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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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Cavagna RDO, Pinto IA, Escremim de Paula F, Berardinelli GN, Sant'Anna D, Santana I, da Silva VD, Da Silva ECA, Miziara JE, Mourão Dias J, Antoniazzi A, Jacinto A, De Marchi P, Molina-Vila MA, Ferro Leal L, Reis RM. Disruptive and Truncating TP53 Mutations Are Associated with African-Ancestry and Worse Prognosis in Brazilian Patients with Lung Adenocarcinoma. Pathobiology 2023; 90:344-355. [PMID: 37031678 DOI: 10.1159/000530587] [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: 10/27/2022] [Accepted: 04/03/2023] [Indexed: 04/11/2023] Open
Abstract
INTRODUCTION TP53 is the most frequently mutated gene in lung tumors, but its prognostic role in admixed populations, such as Brazilians, remains unclear. In this study, we aimed to evaluate the frequency and clinicopathological impact of TP53 mutations in non-small cell lung cancer (NSCLC) patients in Brazil. METHODS We analyzed 446 NSCLC patients from Barretos Cancer Hospital. TP53 mutational status was evaluated through targeted next-generation sequencing (NGS) and the variants were biologically classified as disruptive/nondisruptive and as truncating/nontruncating. We also assessed genetic ancestry using 46 ancestry-informative markers. Analysis of lung adenocarcinomas from the cBioportal dataset was performed. We further examined associations of TP53 mutations with patients' clinicopathological features. RESULTS TP53 mutations were detected in 64.3% (n = 287/446) of NSCLC cases, with a prevalence of 60.4% (n = 221/366) in lung adenocarcinomas. TP53 mutations were associated with brain metastasis at diagnosis, tobacco consumption, and higher African ancestry. Disruptive and truncating mutations were associated with a younger age at diagnosis. Additionally, cBioportal dataset revealed that TP53 mutations were associated with younger age and Black skin color. Patients harboring disruptive/truncating TP53 mutations had worse overall survival than nondisruptive/nontruncating and wild-type patients. CONCLUSION TP53 mutations are common in Brazilian lung adenocarcinomas, and their biological characterization as disruptive and truncating mutations is associated with African ancestry and shorter overall survival.
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Affiliation(s)
| | - Icaro Alves Pinto
- Molecular Oncology Research Center, Barretos Cancer Hospital, São Paulo, Brazil
| | | | | | - Débora Sant'Anna
- Molecular Oncology Research Center, Barretos Cancer Hospital, São Paulo, Brazil
| | - Iara Santana
- Department of Pathology, Barretos Cancer Hospital, São Paulo, Brazil
| | | | | | - José Elias Miziara
- Department Thoracic Surgery, Barretos Cancer Hospital, São Paulo, Brazil
- Department of Medical Oncology, Barretos Cancer Hospital, São Paulo, Brazil
| | | | - Augusto Antoniazzi
- Department of Medical Oncology, Barretos Cancer Hospital, São Paulo, Brazil
- Department of Oncogenetics / Barretos Cancer Hospital, São Paulo, Brazil
| | - Alexandre Jacinto
- Department of Radiotherapy, Barretos Cancer Hospital, São Paulo, Brazil
| | - Pedro De Marchi
- Molecular Oncology Research Center, Barretos Cancer Hospital, São Paulo, Brazil
- Department of Medical Oncology, Barretos Cancer Hospital, São Paulo, Brazil
- Department of Medical Oncology, Oncoclinicas, Rio de Janeiro, Brazil
| | | | - Leticia Ferro Leal
- Molecular Oncology Research Center, Barretos Cancer Hospital, São Paulo, Brazil
- Barretos School of Health Sciences Dr. Paulo Prata, FACISB, São Paulo, Brazil
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, São Paulo, Brazil
- Molecular Diagnostic Laboratory, Barretos Cancer Hospital, São Paulo, Brazil
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's - PT Government Associate Laboratory, Braga-Guimarães, Portugal
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Cosemans C, Wang C, Martens DS, Janssen BG, Vanpoucke C, Lefebvre W, Smeets K, Nawrot TS, Plusquin M. In Utero Exposure to Air Pollutants and Mitochondrial Heteroplasmy in Neonates. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:350-359. [PMID: 36516295 DOI: 10.1021/acs.est.2c02556] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Mitochondria are sensitive to oxidative stress, which can be caused by traffic-related air pollution. Placental mitochondrial DNA (mtDNA) mutations have been previously linked with air pollution. However, the relationship between prenatal air pollution and cord-blood mtDNA mutations has been poorly understood. Therefore, we hypothesized that prenatal particulate matter (PM2.5) and NO2 exposures are associated with cord-blood mtDNA heteroplasmy. As part of the ENVIRONAGE cohort, 200 mother-newborn pairs were recruited. Cord-blood mitochondrial single-nucleotide polymorphisms were identified by whole mitochondrial genome sequencing, and heteroplasmy levels were evaluated based on the variant allele frequency (VAF). Outdoor PM2.5 and NO2 concentrations were determined by a high-resolution spatial-temporal interpolation method based on the maternal residential address. Distributed lag linear models were used to determine sensitive time windows for the association between NO2 exposure and cord-blood mtDNA heteroplasmy. A 5 μg/m3 increment in NO2 was linked with MT-D-Loop16311T>C heteroplasmy from gestational weeks 17-25. MT-CYTB14766C>T was negatively associated with NO2 exposure in mid pregnancy, from weeks 14-17, and positively associated in late pregnancy, from weeks 31-36. No significant associations were observed with prenatal PM2.5 exposure. This is the first study to show that prenatal NO2 exposure is associated with cord-blood mitochondrial mutations and suggests two critical windows of exposure in mid-to-late pregnancy.
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Affiliation(s)
- Charlotte Cosemans
- Centre for Environmental Sciences, Hasselt University, 3590 Diepenbeek, Belgium
| | - Congrong Wang
- Centre for Environmental Sciences, Hasselt University, 3590 Diepenbeek, Belgium
| | - Dries S Martens
- Centre for Environmental Sciences, Hasselt University, 3590 Diepenbeek, Belgium
| | - Bram G Janssen
- Centre for Environmental Sciences, Hasselt University, 3590 Diepenbeek, Belgium
| | - Charlotte Vanpoucke
- Belgian Interregional Environment Agency, IRCEL-CELINE, 1000 Brussels, Belgium
| | - Wouter Lefebvre
- Flemish Institute for Technological Research, VITO, 2400 Mol, Belgium
| | - Karen Smeets
- Centre for Environmental Sciences, Hasselt University, 3590 Diepenbeek, Belgium
| | - Tim S Nawrot
- Centre for Environmental Sciences, Hasselt University, 3590 Diepenbeek, Belgium
- School of Public Health, Occupational & Environmental Medicine, Leuven University, 3000 Leuven, Belgium
| | - Michelle Plusquin
- Centre for Environmental Sciences, Hasselt University, 3590 Diepenbeek, Belgium
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Diagnostic Validation of a Comprehensive Targeted Panel for Broad Mutational and Biomarker Analysis in Solid Tumors. Cancers (Basel) 2022; 14:cancers14102457. [PMID: 35626061 PMCID: PMC9139650 DOI: 10.3390/cancers14102457] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/11/2022] [Accepted: 05/13/2022] [Indexed: 11/25/2022] Open
Abstract
The use of targeted Next Generation Sequencing (NGS) for the diagnostic screening of somatic variants in solid tumor samples has proven its high clinical value. Because of the large number of ongoing clinical trials for a multitude of variants in a growing number of genes, as well as the detection of proven and emerging pan-cancer biomarkers including microsatellite instability (MSI) and tumor mutation burden (TMB), the currently employed diagnostic gene panels will become vastly insufficient in the near future. Here, we describe the validation and implementation of the hybrid capture-based comprehensive TruSight Oncology (TSO500) assay that is able to detect single-nucleotide variants (SNVs) and subtle deletions and insertions (indels) in 523 tumor-associated genes, copy-number variants (CNVs) of 69 genes, fusions with 55 cancer driver genes, and MSI and TMB. Extensive validation of the TSO500 assay was performed on DNA or RNA from 170 clinical samples with neoplastic content down to 10%, using multiple tissue and specimen types. Starting with 80 ng DNA and 40 ng RNA extracted from formalin-fixed and paraffine-embedded (FFPE) samples revealed a precision and accuracy >99% for all variant types. The analytical sensitivity and specificity were at least 99% for SNVs, indels, CNVs, MSI, and gene rearrangements. For TMB, only values around the threshold could yield a deviating outcome. The limit-of-detection for SNVs and indels was well below the set threshold of 5% variant allele frequency (VAF). This validated comprehensive genomic profiling assay was then used to screen 624 diagnostic samples, and its success rate for adoption in a clinical diagnostic setting of broad solid tumor screening was assessed on this cohort.
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Oben B, Cosemans C, Geerdens E, Linsen L, Vanhees K, Maes B, Theunissen K, Cruys B, Lionetti M, Arijs I, Bolli N, Froyen G, Rummens JL. The Dynamics of Nucleotide Variants in the Progression from Low-Intermediate Myeloma Precursor Conditions to Multiple Myeloma: Studying Serial Samples with a Targeted Sequencing Approach. Cancers (Basel) 2022; 14:cancers14041035. [PMID: 35205782 PMCID: PMC8870380 DOI: 10.3390/cancers14041035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/28/2022] [Accepted: 02/16/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Multiple myeloma (MM), characterized by the expansion of plasma cells in the bone marrow, is the second most common hematological malignancy. This incurable cancer is consistently preceded by non-malignant asymptomatic precursor conditions known as monoclonal gammopathy of undetermined significance (MGUS) and/or smoldering multiple myeloma (SMM). These pre-stages are relatively frequent, but only a select percentage of them will progress to MM. However, it is still not possible to individually predict when and which patients will develop MM. Therefore, this study aimed to investigate the mutational profile in the progression in serial bone marrow samples with a custom targeted sequencing panel, designed to detect variants in myeloma-related genes. Remarkably, almost all variants identified in the MM samples were also already present in the pre-stages, sometimes even many years before the progression. These results provide new important insights into the molecular mechanisms of the precursor conditions and progression to MM. Abstract Multiple myeloma (MM), or Kahler’s disease, is an incurable plasma cell (PC) cancer in the bone marrow (BM). This malignancy is preceded by one or more asymptomatic precursor conditions, monoclonal gammopathy of undetermined significance (MGUS) and/or smoldering multiple myeloma (SMM). The molecular mechanisms and exact cause of this progression are still not completely understood. In this study, the mutational profile underlying the progression from low–intermediate risk myeloma precursor conditions to MM was studied in serial BM smears. A custom capture-based sequencing platform was developed, including 81 myeloma-related genes. The clonal evolution of single nucleotide variants and short insertions and deletions was studied in serial BM smears from 21 progressed precursor patients with a median time of progression of six years. From the 21 patients, four patients had no variation in one of the 81 studied genes. Interestingly, in 16 of the 17 other patients, at least one variant present in MM was also detected in its precursor BM, even years before progression. Here, the variants were present in the pre-stage at a median of 62 months before progression to MM. Studying these paired BM samples contributes to the knowledge of the evolutionary genetic landscape and provides additional insight into the mutational behavior of mutant clones over time throughout progression.
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Affiliation(s)
- Bénedith Oben
- Laboratory Experimental Hematology, Department Clinical Biology, Jessa Hospital, 3500 Hasselt, Belgium; (C.C.); (L.L.); (J.-L.R.)
- Faculty of Medicine and Life Sciences, Hasselt University, 3500 Hasselt, Belgium; (K.V.); (I.A.); (G.F.)
- Correspondence:
| | - Charlotte Cosemans
- Laboratory Experimental Hematology, Department Clinical Biology, Jessa Hospital, 3500 Hasselt, Belgium; (C.C.); (L.L.); (J.-L.R.)
- Faculty of Medicine and Life Sciences, Hasselt University, 3500 Hasselt, Belgium; (K.V.); (I.A.); (G.F.)
- Centre for Environmental Sciences, Hasselt University, 3590 Diepenbeek, Belgium
| | - Ellen Geerdens
- Laboratory Molecular Diagnostics, Department Clinical Biology, Jessa Hospital, 3500 Hasselt, Belgium; (E.G.); (B.M.); (B.C.)
| | - Loes Linsen
- Laboratory Experimental Hematology, Department Clinical Biology, Jessa Hospital, 3500 Hasselt, Belgium; (C.C.); (L.L.); (J.-L.R.)
- Activity Center Biobanking, University Hospitals Leuven, 3000 Leuven, Belgium
- University Biobank Limburg (UBiLim), Clinical Biobank, Jessa Hospital, 3500 Hasselt, Belgium
| | - Kimberly Vanhees
- Faculty of Medicine and Life Sciences, Hasselt University, 3500 Hasselt, Belgium; (K.V.); (I.A.); (G.F.)
- University Biobank Limburg (UBiLim), Clinical Biobank, Jessa Hospital, 3500 Hasselt, Belgium
| | - Brigitte Maes
- Laboratory Molecular Diagnostics, Department Clinical Biology, Jessa Hospital, 3500 Hasselt, Belgium; (E.G.); (B.M.); (B.C.)
| | - Koen Theunissen
- Department Hematology, Jessa Hospital, 3500 Hasselt, Belgium;
| | - Bert Cruys
- Laboratory Molecular Diagnostics, Department Clinical Biology, Jessa Hospital, 3500 Hasselt, Belgium; (E.G.); (B.M.); (B.C.)
| | - Marta Lionetti
- Department Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy; (M.L.); (N.B.)
| | - Ingrid Arijs
- Faculty of Medicine and Life Sciences, Hasselt University, 3500 Hasselt, Belgium; (K.V.); (I.A.); (G.F.)
- Laboratory for Translational Genetics, Department Human Genetics, University of Leuven, 3000 Leuven, Belgium
- Belgian Inflammatory Bowel Disease Research and Development (BIRD), 1930 Zaventem, Belgium
| | - Niccolò Bolli
- Department Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy; (M.L.); (N.B.)
- Unità Operativa Complessa di Ematologia, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Guy Froyen
- Faculty of Medicine and Life Sciences, Hasselt University, 3500 Hasselt, Belgium; (K.V.); (I.A.); (G.F.)
- Laboratory Molecular Diagnostics, Department Clinical Biology, Jessa Hospital, 3500 Hasselt, Belgium; (E.G.); (B.M.); (B.C.)
| | - Jean-Luc Rummens
- Laboratory Experimental Hematology, Department Clinical Biology, Jessa Hospital, 3500 Hasselt, Belgium; (C.C.); (L.L.); (J.-L.R.)
- Faculty of Medicine and Life Sciences, Hasselt University, 3500 Hasselt, Belgium; (K.V.); (I.A.); (G.F.)
- University Biobank Limburg (UBiLim), Clinical Biobank, Jessa Hospital, 3500 Hasselt, Belgium
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Wang D, Ma K, Deng W, Li J, Xiang S, Zhang Y, Fu Y, Dai H, Huang B. Development and Analytical Validation of a Targeted Next-Generation Sequencing Panel to Detect Actionable Mutations for Targeted Therapy. Onco Targets Ther 2021; 14:2423-2431. [PMID: 33854338 PMCID: PMC8039190 DOI: 10.2147/ott.s299381] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 03/18/2021] [Indexed: 11/23/2022] Open
Abstract
Background The ability to rapidly, inexpensively, and accurately identify cancer patients based on actionable genomic mutations in tumour specimens is becoming critically important in routine clinical diagnostics. Targeted panel sequencing is becoming popular because it enables comprehensive and cost-effective diagnosis. However, the implementation of a next-generation sequencing (NGS) assay in clinical settings requires careful analytical validation to demonstrate its ability to detect multiple genomic variants. Materials and Methods Here, we developed a custom-targeted NGS panel to identify actionable variants, including single nucleotide variants, insertions, and deletions; copy number variants; and gene fusions, across 73 genes for targeted cancer therapy. We implemented a practical validation strategy with diluted samples and reference standard samples that modelled key determinants of accuracy, including mutant allele frequency, insertion/deletion length, amplitude of copy number, and hotspot gene fusions. Results The analytical validation results demonstrated that our panel can identify different types of genomic alterations in these test samples with high levels of accuracy, sensitivity, and reproducibility. Conclusion Our panel could be deployed as a routine clinical test to comprehensively detect actionable variants in cancer patients to guide targeted therapy decisions.
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Affiliation(s)
- Dandan Wang
- College of Big Data and Internet, Shenzhen Technology University, Shenzhen, Guangdong, 518118, People's Republic of China.,Department of Research and Development, Sinotech Genomics Inc., Shanghai, 230001, People's Republic of China
| | - Kai Ma
- Department of Thoracic Surgery, National Cancer Center, Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, Guangdong, 518116, People's Republic of China
| | - Wei Deng
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University & National Clinical Research Center for Digestive Disease, Beijing, 100050, People's Republic of China
| | - Jingyu Li
- College of Big Data and Internet, Shenzhen Technology University, Shenzhen, Guangdong, 518118, People's Republic of China
| | - Shaohua Xiang
- College of Big Data and Internet, Shenzhen Technology University, Shenzhen, Guangdong, 518118, People's Republic of China
| | - Yang Zhang
- Department of Research and Development, Sinotech Genomics Inc., Shanghai, 230001, People's Republic of China
| | - Ying Fu
- Department of Research and Development, Sinotech Genomics Inc., Shanghai, 230001, People's Republic of China
| | - Heng Dai
- Department of Research and Development, Sinotech Genomics Inc., Shanghai, 230001, People's Republic of China
| | - Bingding Huang
- College of Big Data and Internet, Shenzhen Technology University, Shenzhen, Guangdong, 518118, People's Republic of China.,Department of Research and Development, Sinotech Genomics Inc., Shanghai, 230001, People's Republic of China
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Xu C, Peng D, Li J, Chen M, Hu Y, Hou M, Shang Q, Liang Q, Li J, Li W, Wu X, Liu C, Hu W, Cai M, Zhang H, Chen G, Yu L, Zheng X, Jiang F, Luan J, Jin S, Ding C. Highly multiplexed quantifications of 299 somatic mutations in colorectal cancer patients by automated MALDI-TOF mass spectrometry. BMC Med Genomics 2020; 13:143. [PMID: 33008377 PMCID: PMC7532609 DOI: 10.1186/s12920-020-00804-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 09/24/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Detection of somatic mutations in tumor tissues helps to understand tumor biology and guide treatment selection. Methods such as quantitative PCR can analyze a few mutations with high efficiency, while next generation sequencing (NGS) based methods can analyze hundreds to thousands of mutations. However, there is a lack of cost-effective method for quantitatively analyzing tens to a few hundred mutations of potential biological and clinical significance. METHODS Through a comprehensive database and literature review we selected 299 mutations associated with colorectal cancer. We then designed a highly multiplexed assay panel (8-wells covering 299 mutations in 109 genes) based on an automated MADLI-TOF mass spectrometry (MS) platform. The multiplex panel was tested with a total of 319 freshly frozen tissues and 92 FFPE samples from 229 colorectal cancer patients, with 13 samples also analyzed by a targeted NGS method covering 532 genes. RESULTS Multiplex somatic mutation panel based on MALDI-TOF MS detected and quantified at least one somatic mutation in 142 patients, with KRAS, TP53 and APC being the most frequently mutated genes. Extensive validation by both capillary sequencing and targeted NGS demonstrated high accuracy of the multiplex MS assay. Out of 35 mutations tested with plasmid constructs, sensitivities of 5 and 10% mutant allele frequency were achieved for 19 and 16 mutations, respectively. CONCLUSIONS Automated MALDI-TOF MS offers an efficient and cost-effective platform for highly multiplexed quantitation of 299 somatic mutations, which may be useful in studying the biological and clinical significance of somatic mutations with large numbers of cancer tissues.
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Affiliation(s)
- Chang Xu
- Department of Colorectal and Anal Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Danli Peng
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
- Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Jialu Li
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
- Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Meihua Chen
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
- Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Yujie Hu
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
- Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Mingliang Hou
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
- Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Qingjuan Shang
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
- Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Qi Liang
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
- Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Jie Li
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
- Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Wenfeng Li
- Department of Radiotherapy and Chemotherapy, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Xiaoli Wu
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Changbao Liu
- Department of Coloproctology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Wanle Hu
- Department of Coloproctology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Mao Cai
- Department of Coloproctology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Huxiang Zhang
- Department of Pathology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Guorong Chen
- Department of Pathology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Lingling Yu
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Xiaoqun Zheng
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Feizhao Jiang
- Department of Colorectal and Anal Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Ju Luan
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, China.
- Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang Province, China.
| | - Shengnan Jin
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, China.
- Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang Province, China.
| | - Chunming Ding
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, China.
- Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou Medical University, Wenzhou, Zhejiang Province, China.
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Next-Generation Sequencing in High-Sensitive Detection of Mutations in Tumors: Challenges, Advances, and Applications. J Mol Diagn 2020; 22:994-1007. [PMID: 32480002 DOI: 10.1016/j.jmoldx.2020.04.213] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/17/2020] [Accepted: 04/23/2020] [Indexed: 02/06/2023] Open
Abstract
Next-generation sequencing (NGS) technologies have come of age as preferred technologies for screening of genomic variants of pathologic and therapeutic potential. Because of their capability for high-throughput and massively parallel sequencing, they can screen for a variety of genomic changes in multiple samples simultaneously. This has made them platforms of choice for clinical testing of solid tumors and hematological malignancies. Consequently, they are increasingly replacing conventional technologies, such as Sanger sequencing and pyrosequencing, expression arrays, real-time PCR, and fluorescence in situ hybridization methods, for routine molecular testing of tumors. However, one limitation of routinely used NGS technologies is the inability to detect low-level genomic variants with high accuracy. This can be attributed to the frequent occurrence of low-level sequencing errors and artifacts in NGS workflow that need specialized approaches to be identified and eliminated. This review focuses on the origins and nature of these artifacts and recent improvements in the NGS technologies to overcome them to facilitate accurate high-sensitive detection of low-level mutations. Potential applications of high-sensitive NGS in oncology and comparisons with non-NGS technologies of similar capabilities are also summarized.
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McCabe MJ, Gauthier MEA, Chan CL, Thompson TJ, De Sousa SMC, Puttick C, Grady JP, Gayevskiy V, Tao J, Ying K, Cipponi A, Deng N, Swarbrick A, Thomas ML, Lord RV, Johns AL, Kohonen-Corish M, O'Toole SA, Clark J, Mueller SA, Gupta R, McCormack AI, Dinger ME, Cowley MJ. Development and validation of a targeted gene sequencing panel for application to disparate cancers. Sci Rep 2019; 9:17052. [PMID: 31745186 PMCID: PMC6864073 DOI: 10.1038/s41598-019-52000-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 10/09/2019] [Indexed: 02/08/2023] Open
Abstract
Next generation sequencing has revolutionised genomic studies of cancer, having facilitated the development of precision oncology treatments based on a tumour's molecular profile. We aimed to develop a targeted gene sequencing panel for application to disparate cancer types with particular focus on tumours of the head and neck, plus test for utility in liquid biopsy. The final panel designed through Roche/Nimblegen combined 451 cancer-associated genes (2.01 Mb target region). 136 patient DNA samples were collected for performance and application testing. Panel sensitivity and precision were measured using well-characterised DNA controls (n = 47), and specificity by Sanger sequencing of the Aryl Hydrocarbon Receptor Interacting Protein (AIP) gene in 89 patients. Assessment of liquid biopsy application employed a pool of synthetic circulating tumour DNA (ctDNA). Library preparation and sequencing were conducted on Illumina-based platforms prior to analysis with our accredited (ISO15189) bioinformatics pipeline. We achieved a mean coverage of 395x, with sensitivity and specificity of >99% and precision of >97%. Liquid biopsy revealed detection to 1.25% variant allele frequency. Application to head and neck tumours/cancers resulted in detection of mutations aligned to published databases. In conclusion, we have developed an analytically-validated panel for application to cancers of disparate types with utility in liquid biopsy.
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Affiliation(s)
- Mark J McCabe
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Hormones and Cancer Group, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- St Vincent's Clinical School, UNSW Australia, Sydney, NSW, Australia
| | - Marie-Emilie A Gauthier
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- The Sydney Head and Neck Cancer Institute, Chris O'Brien Lifehouse, Sydney, Australia
- Children's Cancer Institute, Randwick, NSW, Australia
| | - Chia-Ling Chan
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Tanya J Thompson
- Hormones and Cancer Group, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Sunita M C De Sousa
- Endocrine and Metabolic Unit, Royal Adelaide Hospital, Adelaide, SA, Australia
- Adult Genetics Unit, Royal Adelaide Hospital, Adelaide, SA, Australia
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, an SA Pathology and University of South Australia alliance, Adelaide, SA, Australia
- School of Medicine, University of Adelaide, Adelaide, SA, Australia
| | - Clare Puttick
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - John P Grady
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Velimir Gayevskiy
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Jiang Tao
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Kevin Ying
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Arcadi Cipponi
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Niantao Deng
- St Vincent's Clinical School, UNSW Australia, Sydney, NSW, Australia
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Alex Swarbrick
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Melissa L Thomas
- St Vincent's Centre for Applied Medical Research, Darlinghurst, NSW, Australia
| | - Reginald V Lord
- St Vincent's Centre for Applied Medical Research, Darlinghurst, NSW, Australia
- Notre Dame University School of Medicine, Sydney, NSW, Australia
| | - Amber L Johns
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Maija Kohonen-Corish
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- St George and Sutherland Clinical School, UNSW Australia, Sydney, NSW, Australia
- Woolcock Institute of Medical Research, University of Sydney, Sydney, NSW, Australia
| | - Sandra A O'Toole
- Northern Clinical School, The University of Sydney, Royal North Shore Hospital, St Leonards, NSW, Australia
- Sydney Medical School, The University of Sydney, Camperdown,, NSW, Australia
- Western Sydney University Medical School, Campbelltown, NSW, Australia
- Australian Clinical Labs, Bella Vista, NSW, Australia
| | - Jonathan Clark
- The Sydney Head and Neck Cancer Institute, Chris O'Brien Lifehouse, Sydney, Australia
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
- Central Clinical School, The University of Sydney, Sydney, NSW, Australia
| | - Simon A Mueller
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- The Sydney Head and Neck Cancer Institute, Chris O'Brien Lifehouse, Sydney, Australia
- Department for Oto-Rhino-Laryngology, Head and Neck Surgery, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Ruta Gupta
- The Sydney Head and Neck Cancer Institute, Chris O'Brien Lifehouse, Sydney, Australia
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
- Central Clinical School, The University of Sydney, Sydney, NSW, Australia
| | - Ann I McCormack
- Hormones and Cancer Group, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- St Vincent's Clinical School, UNSW Australia, Sydney, NSW, Australia
- Department of Endocrinology, St Vincent's Hospital, Darlinghurst, NSW, Australia
| | - Marcel E Dinger
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- St Vincent's Clinical School, UNSW Australia, Sydney, NSW, Australia
| | - Mark J Cowley
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.
- St Vincent's Clinical School, UNSW Australia, Sydney, NSW, Australia.
- Children's Cancer Institute, Randwick, NSW, Australia.
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10
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Analytical Evaluation of an NGS Testing Method for Routine Molecular Diagnostics on Melanoma Formalin-Fixed, Paraffin-Embedded Tumor-Derived DNA. Diagnostics (Basel) 2019; 9:diagnostics9030117. [PMID: 31547467 PMCID: PMC6787639 DOI: 10.3390/diagnostics9030117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 09/06/2019] [Accepted: 09/10/2019] [Indexed: 12/12/2022] Open
Abstract
Next Generation Sequencing (NGS) is a promising tool for the improvement of tumor molecular profiling in view of the identification of a personalized treatment in oncologic patients. To verify the potentiality of a targeted NGS (Ion AmpliSeq™ Cancer Hotspot Panel v2), selected melanoma samples (n = 21) were retrospectively analyzed on S5 platform in order to compare NGS performance with the conventional techniques adopted in our routine clinical setting (Sequenom MassARRAY system, Sanger sequencing, allele-specific real-time PCR). The capability in the identification of rare and low-frequency mutations in the main genes involved in melanoma (BRAF and NRAS genes) was verified and integrated with the results deriving from other oncogenes and tumor suppressor genes. The analytical evaluation was carried out by the analysis of DNA derived from control cell lines and FFPE (Formalin-Fixed, Paraffin-Embedded) samples to verify that the achieved resolution of uncommon mutations and low-frequency variants was suitable to meet the technical and clinical requests. Our results demonstrate that the amplicon-based NGS approach can reach the sensitivity proper of the allele-specific assays together with the high specificity of a sequencing method. An overall concordance among the tested methods was observed in the identification of classical and uncommon mutations. The assessment of the quality parameters and the comparison with the orthogonal methods suggest that the NGS method could be implemented in the clinical setting for melanoma molecular characterization.
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Abstract
Large-scale tumor profiling studies have generated massive amounts of data that have been instrumental for the detection of recurrent driver mutations in many tumor types. These driver mutations as well as the concurrent passenger mutations are now being used for a more accurate diagnosis of the tumor and prognosis for the patient. Moreover, therapeutic inhibitors toward specific mutations are already on the market and many clinical trials are ongoing to approve novel therapeutic drugs. The broad-range identification of these somatic mutations is key to this tailored personalized medicine approach, which preferentially has to be performed by a multigene multihotspot method such as massive parallel sequencing, also called next generation sequencing (NGS). The implementation of NGS in molecular diagnostics of tumor profiling however, requires a firm validation to minimize the occurrence of false positives and false negatives, thereby yielding highly accurate and robust clinical data.Here, we describe the different performance characteristics as well as quality metrics that should be analyzed for the robust diagnostic validation of tumor profiling in order to meet the requirements of international standards specific for medical laboratories, such as the ISO15189:2012 standard. These metrics include assays that assess the precision, limit of detection, accuracy, sensitivity, specificity, and robustness of the entire workflow from DNA enrichment up to the final report.
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Affiliation(s)
- Guy Froyen
- Laboratory for Molecular Diagnostics, Department of Clinical Biology, Jessa Hospital, Hasselt, Belgium.
| | - Brigitte Maes
- Laboratory for Molecular Diagnostics, Department of Clinical Biology, Jessa Hospital, Hasselt, Belgium
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12
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Oben B, Cosemans C, Arijs I, Linsen L, Daniëls A, Declercq J, Maes B, Vanhees K, Froyen G, Rummens JL. Archival May-Grünwald-Giemsa-Stained Bone Marrow Smears Are an Eligible Source for Molecular DNA Research. Biopreserv Biobank 2018; 17:274-281. [PMID: 30412415 DOI: 10.1089/bio.2018.0062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Biobanking is increasingly important in studying complex heterogeneous diseases. Therefore, it is essential to ensure the sample quality after long-term storage for reliable downstream analyses. The Clinical Biobank of the Jessa Hospital and the University Biobank Limburg (UBiLim) hold a continuously growing collection of hematological samples, including May-Grünwald-Giemsa (MGG)- and Perls' Prussian Blue (PPB)-stained bone marrow (BM) smears, stored at room temperature (RT) for up to 20 years. In this study, we investigated the effect of short- and long-term storage on the quality of DNA and RNA extracted from these BM smears to assess their fitness-for-purpose in downstream molecular applications, including agarose gel electrophoresis, bio-analyzer analysis, quantitative polymerase chain reaction (qPCR), and targeted next-generation sequencing (NGS). The RNA quality was very low for all samples, independent of storage time or staining method. The DNA from PPB-stained BM smears was already degraded after 1 year of storage and correspondingly could not be used for reliable downstream molecular analysis. In contrast, DNA extracted from MGG-stained BM smears stored for up to 10 years was able to generate high-quality data in qPCR and targeted NGS analyses. Longer storage periods (>15 years) of these samples revealed a high degree of degradation and a significant amount of DNA transitions and transversions. In conclusion, the DNA extracted from archival MGG-stained BM smears with a storage time up to at least 10 years was qualitatively good and fit for downstream analysis, including targeted NGS. This indicates that these samples are an eligible source for molecular DNA research and for studying complex diseases.
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Affiliation(s)
- Bénedith Oben
- 1Department of Experimental Hematology, Jessa Hospital, Hasselt, Belgium.,2Faculty of Medicine and Life Sciences, Hasselt University, Hasselt, Belgium
| | - Charlotte Cosemans
- 1Department of Experimental Hematology, Jessa Hospital, Hasselt, Belgium.,2Faculty of Medicine and Life Sciences, Hasselt University, Hasselt, Belgium
| | - Ingrid Arijs
- 1Department of Experimental Hematology, Jessa Hospital, Hasselt, Belgium.,2Faculty of Medicine and Life Sciences, Hasselt University, Hasselt, Belgium
| | - Loes Linsen
- 1Department of Experimental Hematology, Jessa Hospital, Hasselt, Belgium.,2Faculty of Medicine and Life Sciences, Hasselt University, Hasselt, Belgium.,3University Biobank Limburg (UBiLim) and Clinical Biobank Jessa Hospital, Hasselt, Belgium
| | - Annick Daniëls
- 1Department of Experimental Hematology, Jessa Hospital, Hasselt, Belgium
| | - Jeroen Declercq
- 1Department of Experimental Hematology, Jessa Hospital, Hasselt, Belgium.,2Faculty of Medicine and Life Sciences, Hasselt University, Hasselt, Belgium
| | - Brigitte Maes
- 1Department of Experimental Hematology, Jessa Hospital, Hasselt, Belgium.,2Faculty of Medicine and Life Sciences, Hasselt University, Hasselt, Belgium.,4Department of Clinical Biology, Jessa Hospital, Hasselt, Belgium
| | - Kimberly Vanhees
- 2Faculty of Medicine and Life Sciences, Hasselt University, Hasselt, Belgium.,3University Biobank Limburg (UBiLim) and Clinical Biobank Jessa Hospital, Hasselt, Belgium
| | - Guy Froyen
- 1Department of Experimental Hematology, Jessa Hospital, Hasselt, Belgium.,2Faculty of Medicine and Life Sciences, Hasselt University, Hasselt, Belgium.,4Department of Clinical Biology, Jessa Hospital, Hasselt, Belgium
| | - Jean-Luc Rummens
- 1Department of Experimental Hematology, Jessa Hospital, Hasselt, Belgium.,2Faculty of Medicine and Life Sciences, Hasselt University, Hasselt, Belgium.,3University Biobank Limburg (UBiLim) and Clinical Biobank Jessa Hospital, Hasselt, Belgium.,4Department of Clinical Biology, Jessa Hospital, Hasselt, Belgium
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13
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Tack V, Spans L, Schuuring E, Keppens C, Zwaenepoel K, Pauwels P, Van Houdt J, Dequeker EMC. Describing the Reportable Range Is Important for Reliable Treatment Decisions: A Multiple Laboratory Study for Molecular Tumor Profiling Using Next-Generation Sequencing. J Mol Diagn 2018; 20:743-753. [PMID: 30055348 DOI: 10.1016/j.jmoldx.2018.06.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 05/14/2018] [Accepted: 06/05/2018] [Indexed: 01/04/2023] Open
Abstract
Because interpretation of next-generation sequencing (NGS) data remains challenging, optimization of the NGS process is needed to obtain correct sequencing results. Therefore, extensive validation and continuous monitoring of the quality is essential. NGS performance was compared with traditional detection methods and technical quality of nine NGS technologies was assessed. First, nine formalin-fixed, paraffin-embedded patient samples were analyzed by 114 laboratories by using different detection methods. No significant differences in performance were observed between analyses with NGS and traditional techniques. Second, two DNA control samples were analyzed for a selected number of variants by 26 participants with the use of nine different NGS technologies. Quality control metrics were analyzed from raw data files and a survey about routine procedures. Results showed large differences in coverages, but observed variant allele frequencies in raw data files were in line with predefined variant allele frequencies. Many false negative results were found because of low-quality regions, which were not reported as such. It is recommended to disclose the reportable range, the fraction of targeted genomic regions for which calls of acceptable quality can be generated, to avoid any errors in therapy decisions. NGS can be a reliable technique, only if essential quality control during analysis is applied and reported.
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Affiliation(s)
- Véronique Tack
- Biomedical Quality Assurance Research Unit, Department of Public Health and Primary Care, University of Leuven, Leuven, Belgium
| | - Lien Spans
- Center for Human Genetics, University of Leuven, Leuven, Belgium
| | - Ed Schuuring
- Department of Pathology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Cleo Keppens
- Biomedical Quality Assurance Research Unit, Department of Public Health and Primary Care, University of Leuven, Leuven, Belgium
| | - Karen Zwaenepoel
- Department of Pathology, University Hospital Antwerp, Edegem, Belgium
| | - Patrick Pauwels
- Center for Oncologic Research (CORE), University of Antwerp, Antwerp, Belgium
| | | | - Elisabeth M C Dequeker
- Biomedical Quality Assurance Research Unit, Department of Public Health and Primary Care, University of Leuven, Leuven, Belgium; Department of Medical Diagnostics, University Hospital Leuven, Leuven, Belgium.
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14
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Dou Y, Gold HD, Luquette LJ, Park PJ. Detecting Somatic Mutations in Normal Cells. Trends Genet 2018; 34:545-557. [PMID: 29731376 PMCID: PMC6029698 DOI: 10.1016/j.tig.2018.04.003] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/03/2018] [Accepted: 04/05/2018] [Indexed: 01/12/2023]
Abstract
Somatic mutations have been studied extensively in the context of cancer. Recent studies have demonstrated that high-throughput sequencing data can be used to detect somatic mutations in non-tumor cells. Analysis of such mutations allows us to better understand the mutational processes in normal cells, explore cell lineages in development, and examine potential associations with age-related disease. We describe here approaches for characterizing somatic mutations in normal and non-tumor disease tissues. We discuss several experimental designs and common pitfalls in somatic mutation detection, as well as more recent developments such as phasing and linked-read technology. With the dramatically increasing numbers of samples undergoing genome sequencing, bioinformatic analysis will enable the characterization of somatic mutations and their impact on non-cancer tissues.
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Affiliation(s)
- Yanmei Dou
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; Equal contributions
| | - Heather D Gold
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; Bioinformatics and Integrative Genomics PhD Program, Harvard Medical School, Boston, MA, USA; Equal contributions
| | - Lovelace J Luquette
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; Bioinformatics and Integrative Genomics PhD Program, Harvard Medical School, Boston, MA, USA; Equal contributions
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA.
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15
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Frequency of Somatic TP53 Mutations in Combination with Known Pathogenic Mutations in Colon Adenocarcinoma, Non-Small Cell Lung Carcinoma, and Gliomas as Identified by Next-Generation Sequencing. Neoplasia 2018; 20:256-262. [PMID: 29454261 PMCID: PMC5849803 DOI: 10.1016/j.neo.2017.12.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 12/14/2017] [Accepted: 12/18/2017] [Indexed: 12/20/2022] Open
Abstract
The tumor suppressor gene TP53 is the most frequently mutated gene in human cancer. It encodes p53, a DNA-binding transcription factor that regulates multiple genes involved in DNA repair, metabolism, cell cycle arrest, apoptosis, and senescence. TP53 is associated with human cancer by mutations that lead to a loss of wild-type p53 function as well as mutations that confer alternate oncogenic functions that enable them to promote invasion, metastasis, proliferation, and cell survival. Identifying the discrete TP53 mutations in tumor cells may help direct therapies that are more effective. In this study, we identified the frequency of individual TP53 mutations in patients with colon adenocarcinoma (48%), non–small cell lung carcinoma (NSCLC) (36%), and glioma/glioblastoma (28%) at our institution using next-generation sequencing. We also identified the occurrence of somatic mutations in numerous actionable genes including BRAF, EGFR, KRAS, IDH1, and PIK3CA that occurred concurrently with these TP53 mutations. Of the 480 tumors examined that contained one or more mutations in the TP53 gene, 219 were colon adenocarcinomas, 215 were NSCLCs, and 46 were gliomas/glioblastomas. Among the patients positive for TP53 mutations diagnosed with colon adenocarcinoma, 50% also showed at least one mutation in pathogenic genes of which 14% were BRAF, 33% were KRAS, and 3% were NRAS. Forty-seven percent of NSCLC patients harboring TP53 mutations also had a mutation in at least one actionable pathogenic variant with the following frequencies: BRAF: 4%, EGFR: 10%, KRAS: 28%, and PIK3CA: 4%. Fifty-two percent of patients diagnosed with glioma/glioblastoma with a positive TP53 mutation had at least one concurrent mutation in a known pathogenic gene of which 9% were CDKN2A, 41% were IDH1, and 11% were PIK3CA.
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16
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Yohe S, Thyagarajan B. Review of Clinical Next-Generation Sequencing. Arch Pathol Lab Med 2017; 141:1544-1557. [PMID: 28782984 DOI: 10.5858/arpa.2016-0501-ra] [Citation(s) in RCA: 203] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT - Next-generation sequencing (NGS) is a technology being used by many laboratories to test for inherited disorders and tumor mutations. This technology is new for many practicing pathologists, who may not be familiar with the uses, methodology, and limitations of NGS. OBJECTIVE - To familiarize pathologists with several aspects of NGS, including current and expanding uses; methodology including wet bench aspects, bioinformatics, and interpretation; validation and proficiency; limitations; and issues related to the integration of NGS data into patient care. DATA SOURCES - The review is based on peer-reviewed literature and personal experience using NGS in a clinical setting at a major academic center. CONCLUSIONS - The clinical applications of NGS will increase as the technology, bioinformatics, and resources evolve to address the limitations and improve quality of results. The challenge for clinical laboratories is to ensure testing is clinically relevant, cost-effective, and can be integrated into clinical care.
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Affiliation(s)
- Sophia Yohe
- From the Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis
| | - Bharat Thyagarajan
- From the Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis
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17
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Maes B, Willemse J, Broekmans A, Smets R, Cruys B, Put N, Madoe V, Janssen M, Soepenberg O, Bries G, Vrelust I, Achten R, Van Pelt K, Buvé K, Theunissen K, Peeters V, Froyen G. Targeted next-generation sequencing using a multigene panel in myeloid neoplasms: Implementation in clinical diagnostics. Int J Lab Hematol 2017; 39:604-612. [DOI: 10.1111/ijlh.12709] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 05/23/2017] [Indexed: 01/22/2023]
Affiliation(s)
- B. Maes
- Department of Clinical Biology; Jessa Ziekenhuis; Hasselt Belgium
| | - J. Willemse
- Department of Clinical Biology; Jessa Ziekenhuis; Hasselt Belgium
- Department of Clinical Biology; AZ Turnhout; Turnhout Belgium
| | - A. Broekmans
- Department of Clinical Biology; Jessa Ziekenhuis; Hasselt Belgium
| | - R. Smets
- Department of Clinical Biology; Jessa Ziekenhuis; Hasselt Belgium
| | - B. Cruys
- Department of Clinical Biology; Jessa Ziekenhuis; Hasselt Belgium
| | - N. Put
- Department of Hematology; Jessa Ziekenhuis; Hasselt Belgium
| | - V. Madoe
- Department of Hematology; Jessa Ziekenhuis; Hasselt Belgium
| | - M. Janssen
- Department of Hematology; Ziekenhuis Oost-Limburg; Genk Belgium
| | - O. Soepenberg
- Department of Hematology; Mariaziekenhuis Noord-Limburg; Overpelt Belgium
| | - G. Bries
- Department of Hematology; AZ Turnhout; Turnhout Belgium
| | - I. Vrelust
- Department of Hematology; AZ Turnhout; Turnhout Belgium
| | - R. Achten
- Department of Pathology; Jessa Ziekenhuis; Hasselt Belgium
| | - K. Van Pelt
- Department of Clinical Biology; Ziekenhuis Oost-Limburg; Genk Belgium
| | - K. Buvé
- Department of Hematology; Jessa Ziekenhuis; Hasselt Belgium
| | - K. Theunissen
- Department of Hematology; Jessa Ziekenhuis; Hasselt Belgium
| | - V. Peeters
- Department of Clinical Biology; Jessa Ziekenhuis; Hasselt Belgium
| | - G. Froyen
- Department of Clinical Biology; Jessa Ziekenhuis; Hasselt Belgium
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18
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Technical Validation of a Next-Generation Sequencing Assay for Detecting Clinically Relevant Levels of Breast Cancer–Related Single-Nucleotide Variants and Copy Number Variants Using Simulated Cell-Free DNA. J Mol Diagn 2017; 19:525-536. [DOI: 10.1016/j.jmoldx.2017.04.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 04/02/2017] [Accepted: 04/05/2017] [Indexed: 12/28/2022] Open
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19
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Variant call concordance between two laboratory-developed, solid tumor targeted genomic profiling assays using distinct workflows and sequencing instruments. Exp Mol Pathol 2017; 102:215-218. [DOI: 10.1016/j.yexmp.2017.02.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 02/07/2017] [Indexed: 11/22/2022]
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20
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Shimoda Y, Nagashima T, Urakami K, Tanabe T, Saito J, Naruoka A, Serizawa M, Mochizuki T, Ohshima K, Ohnami S, Ohnami S, Kusuhara M, Yamaguchi K. Integrated next-generation sequencing analysis of whole exome and 409 cancer-related genes. Biomed Res 2017; 37:367-379. [PMID: 28003584 DOI: 10.2220/biomedres.37.367] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The use of next-generation sequencing (NGS) techniques to analyze the genomes of cancer cells has identified numerous genomic alterations, including single-base substitutions, small insertions and deletions, amplification, recombination, and epigenetic modifications. NGS contributes to the clinical management of patients as well as new discoveries that identify the mechanisms of tumorigenesis. Moreover, analysis of gene panels targeting actionable mutations enhances efforts to optimize the selection of chemotherapeutic regimens. However, whole genome sequencing takes several days and costs at least $10,000, depending on sequence coverage. Therefore, laboratories with relatively limited resources must employ a more economical approach. For this purpose, we conducted an integrated nucleotide sequence analysis of a panel of 409-cancer related genes (409-CRG) combined with whole exome sequencing (WES). Analysis of the 409-CRG panel detected low-frequency variants with high sensitivity, and WES identified moderate and high frequency somatic variants as well as germline variants.
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Affiliation(s)
- Yuji Shimoda
- Cancer Diagnostics Reseach Division, Shizuoka Cancer Center Research Institute
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21
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Kyrochristos ID, Glantzounis GK, Ziogas DE, Gizas I, Schizas D, Lykoudis EG, Felekouras E, Machairas A, Katsios C, Liakakos T, Cho WC, Roukos DH. From Clinical Standards to Translating Next-Generation Sequencing Research into Patient Care Improvement for Hepatobiliary and Pancreatic Cancers. Int J Mol Sci 2017; 18:E180. [PMID: 28106782 PMCID: PMC5297812 DOI: 10.3390/ijms18010180] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Revised: 12/19/2016] [Accepted: 12/27/2016] [Indexed: 02/06/2023] Open
Abstract
Hepatobiliary and pancreatic (HBP) cancers are associated with high cancer-related death rates. Surgery aiming for complete tumor resection (R0) remains the cornerstone of the treatment for HBP cancers. The current progress in the adjuvant treatment is quite slow, with gemcitabine chemotherapy available only for pancreatic ductal adenocarcinoma (PDA). In the advanced and metastatic setting, only two targeted drugs have been approved by the Food & Drug Administration (FDA), which are sorafenib for hepatocellular carcinoma and erlotinib for PDA. It is a pity that multiple Phase III randomized control trials testing the efficacy of targeted agents have negative results. Failure in the development of effective drugs probably reflects the poor understanding of genome-wide alterations and molecular mechanisms orchestrating therapeutic resistance and recurrence. In the post-ENCODE (Encyclopedia of DNA Elements) era, cancer is referred to as a highly heterogeneous and systemic disease of the genome. The unprecedented potential of next-generation sequencing (NGS) technologies to accurately identify genetic and genomic variations has attracted major research and clinical interest. The applications of NGS include targeted NGS with potential clinical implications, while whole-exome and whole-genome sequencing focus on the discovery of both novel cancer driver genes and therapeutic targets. These advances dictate new designs for clinical trials to validate biomarkers and drugs. This review discusses the findings of available NGS studies on HBP cancers and the limitations of genome sequencing analysis to translate genome-based biomarkers and drugs into patient care in the clinic.
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Affiliation(s)
- Ioannis D Kyrochristos
- Centre for Biosystems and Genome Network Medicine, Ioannina University, 45110 Ioannina, Greece.
- Department of Surgery, Ioannina University Hospital, 45110 Ioannina, Greece.
| | | | - Demosthenes E Ziogas
- Centre for Biosystems and Genome Network Medicine, Ioannina University, 45110 Ioannina, Greece.
- Department of Surgery, 'G. Hatzikosta' General Hospital, 45001 Ioannina, Greece.
| | | | - Dimitrios Schizas
- 1st Department of Surgery, Laikon General Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece.
| | - Efstathios G Lykoudis
- Department of Plastic Surgery, Ioannina University School of Medicine, 45110 Ioannina, Greece.
| | - Evangelos Felekouras
- 1st Department of Surgery, Laikon General Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece.
| | - Anastasios Machairas
- Third Department of Surgery, Attikon General Hospital, Medical School, National and Kapodistrian University of Athens, 12462 Athens, Greece.
| | - Christos Katsios
- Department of Surgery, Ioannina University Hospital, 45110 Ioannina, Greece.
| | - Theodoros Liakakos
- 1st Department of Surgery, Laikon General Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece.
| | - William C Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong, China.
| | - Dimitrios H Roukos
- Centre for Biosystems and Genome Network Medicine, Ioannina University, 45110 Ioannina, Greece.
- Department of Surgery, Ioannina University Hospital, 45110 Ioannina, Greece.
- Biomedical Research Foundation of the Academy of Athens (BRFAA), 11527 Athens, Greece.
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22
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Fontanges Q, De Mendonca R, Salmon I, Le Mercier M, D'Haene N. Clinical Application of Targeted Next Generation Sequencing for Colorectal Cancers. Int J Mol Sci 2016; 17:ijms17122117. [PMID: 27999270 PMCID: PMC5187917 DOI: 10.3390/ijms17122117] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 12/01/2016] [Accepted: 12/09/2016] [Indexed: 01/01/2023] Open
Abstract
Promising targeted therapy and personalized medicine are making molecular profiling of tumours a priority. For colorectal cancer (CRC) patients, international guidelines made RAS (KRAS and NRAS) status a prerequisite for the use of anti-epidermal growth factor receptor agents (anti-EGFR). Daily, new data emerge on the theranostic and prognostic role of molecular biomarkers, which is a strong incentive for a validated, sensitive and broadly available molecular screening test in order to implement and improve multi-modal therapy strategy and clinical trials. Next generation sequencing (NGS) has begun to supplant other technologies for genomic profiling. Targeted NGS is a method that allows parallel sequencing of thousands of short DNA sequences in a single test offering a cost-effective approach for detecting multiple genetic alterations with a minimum amount of DNA. In the present review, we collected data concerning the clinical application of NGS technology in the setting of colorectal cancer.
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Affiliation(s)
- Quitterie Fontanges
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, 1070 Brussels, Belgium.
| | - Ricardo De Mendonca
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, 1070 Brussels, Belgium.
| | - Isabelle Salmon
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, 1070 Brussels, Belgium.
| | - Marie Le Mercier
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, 1070 Brussels, Belgium.
| | - Nicky D'Haene
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, 1070 Brussels, Belgium.
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23
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Horak P, Fröhling S, Glimm H. Integrating next-generation sequencing into clinical oncology: strategies, promises and pitfalls. ESMO Open 2016; 1:e000094. [PMID: 27933214 PMCID: PMC5133384 DOI: 10.1136/esmoopen-2016-000094] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 10/06/2016] [Accepted: 10/17/2016] [Indexed: 12/24/2022] Open
Abstract
We live in an era of genomic medicine. The past five years brought about many significant achievements in the field of cancer genetics, driven by rapidly evolving technologies and plummeting costs of next-generation sequencing (NGS). The official completion of the Cancer Genome Project in 2014 led many to envision the clinical implementation of cancer genomic data as the next logical step in cancer therapy. Stemming from this vision, the term 'precision oncology' was coined to illustrate the novelty of this individualised approach. The basic assumption of precision oncology is that molecular markers detected by NGS will predict response to targeted therapies independently from tumour histology. However, along with a ubiquitous availability of NGS, the complexity and heterogeneity at the individual patient level had to be acknowledged. Not only does the latter present challenges to clinical decision-making based on sequencing data, it is also an obstacle to the rational design of clinical trials. Novel tissue-agnostic trial designs were quickly developed to overcome these challenges. Results from some of these trials have recently demonstrated the feasibility and efficacy of this approach. On the other hand, there is an increasing amount of whole-exome and whole-genome NGS data which allows us to assess ever smaller differences between individual patients with cancer. In this review, we highlight different tumour sequencing strategies currently used for precision oncology, describe their individual strengths and weaknesses, and emphasise their feasibility in different clinical settings. Further, we evaluate the possibility of NGS implementation in current and future clinical trials, and point to the significance of NGS for translational research.
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Affiliation(s)
- Peter Horak
- Department of Translational Oncology , National Center for Tumor Diseases Heidelberg, German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Stefan Fröhling
- Department of Translational Oncology , National Center for Tumor Diseases Heidelberg, German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Hanno Glimm
- Department of Translational Oncology , National Center for Tumor Diseases Heidelberg, German Cancer Research Center (DKFZ) , Heidelberg , Germany
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24
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Cree IA. Progress and potential of RAS mutation detection for diagnostics and companion diagnostics. Expert Rev Mol Diagn 2016; 16:1067-1072. [PMID: 27494709 DOI: 10.1080/14737159.2016.1221345] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION The importance of RAS mutation in carcinogenesis is established, and knowledge of an individual cancer's mutation status is important for optimal treatment. Areas covered: This paper is restricted to RAS testing in cancer, and highlights papers relevant to current practice. Expert commentary: Multiple laboratory methods are available for RAS gene analysis. PCR is commonly used to determine RAS status, providing a robust and inexpensive technology for clinical use. Next generation sequencing (NGS) platforms are changing the way in which mutation status is determined, though they require considerable expertise. Pre-analytical issues affect both methods and should be considered. The interpretation and reporting of results is not simple, particularly for NGS. External quality assurance is a pre-requisite for success, and is mandated by most laboratory accreditation schemes. The use of RAS testing is now extending beyond biopsy material to include the detection of mutations in circulating cell-free DNA and tumour cells.
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Affiliation(s)
- Ian A Cree
- a Department of Pathology , University Hospitals Coventry and Warwickshire , Coventry , United Kingdom
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