor-driving molecular characteristics of the tissue. Technological advancements in mass spectrometry-based proteomics enable the robust, rapid, and sensitive detection of thousands of proteins in minimal sample amounts, paving the way for clinical proteomics and the probing of oncogenic signaling activity. Therefore, proteomics is currently being integrated into molecular diagnostics within MTBs and holds promising potential in aiding tumor classification and identifying personalized treatment strategies. This review introduces MTBs and describes current clinical proteomics, its potential in precision oncology, and highlights the benefits of multi-omic data integration.
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Affiliation(s)
- Johanna Thiery
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Matthias Fahrner
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Freiburg, Germany
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2
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Vanni I, Pastorino L, Andreotti V, Comandini D, Fornarini G, Grassi M, Puccini A, Tanda ET, Pastorino A, Martelli V, Mastracci L, Grillo F, Cabiddu F, Guadagno A, Coco S, Allavena E, Barbero F, Bruno W, Dalmasso B, Bellomo SE, Marchiò C, Spagnolo F, Sciallero S, Berrino E, Ghiorzo P. Combining germline, tissue and liquid biopsy analysis by comprehensive genomic profiling to improve the yield of actionable variants in a real-world cancer cohort. J Transl Med 2024; 22:462. [PMID: 38750555 PMCID: PMC11097509 DOI: 10.1186/s12967-024-05227-2] [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: 02/23/2024] [Accepted: 04/22/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND Comprehensive next-generation sequencing is widely used for precision oncology and precision prevention approaches. We aimed to determine the yield of actionable gene variants, the capacity to uncover hereditary predisposition and liquid biopsy appropriateness instead of, or in addition to, tumor tissue analysis, in a real-world cohort of cancer patients, who may benefit the most from comprehensive genomic profiling. METHODS Seventy-eight matched germline/tumor tissue/liquid biopsy DNA and RNA samples were profiled using the Hereditary Cancer Panel (germline) and the TruSight Oncology 500 panel (tumor tissue/cfDNA) from 23 patients consecutively enrolled at our center according to at least one of the following criteria: no available therapeutic options; long responding patients potentially fit for other therapies; rare tumor; suspected hereditary cancer; primary cancer with high metastatic potential; tumor of unknown primary origin. Variants were annotated for OncoKB and AMP/ASCO/CAP classification. RESULTS The overall yield of actionable somatic and germline variants was 57% (13/23 patients), and 43.5%, excluding variants previously identified by somatic or germline routine testing. The accuracy of tumor/cfDNA germline-focused analysis was demonstrated by overlapping results of germline testing. Five germline variants in BRCA1, VHL, CHEK1, ATM genes would have been missed without extended genomic profiling. A previously undetected BRAF p.V600E mutation was emblematic of the clinical utility of this approach in a patient with a liver undifferentiated embryonal sarcoma responsive to BRAF/MEK inhibition. CONCLUSIONS Our study confirms the clinical relevance of performing extended parallel tumor DNA and cfDNA testing to broaden therapeutic options, to longitudinally monitor cfDNA during patient treatment, and to uncover possible hereditary predisposition following tumor sequencing in patient care.
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Affiliation(s)
- I Vanni
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - L Pastorino
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, 16132, Genoa, Italy
| | - V Andreotti
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - D Comandini
- Medical Oncology Unit 1, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - G Fornarini
- Medical Oncology Unit 1, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - M Grassi
- Medical Oncology Unit 1, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - A Puccini
- Medical Oncology Unit 1, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - E T Tanda
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, 16132, Genoa, Italy
- Medical Oncology Unit 2, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - A Pastorino
- Medical Oncology Unit 1, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - V Martelli
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, 16132, Genoa, Italy
- Medical Oncology Unit 1, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - L Mastracci
- Pathology Unit, Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, 16132, Genoa, Italy
- Pathology Unit, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - F Grillo
- Pathology Unit, Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, 16132, Genoa, Italy
- Pathology Unit, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - F Cabiddu
- Pathology Unit, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - A Guadagno
- Pathology Unit, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - S Coco
- Lung Cancer Unit, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - E Allavena
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, 16132, Genoa, Italy
| | - F Barbero
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - W Bruno
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, 16132, Genoa, Italy
| | - B Dalmasso
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - S E Bellomo
- Pathology Unit, Candiolo Cancer Institute, FPO - IRCCS, 10060, Candiolo, Turin, Italy
| | - C Marchiò
- Pathology Unit, Candiolo Cancer Institute, FPO - IRCCS, 10060, Candiolo, Turin, Italy
- Department of Medical Sciences, University of Torino, 10060, Turin, Italy
| | - F Spagnolo
- Medical Oncology Unit 2, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
- Plastic Surgery, Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, 16132, Genoa, Italy
| | - S Sciallero
- Medical Oncology Unit 1, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy
| | - E Berrino
- Pathology Unit, Candiolo Cancer Institute, FPO - IRCCS, 10060, Candiolo, Turin, Italy
- Department of Medical Sciences, University of Torino, 10060, Turin, Italy
| | - P Ghiorzo
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, 16132, Genoa, Italy.
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, 16132, Genoa, Italy.
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3
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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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Meireles SI, Cruz MV, de Godoy CD, de Testagrossa L. Performance of non-formalin fixed paraffin embedded samples in hybrid capture and amplicon next-generation sequencing panels. Diagn Cytopathol 2024; 52:171-182. [PMID: 38124281 DOI: 10.1002/dc.25267] [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: 09/06/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND Genomic profiling using next-generation sequencing (NGS) is fundamental for driving prognostic and therapy in cancer. Formalin-fixed paraffin embedded (FFPE) tissue is the widely used material, whereas non-FFPE may represent an alternative. However, studies comparing the NGS performance of non-FFPE materials to FFPE are still lacking in the literature. The objective of this study was to characterize in non-FFPE preparations the nucleic acid yield and NGS performance on both a capture-based and an amplicon-based NGS platform. NGS quality metrics obtained from non-FFPE preparations were compared to FFPE. METHODS We analyzed the cellularity and nucleic acid yield in 111 tumors from non-FFPE preparations. In addition, comprehensive hybrid capture panel sequencing metrics obtained from DNA and RNA libraries were compared between independent non-FFPE and FFPE samples. A paired comparison between non-FFPE and FFPE samples was performed to analyze concordance in mutant allele detection using an amplicon panel. RESULTS The mean target coverage from DNA libraries was 2× higher in non-FFPE samples than in FFPE. The detection of exogenous DNA was 2.5× higher in non-FFPE than in FFPE. Conversely, a lower performance was observed in non-FFPE RNA libraries in comparison to FFPE DNA libraries with no impact in minimum standard cutoffs. The variant allele detection in non-FFPE was found to be comparable to that of FFPE tumor samples in matched samples. CONCLUSIONS Non-FFPE was demonstrated to be a suitable material for DNA and RNA library preparations using a comprehensive NGS panel. This is the first study reporting library quality metrics according to the TSO500 analysis pipeline.
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Affiliation(s)
- Sibele Inácio Meireles
- Departamento de Anatomia Patológica e Molecular, Hospital Sírio Libanês, São Paulo, Brazil
| | - Mariana Vargas Cruz
- Departamento de Anatomia Patológica e Molecular, Hospital Sírio Libanês, São Paulo, Brazil
| | - Carla Daniele de Godoy
- Departamento de Anatomia Patológica e Molecular, Hospital Sírio Libanês, São Paulo, Brazil
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Mosteiro M, Azuara D, Villatoro S, Alay A, Gausachs M, Varela M, Baixeras N, Pijuan L, Ajenjo-Bauza M, Lopez-Doriga A, Teulé Á, Solanes A, Palmero R, Brenes J, Jové M, Padrones S, Moreno V, Cordero D, Matías-Guiu X, Lázaro C, Nadal E. Molecular profiling and feasibility using a comprehensive hybrid capture panel on a consecutive series of non-small-cell lung cancer patients from a single centre. ESMO Open 2023; 8:102197. [PMID: 38070435 PMCID: PMC10774954 DOI: 10.1016/j.esmoop.2023.102197] [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: 07/03/2023] [Revised: 11/04/2023] [Accepted: 11/13/2023] [Indexed: 12/31/2023] Open
Abstract
BACKGROUND Targeted next-generation sequencing (NGS) is recommended to screen actionable genomic alterations (GAs) in patients with non-small-cell lung cancer (NSCLC). We determined the feasibility to detect actionable GAs using TruSight™ Oncology 500 (TSO500) in 200 consecutive patients with NSCLC. MATERIALS AND METHODS DNA and RNA were sequenced on an Illumina® NextSeq 550 instrument and processed using the TSO500 Docker pipeline. Clinical actionability was defined within the molecular tumour board following European Society for Medical Oncology (ESMO) guidelines for oncogene-addicted NSCLC. Overall survival (OS) was estimated as per the presence of druggable GAs and treatment with targeted therapy. RESULTS Most patients were males (69.5%) and former or current smokers (86.5%). Median age was 64 years. The most common histological type and tumour stage were lung adenocarcinoma (81%) and stage IV (64%), respectively. Sequencing was feasible in most patients (93.5%) and actionable GAs were found in 26.5% of patients. A high concordance was observed between single-gene testing and TSO500 NGS panel. Patients harbouring druggable GAs and receiving targeted therapy achieved longer OS compared to patients without druggable GAs. Conversely, patients with druggable GAs not receiving targeted therapy had a trend toward shorter OS compared with driver-negative patients. CONCLUSIONS Hybrid capture sequencing using TSO500 panel is feasible to analyse clinical samples from patients with NSCLC and is an efficient tool for screening actionable GAs.
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Affiliation(s)
- M Mosteiro
- Department of Medical Oncology, Catalan Institute of Oncology (ICO), L'Hospitalet del Llobregat, Barcelona, Spain; Preclinical and Experimental Research in Thoracic Tumors (PReTT), Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - D Azuara
- Laboratory Core Molecular Analysis (L-CAM), Hospital Universitari de Bellvitge and Catalan Institute of Oncology, L'Hospitalet del Llobregat, Barcelona, Spain; Hereditary Cancer Program, Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell) Program, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Spain
| | - S Villatoro
- Laboratory Core Molecular Analysis (L-CAM), Hospital Universitari de Bellvitge and Catalan Institute of Oncology, L'Hospitalet del Llobregat, Barcelona, Spain; Department of Pathology, Hospital Universitari de Bellvitge and Catalan Institute of Oncology (ICO), L'Hospitalet del Llobregat, Barcelona, Spain
| | - A Alay
- Preclinical and Experimental Research in Thoracic Tumors (PReTT), Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain; Unit of Bioinformatics for Precision Oncology (UBOP), Catalan Institute of Oncology (ICO), L'Hospitalet de Llobregat, Barcelona, Spain
| | - M Gausachs
- Department of Medical Oncology, Catalan Institute of Oncology (ICO), L'Hospitalet del Llobregat, Barcelona, Spain; Preclinical and Experimental Research in Thoracic Tumors (PReTT), Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - M Varela
- Laboratory Core Molecular Analysis (L-CAM), Hospital Universitari de Bellvitge and Catalan Institute of Oncology, L'Hospitalet del Llobregat, Barcelona, Spain; Department of Pathology, Hospital Universitari de Bellvitge and Catalan Institute of Oncology (ICO), L'Hospitalet del Llobregat, Barcelona, Spain
| | - N Baixeras
- Department of Pathology, Hospital Universitari de Bellvitge and Catalan Institute of Oncology (ICO), L'Hospitalet del Llobregat, Barcelona, Spain
| | - L Pijuan
- Department of Pathology, Hospital Universitari de Bellvitge and Catalan Institute of Oncology (ICO), L'Hospitalet del Llobregat, Barcelona, Spain
| | - M Ajenjo-Bauza
- Unit of Bioinformatics for Precision Oncology (UBOP), Catalan Institute of Oncology (ICO), L'Hospitalet de Llobregat, Barcelona, Spain
| | - A Lopez-Doriga
- Preclinical and Experimental Research in Thoracic Tumors (PReTT), Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain; Unit of Bioinformatics for Precision Oncology (UBOP), Catalan Institute of Oncology (ICO), L'Hospitalet de Llobregat, Barcelona, Spain; Centro de Investigación Biomédica en Red de Epidemiologia y Salud Pública (CIBERESP), Madrid, Spain
| | - Á Teulé
- Department of Medical Oncology, Catalan Institute of Oncology (ICO), L'Hospitalet del Llobregat, Barcelona, Spain; Hereditary Cancer Program, Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell) Program, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Spain
| | - A Solanes
- Department of Medical Oncology, Catalan Institute of Oncology (ICO), L'Hospitalet del Llobregat, Barcelona, Spain; Hereditary Cancer Program, Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell) Program, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Spain
| | - R Palmero
- Department of Medical Oncology, Catalan Institute of Oncology (ICO), L'Hospitalet del Llobregat, Barcelona, Spain; Preclinical and Experimental Research in Thoracic Tumors (PReTT), Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - J Brenes
- Department of Medical Oncology, Catalan Institute of Oncology (ICO), L'Hospitalet del Llobregat, Barcelona, Spain; Preclinical and Experimental Research in Thoracic Tumors (PReTT), Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - M Jové
- Department of Medical Oncology, Catalan Institute of Oncology (ICO), L'Hospitalet del Llobregat, Barcelona, Spain; Preclinical and Experimental Research in Thoracic Tumors (PReTT), Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - S Padrones
- Department of Respiratory Medicine, Hospital Universitari de Bellvitge, L'Hospitalet del Llobregat, Barcelona, Spain
| | - V Moreno
- Centro de Investigación Biomédica en Red de Epidemiologia y Salud Pública (CIBERESP), Madrid, Spain; Oncology Data Analytics Program, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain; Department of Clinical Sciences, Faculty of Medicine, and Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona, Barcelona, Spain
| | - D Cordero
- Preclinical and Experimental Research in Thoracic Tumors (PReTT), Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain; Department of Pathology, Hospital Universitari de Bellvitge and Catalan Institute of Oncology (ICO), L'Hospitalet del Llobregat, Barcelona, Spain; Unit of Bioinformatics for Precision Oncology (UBOP), Catalan Institute of Oncology (ICO), L'Hospitalet de Llobregat, Barcelona, Spain; Centro de Investigación Biomédica en Red de Epidemiologia y Salud Pública (CIBERESP), Madrid, Spain.
| | - X Matías-Guiu
- Laboratory Core Molecular Analysis (L-CAM), Hospital Universitari de Bellvitge and Catalan Institute of Oncology, L'Hospitalet del Llobregat, Barcelona, Spain; Department of Pathology, Hospital Universitari de Bellvitge and Catalan Institute of Oncology (ICO), L'Hospitalet del Llobregat, Barcelona, Spain.
| | - C Lázaro
- Laboratory Core Molecular Analysis (L-CAM), Hospital Universitari de Bellvitge and Catalan Institute of Oncology, L'Hospitalet del Llobregat, Barcelona, Spain; Hereditary Cancer Program, Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell) Program, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
| | - E Nadal
- Department of Medical Oncology, Catalan Institute of Oncology (ICO), L'Hospitalet del Llobregat, Barcelona, Spain; Preclinical and Experimental Research in Thoracic Tumors (PReTT), Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain.
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6
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Delsupehe L, Steelandt T, Lemahieu J, Volders PJ, Geerdens E, Berden S, Daniels A, Froyen G, Maes B. Novel gene fusion discovery in Spitz tumours and its relevance in diagnostics. Virchows Arch 2023:10.1007/s00428-023-03649-9. [PMID: 37731064 DOI: 10.1007/s00428-023-03649-9] [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: 06/07/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 09/22/2023]
Abstract
In addition to morphologic analysis, molecular diagnostic work up of Spitz tumours is often of great value for their accurate diagnosis/classification. Nowadays, next-generation sequencing (NGS) is the predominant screening method in molecular diagnostics. Up to 80% of these melanocytic neoplasms comprise gene fusions as genetic anomalies for which the driver codes for a protein harbouring a kinase domain. However, because of the variety of fusion partners the use of PCR-based targeted enrichment NGS methods is not recommended. We describe a series of four Spitz tumour samples in which distinct gene fusions were detected by hybridisation-based capture NGS (TPM3::ALK, LIMA1::ROS1, LRRFIP2::ROS1 and MYO5A::RET). Two of these fusions are not previously described. All 4 fusions were confirmed by reverse transcription-PCR. These findings demonstrate the need for molecular analysis that can detect unknown fusions in Spitz neoplasms for optimal diagnosis.
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Affiliation(s)
- Louis Delsupehe
- Laboratory for Molecular Diagnostics, Department of Clinical Biology, Jessa Hospital, Hasselt, Belgium
- Department Jessa & Science, LCRC (-MHU), Hasselt, Belgium
- Faculty of Medicine and Life Sciences, University of Hasselt, Hasselt, Belgium
| | - Thomas Steelandt
- Laboratory of Pathological Anatomy, Jessa Hospital, Hasselt, Belgium
| | - Julie Lemahieu
- Laboratory for Dermatopathology, Dermpat, Ghent, Belgium
| | - Pieter-Jan Volders
- Laboratory for Molecular Diagnostics, Department of Clinical Biology, Jessa Hospital, Hasselt, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Ellen Geerdens
- Laboratory for Molecular Diagnostics, Department of Clinical Biology, Jessa Hospital, Hasselt, Belgium
| | - Severine Berden
- Laboratory for Molecular Diagnostics, Department of Clinical Biology, Jessa Hospital, Hasselt, Belgium
| | - Annick Daniels
- Laboratory for Molecular Diagnostics, Department of Clinical Biology, Jessa Hospital, Hasselt, Belgium
| | - Guy Froyen
- Laboratory for Molecular Diagnostics, Department of Clinical Biology, Jessa Hospital, Hasselt, Belgium
- Department Jessa & Science, LCRC (-MHU), Hasselt, Belgium
- Faculty of Medicine and Life Sciences, University of Hasselt, Hasselt, Belgium
| | - Brigitte Maes
- Laboratory for Molecular Diagnostics, Department of Clinical Biology, Jessa Hospital, Hasselt, Belgium.
- Department Jessa & Science, LCRC (-MHU), Hasselt, Belgium.
- Faculty of Medicine and Life Sciences, University of Hasselt, Hasselt, Belgium.
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Nicolini A. Experimental and Clinical Advances in Counteracting Progression of Solid Cancers. Cancers (Basel) 2023; 15:cancers15071956. [PMID: 37046618 PMCID: PMC10093485 DOI: 10.3390/cancers15071956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 03/22/2023] [Indexed: 04/14/2023] Open
Abstract
In recent decades, impressing technological developments have significantly advanced our understanding of cancer [...].
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Affiliation(s)
- Andrea Nicolini
- Department of Oncology, Transplantations and New Technologies in Medicine, University of Pisa, 56126 Pisa, Italy
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A Computational Framework for Comprehensive Genomic Profiling in Solid Cancers: The Analytical Performance of a High-Throughput Assay for Small and Copy Number Variants. Cancers (Basel) 2022; 14:cancers14246152. [PMID: 36551638 PMCID: PMC9776229 DOI: 10.3390/cancers14246152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/25/2022] [Accepted: 12/10/2022] [Indexed: 12/15/2022] Open
Abstract
In January 2022, our institution launched a comprehensive cancer genome profiling program on 10 cancer types using a non-IVD solution named the TruSight Oncology 500 Assay provided by Illumina®. The assay analyzes both DNA and RNA, identifying Single-Nucleotide Variants (SNV)s and Insertion-Deletion (InDel) in 523 genes, as well as known and unknown fusions and splicing variants in 55 genes and Copy Number Alterations (CNVs), Mutational Tumor Burden (MTB) and Microsatellite Instability (MSI). According to the current European IVD Directive 98/79/EC, an internal validation was performed before running the test. A dedicated open-source bioinformatics pipeline was developed for data postprocessing, panel assessment and embedding in high-performance computing framework using the container technology to ensure scalability and reproducibility. Our protocols, applied to 71 DNA and 64 RNA samples, showed full agreement between the TruSight Oncology 500 assay and standard approaches, with only minor limitations, allowing to routinely perform our protocol in patient screening.
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