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Roemen GMJM, Theunissen TEJ, Hoezen WWJ, Steyls ARM, Paulussen ADC, Mosterd K, Rahikkala E, zur Hausen A, Speel EJM, van Geel M. Detection of PTCH1 Copy-Number Variants in Mosaic Basal Cell Nevus Syndrome. Biomedicines 2024; 12:330. [PMID: 38397932 PMCID: PMC10886644 DOI: 10.3390/biomedicines12020330] [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: 12/28/2023] [Revised: 01/20/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
Basal cell nevus syndrome (BCNS) is an inherited disorder characterized mainly by the development of basal cell carcinomas (BCCs) at an early age. BCNS is caused by heterozygous small-nucleotide variants (SNVs) and copy-number variants (CNVs) in the Patched1 (PTCH1) gene. Genetic diagnosis may be complicated in mosaic BCNS patients, as accurate SNV and CNV analysis requires high-sensitivity methods due to possible low variant allele frequencies. We compared test outcomes for PTCH1 CNV detection using multiplex ligation-probe amplification (MLPA) and digital droplet PCR (ddPCR) with samples from a BCNS patient heterozygous for a PTCH1 CNV duplication and the patient's father, suspected to have a mosaic form of BCNS. ddPCR detected a significantly increased PTCH1 copy-number ratio in the index patient's blood, and the father's blood and tissues, indicating that the father was postzygotic mosaic and the index patient inherited the CNV from him. MLPA only detected the PTCH1 duplication in the index patient's blood and in hair and saliva from the mosaic father. Our data indicate that ddPCR more accurately detects CNVs, even in low-grade mosaic BCNS patients, which may be missed by MLPA. In general, quantitative ddPCR can be of added value in the genetic diagnosis of mosaic BCNS patients and in estimating the recurrence risk for offspring.
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Affiliation(s)
- Guido M. J. M. Roemen
- Department of Pathology, Maastricht University Medical Center, 6229 HX Maastricht, The Netherlands; (T.E.J.T.)
- GROW School for Oncology and Reproduction, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.D.C.P.)
| | - Tom E. J. Theunissen
- Department of Pathology, Maastricht University Medical Center, 6229 HX Maastricht, The Netherlands; (T.E.J.T.)
- GROW School for Oncology and Reproduction, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.D.C.P.)
| | - Ward W. J. Hoezen
- Department of Dermatology, Maastricht University Medical Center, 6229 HX Maastricht, The Netherlands
| | - Anja R. M. Steyls
- Department of Clinical Genetics, Maastricht University Medical Center, 6229 HX Maastricht, The Netherlands;
| | - Aimee D. C. Paulussen
- GROW School for Oncology and Reproduction, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.D.C.P.)
- Department of Clinical Genetics, Maastricht University Medical Center, 6229 HX Maastricht, The Netherlands;
| | - Klara Mosterd
- GROW School for Oncology and Reproduction, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.D.C.P.)
- Department of Dermatology, Maastricht University Medical Center, 6229 HX Maastricht, The Netherlands
| | - Elisa Rahikkala
- Research Unit of Clinical Medicine, Department of Clinical Genetics, Medical Research Center Oulu, Oulu University Hospital, University of Oulu, 90570 Oulu, Finland
| | - Axel zur Hausen
- Department of Pathology, Maastricht University Medical Center, 6229 HX Maastricht, The Netherlands; (T.E.J.T.)
- GROW School for Oncology and Reproduction, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.D.C.P.)
| | - Ernst Jan M. Speel
- Department of Pathology, Maastricht University Medical Center, 6229 HX Maastricht, The Netherlands; (T.E.J.T.)
- GROW School for Oncology and Reproduction, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.D.C.P.)
| | - Michel van Geel
- GROW School for Oncology and Reproduction, Maastricht University, 6229 ER Maastricht, The Netherlands; (A.D.C.P.)
- Department of Dermatology, Maastricht University Medical Center, 6229 HX Maastricht, The Netherlands
- Department of Clinical Genetics, Maastricht University Medical Center, 6229 HX Maastricht, The Netherlands;
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Gurav M, Epari S, Gogte P, Pai T, Deshpande G, Karnik N, Shetty O, Desai S. Targeted molecular profiling of solid tumours-Indian tertiary cancer centre experience. J Cancer Res Clin Oncol 2023; 149:7413-7425. [PMID: 36935431 DOI: 10.1007/s00432-023-04693-3] [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: 01/16/2023] [Accepted: 03/12/2023] [Indexed: 03/21/2023]
Abstract
PURPOSE Molecular Profiling of solid tumours is extensively used for prognostic, theranostic, and risk prediction. Next generation sequencing (NGS) has emerged as powerful method for molecular profiling. The present study was performed to identify molecular alterations present in solid tumours in Indian tertiary cancer centre. METHODS Study included 1140 formalin Fixed paraffin embedded samples. NGS was performed using two targeted gene panels viz. Ampliseq Focus panel and Sophia Solid Tumor Plus Solution. Data was analyzed using Illumina's Local Run Manager and SOPHiA DDM software. Variant interpretation and annotations were done as per AMP/ACMG guidelines. RESULTS Total 896 cases were subjected to NGS after excluding cases with suboptimal nucleic acid quality/quantity. DNA alterations were detected in 64.9% and RNA fusions in 6.9% cases. Among detected variants, 86.7% were clinically relevant aberrations. Mutation frequency among different solid tumours was 70.8%, 67.4%, 64.4% in non-small cell lung (NSCLC), lung squamous cell carcinomas and head neck tumours respectively. EGFR, KRAS, BRAF, ALK and ROS1were commonly altered in NSCLC. Gastrointestinal tumours showed mutations in 63.6% with predominant alterations in pancreatic (88.2%), GIST (87.5%), colorectal (78.7%), cholangiocarcinoma (52.9%), neuroendocrine (45.5%), gall bladder (36.7%) and gastric adenocarcinomas (16.7%). The key genes affected were KRAS, NRAS, BRAF and PIK3CA. NGS evaluation identified co-occurring alterations in 37.7% cases otherwise missed by conventional assays. Resistance mutations were detected in progressive lung tumours (39.5%) against EGFR TKIs and ALK/ROS inhibitors. CONCLUSION This is the largest Indian study on molecular profiling of solid tumours providing extensive information about mutational signatures using NGS.
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Affiliation(s)
- Mamta Gurav
- Molecular Pathology laboratory, Department of Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
| | - Sridhar Epari
- Department of Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
| | - Prachi Gogte
- Molecular Pathology laboratory, Department of Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
| | - Trupti Pai
- Department of Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
| | - Gauri Deshpande
- Department of Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
| | - Nupur Karnik
- Department of Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
| | - Omshree Shetty
- Molecular Pathology laboratory, Department of Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India.
| | - Sangeeta Desai
- Department of Pathology, Tata Memorial Hospital, Homi Bhabha National Institute, Mumbai, India
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Jardim DL, Murugesan K, Elvin JA, Huang RSP, Kurzrock R. PD-L1 gene amplification and focality: relationship with protein expression. J Immunother Cancer 2023; 11:jitc-2022-006311. [PMID: 36849197 PMCID: PMC9972417 DOI: 10.1136/jitc-2022-006311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2023] [Indexed: 03/01/2023] Open
Abstract
PD-L1 (CD274) amplification occurs in a small subset of malignancies and may predict anti-PD-1/PD-L1 immunotherapy responsiveness. We hypothesized that both copy number (CN) and focality of cancer-related PD-L1 amplifications impact protein expression, and, thus, analyzed solid tumors that underwent comprehensive genomic profiling between March 2016 and February 2022 at Foundation Medicine. PD-L1 CN alterations were detected using a comparative genomic hybridization-like method. PD-L1 CN changes were correlated with PD-L1 protein expression (DAKO 22C3 antibody) by immunohistochemistry (IHC). Overall, 60,793 samples were analyzed (most frequent histologies: lung adenocarcinoma (20%), colon adenocarcinoma (12%), lung squamous carcinoma (8%)). Using a definition of CD274 CN ≥ specimen ploidy +4 (6 copies), 1.21% of tumors (738/60,793) were PD-L1 amplified. Focality category distribution was as follows: <0.1 mB (n=18 (2.4%)), ≥0.1 to <4 mB (n=230 (31.1%)), ≥4 to <20 mB (n=310 (42%)), ≥20mB (n=180 (24.4%)). Lower levels of PD-L1 amplification (below specimen ploidy +4) were more frequently non-focal amplifications compared to higher levels. In addition, more focal amplification (<0.1 mB) correlated with higher PD-L1 IHC expression. Median tumor proportion score (TPS) for samples with PD-L1 amplification (ploidy ≥+4) according to focality were 87.5% (<0.1 mB), 80% (≥0.1 to <4 mB), 40% (≥4 to <20 mB), 1% (≥20mB). In specimens with PD-L1 ploidy less than +4, but highly focal (<0.1 mB), the 75th percentile of PD-L1 expression by TPS was 80%. Conversely, non-focal (≥20 mB) PD-L1 amplification (ploidy ≥+4) can present high PD-L1 expression (TPS≥50%), albeit infrequently (0.09% of our cohort). In conclusion, PD-L1 expression measured by IHC is influenced by PD-L1 amplification level and focality. Further correlation between amplification, focality, protein expression and therapeutic outcome for PD-L1 and other targetable genes warrants exploration.
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Affiliation(s)
| | - Karthikeyan Murugesan
- Cancer Genomics Research, Foundation Medicine Inc, Cambridge, Massachusetts, USA,Foundation Medicine Inc, Cambridge, Massachusetts, USA
| | | | | | - Razelle Kurzrock
- Department of Medicine, WIN Consortium for Personalized Cancer Therapy, La Jolla, San Diego, USA,Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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Kapteijn MY, Kaptein FHJ, Stals MAM, Klaase EE, García-Ortiz I, van Eijk R, Ruano D, van Duinen SG, Cannegieter SC, Taphoorn MJB, Dirven L, Koekkoek JAF, Klok FA, Versteeg HH, Buijs JT. Targeted DNA sequencing to identify genetic aberrations in glioblastoma that underlie venous thromboembolism; a cohort study. Thromb Res 2023; 221:10-18. [PMID: 36435047 DOI: 10.1016/j.thromres.2022.11.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 11/19/2022]
Abstract
BACKGROUND AND OBJECTIVES Patients with glioblastoma have a high risk of developing venous thromboembolism (VTE). However, the role of underlying genetic risk factors remains largely unknown. Therefore, the aim of this study was to discover whether genetic aberrations in glioblastoma associate with VTE risk. METHODS In this cohort study, all consecutive patients diagnosed with glioblastoma in two Dutch hospitals between February 2017 and August 2020 were included. Targeted DNA next-generation sequencing of all glioblastomas was performed for diagnostic purposes and included mutational status of the genes ATRX, BRAF, CIC, FUBP1, H3F3A, IDH1, IDH2, PIK3CA, PTEN and TP53 and amplification/gain or deletion of BRAF, CDKN2A, EGFR, NOTCH1 and PTEN. The primary outcome was VTE within three months before glioblastoma diagnosis until two years after. Cumulative incidences were determined using competing risk analysis adjusting for mortality. Univariable Cox regression analysis was performed to determine hazard ratios. RESULTS From 324 patients with glioblastoma, 25 were diagnosed with VTE. Patients with a CDKN2A deletion had a 12-month adjusted cumulative incidence of VTE of 12.5 % (95%CI: 7.3-19.3) compared with 5.4 % (95%CI: 2.6-9.6) in patients with CDKN2A wildtype (p = 0.020), corresponding to a HR of 2.53 (95%CI: 1.12-5.73, p = 0.026). No significant associations were found between any of the other investigated genes and VTE. CONCLUSION This study suggests a potential role for CDKN2A deletion in glioblastoma-related VTE. Therefore, once independently validated, CDKN2A mutational status may be a promising predictor to identify glioblastoma patients at high risk for VTE, who may benefit from thromboprophylaxis.
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Affiliation(s)
- Maaike Y Kapteijn
- Einthoven Laboratory for Vascular and Regenerative Medicine, Div. of Thrombosis & Hemostasis, Dept. of Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Fleur H J Kaptein
- Einthoven Laboratory for Vascular and Regenerative Medicine, Div. of Thrombosis & Hemostasis, Dept. of Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Milou A M Stals
- Einthoven Laboratory for Vascular and Regenerative Medicine, Div. of Thrombosis & Hemostasis, Dept. of Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Eva E Klaase
- Einthoven Laboratory for Vascular and Regenerative Medicine, Div. of Thrombosis & Hemostasis, Dept. of Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Inés García-Ortiz
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Ronald van Eijk
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Dina Ruano
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Sjoerd G van Duinen
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Suzanne C Cannegieter
- Einthoven Laboratory for Vascular and Regenerative Medicine, Div. of Thrombosis & Hemostasis, Dept. of Medicine, Leiden University Medical Center, Leiden, the Netherlands; Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Martin J B Taphoorn
- Department of Neurology, Leiden University Medical Center, Leiden, the Netherlands; Department of Neurology, Haaglanden Medical Center, The Hague, the Netherlands
| | - Linda Dirven
- Department of Neurology, Leiden University Medical Center, Leiden, the Netherlands; Department of Neurology, Haaglanden Medical Center, The Hague, the Netherlands
| | - Johan A F Koekkoek
- Department of Neurology, Leiden University Medical Center, Leiden, the Netherlands; Department of Neurology, Haaglanden Medical Center, The Hague, the Netherlands
| | - Frederikus A Klok
- Einthoven Laboratory for Vascular and Regenerative Medicine, Div. of Thrombosis & Hemostasis, Dept. of Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Henri H Versteeg
- Einthoven Laboratory for Vascular and Regenerative Medicine, Div. of Thrombosis & Hemostasis, Dept. of Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Jeroen T Buijs
- Einthoven Laboratory for Vascular and Regenerative Medicine, Div. of Thrombosis & Hemostasis, Dept. of Medicine, Leiden University Medical Center, Leiden, the Netherlands.
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Ahn MJ, Mendoza MJL, Pavlakis N, Kato T, Soo RA, Kim DW, Liam CK, Hsia TC, Lee CK, Reungwetwattana T, Geater S, Chan OSH, Prasongsook N, Solomon BJ, Nguyen TTH, Kozuki T, Yang JCH, Wu YL, Mok TSK, Tan DSW, Yatabe Y. Asian Thoracic Oncology Research Group (ATORG) Expert Consensus Statement on MET Alterations in NSCLC: Diagnostic and Therapeutic Considerations. Clin Lung Cancer 2022; 23:670-685. [PMID: 36151006 DOI: 10.1016/j.cllc.2022.07.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/29/2022] [Indexed: 01/27/2023]
Abstract
Non-small cell lung cancer (NSCLC) is a heterogeneous disease, with many oncogenic driver mutations, including de novo mutations in the Mesenchymal Epithelial Transition (MET) gene (specifically in Exon 14 [ex14]), that lead to tumourigenesis. Acquired alterations in the MET gene, specifically MET amplification is also associated with the development of epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI) resistance in patients with EGFR-mutant NSCLC. Although MET has become an actionable biomarker with the availability of MET-specific inhibitors in selected countries, there is differential accessibility to diagnostic platforms and targeted therapies across countries in Asia-Pacific (APAC). The Asian Thoracic Oncology Research Group (ATORG), an interdisciplinary group of experts from Australia, Hong Kong, Japan, Korea, Mainland China, Malaysia, the Philippines, Singapore, Taiwan, Thailand and Vietnam, discussed testing for MET alterations and considerations for using MET-specific inhibitors at a consensus meeting in January 2022, and in subsequent offline consultation. Consensus recommendations are provided by the ATORG group to address the unmet need for standardised approaches to diagnosing MET alterations in NSCLC and for using these therapies. MET inhibitors may be considered for first-line or second or subsequent lines of treatment for patients with advanced and metastatic NSCLC harbouring MET ex14 skipping mutations; MET ex14 testing is preferred within multi-gene panels for detecting targetable driver mutations in NSCLC. For patients with EGFR-mutant NSCLC and MET amplification leading to EGFR TKI resistance, enrolment in combination trials of EGFR TKIs and MET inhibitors is encouraged.
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Affiliation(s)
- Myung-Ju Ahn
- Division of Hematology-Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | | | - Nick Pavlakis
- Department of Medical Oncology, Royal North Shore Hospital, University of Sydney, Sydney, NSW, Australia
| | - Terufumi Kato
- Department of Thoracic Oncology, Kanagawa Cancer Center, Yokohama, Japan
| | - Ross A Soo
- Department of Haematology-Oncology, National University Cancer Institute Singapore, Singapore
| | - Dong-Wan Kim
- Department of Internal Medicine, Seoul National University College of Medicine and Seoul National University Hospital, Seoul, Republic of Korea
| | - Chong Kin Liam
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Te-Chun Hsia
- Department of Respiratory Therapy, China Medical University, Taichung, Taiwan; Department of Internal Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Chee Khoon Lee
- National Health and Medical Research Council Clinical Trials Centre, The University of Sydney, Sydney, NSW, Australia
| | - Thanyanan Reungwetwattana
- Division of Medical Oncology, Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Sarayut Geater
- Division of Internal Medicine, Faculty of Medicine, Songklanagarind Hospital, Prince of Songkla University, Songkhla, Thailand
| | - Oscar Siu Hong Chan
- Department of Clinical Oncology, Hong Kong Integrated Oncology Centre, Hong Kong SAR, China
| | - Naiyarat Prasongsook
- Division of Medical Oncology, Department of Medicine, Phramongkutklao Hospital, Bangkok, Thailand
| | - Benjamin J Solomon
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | | | - Toshiyuki Kozuki
- Department of Thoracic Oncology and Medicine, National Hospital Organization Shikoku Cancer Center, Matsuyama, Ehime, Japan
| | - James Chih-Hsin Yang
- Department of Medical Oncology, National Taiwan University Cancer Center and National Taiwan University Hospital, Taipei, Taiwan
| | - Yi-Long Wu
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Tony Shu Kam Mok
- Department of Clinical Oncology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | | | - Yasushi Yatabe
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan
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Tsuriel S, Hannes V, Hasona A, Raz M, Hershkovitz D. Digital PCR-Based Method for Detecting CDKN2A Loss in Brain Tumours. Mol Diagn Ther 2022; 26:689-698. [PMID: 36129665 DOI: 10.1007/s40291-022-00610-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2022] [Indexed: 12/30/2022]
Abstract
INTRODUCTION CDKN2A is a key tumour suppressor gene and loss of CDKN2A can be found in many tumours. In astrocytoma grade IV, CDKN2A is deleted in more than 50% of tumours. In many instances, low-grade gliomas with homozygous loss of CDKN2A behave like high grade tumours. The available techniques for CDKN2A loss are laborious, expensive, unreliable, or unavailable in most pathology institutes. Therefore, although it is essential for accurate brain tumour diagnosis, the routine diagnosis does not include testing for CDKN2A deletion. METHODS We developed a digital polymerase chain reaction (dPCR) assay for CDKN2A loss detection. The assay is based on counting the copy number of CDKN2A gene and of a reference gene on the same chromosome. It was tested for the detection limit with regard to tumour content and minimal DNA quantity. It was then tested on 24 clinical samples with known CDKN2A status. Additionally, we tested 44 gliomas with unknown CDKN2A status. RESULTS We found that the newly developed assay is reliable in tissue with more than 50% tumour content and more than 0.4 ng of DNA. The validation cohort showed complete concordance, and we were able to detect homozygous loss in 16 gliomas with unknown CDKN2A status. DISCUSSION The method presented can give a fast, cost-effective, clinically reliable evaluation of CDKN2A loss in tissue with more than 50% tumour content. Its ability to work with old samples and with low amounts of DNA makes it the favoured assay in cases where other techniques fail.
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Affiliation(s)
- Shlomo Tsuriel
- Institute of Pathology, Tel-Aviv Sourasky Medical Center, 62431, Tel-Aviv, Israel.
| | - Victoria Hannes
- Institute of Pathology, Tel-Aviv Sourasky Medical Center, 62431, Tel-Aviv, Israel
| | - Asala Hasona
- Institute of Pathology, Tel-Aviv Sourasky Medical Center, 62431, Tel-Aviv, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, 69978, Tel-Aviv, Israel
| | - Michal Raz
- Institute of Pathology, Tel-Aviv Sourasky Medical Center, 62431, Tel-Aviv, Israel
| | - Dov Hershkovitz
- Institute of Pathology, Tel-Aviv Sourasky Medical Center, 62431, Tel-Aviv, Israel.
- Sackler Faculty of Medicine, Tel-Aviv University, 69978, Tel-Aviv, Israel.
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Identification of Fusion Genes and Targets for Genetically Matched Therapies in a Large Cohort of Salivary Gland Cancer Patients. Cancers (Basel) 2022; 14:cancers14174156. [PMID: 36077692 PMCID: PMC9454424 DOI: 10.3390/cancers14174156] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/15/2022] [Accepted: 08/25/2022] [Indexed: 11/19/2022] Open
Abstract
Simple Summary Salivary gland cancer (SGC) is a rare and heterogeneous cancer for which limited treatment options are available in the palliative treatment setting. Characterization of the SGC genetic landscape to identify actionable aberrations is therefore important. This research aimed to comprehensively assess the prevalence of various types of actionable aberrations, including gene fusions, in a large cohort of patients with different SGC subtypes. The combined approach using RNA- and DNA-based targeted next-generation sequencing panels revealed the presence of gene fusions in half of the cases, including several fusions not previously described in SGC. Targets for genetically matched therapies were identified in 28.3–81.8% of cases, depending on the SGC subtype (overall 53.7% of the cases). This highlights the potential of molecular diagnostics to select systemic treatment in SGC. Abstract Introduction: Salivary gland cancer (SGC) is a rare cancer for which systemic treatment options are limited. Therefore, it is important to characterize its genetic landscape in search for actionable aberrations, such as NTRK gene fusions. This research aimed to identify these actionable aberrations by combining NGS-based analysis of RNA (gene fusions) and DNA (single and multiple nucleotide variants, copy number variants, microsatellite instability and tumor mutational burden) in a large cohort of SGC patients. Methods: RNA and DNA were extracted from archival tissue of 121 patients with various SGC subtypes. Gene fusion analysis was performed using a customized RNA-based targeted NGS panel. DNA was sequenced using a targeted NGS panel encompassing 523 cancer-related genes. Cross-validation of NGS-based NTRK fusion detection and pan-TRK immunohistochemistry (IHC) was performed. Results: Fusion transcripts were detected in 50% of the cases and included both known (MYB-NFIB, MYBL1-NFIB, CRTC1-MAML2) and previously unknown fusions (including transcripts involving RET, BRAF or RAD51B). Only one NTRK fusion transcript was detected, in a secretory carcinoma case. Pan-TRK IHC (clone EPR17341) was false positive in 74% of cases. The proportion of patients with targets for genetically matched therapies differed among subtypes (salivary duct carcinoma: 82%, adenoid cystic carcinoma 28%, mucoepidermoid carcinoma 50%, acinic cell carcinoma 33%). Actionable aberrations were most often located in PIK3CA (n = 18, 15%), ERBB2 (n = 15, 12%), HRAS and NOTCH1 (both n = 9, 7%). Conclusions: Actionable genetic aberrations were seen in 53.7% of all SGC cases on the RNA and DNA level, with varying percentages between subtypes.
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Grafodatskaya D, O'Rielly DD, Bedard K, Butcher DT, Howlett CJ, Lytwyn A, McCready E, Parboosingh J, Spriggs EL, Vaags AK, Stockley TL. Practice guidelines for BRCA1/2 tumour testing in ovarian cancer. J Med Genet 2022; 59:727-736. [PMID: 35393334 PMCID: PMC9340048 DOI: 10.1136/jmedgenet-2021-108238] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 02/24/2022] [Indexed: 12/26/2022]
Abstract
The purpose of this document is to provide pre-analytical, analytical and post-analytical considerations and recommendations to Canadian clinical laboratories developing, validating and offering next-generation sequencing (NGS)-based BRCA1 and BRCA2 (BRCA1/2) tumour testing in ovarian cancers. This document was drafted by the members of the Canadian College of Medical Geneticists (CCMG) somatic BRCA Ad Hoc Working Group, and representatives from the Canadian Association of Pathologists. The document was circulated to the CCMG members for comment. Following incorporation of feedback, this document has been approved by the CCMG board of directors. The CCMG is a Canadian organisation responsible for certifying medical geneticists and clinical laboratory geneticists, and for establishing professional and ethical standards for clinical genetics services in Canada. The current CCMG Practice Guidelines were developed as a resource for clinical laboratories in Canada; however, they are not inclusive of all information laboratories should consider in the validation and use of NGS for BRCA1/2 tumour testing in ovarian cancers.
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Affiliation(s)
- Daria Grafodatskaya
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada.,Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, Ontario, Canada
| | - Darren D O'Rielly
- Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada.,Centre for Translational Genomes & Division of Genetics, Eastern Regional Health Authority, St. John's, Newfoundland, Canada
| | - Karine Bedard
- Département de Pathologie et Biologie cellulaire, Université de Montréal, Montreal, Québec, Canada.,Laboratoire de Diagnostic Moléculaire, Centre hospitalier de l'Université de Montréal, Montreal, Québec, Canada
| | - Darci T Butcher
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada.,Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, Ontario, Canada
| | - Christopher J Howlett
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine & Dentistry, Wester University, London, Ontario, Canada
| | - Alice Lytwyn
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada.,Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, Ontario, Canada
| | - Elizabeth McCready
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada.,Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, Ontario, Canada
| | - Jillian Parboosingh
- Department of Medical Genetics, Alberta Children's Hospital Research Institute for Child and Maternal Health, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Genetics and Genomics, Alberta Precision Laboratories, Calgary, Alberta, Canada
| | - Elizabeth L Spriggs
- Genomics, Diagnostic Services, Shared Health Manitoba, Winnipeg, Manitoba, Canada.,Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Andrea K Vaags
- Laboratory Medicine and Genetics, Trillium Health Partners, Mississauga, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Tracy L Stockley
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada .,Department of Clinical Laboratory Genetics, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
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9
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Boichard A, Lippman SM, Kurzrock R. Therapeutic implications of cancer gene amplifications without mRNA overexpression: silence may not be golden. J Hematol Oncol 2021; 14:201. [PMID: 34857015 PMCID: PMC8638100 DOI: 10.1186/s13045-021-01211-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/04/2021] [Indexed: 01/04/2023] Open
Abstract
Amplifications of oncogenic genes are often considered actionable. However, not all patients respond. Questions have therefore arisen regarding the degree to which amplifications, especially non-focal ones, mediate overexpression. We found that a subset of high-level gene amplifications (≥ 6 copies) (from The Cancer Genome Atlas database) was not over-expressed at the RNA level. Unexpectedly, focal amplifications were more frequently silenced than non-focal amplifications. Most non-focal amplifications were not silenced; therefore, non-focal amplifications, if over-expressed, may be therapeutically tractable. Furthermore, specific silencing of high-level focal or non-focal gene amplifications may explain resistance to drugs that target the relevant gene product.
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Affiliation(s)
- Amélie Boichard
- Department of Molecular Cancer Genetics, University of Strasbourg Hospitals, 67000, Strasbourg, France.
| | - Scott M Lippman
- Center for Personalized Cancer Therapy, Moores Cancer Center, University of California, La Jolla, CA, 92093, USA
| | - Razelle Kurzrock
- Center for Personalized Cancer Therapy, Moores Cancer Center, University of California, La Jolla, CA, 92093, USA.,WIN Consortium, Paris, France
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10
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Schmitt C, Schulz AA, Winkelmann R, Smith K, Wild PJ, Demes M. Comparison of MET gene amplification analysis by next-generation sequencing and fluorescence in situ hybridization. Oncotarget 2021; 12:2273-2282. [PMID: 34733418 PMCID: PMC8555686 DOI: 10.18632/oncotarget.28092] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 09/28/2021] [Indexed: 11/25/2022] Open
Abstract
MET gene alterations are known to be involved in acquired resistance to epidermal growth factor receptor inhibition. MET amplifications present a potential therapeutic target in non-small cell lung cancer. Although next-generation sequencing (NGS) and fluorescence in situ hybridization (FISH) are conventionally used to assess MET amplifications, there are currently no clinically defined cut-off values for NGS, with FISH still being the gold standard. A collective of 20 formalin-fixed paraffin-embedded lung cancer tissue samples (mean age 64 years) were selected based on increased MET gene copy number (CNV) status or the presence of mutations detected by NGS (GeneReader, QIAGEN) and were further assessed by FISH (MET/CEN7, Zytomed). Of these, 17 tumor samples were MET-amplified and one patient was found to have a MET rearrangement by NGS, while two samples had no MET gene alteration. In contrast to the NGS result, FISH analysis showed only one highly amplified sample and 19 negative samples. The single highly amplified case detected by FISH was also positive by NGS with a fold change (FC) of 3.18 and a mean copy number (CNMV 10−100%) of 20.5. Therefore, for the assessment of MET amplifications using the QIAGEN NGS workflow, we suggest detecting amplified cases with an FC value of ≥ 3.0 and a CNMV 10−100% value of ≥ 20.0 by FISH. In summary, NGS allows for DNA- and RNA-based analysis of specific MET gene amplifications, point mutations or rearrangements.
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Affiliation(s)
- Christina Schmitt
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt am Main 60590, Germany
| | - Anna-Alice Schulz
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt am Main 60590, Germany
| | - Ria Winkelmann
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt am Main 60590, Germany
| | - Kevin Smith
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt am Main 60590, Germany
| | - Peter J Wild
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt am Main 60590, Germany.,Wildlab, University Hospital Frankfurt MVZ GmbH, Frankfurt am Main 60590, Germany.,Frankfurt Institute for Advanced Studies (FIAS), Frankfurt am Main 60438, Germany
| | - Melanie Demes
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt am Main 60590, Germany.,Wildlab, University Hospital Frankfurt MVZ GmbH, Frankfurt am Main 60590, Germany
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11
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Validation of the EuroClonality-NGS DNA capture panel as an integrated genomic tool for lymphoproliferative disorders. Blood Adv 2021; 5:3188-3198. [PMID: 34424321 DOI: 10.1182/bloodadvances.2020004056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/16/2021] [Indexed: 11/20/2022] Open
Abstract
Current diagnostic standards for lymphoproliferative disorders include multiple tests for detection of clonal immunoglobulin (IG) and/or T-cell receptor (TCR) rearrangements, translocations, copy-number alterations (CNAs), and somatic mutations. The EuroClonality-NGS DNA Capture (EuroClonality-NDC) assay was designed as an integrated tool to characterize these alterations by capturing IGH switch regions along with variable, diversity, and joining genes of all IG and TCR loci in addition to clinically relevant genes for CNA and mutation analysis. Diagnostic performance against standard-of-care clinical testing was assessed in a cohort of 280 B- and T-cell malignancies from 10 European laboratories, including 88 formalin-fixed paraffin-embedded samples and 21 reactive lesions. DNA samples were subjected to the EuroClonality-NDC protocol in 7 EuroClonality-NGS laboratories and analyzed using a bespoke bioinformatic pipeline. The EuroClonality-NDC assay detected B-cell clonality in 191 (97%) of 197 B-cell malignancies and T-cell clonality in 71 (97%) of 73 T-cell malignancies. Limit of detection (LOD) for IG/TCR rearrangements was established at 5% using cell line blends. Chromosomal translocations were detected in 145 (95%) of 152 cases known to be positive. CNAs were validated for immunogenetic and oncogenetic regions, highlighting their novel role in confirming clonality in somatically hypermutated cases. Single-nucleotide variant LOD was determined as 4% allele frequency, and an orthogonal validation using 32 samples resulted in 98% concordance. The EuroClonality-NDC assay is a robust tool providing a single end-to-end workflow for simultaneous detection of B- and T-cell clonality, translocations, CNAs, and sequence variants.
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12
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Shetty O, Gurav M, Bapat P, Karnik N, Wagh G, Pai T, Epari S, Desai S. Moving Next-Generation Sequencing into the Clinic. Indian J Med Paediatr Oncol 2021. [DOI: 10.1055/s-0041-1732854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
AbstractWith an advancement in the field of molecular diagnostics, there has been a profound evolution in the testing modalities, especially in the field of oncology. In the past decade, sequencing technology has evolved drastically with the advent of high-throughput next-generation sequencing (NGS). Subsequently, the single-gene tests have been replaced by multigene panel-based assays, deep sequencing, massively parallel whole genome, whole-exome sequencing, and so on. NGS has provided molecular diagnostics professionals a wonderful tool to explore and unearth the genetic alterations, underpinning the pathophysiology of the disease. However, this development has posed new challenges which consist of the following; understanding the technology, types of platforms available, various sequencing strategies, bioinformatics and data analysis algorithm, reporting of various variants, and validation of assays and overall for developing NGS assay for clinical utility. The challenges involved sometimes impede development of these high-end assays in laboratories. The present article provides a broad overview of our journey in setting up the NGS assay in a molecular pathology laboratory at a tertiary care oncology center. We hereby describe various important points and steps to be followed while working on the NGS setup, right from its inception to final drafting of the reports, with inclusion of various validation steps. We aim at providing a beginner’s guide to set up NGS assays in the laboratory using recommended best practices and various international guidelines.
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Affiliation(s)
- Omshree Shetty
- Division of Molecular Pathology, Department of Pathology, Tata Memorial Centre, Homi Bhabha National Institute, Mumbai, Maharashtra, India
| | - Mamta Gurav
- Division of Molecular Pathology, Department of Pathology, Tata Memorial Centre, Homi Bhabha National Institute, Mumbai, Maharashtra, India
| | - Prachi Bapat
- Division of Molecular Pathology, Department of Pathology, Tata Memorial Centre, Homi Bhabha National Institute, Mumbai, Maharashtra, India
| | - Nupur Karnik
- Department of Pathology, Tata Memorial Centre, Homi Bhabha National Institute, Mumbai, Maharashtra, India
| | - Gauri Wagh
- Department of Pathology, Tata Memorial Centre, Homi Bhabha National Institute, Mumbai, Maharashtra, India
| | - Trupti Pai
- Department of Pathology, Tata Memorial Centre, Homi Bhabha National Institute, Mumbai, Maharashtra, India
| | - Sridhar Epari
- Department of Pathology, Tata Memorial Centre, Homi Bhabha National Institute, Mumbai, Maharashtra, India
| | - Sangeeta Desai
- Department of Pathology, Tata Memorial Centre, Homi Bhabha National Institute, Mumbai, Maharashtra, India
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13
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Roepman P, de Bruijn E, van Lieshout S, Schoenmaker L, Boelens MC, Dubbink HJ, Geurts-Giele WRR, Groenendijk FH, Huibers MMH, Kranendonk MEG, Roemer MGM, Samsom KG, Steehouwer M, de Leng WWJ, Hoischen A, Ylstra B, Monkhorst K, van der Hoeven JJM, Cuppen E. Clinical Validation of Whole Genome Sequencing for Cancer Diagnostics. J Mol Diagn 2021; 23:816-833. [PMID: 33964451 DOI: 10.1016/j.jmoldx.2021.04.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 02/17/2021] [Accepted: 04/12/2021] [Indexed: 02/08/2023] Open
Abstract
Whole genome sequencing (WGS) using fresh-frozen tissue and matched blood samples from cancer patients may become the most complete genetic tumor test. With the increasing availability of small biopsies and the need to screen more number of biomarkers, the use of a single all-inclusive test is preferable over multiple consecutive assays. To meet high-quality diagnostics standards, we optimized and clinically validated WGS sample and data processing procedures, resulting in a technical success rate of 95.6% for fresh-frozen samples with sufficient (≥20%) tumor content. Independent validation of identified biomarkers against commonly used diagnostic assays showed a high sensitivity (recall; 98.5%) and precision (positive predictive value; 97.8%) for detection of somatic single-nucleotide variants and insertions and deletions (across 22 genes), and high concordance for detection of gene amplification (97.0%; EGFR and MET) as well as somatic complete loss (100%; CDKN2A/p16). Gene fusion analysis showed a concordance of 91.3% between DNA-based WGS and an orthogonal RNA-based gene fusion assay. Microsatellite (in)stability assessment showed a sensitivity of 100% with a precision of 94%, and virus detection (human papillomavirus), an accuracy of 100% compared with standard testing. In conclusion, whole genome sequencing has a >95% sensitivity and precision compared with routinely used DNA techniques in diagnostics, and all relevant mutation types can be detected reliably in a single assay.
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Affiliation(s)
- Paul Roepman
- Hartwig Medical Foundation, Amsterdam, the Netherlands.
| | | | | | | | - Mirjam C Boelens
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Hendrikus J Dubbink
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | | | - Floris H Groenendijk
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Manon M H Huibers
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Margaretha G M Roemer
- Department of Pathology, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Kris G Samsom
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Marloes Steehouwer
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Wendy W J de Leng
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Department Internal Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Bauke Ylstra
- Department of Pathology, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Kim Monkhorst
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | | | - Edwin Cuppen
- Hartwig Medical Foundation, Amsterdam, the Netherlands; Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, the Netherlands
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14
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de Bitter TJJ, Kroeze LI, de Reuver PR, van Vliet S, Vink-Börger E, von Rhein D, Jansen EAM, Nagtegaal ID, Ligtenberg MJL, van der Post RS. Unraveling Neuroendocrine Gallbladder Cancer: Comprehensive Clinicopathologic and Molecular Characterization. JCO Precis Oncol 2021; 5:PO.20.00487. [PMID: 34036234 PMCID: PMC8140808 DOI: 10.1200/po.20.00487] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/19/2021] [Accepted: 02/01/2021] [Indexed: 12/23/2022] Open
Abstract
PURPOSE Neuroendocrine carcinomas and mixed neuroendocrine non-neuroendocrine neoplasms of the gallbladder (NE GBC) are rare and highly aggressive entities. The cell of origin of NE GBC has been a matter of controversy. Here, we performed a comparative histopathologic and molecular analysis of NE GBC cases and, if present, associated precancerous lesions. PATIENTS AND METHODS We selected cases diagnosed between 2000 and 2019 in the Netherlands. Precursors and carcinomas were immunohistochemically compared and analyzed for mutations, gene amplifications, microsatellite instability, and tumor mutational burden using an next-generation sequencing panel containing 523 cancer-related genes. In addition, presence of fusion genes was analyzed using a panel of 55 genes. RESULTS Sixty percent of neuroendocrine cases (6/10) presented with a precursor lesion, either intracholecystic papillary neoplasm (n = 3) or biliary intraepithelial neoplasia (n = 3). Immunohistochemically, neuroendocrine components were different from the epithelial precursor lesions. Molecular profiling, however, revealed TP53 mutations shared between different components in five of six cases, indicating a clonal relation. Furthermore, 40% of cases (4/10) harbored at least one potentially actionable alteration. This included (likely) pathogenic mutations in RAD54L, ATM, and BRCA2; amplifications of ERBB2 and MDM2; and a gene fusion involving FGFR3-TACC3. All cases were microsatellite-stable and had a tumor mutational burden of < 10 mutations/Mb. CONCLUSION Our data provide insight into the development of NE GBC and suggest a common origin of precancerous epithelial lesions and invasive neuroendocrine components, favoring the hypothesis of lineage transformation. Moreover, nearly half of the NE GBCs carried at least one potentially actionable molecular alteration, highlighting the importance of molecular testing in this highly lethal cancer.
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Affiliation(s)
- Tessa J J de Bitter
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Leonie I Kroeze
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Philip R de Reuver
- Department of Surgery, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Shannon van Vliet
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Elisa Vink-Börger
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Daniel von Rhein
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Erik A M Jansen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Iris D Nagtegaal
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Marjolijn J L Ligtenberg
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Rachel S van der Post
- Department of Pathology, Radboud University Medical Center, Nijmegen, the Netherlands
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15
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Wei J, Meng P, Terpstra MM, van Rijk A, Tamminga M, Scherpen F, Ter Elst A, Alimohamed MZ, Johansson LF, Stigt J, Gijtenbeek RPG, van Putten J, Hiltermann TJN, Groen HJM, Kok K, van der Wekken AJ, van den Berg A. Clinical Value of EGFR Copy Number Gain Determined by Amplicon-Based Targeted Next Generation Sequencing in Patients with EGFR-Mutated NSCLC. Target Oncol 2021; 16:215-226. [PMID: 33606136 PMCID: PMC7935828 DOI: 10.1007/s11523-021-00798-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/03/2021] [Indexed: 02/05/2023]
Abstract
BACKGROUND The clinical relevance of epidermal growth factor receptor (EGFR) copy number gain in patients with EGFR mutated advanced non-small cell lung cancer on first-line tyrosine kinase inhibitor treatment has not been fully elucidated. OBJECTIVE We aimed to estimate EGFR copy number gain using amplicon-based next generation sequencing data and explored its prognostic value. PATIENTS AND METHODS Next generation sequencing data were obtained for 1566 patients with non-small cell lung cancer. EGFR copy number gain was defined based on an increase in EGFR read counts relative to internal reference amplicons and normal controls in combination with a modified z-score ≥ 3.5. Clinical follow-up data were available for 60 patients treated with first-line EGFR-tyrosine kinase inhibitors. RESULTS Specificity and sensitivity of next generation sequencing-based EGFR copy number estimations were above 90%. EGFR copy number gain was observed in 27.9% of EGFR mutant cases and in 7.4% of EGFR wild-type cases. EGFR gain was not associated with progression-free survival but showed a significant effect on overall survival with an adjusted hazard ratio of 3.14 (95% confidence interval 1.46-6.78, p = 0.003). Besides EGFR copy number gain, osimertinib in second or subsequent lines of treatment and the presence of T790M at relapse revealed significant effects in a multivariate analysis with adjusted hazard ratio of 0.43 (95% confidence interval 0.20-0.91, p = 0.028) and 0.24 (95% confidence interval 0.1-0.59, p = 0.001), respectively. CONCLUSIONS Pre-treatment EGFR copy number gain determined by amplicon-based next generation sequencing data predicts worse overall survival in EGFR-mutated patients treated with first-line EGFR-tyrosine kinase inhibitors. T790M at relapse and subsequent treatment with osimertinib predict longer overall survival.
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Affiliation(s)
- Jiacong Wei
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Pathology, Cancer Hospital Chinese Academy of Medical Sciences, Beijing, China
| | - Pei Meng
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, HPC: EA10, Room F0-15, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
- Department of Pathology, Collaborative and Creative Centre, Shantou University Medical College, Shantou, Guangdong, China
| | - Miente Martijn Terpstra
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Anke van Rijk
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, HPC: EA10, Room F0-15, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - Menno Tamminga
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Frank Scherpen
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, HPC: EA10, Room F0-15, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - Arja Ter Elst
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, HPC: EA10, Room F0-15, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands
| | - Mohamed Z Alimohamed
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Haematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar-es-Salaam, Tanzania
| | - Lennart F Johansson
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jos Stigt
- Department of Pulmonary Diseases, Isala Clinic, Zwolle, The Netherlands
| | - Rolof P G Gijtenbeek
- Department of Pulmonary Diseases, Medical Center Leeuwarden, Leeuwarden, The Netherlands
| | - John van Putten
- Department of Pulmonary Diseases, Martini Hospital, Groningen, The Netherlands
| | - T Jeroen N Hiltermann
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Harry J M Groen
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Klaas Kok
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Anthonie J van der Wekken
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Anke van den Berg
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, HPC: EA10, Room F0-15, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands.
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16
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Evaluation of a Hybrid Capture–Based Pan-Cancer Panel for Analysis of Treatment Stratifying Oncogenic Aberrations and Processes. J Mol Diagn 2020; 22:757-769. [DOI: 10.1016/j.jmoldx.2020.02.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 01/22/2020] [Accepted: 02/26/2020] [Indexed: 12/12/2022] Open
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17
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Beagan JJ, Bach S, van Boerdonk RA, van Dijk E, Thunnissen E, van den Broek D, Weiss J, Kazemier G, Pegtel DM, Bahce I, Ylstra B, Heideman DAM. Circulating tumor DNA analysis of EGFR-mutant non-small cell lung cancer patients receiving osimertinib following previous tyrosine kinase inhibitor treatment. Lung Cancer 2020; 145:173-180. [PMID: 32460198 DOI: 10.1016/j.lungcan.2020.04.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 04/19/2020] [Accepted: 04/29/2020] [Indexed: 12/21/2022]
Abstract
OBJECTIVES Circulating tumor (ct)DNA analysis is rapidly gaining acceptance as a diagnostic tool to guide clinical management of advanced non-small cell lung cancer (NSCLC). Clinically-actionable EGFR mutations can be detected in ctDNA before or after first-line EGFR-Tyrosine Kinase Inhibitor (TKI) treatment, but data are limited for patients with a complex treatment history. This study aimed to explore the feasibility of ctDNA testing in a clinical setting of NSCLC patients receiving osimertinib as a second or third line EGFR-TKI. MATERIALS AND METHODS Twenty EGFR T790M-positive NSCLC patients, who had received osimertinib as a second or third line EGFR-TKI and had donated blood samples while attending routine follow-up consultations between April and November 2016, were retrospectively selected to test plasma cfDNA for tumor-guided EGFR mutations. We used EGFR mutations previously identified in tumor-tissue to retrospectively test plasma ctDNA from 20 patients who had received osimertinib as a second or third line EGFR-TKI. Both EGFR-TKI sensitising and T790 M resistance mutations were analysed by droplet digital PCR (ddPCR) in plasma taken alongside routine consultations and ctDNA detection was correlated with response under osimertinib. Follow-up solid-tissue biopsies were obtained after disease progression. RESULTS CtDNA was detected under osimertinib treatment in four out of the eight patients (50 %) who showed no response, two out of the seven (29 %) who showed an initial response and none of the five patients (0 %) who showed an ongoing response. The fraction of EGFR-mutant ctDNA in plasma tended to be higher in non-responders (0.1-68 %), compared to the initial responders (0.2-1.1 %). Blood samples were donated up to 34, 27 and 49 weeks after the start of osimertinib for the non-, initial and ongoing responders, respectively. CONCLUSIONS These findings support a potential role for ctDNA analysis in response monitoring of NSCLC patients with a complex EGFR-TKI treatment history. The weak trend between ctDNA detection and disease progression warrants larger studies to further investigate potential clinical utility.
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Affiliation(s)
- Jamie J Beagan
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, the Netherlands.
| | - Sander Bach
- Amsterdam UMC, Vrije Universiteit Amsterdam, Surgery, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, the Netherlands.
| | - Robert A van Boerdonk
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, the Netherlands.
| | - Erik van Dijk
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, the Netherlands.
| | - Erik Thunnissen
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, the Netherlands.
| | - Daan van den Broek
- Department of Laboratory Medicine, The Netherlands Cancer Institute, Amsterdam, the Netherlands.
| | - Janneke Weiss
- Amsterdam UMC, Vrije Universiteit Amsterdam, Clinical Genetics, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, the Netherlands.
| | - Geert Kazemier
- Amsterdam UMC, Vrije Universiteit Amsterdam, Surgery, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, the Netherlands.
| | - D Michiel Pegtel
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, the Netherlands.
| | - Idris Bahce
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pulmonary Diseases, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, the Netherlands.
| | - Bauke Ylstra
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, the Netherlands.
| | - Daniëlle A M Heideman
- Amsterdam UMC, Vrije Universiteit Amsterdam, Pathology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, the Netherlands.
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18
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Steeghs EMP, Kroeze LI, Tops BBJ, van Kempen LC, Ter Elst A, Kastner-van Raaij AWM, Hendriks-Cornelissen SJB, Hermsen MJW, Jansen EAM, Nederlof PM, Schuuring E, Ligtenberg MJL, Eijkelenboom A. Comprehensive routine diagnostic screening to identify predictive mutations, gene amplifications, and microsatellite instability in FFPE tumor material. BMC Cancer 2020; 20:291. [PMID: 32264863 PMCID: PMC7137451 DOI: 10.1186/s12885-020-06785-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 03/25/2020] [Indexed: 02/08/2023] Open
Abstract
Background Sensitive and reliable molecular diagnostics is needed to guide therapeutic decisions for cancer patients. Although less material becomes available for testing, genetic markers are rapidly expanding. Simultaneous detection of predictive markers, including mutations, gene amplifications and MSI, will save valuable material, time and costs. Methods Using a single-molecule molecular inversion probe (smMIP)-based targeted next-generation sequencing (NGS) approach, we developed an NGS panel allowing detection of predictive mutations in 33 genes, gene amplifications of 13 genes and microsatellite instability (MSI) by the evaluation of 55 microsatellite markers. The panel was designed to target all clinically relevant single and multiple nucleotide mutations in routinely available lung cancer, colorectal cancer, melanoma, and gastro-intestinal stromal tumor samples, but is useful for a broader set of tumor types. Results The smMIP-based NGS panel was successfully validated and cut-off values were established for reliable gene amplification analysis (i.e. relative coverage ≥3) and MSI detection (≥30% unstable loci). After validation, 728 routine diagnostic tumor samples including a broad range of tumor types were sequenced with sufficient sensitivity (2.4% drop-out), including samples with low DNA input (< 10 ng; 88% successful), low tumor purity (5–10%; 77% successful), and cytological material (90% successful). 75% of these tumor samples showed ≥1 (likely) pathogenic mutation, including targetable mutations (e.g. EGFR, BRAF, MET, ERBB2, KIT, PDGFRA). Amplifications were observed in 5.5% of the samples, comprising clinically relevant amplifications (e.g. MET, ERBB2, FGFR1). 1.5% of the tumor samples were classified as MSI-high, including both MSI-prone and non-MSI-prone tumors. Conclusions We developed a comprehensive workflow for predictive analysis of diagnostic tumor samples. The smMIP-based NGS analysis was shown suitable for limited amounts of histological and cytological material. As smMIP technology allows easy adaptation of panels, this approach can comply with the rapidly expanding molecular markers.
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Affiliation(s)
- Elisabeth M P Steeghs
- Department of Pathology, Radboud university medical center, PO Box 9101, 6500, HB, Nijmegen, the Netherlands
| | - Leonie I Kroeze
- Department of Pathology, Radboud university medical center, PO Box 9101, 6500, HB, Nijmegen, the Netherlands
| | - Bastiaan B J Tops
- Department of Pathology, Radboud university medical center, PO Box 9101, 6500, HB, Nijmegen, the Netherlands.,Department of Pathology, Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Leon C van Kempen
- Department of Pathology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Arja Ter Elst
- Department of Pathology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | | | | | - Mandy J W Hermsen
- Department of Pathology, Radboud university medical center, PO Box 9101, 6500, HB, Nijmegen, the Netherlands
| | - Erik A M Jansen
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Petra M Nederlof
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ed Schuuring
- Department of Pathology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Marjolijn J L Ligtenberg
- Department of Pathology, Radboud university medical center, PO Box 9101, 6500, HB, Nijmegen, the Netherlands.,Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
| | - Astrid Eijkelenboom
- Department of Pathology, Radboud university medical center, PO Box 9101, 6500, HB, Nijmegen, the Netherlands.
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Van Bockstal MR, Agahozo MC, van Marion R, Atmodimedjo PN, Sleddens HFBM, Dinjens WNM, Visser LL, Lips EH, Wesseling J, van Deurzen CHM. Somatic mutations and copy number variations in breast cancers with heterogeneous HER2 amplification. Mol Oncol 2020; 14:671-685. [PMID: 32058674 PMCID: PMC7138394 DOI: 10.1002/1878-0261.12650] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 01/13/2020] [Accepted: 02/13/2020] [Indexed: 12/14/2022] Open
Abstract
Intratumour heterogeneity fuels carcinogenesis and allows circumventing specific targeted therapies. HER2 gene amplification is associated with poor outcome in invasive breast cancer. Heterogeneous HER2 amplification has been described in 5–41% of breast cancers. Here, we investigated the genetic differences between HER2‐positive and HER2‐negative admixed breast cancer components. We performed an in‐depth analysis to explore the potential heterogeneity in the somatic mutational landscape of each individual tumour component. Formalin‐fixed, paraffin‐embedded breast cancer tissue of ten patients with at least one HER2‐negative and at least one HER2‐positive component was microdissected. Targeted next‐generation sequencing was performed using a customized 53‐gene panel. Somatic mutations and copy number variations were analysed. Overall, the tumours showed a heterogeneous distribution of 12 deletions, 9 insertions, 32 missense variants and 7 nonsense variants in 26 different genes, which are (likely) pathogenic. Three splice site alterations were identified. One patient had an EGFR copy number gain restricted to a HER2‐negative in situ component, resulting in EGFR protein overexpression. Two patients had FGFR1 copy number gains in at least one tumour component. Two patients had an 8q24 gain in at least one tumour component, resulting in a copy number increase in MYC and PVT1. One patient had a CCND1 copy number gain restricted to a HER2‐negative tumour component. No common alternative drivers were identified in the HER2‐negative tumour components. This series of 10 breast cancers with heterogeneous HER2 gene amplification illustrates that HER2 positivity is not an unconditional prerequisite for the maintenance of tumour growth. Many other molecular aberrations are likely to act as alternative or collaborative drivers. This study demonstrates that breast carcinogenesis is a dynamically evolving process characterized by a versatile somatic mutational profile, of which some genetic aberrations will be crucial for cancer progression, and others will be mere ‘passenger’ molecular anomalies.
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Affiliation(s)
| | | | - Ronald van Marion
- Department of Pathology, Erasmus MC Cancer Institute Rotterdam, The Netherlands
| | - Peggy N Atmodimedjo
- Department of Pathology, Erasmus MC Cancer Institute Rotterdam, The Netherlands
| | - Hein F B M Sleddens
- Department of Pathology, Erasmus MC Cancer Institute Rotterdam, The Netherlands
| | - Winand N M Dinjens
- Department of Pathology, Erasmus MC Cancer Institute Rotterdam, The Netherlands
| | - Lindy L Visser
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Esther H Lips
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jelle Wesseling
- Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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