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Protásio BM, de Castria TB, Natalino R, Mangone FR, Saragiotto DF, Sabbaga J, Hoff PM, Chammas R. Prognostic Impact of Primary Tumor Sidedness in Stage III Colorectal Cancer: Real-World Evidence from a Brazilian Cohort. Clin Colorectal Cancer 2024; 23:73-84. [PMID: 38151358 DOI: 10.1016/j.clcc.2023.12.001] [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: 08/18/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 12/29/2023]
Abstract
BACKGROUND Primary tumor sidedness (PTS) is an independent prognostic factor in patients with metastatic colorectal cancer (CRC), with a worse prognosis for right-sided tumors. There are limited data on the prognostic impact of PTS in stage III CRC. The main objective of this study was to analyze the prognostic impact of PTS in stage III CRC. PATIENTS AND METHODS A retrospective and uni-institutional cohort study was performed in an oncology reference center. Patients with stage III CRC treated with a 5-fluorouracil and oxaliplatin-based chemotherapy regimen (mFLOX regimen) from October 2007 to February 2013 were included. The primary outcome was the probability of overall survival (OS) at 5 years stratified by PTS. Secondary outcomes were the probability of disease-free survival (DFS) at 5 years and an analysis of the prognostic impact of clinical and molecular biomarkers. Kaplan‒Meier curves were used, and Cox models were used to evaluate prognostic factors associated with OS and DFS. RESULTS Overall, 265 patients were evaluated. Transverse colon tumors, multicentric tumors, and undetermined primary subsites were excluded, resulting in 234 patients classified according to PTS: 95 with right sidedness (40.6%) and 139 with left sidedness (59.4%). The median follow-up time was 66 months [interquartile range (IQR): 39-81]. The 5-year OS probabilities for right-sided and left-sided tumors were 67% (95% CI: 58%-77%) and 82% (75%-89%), respectively [hazard ratio (HR): 2.02, 95% CI: 1.18-3.46; P = .010]. The 5-year probabilities of DFS for right-sided and left-sided tumors were 58% (49%-69%) and 65% (58%-74%), respectively (HR: 1.29, 0.84-1.97; P = 0.248). CONCLUSION These data suggest that there may be a worse prognosis (inferior OS at 5 years) for resected right-sided stage III CRC patients treated in the real world. However, these data need to be confirmed by prospective studies with a larger number of participants.
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Affiliation(s)
- Bruno Medonça Protásio
- Programa de Pós-Graduação em Oncologia, Faculdade de Medicina da Universidade de São Paulo- FMUSP, Sao Paulo, Brazil; Núcleo de Oncologia da Bahia- NOB. Grupo Oncoclínicas, Salvador, Brazil.
| | | | - Renato Natalino
- Centro de Investigação Translacional em Oncologia- CTO. Instituto do Câncer do Estado de São Paulo-ICESP. Faculdade de Medicina da Universidade de São Paulo- FMUSP, Sao Paulo, Brazil
| | - Flávia R Mangone
- Centro de Investigação Translacional em Oncologia- CTO. Instituto do Câncer do Estado de São Paulo-ICESP. Faculdade de Medicina da Universidade de São Paulo- FMUSP, Sao Paulo, Brazil; Comprehensive Center for Precision Oncology, Universidade de São Paulo, Sao Paulo, Brazil
| | - Daniel Fernandes Saragiotto
- Departamento de Oncologia do Hospital Santa Catarina Paulista, São Paulo, Brazil; Centro Brasileiro de Radioterapia, Oncologia e Mastologia- CEBROM. Grupo Oncoclínicas, Goiania, Brazil
| | - Jorge Sabbaga
- IDOR- Intituto D'Or de Pesquisa e Ensino, Sao Paulo, Brazil; Disciplina de Oncologia Clínica do Departamento de Radiologia e Oncologia da Faculdade de Medicina da Universidade de São Paulo- FMUSP. Instituto do Câncer do Estado de São Paulo- ICESP, Sao Paulo, Brazil
| | - Paulo M Hoff
- IDOR- Intituto D'Or de Pesquisa e Ensino, Sao Paulo, Brazil; Disciplina de Oncologia Clínica do Departamento de Radiologia e Oncologia da Faculdade de Medicina da Universidade de São Paulo- FMUSP. Instituto do Câncer do Estado de São Paulo- ICESP, Sao Paulo, Brazil
| | - Roger Chammas
- Centro de Investigação Translacional em Oncologia- CTO. Instituto do Câncer do Estado de São Paulo-ICESP. Faculdade de Medicina da Universidade de São Paulo- FMUSP, Sao Paulo, Brazil; Comprehensive Center for Precision Oncology, Universidade de São Paulo, Sao Paulo, Brazil
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Yang H, Xiao X, Zeng L, Zeng H, Zheng Y, Wang J, Li G, Dai W, He Y, Wang S, Peng J, Chen W. Integrating cfDNA liquid biopsy and organoid-based drug screening reveals PI3K signaling as a promising therapeutic target in colorectal cancer. J Transl Med 2024; 22:132. [PMID: 38310289 PMCID: PMC10837874 DOI: 10.1186/s12967-023-04675-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 10/29/2023] [Indexed: 02/05/2024] Open
Abstract
BACKGROUND The current precision medicine relies on biomarkers, which are mainly obtained through next-generation sequencing (NGS). However, this model failed to find effective drugs for most cancer patients. This study tried to combine liquid biopsy with functional drug tests using organoid models to find potential drugs for cancer patients. METHODS Colorectal cancer (CRC) patients were prospectively enrolled and blood samples were collected from patients before the start of treatment. Targeted deep sequencing of cfDNA samples was performed using a 14-gene panel. Gastrointestinal (GI) cancer organoids were established and PI3K and mTOR inhibitors were evaluated on organoid models. RESULTS A total of 195 mutations were detected across 58 cfDNA samples. The most frequently mutated genes were KRAS, TP53, PIK3CA, and BRAF, all of which exhibited higher mutation rates than tissue biopsy. Although 81% of variants had an allele frequency of less than 1%, certain mutations in KRAS, TP53, and SMAD4 had high allele frequencies exceeding 10%. Notably, among the seven patients with high allele frequency mutations, six had metastatic tumors, indicating that a high allele frequency of ctDNA could potentially serve as a biomarker of later-stage cancer. A high rate of PIK3CA mutation (31 out of 67, or 46.3%) was discovered in CRC patients, suggesting possible tumor progression mechanisms and targeted therapy opportunities. To evaluate the value of anti PI3K strategy in GI cancer, different lines of GI cancer organoids were established. The organoids recapitulated the morphologies of the original tumors. Organoids were generally insensitive to PI3K inhibitors. However, CRC-3 and GC-4 showed response to mTOR inhibitor Everolimus, and GC-3 was sensitive to PI3Kδ inhibitor Idelalisib. The CRC organoid with a PIK3CA mutation showed greater sensitivity to the PI3K inhibitor Alpelisib than wildtype organoids, suggesting potential treatment options for the corresponding patients. CONCLUSION Liquid biopsy holds significant promise for improving precision treatment and tumor prognosis in colorectal cancer patients. The combination of biomarker-based drug prediction with organoid-based functional drug sensitivity assay may lead to more effective cancer treatment.
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Affiliation(s)
- Huan Yang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, Shenzhen, Guangdong, China
| | - Xing Xiao
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, Shenzhen, Guangdong, China
| | - Leli Zeng
- Department of Biobank, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, Guangdong, China
| | - Haiteng Zeng
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, Shenzhen, Guangdong, China
| | - Yueyuan Zheng
- Clinical Big Data Research Center, Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, China
| | - Jingshu Wang
- Department of Oncology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Guanghua Li
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Weigang Dai
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Yulong He
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, Shenzhen, Guangdong, China
- Department of Gastrointestinal Surgery, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, Guangdong, China
| | - Suihai Wang
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong, China.
| | - Jianjun Peng
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China.
| | - Wei Chen
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, Shenzhen, Guangdong, China.
- Department of Gastrointestinal Surgery, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, Guangdong, China.
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Lee S, Jung S, You H, Lee Y, Park Y, Lee H, Hyun S. Effect of Fermented Red Ginseng Concentrate Intake on Stool Characteristic, Biochemical Parameters, and Gut Microbiota in Elderly Korean Women. Nutrients 2022; 14:nu14091693. [PMID: 35565660 PMCID: PMC9105854 DOI: 10.3390/nu14091693] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/15/2022] [Accepted: 04/18/2022] [Indexed: 12/05/2022] Open
Abstract
Fermented red ginseng (FRG) has been used as a general stimulant and herbal medicine for health promotion in Asia for thousands of years. Few studies have investigated the effects of FRG containing prebiotics on the gut microbiota. Here, 29 Korean women aged ≥ 50 years were administered FRG for three weeks to determine its effect on stool characteristics, biochemical parameters, and gut microbiome. Gut microbial DNA was subjected to 16S rRNA V3–V4 region sequencing to assess microbial distribution in different stages. Additionally, the stool consistency, frequency of bowel movements, and biochemical parameters of blood were evaluated. We found that FRG intake improved stool consistency and increased the frequency of bowel movements compared to before intake. Biochemical parameters such as glucose, triglyceride, cholesterol, low-density lipoprotein cholesterol, creatinine, alkaline phosphatase, and lactate dehydrogenase decreased and high-density lipoprotein cholesterol increased with FRG intake. Gut microbiome analysis revealed 20 specific bacteria after three weeks of FRG intake. Additionally, 16 pathways correlated with the 20 specific bacteria were enhanced after red ginseng intake. In conclusion, FRG promoted health in elderly women by lowering blood glucose levels and improving bowel movement frequency. The increase in bacteria observed with FRG ingestion supports these findings.
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Affiliation(s)
- Songhee Lee
- Department of Biomedical Laboratory Science, Graduate School, Eulji University, Uijeongbu-si 11759, Korea; (S.L.); (Y.L.)
| | - Sunghee Jung
- Department of Internal Medicine, College of Medicine, Eulji University, Daejeon-si 35233, Korea;
| | - Heesang You
- Department of Senior Healthcare, Graduate School, Eulji University, Uijeongbu-si 11759, Korea;
| | - Yeongju Lee
- Department of Biomedical Laboratory Science, Graduate School, Eulji University, Uijeongbu-si 11759, Korea; (S.L.); (Y.L.)
| | - Youngsook Park
- Department of Gastroenterology, Nowon Eulji University Hospital, Eulji University School of Medicine, Seoul 01830, Korea;
| | - Hyunkoo Lee
- LHK Fermentation Lab., Seongnam-si 13209, Korea;
| | - Sunghee Hyun
- Department of Biomedical Laboratory Science, Graduate School, Eulji University, Uijeongbu-si 11759, Korea; (S.L.); (Y.L.)
- Department of Internal Medicine, College of Medicine, Eulji University, Daejeon-si 35233, Korea;
- Correspondence: ; Tel.: +82-10-9412-8853
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Angerilli V, Sabella G, Centonze G, Lonardi S, Bergamo F, Mangogna A, Pietrantonio F, Fassan M, Milione M. BRAF-mutated colorectal adenocarcinomas: pathological heterogeneity and clinical implications. Crit Rev Oncol Hematol 2022; 172:103647. [PMID: 35248712 DOI: 10.1016/j.critrevonc.2022.103647] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/24/2022] [Accepted: 02/28/2022] [Indexed: 02/07/2023] Open
Abstract
Advances in molecular biology have markedly increased our understanding of the heterogeneous molecular landscape of colorectal cancer (CRC). Up to 15% of CRCs harbor the BRAF p.V600E somatic mutation (BRAFmt), a well-established negative prognostic marker in patients with metastatic CRC (mCRC). The BEACON CRC trial set a new standard of care in patients with progressive BRAFmt cancers, consisting of the combination of encorafenib and cetuximab. On these bases, BRAF mutational testing is now recommended in patients with mCRC. However, efforts are needed to further stratify patients carrying this mutation. Here, we discuss the heterogeneous pathologic and molecular landscape of BRAFmt CRCs, focusing on the promises and pitfalls of molecular diagnostics, on novel biomarkers to improve patients' stratification and on the current diagnostic scenario for CRC. We believe that a better stratification based on histopathological features and novel molecular biomarkers should be performed to optimize patient management and therapeutic decision-making.
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Affiliation(s)
| | - Giovanna Sabella
- Pathology Unit 1, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy
| | - Giovanni Centonze
- Pathology Unit 1, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy
| | - Sara Lonardi
- Oncology Unit 1, Department of Oncology, Veneto Institute of Oncology, IOV-IRCCS, Padua
| | - Francesca Bergamo
- Oncology Unit 1, Department of Oncology, Veneto Institute of Oncology, IOV-IRCCS, Padua
| | - Alessandro Mangogna
- Institute for Maternal and Child Health, IRCCS Burlo Garofalo, 34137 Trieste, Italy
| | | | - Matteo Fassan
- Department of Medicine, Surgical Pathology Unit, University of Padua; Veneto Institute of Oncology, IOV-IRCCS, Padua
| | - Massimo Milione
- Pathology Unit 1, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy.
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Karimi E, Mahmoudian F, Reyes SOL, Bargir UA, Madkaikar M, Artac H, Sabzevari A, Lu N, Azizi G, Abolhassani H. Approach to genetic diagnosis of inborn errors of immunity through next-generation sequencing. Mol Immunol 2021; 137:57-66. [PMID: 34216999 DOI: 10.1016/j.molimm.2021.06.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/18/2021] [Accepted: 06/23/2021] [Indexed: 01/02/2023]
Abstract
Patients with inborn errors of immunity (IEI) present with a heterogeneous clinical and immunological phenotype, therefore a correct molecular diagnosis is crucial for the classification and subsequent therapeutic management. On the other hand, IEI are a group of rare congenital diseases with highly diverse features and, in most cases, an as yet unknown genetic etiology. Next generation sequencing has facilitated genetic examinations of rare inherited disorders during the recent years, thus allowing a suitable molecular diagnosis in the IEI patients. This review aimed to investigate the current findings about these techniques in the field of IEI, suggesting an efficient stepwise approach to molecular diagnosis of inborn errors of immunity.
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Affiliation(s)
- Esmat Karimi
- Department of Cellular and Molecular Medicine, College of Medicine, University of Arizona, Tucson, AZ, 85721, USA; Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Science, Tehran, Iran
| | - Fatemeh Mahmoudian
- Department of Molecular Medicine, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Saul O Lugo Reyes
- Immune Deficiencies Lab, National Institute of Pediatrics, Mexico City, Mexico
| | - Umair Ahmed Bargir
- Department of Pediatric Immunology and Leukocyte Biology, ICMR-National Institute of Immunohaematology, Mumbai, India
| | - Manisha Madkaikar
- Department of Pediatric Immunology and Leukocyte Biology, ICMR-National Institute of Immunohaematology, Mumbai, India
| | - Hasibe Artac
- Department of Pediatric Immunology and Allergy, Faculty of Medicine, Selcuk University, Konya, Turkey
| | - Araz Sabzevari
- CinnaGen Medical Biotechnology Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Na Lu
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Gholamreza Azizi
- Non-communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran.
| | - Hassan Abolhassani
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Science, Tehran, Iran; Division of Clinical Immunology, Department of Biosciences and Nutrition, Karolinska Institute, Stockholm, Sweden; Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institute at Karolinska University Hospital Huddinge, Stockholm, Sweden.
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CANDIDATE GENES IDENTIFICATION OF OIL PALM (Elaeis guineensis Jacq.) INTEREST CHARACTERS USING PUBLISHED DATABASE. BIOVALENTIA: BIOLOGICAL RESEARCH JOURNAL 2021. [DOI: 10.24233/biov.7.1.2021.188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Palm oil has supplied more than 30% of vegetable oil consumption worldwide. Rising demand has pushed oil palm plantations to increase the yield. It is well known that genetic has played a significant role in phenotypic performance. Moreover, in recent years, genomic data has emerged tremendously. Unfortunately on the gene related to oil palm yield. Therefore, a preliminary study to classify and select oil palm candidate genes associated with characteristic by scanning existing genes in oil palm or other in-silico species were conducted. Based on Blast2Go results, 22 genes related to oil biosynthesis, two specifically related to fruit number and fruit weight were analysed. Furthermore, 19 candidate genes were able to amplify.
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Lee S, You H, Lee M, Kim D, Jung S, Park Y, Hyun S. Different Reactions in Each Enterotype Depending on the Intake of Probiotic Yogurt Powder. Microorganisms 2021; 9:1277. [PMID: 34208176 PMCID: PMC8230767 DOI: 10.3390/microorganisms9061277] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 06/05/2021] [Accepted: 06/08/2021] [Indexed: 12/12/2022] Open
Abstract
Probiotics can be used as a nutritional strategy to improve gut homeostasis. We aimed to evaluate the intestinal microbiota profile of 18 subjects after ingestion of probiotic yogurt powder (PYP) based on enterotype. The subjects were classified into three enterotypes according to their microbial community: Bacteroides (n = 9, type B), Prevotella (n = 3, type P), and Ruminococcus (n = 6, type R). We performed controlled termination in a transient series that included a control period of three weeks before probiotic intake, PYP intake for three weeks, and a three-week washout period. Fecal microbiota composition was analyzed by sequencing the V3-V4 super variable region of 16S rRNA. Based on the Bristol stool shape scale, abnormal stool shape improved with PYP intake, and bowel movements were activated. The abundance of Faecalibacterium, Eggerthella, and Leuconostoc, which ferment and metabolize glucose, showed a strong correlation with type B Bacteroides, and glucose metabolism improvement was observed in all type B subjects. Alkaline phosphatase was significantly improved only in type B. In addition, the abundance of type B Bacteroides showed a negative correlation with that of Lactobacillus. The abundance of Streptococcus, Agathobacter, and Christensenella, which are involved in lipid metabolism, showed a strong correlation with that of type P Prevotella, and triglyceride metabolism improvement was observed in all type P subjects. The gut microbiota showed only short-term changes after PYP intake and showed resilience by returning to its original state when PYP intake was interrupted. In summary, the different responses to PYP intake may result from the different enterotypes and associated strains; therefore, the probiotic composition should be adjusted based on the individual enterotype.
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Affiliation(s)
- Songhee Lee
- Department of Biomedical Laboratory Science, Graduate School, Eulji University, Dongil-ro 712, Uijeongbu-si 11759, Korea;
| | - Heesang You
- Department of Senior Healthcare, Graduate School, Eulji University, Dongil-ro 712, Uijeongbu-si 11759, Korea;
| | - Minho Lee
- Department of Food Science and Service, College of Bio-Convergence, Eulji University, Sansung daero 553, Seongnam-si 13135, Korea;
| | - Doojin Kim
- Department of Biomedical Laboratory Science, College of Health Sciences, Eulji University, Sansung daero 553, Seongnam-si 13135, Korea;
| | - Sunghee Jung
- Department of Internal Medicine, College of Medicine, Eulji University, Dunsan-seo 95, Daejeon-si 35233, Korea;
| | - Youngsook Park
- Department of Gastroenterology, Nowon Eulji University Hospital, Eulji University School of Medicine, Hangeul Biseok-ro 68, Seoul 01830, Korea;
| | - Sunghee Hyun
- Department of Biomedical Laboratory Science, Graduate School, Eulji University, Dongil-ro 712, Uijeongbu-si 11759, Korea;
- Department of Senior Healthcare, Graduate School, Eulji University, Dongil-ro 712, Uijeongbu-si 11759, Korea;
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Liu J, Deng Y, Yu B, Mo B, Luo L, Yang J, Zhang X, Wang Z, Wang Y, Zhu J, Yang H, Fang S, Cheng Z, Li J, Shu Y, Luo G, Xiong W, Wei J, Li Z. Targeted resequencing showing novel common and rare genetic variants increases the risk of asthma in the Chinese Han population. J Clin Lab Anal 2021; 35:e23813. [PMID: 33969541 DOI: 10.1002/jcla.23813] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 04/16/2021] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Although studies have identified hundreds of genetic variants associated with asthma risk, a large fraction of heritability remains unexplained, especially in Chinese individuals. METHODS To identify genetic risk factors for asthma in a Han Chinese population, 211 asthma-related genes were first selected based on database searches. The genes were then sequenced for subjects in a Discovery Cohort (284 asthma patients and 205 older healthy controls) using targeted next-generation sequencing. Bioinformatics analysis and statistical association analyses were performed to reveal the associations between rare/common variants and asthma, respectively. The identified common risk variants underwent a validation analysis using a Replication Cohort (664 patients and 650 controls). RESULTS First, we identified 18 potentially functional rare loss-of-function (LOF) variants in 21/284 (7.4%) of the asthma cases. Second, using burden tests, we found that the asthma group had nominally significant (p < 0.05) burdens of rare nonsynonymous variants in 10 genes. Third, 23 common single-nucleotide polymorphisms were associated with the risk of asthma, 7/23 (30.4%) and 9/23 (39.1%) of which were modestly significant (p < 9.1 × 10-4 ) in the Replication Cohort and Combined Cohort, respectively. According to our cumulative risk model involving the modestly associated alleles, middle- and high-risk subjects had a 2.0-fold (95% CI: 1.621-2.423, p = 2.624 × 10-11 ) and 6.0-fold (95% CI: 3.623-10.156, p = 7.086 × 10-12 ) increased risk of asthma, respectively, compared with low-risk subjects. CONCLUSION This study revealed novel rare and common genetic risk factors for asthma, and provided a cumulative risk model for asthma risk prediction and stratification in Han Chinese individuals.
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Affiliation(s)
- Juan Liu
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Pulmonary Diseases of Health Ministry, Key Cite of National Clinical Research Center for Respiratory Disease, Wuhan Clinical Medical Research Center for Chronic Airway Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Yanhan Deng
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Pulmonary Diseases of Health Ministry, Key Cite of National Clinical Research Center for Respiratory Disease, Wuhan Clinical Medical Research Center for Chronic Airway Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Bo Yu
- Division of Cardiology, Departments of Internal Medicine and Genetic Diagnosis Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Biwen Mo
- Department of Respiratory Medicine, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Liman Luo
- Department of Pediatrics, The 306 Hospital of People's Liberation Army, Beijing, China
| | - Jingping Yang
- Department of Respiratory and Critical Care Medicine, The Third Affiliated Hospital of Inner Mongolia Medical University, Baotou, China
| | - Xiaoju Zhang
- Department of Respiratory Medicine, Henan Provincial People's Hospital & the People's Hospital of Zhengzhou University, Zhengzhou, China
| | - Zheng Wang
- Department of Respiratory Medicine, Henan Provincial People's Hospital & the People's Hospital of Zhengzhou University, Zhengzhou, China
| | - Yingnan Wang
- Department of Respiratory and Critical Care Medicine, Renmin Hospital of Three Gorges University, Yichang, China
| | - Jing Zhu
- Department of Respiratory and Critical Care Medicine, Renmin Hospital of Three Gorges University, Yichang, China
| | - Hua Yang
- Department of Respiratory Medicine, University Hospital of Hubei University for Nationalities, Enshi, China
| | - Shirong Fang
- Department of Respiratory Medicine, University Hospital of Hubei University for Nationalities, Enshi, China
| | - Zhenshun Cheng
- Department of Respiratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Jingping Li
- Department of Respiratory Medicine, Qianjiang Central Hospital, Qianjiang, China
| | - Ying Shu
- Department of Respiratory Medicine, Qianjiang Central Hospital, Qianjiang, China
| | - Guangwei Luo
- Department of Respiratory Medicine, Wuhan No. 1 Hospital, Wuhan, China
| | - Weining Xiong
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Pulmonary Diseases of Health Ministry, Key Cite of National Clinical Research Center for Respiratory Disease, Wuhan Clinical Medical Research Center for Chronic Airway Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China.,Department of Respiratory Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianghong Wei
- Department of Respiratory Medicine, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Zongzhe Li
- Division of Cardiology, Departments of Internal Medicine and Genetic Diagnosis Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Angerilli V, Galuppini F, Pagni F, Fusco N, Malapelle U, Fassan M. The Role of the Pathologist in the Next-Generation Era of Tumor Molecular Characterization. Diagnostics (Basel) 2021; 11:339. [PMID: 33670699 PMCID: PMC7922586 DOI: 10.3390/diagnostics11020339] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 12/14/2022] Open
Abstract
Current pathology practice is being shaped by the increasing complexity of modern medicine, in particular of precision oncology, and major technological advances. In the "next-generation technologies era", the pathologist has become the person responsible for the integration and interpretation of morphologic and molecular information and for the delivery of critical answers to diagnostic, prognostic and predictive queries, acquiring a prominent position in the molecular tumor boards.
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Affiliation(s)
- Valentina Angerilli
- Department of Medicine (DIMED), Surgical Pathology Unit, University of Padua, 35121 Padua, Italy; (V.A.); (F.G.)
| | - Francesca Galuppini
- Department of Medicine (DIMED), Surgical Pathology Unit, University of Padua, 35121 Padua, Italy; (V.A.); (F.G.)
| | - Fabio Pagni
- Department of Medicine and Surgery, Pathology, San Gerardo Hospital, University of Milano-Bicocca, 20900 Monza, Italy;
| | - Nicola Fusco
- Division of Pathology, IEO, European Institute of Oncology IRCCS, 20122 Milan, Italy;
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, 80138 Naples, Italy;
| | - Matteo Fassan
- Department of Medicine (DIMED), Surgical Pathology Unit, University of Padua, 35121 Padua, Italy; (V.A.); (F.G.)
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Belardinilli F, Pernazza A, Mahdavian Y, Cerbelli B, Bassi M, Gradilone A, Coppa A, Pignataro MG, Anile M, Venuta F, Della Rocca C, Giannini G, d'Amati G. A multidisciplinary approach for the differential diagnosis between multiple primary lung adenocarcinomas and intrapulmonary metastases. Pathol Res Pract 2021; 220:153387. [PMID: 33647865 DOI: 10.1016/j.prp.2021.153387] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 02/13/2021] [Indexed: 11/26/2022]
Abstract
PURPOSE The distinction between multiple primary lung cancers (MPLCs) and intrapulmonary metastases has a significant impact on tumor staging and therapeutic choices. Several criteria have been proposed to solve this diagnostic issue, but a definitive consensus is still missing. We tested the efficacy of a combined clinical, histopathological and molecular ("real world") approach for the correct classification of multiple lung tumors in a selected cohort of patients. METHODS 24 multiple lung tumors with a diagnosis of adenocarcinoma from 10 patients were retrospectively reviewed. Radiological, pathological and clinical information, including follow-up, were integrated with molecular profiling via a routine multigene panel sequencing. RESULTS Comprehensive histologic assessment revealed readily distinguishable histologic patterns between multiple tumors suggesting unrelated lesions in 7 cases, in agreement with clinical, radiological and molecular data, thus leading to final diagnosis of MPLCs. In the remaining 3 cases, the differential diagnosis between MPLCs and intrapulmonary metastases was challenging, since the histologic features of the lesions were similar or identical. The final interpretation (2 MPLCs and 1 most likely intrapulmonary metastases) was reached thanks to the integration of all available data, and was confirmed by follow-up. CONCLUSIONS A multidisciplinary approach including a routinely affordable multigene panel sequencing is a useful tool to discriminate MPLCs from intrapulmonary metastases in multiple lung nodules sharing the adenocarcinoma histotype.
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Affiliation(s)
- Francesca Belardinilli
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 291, 00161, Rome, Italy
| | - Angelina Pernazza
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University, Latina, 04100, Italy
| | - Yasaman Mahdavian
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 291, 00161, Rome, Italy
| | - Bruna Cerbelli
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University, Latina, 04100, Italy
| | - Massimiliano Bassi
- Department of General and Specialist Surgery "P. Stefanini" Sapienza University, Rome, 00161, Italy
| | - Angela Gradilone
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 291, 00161, Rome, Italy
| | | | - Maria Gemma Pignataro
- Department of Radiological, Oncological and Pathological Sciences, Sapienza University, Rome, 00161, Italy
| | - Marco Anile
- Department of General and Specialist Surgery "P. Stefanini" Sapienza University, Rome, 00161, Italy
| | - Federico Venuta
- Department of General and Specialist Surgery "P. Stefanini" Sapienza University, Rome, 00161, Italy
| | - Carlo Della Rocca
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University, Latina, 04100, Italy
| | - Giuseppe Giannini
- Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 291, 00161, Rome, Italy.
| | - Giulia d'Amati
- Department of Radiological, Oncological and Pathological Sciences, Sapienza University, Rome, 00161, Italy.
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11
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Ramani NS, Chen H, Broaddus RR, Lazar AJ, Luthra R, Medeiros LJ, Patel KP, Rashid A, Routbort MJ, Stewart J, Tang Z, Bassett R, Manekia J, Barkoh BA, Dang H, Roy-Chowdhuri S. Utilization of cytology smears improves success rates of RNA-based next-generation sequencing gene fusion assays for clinically relevant predictive biomarkers. Cancer Cytopathol 2020; 129:374-382. [PMID: 33119213 DOI: 10.1002/cncy.22381] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/21/2020] [Accepted: 07/23/2020] [Indexed: 12/24/2022]
Abstract
BACKGROUND The use of RNA-based next-generation sequencing (NGS) assays to detect gene fusions for targeted therapy has rapidly become an essential component of comprehensive molecular profiling. For cytology specimens, the cell block (CB) is most commonly used for fusion testing; however, insufficient cellularity and/or suboptimal RNA quality are often limiting factors. In the current study, the authors evaluated the factors affecting RNA fusion testing in cytology and the added value of smears in cases with a suboptimal or inadequate CB. METHODS A 12-month retrospective review was performed to identify cytology cases that were evaluated by a targeted RNA-based NGS assay. Samples were sequenced by targeted amplicon-based NGS for 51 clinically relevant genes on a proprietary platform. Preanalytic factors and NGS quality parameters were correlated with the results of RNA fusion testing. RESULTS The overall success rate of RNA fusion testing was 92%. Of the 146 cases successfully sequenced, 14% had a clinically relevant fusion detected. NGS testing success positively correlated with RNA yield (P = .03) but was independent of the tumor fraction, the tumor size, or the number of slides used for extraction. CB preparations were adequate for testing in 45% cases, but the inclusion of direct smears increased the adequacy rate to 92%. There was no significant difference in testing success rates between smears and CB preparations. CONCLUSIONS The success of RNA-based NGS fusion testing depends on the quality and quantity of RNA extracted. The use of direct smears significantly improves the adequacy of cytologic samples for RNA fusion testing for predictive biomarkers.
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Affiliation(s)
- Nisha S Ramani
- Department of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hui Chen
- Department of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Russell R Broaddus
- Department of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Alexander J Lazar
- Department of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rajyalakshmi Luthra
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - L Jeffrey Medeiros
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Keyur P Patel
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Asif Rashid
- Department of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Mark J Routbort
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - John Stewart
- Department of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Zhenya Tang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Roland Bassett
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jawad Manekia
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Bedia A Barkoh
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hyvan Dang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sinchita Roy-Chowdhuri
- Department of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
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12
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Lee SH, You HS, Kang HG, Kang SS, Hyun SH. Association between Altered Blood Parameters and Gut Microbiota after Synbiotic Intake in Healthy, Elderly Korean Women. Nutrients 2020; 12:nu12103112. [PMID: 33053824 PMCID: PMC7650560 DOI: 10.3390/nu12103112] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/25/2020] [Accepted: 10/09/2020] [Indexed: 12/20/2022] Open
Abstract
Synbiotics intake can alter the composition of intestinal microbes beneficially. We aimed to detect the changes in the intestinal microbiomes of 37 healthy elderly Korean women after the intake of a synbiotic drink. This was a longitudinal study controlled with a temporal series, including a control period of 3 weeks before intake, synbiotic intake for 3 weeks, and a washout period of 3 weeks. Fecal microbiota composition was analyzed by sequencing the V3-V4 hypervariable regions of 16S rRNA. Physical fecal activity increased with improvement in fecal shape. Thirty intestinal bacterial taxa were observed to change only after the intake period. In particular, Ellagibacter appeared only after ingestion. In addition, the abundance of Terrisporobacter showed a positive correlation with C-reactive protein, triglyceride. Lachnospiraceae_uc, Eubacterium_g5, and Blautia had a positive correlation with creatinine, whereas PAC001100_g had a negative correlation with creatinine. Short-term (3 weeks) intake of symbiotic organisms changes the composition of the gut microbiota in healthy elderly Korean women.
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Affiliation(s)
- Song Hee Lee
- Department of Biomedical Laboratory Science, School of Medicine, Eulji University, 77 Gyeryong-ro, 771 Beon-gil, Jung-gu, Daejeon 34824, Korea; (S.H.L.); (H.S.Y.)
- Department of Senior Healthcare, BK21 Plus Program, Graduate School, Eulji University, 77 Gyeryong-ro, 771 Beon-gil, Jung-gu, Daejeon 34824, Korea;
| | - Hee Sang You
- Department of Biomedical Laboratory Science, School of Medicine, Eulji University, 77 Gyeryong-ro, 771 Beon-gil, Jung-gu, Daejeon 34824, Korea; (S.H.L.); (H.S.Y.)
- Department of Senior Healthcare, BK21 Plus Program, Graduate School, Eulji University, 77 Gyeryong-ro, 771 Beon-gil, Jung-gu, Daejeon 34824, Korea;
| | - Hee-Gyoo Kang
- Department of Senior Healthcare, BK21 Plus Program, Graduate School, Eulji University, 77 Gyeryong-ro, 771 Beon-gil, Jung-gu, Daejeon 34824, Korea;
- Department of Biomedical Laboratory Science, College of Health Sciences, Eulji University, Seongnam 13135, Korea
| | - Sang Sun Kang
- Department of Biology Education, Chungbuk National University, Chungdae-ro 1, Seowon-gu, Cheongju 28644, Korea;
| | - Sung Hee Hyun
- Department of Biomedical Laboratory Science, School of Medicine, Eulji University, 77 Gyeryong-ro, 771 Beon-gil, Jung-gu, Daejeon 34824, Korea; (S.H.L.); (H.S.Y.)
- Department of Senior Healthcare, BK21 Plus Program, Graduate School, Eulji University, 77 Gyeryong-ro, 771 Beon-gil, Jung-gu, Daejeon 34824, Korea;
- Correspondence: ; Tel.: +82-10-9412-8853
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13
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The Real-Life Data of BRAF Mutation on the Treatment of Colorectal Cancer: a TOG Study. J Gastrointest Cancer 2020; 52:932-939. [PMID: 32914373 DOI: 10.1007/s12029-020-00514-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
PURPOSE Colorectal cancer is the third leading diagnosis accounting for nearly 10% of all new cancers worldwide. The distinct features among BRAF mutant colorectal cancers make these tumor groups hard to treat for oncologists. The median overall survival (OS) of these types of cancers is reported to be 9 to 14 months. METHODS The study was declared on the Turkish Oncology Study Group Conference and approved. The patients' data was received from the centers who confirmed to participate. The BRAF-mutated patients were included in the study. The demographic features (age, gender, etc.), type of mutation, tumor localizations, histology, microsatellite instability (MSI) status, metastasis patterns chemotherapeutic agents and progression, and death times were recorded. RESULTS Thirty-nine patients were enrolled in the study. Sixteen patients had concurrent KRAS mutations, while 7 had NRAS mutations. Most of the patients received doublet chemotherapies in combination with anti-VEGF agents in the first and second line of the treatment. There was a significant difference in OS according to the stage which showed a decreased survival in stage IV patients at the time of diagnosis. Concurrent KRAS mutation resulted in increased OS. The median OS was 47 and 24 months favoring the KRAS mutant group. The patients whose primary tumor operated had better survival when compared with other patients. The median OS of the operated group was 47 months, while the non-operated group was 24 months. Liver metastasis was related to worse prognosis at the time of diagnosis in univariate analysis. CONCLUSION In our study we found a high concurrent RAS mutation ratio in a BRAF mutant patient group which was different from prior studies. The concurrent mutations resulted in a favorable outcome in terms of OS which is also different from the current knowledge. More prospective studies are needed especially BRAF-mutated patient population and especially with concurrent RAS mutations.
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14
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Coquerelle S, Darlington M, Michel M, Durand M, Borget I, Baffert S, Marino P, Perrier L, Durand-Zaleski I. Impact of Next Generation Sequencing on Clinical Practice in Oncology in France: Better Genetic Profiles for Patients Improve Access to Experimental Treatments. VALUE IN HEALTH : THE JOURNAL OF THE INTERNATIONAL SOCIETY FOR PHARMACOECONOMICS AND OUTCOMES RESEARCH 2020; 23:898-906. [PMID: 32762992 DOI: 10.1016/j.jval.2020.03.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 02/11/2020] [Accepted: 03/11/2020] [Indexed: 06/11/2023]
Abstract
OBJECTIVES We evaluated how next generation sequencing (NGS) can modify care pathways in an observational impact study in France. METHODS All patients with lung cancer, colorectal cancer, or melanoma who had NGS analyses of somatic genomic alterations done in 1 of 7 biomolecular platforms certified by the French National Cancer Institute (INCa) between 2013 and 2016 were eligible. We compared patients' pathways before and after their NGS results. Endpoints consisted of the turnaround time in obtaining results, the number of patients with at least 1 genomic alteration identified, the number of actionable alterations, the impact of the genomic multidisciplinary tumor board on care pathways, the number of changes in the treatment plan, and the survival outcome up to 1 year after NGS analyses. RESULTS 1213 patients with a request for NGS analysis were included. NGS was performed for 1155 patients, identified at least 1 genomic alteration for 867 (75%), and provided an actionable alteration for 614 (53%). Turnaround time between analyses and results was on average 8 days (Min: 0; Max: 95) for all cancer types. Before NGS analysis, 33 of 614 patients (5%) were prescribed a targeted therapy compared with 54 of 614 patients (8%) after NGS analysis. Proposition of inclusion in clinical trials with experimental treatments increased from 5% (n = 31 of 614) before to 28% (n = 178 of 614) after NGS analysis. Patients who benefited from a genotype matched treatment after NGS analysis tended to have a better survival outcome at 1 year than patients with nonmatched treatment: 258 days (±107) compared with 234 days (±106), (P = .41). CONCLUSIONS NGS analyses resulted in a change in patients' care pathways for 20% of patients (n = 232 of 1155).
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Affiliation(s)
- Séverine Coquerelle
- Unité de Recherche Clinique en Économie de la Santé d'Ile de France, Assistance Publique Hôpitaux de Paris, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Paris, France; Centre of Research in Epidemiology and Statistics, Institut National de la Santé et de la Recherche Médicale-Joint Research Units, Paris, France.
| | - Meryl Darlington
- Unité de Recherche Clinique en Économie de la Santé d'Ile de France, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Morgane Michel
- Unité de Recherche Clinique en Économie de la Santé d'Ile de France, Assistance Publique Hôpitaux de Paris, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Paris, France; Institut National de la Santé et de la Recherche Médicale, Epidémiologie Clinique et Evaluation Economique, Paris, France
| | - Manon Durand
- Unité de Recherche Clinique en Économie de la Santé d'Ile de France, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Isabelle Borget
- Etudes et Recherche en Economie de la Santé, Gustave Roussy Institute, Villejuif, France
| | | | - Patricia Marino
- Institut Paoli Calmettes, Sciences Economiques et Sociales de la Santé et Traitement de l'information Médicale, Marseille, France
| | - Lionel Perrier
- Université de Lyon, Centre Léon Bérard, Groupe d'Analyse de Théorie Economique, Lyon Saint-Etienne-Joint Research Units, Lyon, France
| | - Isabelle Durand-Zaleski
- Unité de Recherche Clinique en Économie de la Santé d'Ile de France, Assistance Publique Hôpitaux de Paris, Paris, France; Centre of Research in Epidemiology and Statistics, Institut National de la Santé et de la Recherche Médicale-Joint Research Units, Paris, France; Public Health Department, Hôpital Henri-Mondor, Assistance Publique Hôpitaux de Paris, Créteil, France
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15
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Belardinilli F, Capalbo C, Malapelle U, Pisapia P, Raimondo D, Milanetti E, Yasaman M, Liccardi C, Paci P, Sibilio P, Pepe F, Bonfiglio C, Mezi S, Magri V, Coppa A, Nicolussi A, Gradilone A, Petroni M, Di Giulio S, Fabretti F, Infante P, Coni S, Canettieri G, Troncone G, Giannini G. Clinical Multigene Panel Sequencing Identifies Distinct Mutational Association Patterns in Metastatic Colorectal Cancer. Front Oncol 2020; 10:560. [PMID: 32457828 PMCID: PMC7221020 DOI: 10.3389/fonc.2020.00560] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 03/27/2020] [Indexed: 12/12/2022] Open
Abstract
Extensive molecular characterization of human colorectal cancer (CRC) via Next Generation Sequencing (NGS) indicated that genetic or epigenetic dysregulation of a relevant, but limited, number of molecular pathways typically occurs in this tumor. The molecular picture of the disease is significantly complicated by the frequent occurrence of individually rare genetic aberrations, which expand tumor heterogeneity. Inter- and intratumor molecular heterogeneity is very likely responsible for the remarkable individual variability in the response to conventional and target-driven first-line therapies, in metastatic CRC (mCRC) patients, whose median overall survival remains unsatisfactory. Implementation of an extensive molecular characterization of mCRC in the clinical routine does not yet appear feasible on a large scale, while multigene panel sequencing of most commonly mutated oncogene/oncosuppressor hotspots is more easily achievable. Here, we report that clinical multigene panel sequencing performed for anti-EGFR therapy predictive purposes in 639 formalin-fixed paraffin-embedded (FFPE) mCRC specimens revealed previously unknown pairwise mutation associations and a high proportion of cases carrying actionable gene mutations. Most importantly, a simple principal component analysis directed the delineation of a new molecular stratification of mCRC patients in eight groups characterized by non-random, specific mutational association patterns (MAPs), aggregating samples with similar biology. These data were validated on a The Cancer Genome Atlas (TCGA) CRC dataset. The proposed stratification may provide great opportunities to direct more informed therapeutic decisions in the majority of mCRC cases.
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Affiliation(s)
| | - Carlo Capalbo
- Department of Molecular Medicine, University La Sapienza, Rome, Italy
| | | | - Pasquale Pisapia
- Department of Public Health, University Federico II, Naples, Italy
| | - Domenico Raimondo
- Department of Molecular Medicine, University La Sapienza, Rome, Italy
| | | | - Mahdavian Yasaman
- Department of Molecular Medicine, University La Sapienza, Rome, Italy
| | - Carlotta Liccardi
- Department of Molecular Medicine, University La Sapienza, Rome, Italy
| | - Paola Paci
- Institute for System Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Pasquale Sibilio
- Institute for System Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Francesco Pepe
- Department of Public Health, University Federico II, Naples, Italy
| | - Caterina Bonfiglio
- National Institute of Gastroenterology-Research Hospital, IRCCS "S. de Bellis", Bari, Italy
| | - Silvia Mezi
- Department of Radiological Oncological and Pathological Sciences, University La Sapienza, Rome, Italy
| | - Valentina Magri
- Department of Surgery Pietro Valdoni, Faculty of Medicine and Dentistry, Sapienza University of Rome, Rome, Italy
| | - Anna Coppa
- Department of Experimental Medicine, University La Sapienza, Rome, Italy
| | - Arianna Nicolussi
- Department of Experimental Medicine, University La Sapienza, Rome, Italy
| | - Angela Gradilone
- Department of Molecular Medicine, University La Sapienza, Rome, Italy
| | - Marialaura Petroni
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
| | - Stefano Di Giulio
- Department of Molecular Medicine, University La Sapienza, Rome, Italy
| | | | - Paola Infante
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
| | - Sonia Coni
- Department of Molecular Medicine, University La Sapienza, Rome, Italy
| | - Gianluca Canettieri
- Department of Molecular Medicine, University La Sapienza, Rome, Italy.,Pasteur Institute-Cenci Bolognetti Foundation, Rome, Italy
| | | | - Giuseppe Giannini
- Department of Molecular Medicine, University La Sapienza, Rome, Italy.,Pasteur Institute-Cenci Bolognetti Foundation, Rome, Italy
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16
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Garg S, Grenier S, Misyura M, Sukhai MA, Thomas M, Kamel-Reid S, Stockley T. Assessing the Diagnostic Yield of Targeted Next-Generation Sequencing for Melanoma and Gastrointestinal Tumors. J Mol Diagn 2020; 22:467-475. [PMID: 32036084 DOI: 10.1016/j.jmoldx.2019.12.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 11/19/2019] [Accepted: 12/20/2019] [Indexed: 12/21/2022] Open
Abstract
A common rationale in molecular diagnostic laboratories is that implementation of next-generation sequencing (NGS) enables simultaneous multigene testing, allowing increased information benefit compared with non-NGS assays. However, minimal published data exist to support this justification. The current study compared clinical diagnostic yield of TruSight Tumor 26 Sequencing Panel (TST26) in melanoma, colorectal (CRC), and gastrointestinal stromal (GIST) tumors with non-NGS assays. A total of 1041 formalin-fixed, paraffin-embedded tumors, of melanoma, CRC, and GIST, were profiled. NGS results were compared with non-NGS single-gene or single-variant assays with respect to variant output and diagnostic yield. A total of 79% melanoma and 94% CRC tumors were variant positive by panel testing. TST26 panel improved serine/threonine-protein kinase B-raf (BRAF) variant detection in melanoma compared with single-variant BRAF Val600Glu/Lys (V600E/K) routine tests by 24% and detected variants in genes other than BRAF, NRAS, and KIT, which could impact patient management in 20% additional cases. NGS enhanced diagnostic yield in CRC by 36% when compared with routine single-gene assays. In contrast, no added benefit of NGS-based testing for GIST tumors was observed. TST26 panel either missed or inaccurately called complex insertion/deletion variants in KIT exon 11, which were accurately identified by non-NGS methods. Findings of this study demonstrate the differential impact of cancer site and variant type on diagnostic test information yield from NGS assays.
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Affiliation(s)
- Swati Garg
- Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario
| | - Sylvie Grenier
- Division of Genome Diagnostics, Department of Clinical Laboratory Genetics, Laboratory Medicine Program, University Health Network, Toronto, Ontario; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Maksym Misyura
- Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario
| | - Mahadeo A Sukhai
- Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario
| | - Mariam Thomas
- Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario
| | - Suzanne Kamel-Reid
- Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario; Division of Genome Diagnostics, Department of Clinical Laboratory Genetics, Laboratory Medicine Program, University Health Network, Toronto, Ontario; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Tracy Stockley
- Advanced Molecular Diagnostics Laboratory, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario; Division of Genome Diagnostics, Department of Clinical Laboratory Genetics, Laboratory Medicine Program, University Health Network, Toronto, Ontario; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.
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17
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Pepe F, Pisapia P, Del Basso de Caro ML, Conticelli F, Malapelle U, Troncone G, Martinez JC. Next generation sequencing identifies novel potential actionable mutations for grade I meningioma treatment. Histol Histopathol 2019; 35:741-749. [PMID: 31872418 DOI: 10.14670/hh-18-195] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Meningiomas are common brain tumors that arise from the meningeal membranes that envelope the brain and spinal cord. The World Health Organization classifies these tumors into three histopathological grades. Because of tumor recurrence, treating meningiomas may be challenging even in well-differentiated grade I (GI) neoplasms. Indeed, around 5% of completely resected GI meningiomas relapse within 5 years. Therefore, identifying driver mutations in GI meningiomas through next generation sequencing (NGS) assays is paramount. The aim of this study was to validate the use of the 50-gene AmpliSeq Hotspot Cancer Panel v2 to identify the mutational status of 23 GI meningioma, namely, 12 non recurrent and 11 recurrent. In 18 out of the 23 GI meningiomas analyzed, we identified at least one gene mutation (78.2%). The most frequently mutated genes were c-kit (39.1%), ATM (26.1%), TP53 (26.1%), EGFR (26.1%), STK11 (21.7%), NRAS (17.4%), SMAD4 (13%), FGFR3 (13%), and PTPN11 (13%); less frequent mutations were SMARCB1 (8.7%), FLT3 (8.7%), KRAS (8.7%), FBWX7 (8.7%), ABL1 (8.7%), ERBB2 (8.7%), IDH1 (8.7%), BRAF (8.7%), MET (8.7%), HRAS (4.3%), RB1 (4.3%), CTNNB1 (4.3%), PIK3CA (4.3%), VHL (4.3%), KDR (4.3%), APC (4.3%), NOTCH1 (4.3%), JAK3 (4.3%), and SRC (4.3%). To our knowledge, mutations in all of these genes, except for TP53, STK11, SMARCB1, PIK3CA, VHL, and BRAF, have never been described before in meningiomas. Hence, these findings demonstrate the viability of NGS to detect new genetic alterations in GI meningiomas. Equally important, this technology enabled us to detect possible novel actionable mutations not previously associated with GI and for which selective inhibitors already exist.
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Affiliation(s)
- Francesco Pepe
- Department of Public Health, University of Naples "Federico II", Naples, Italy
| | - Pasquale Pisapia
- Department of Public Health, University of Naples "Federico II", Naples, Italy
| | | | - Floriana Conticelli
- Department of Public Health, University of Naples "Federico II", Naples, Italy
| | - Umberto Malapelle
- Department of Public Health, University of Naples "Federico II", Naples, Italy
| | - Giancarlo Troncone
- Department of Public Health, University of Naples "Federico II", Naples, Italy.
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18
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Kim Y, Cho CH, Ha JS, Kim DH, Kwon SY, Oh SC, Lee KA. An optimized BRCA1/2 next-generation sequencing for different clinical sample types. J Gynecol Oncol 2019; 31:e9. [PMID: 31788999 PMCID: PMC6918881 DOI: 10.3802/jgo.2020.31.e9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 07/17/2019] [Accepted: 07/25/2019] [Indexed: 02/04/2023] Open
Abstract
Objective A simultaneous detection of germline and somatic mutations in ovarian cancer (OC) using tumor materials is considered to be cost-effective for BRCA1/2 testing. However, there are limited studies of the analytical performances according to various sample types. The aim of this study is to propose a strategy for routine BRCA1/2 next-generation sequencing (NGS) screening based on analytical performance according to different sample types. Methods We compared BRCA1/2 NGS screening assay using buffy coat, fresh-frozen (FF) and formalin-fixed paraffin-embedded (FFPE) from 130 samples. Results The rate of repeated tests in a total of buffy coat, FF and FFPE was 0%, 8%, and 34%, respectively. The accuracy of BRCA1/2 NGS testing was 100.0%, 99.9% and 99.9% in buffy coat, FFPE and FF, respectively. However, due to the presence of variant allele frequency (VAF) shifted heterozygous variants, tumor materials (FFPE and FF) showed lower sensitivity (95.5%–99.0%) than buffy coat (100%). Furthermore, FFPE showed 51.4% of the positive predictive value (PPV) on account of sequence artifacts. When performed in the post-filtration process, PPV was increased by approximately 20% in FFPE. Buffy coat showed 100% of sensitivity, specificity and accuracy in BRCA1/2 NGS test. Conclusions On the comparison of the analytical performance according to different sample types, the buffy coat was not affected by sequencing artifacts and VAF shifted variants. Therefore, the blood test should be given priority in detecting germline BRCA1/2 mutation, and tumor materials could be suitable to detect somatic mutations in OC patients without identifying germline BRCA1/2 mutation.
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Affiliation(s)
- Yoonjung Kim
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Chi Heum Cho
- Department of Obstetrics and Gynecology, Keimyung University School of Medicine, Daegu, Korea
| | - Jung Sook Ha
- Department of Laboratory Medicine, Keimyung University School of Medicine, Daegu, Korea
| | - Do Hoon Kim
- Department of Laboratory Medicine, Keimyung University School of Medicine, Daegu, Korea
| | - Sun Young Kwon
- Department of Pathology, Keimyung University School of Medicine, Daegu, Korea
| | - Seoung Chul Oh
- Department of Laboratory Medicine, Gangnam Severance Hospital, Seoul, Korea
| | - Kyung A Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea.
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19
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LaCasse Z, Briscoe JR, Nesterov EE, Nesterova IV. Multidimensional Tunability of Nucleic Acids Enables Sensing over Unknown Backgrounds. Anal Chem 2019; 91:14275-14280. [PMID: 31651140 DOI: 10.1021/acs.analchem.9b02420] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A longstanding challenge in quantitative analysis is the relationship between a sensor's dynamic range and a background: the response range must align with the target's background value. If this condition is not met, a reliable measurement is impossible. The requirement is especially critical for sensing systems displaying sharp responses. In this work, we have solved the problem of response range/background misalignment via design of sensing systems that adjust their response to actual unknown backgrounds. The sensing systems are based on nucleic acid scaffolds: due to an intrinsic trait of multidimensional tunability, the sensors can assess the actual background and adjust response range accordingly. We established a general methodology and demonstrated, as a proof-of-concept, a practically meaningful example of detecting very small changes in proton concentrations over unknown aqueous backgrounds using a DNA i-motif sensor. Owing to multidimensional tunability of a DNA i-motif, this sensor could reliably measure changes in proton concentration that are 3 orders of magnitude below currently available methodologies.
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Affiliation(s)
- Zane LaCasse
- Department of Chemistry and Biochemistry , Northern Illinois University , DeKalb , Illinois 60115 , United States
| | - James R Briscoe
- Department of Chemistry , Louisiana State University , Baton Rouge , Louisiana 70803 , United States
| | - Evgueni E Nesterov
- Department of Chemistry and Biochemistry , Northern Illinois University , DeKalb , Illinois 60115 , United States.,Department of Chemistry , Louisiana State University , Baton Rouge , Louisiana 70803 , United States
| | - Irina V Nesterova
- Department of Chemistry and Biochemistry , Northern Illinois University , DeKalb , Illinois 60115 , United States
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20
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Guler I, Askan G, Klostergaard J, Sahin IH. Precision medicine for metastatic colorectal cancer: an evolving era. Expert Rev Gastroenterol Hepatol 2019; 13:919-931. [PMID: 31475851 DOI: 10.1080/17474124.2019.1663174] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Introduction: Metastatic colorectal cancer (CRC) remains a dilemma for cancer researchers with an increasing incidence in the younger patient population. Until the last decade, limited therapeutic options were available for metastatic CRC patients leading to relatively poor clinical outcomes.Areas covered: With advances in genome sequencing technology and reductions in the cost of next-generation sequencing, molecular profiling has become more accessible for cancer researchers and clinical investigators, which has furthered our understanding of the molecular behavior of CRC. This progress has recently translated into significant advances in molecular-based therapeutics and led to the development of new target-specific agents in metastatic CRC patients. In this review article, we extensively elaborate on genomic alterations seen in CRC patients including, but not limited to, EGFR, MMR, BRAF, HER2, NTRKs, FGFR, BRCA1/2, PALB2, POLE, and POLD1 genes, all of which are potentially actionable by either an FDA-approved agent or in a clinical trial setting.Expert opinion: We strongly recommend molecular profiling in metastatic CRC patients during the early course of their disease, as this may provide therapeutic and prognostic information that can guide clinicians to practice precision medicine. Patients with potentially actionable genes should be considered for targeting agents based on molecular alterations.
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Affiliation(s)
- Irem Guler
- Department of Medicine, Baskent University School of Medicine, Ankara, Turkey
| | - Gokce Askan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jim Klostergaard
- Department of Molecular and Cellular Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Ibrahim Halil Sahin
- Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, USA
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21
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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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22
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Capalbo C, Belardinilli F, Raimondo D, Milanetti E, Malapelle U, Pisapia P, Magri V, Prete A, Pecorari S, Colella M, Coppa A, Bonfiglio C, Nicolussi A, Valentini V, Tessitore A, Cardinali B, Petroni M, Infante P, Santoni M, Filetti M, Colicchia V, Paci P, Mezi S, Longo F, Cortesi E, Marchetti P, Troncone G, Bellavia D, Canettieri G, Giannini G. A Simplified Genomic Profiling Approach Predicts Outcome in Metastatic Colorectal Cancer. Cancers (Basel) 2019; 11:cancers11020147. [PMID: 30691222 PMCID: PMC6406354 DOI: 10.3390/cancers11020147] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 01/19/2019] [Accepted: 01/22/2019] [Indexed: 12/22/2022] Open
Abstract
The response of metastatic colorectal cancer (mCRC) to the first-line conventional combination therapy is highly variable, reflecting the elevated heterogeneity of the disease. The genetic alterations underlying this heterogeneity have been thoroughly characterized through omic approaches requiring elevated efforts and costs. In order to translate the knowledge of CRC molecular heterogeneity into a practical clinical approach, we utilized a simplified Next Generation Sequencing (NGS) based platform to screen a cohort of 77 patients treated with first-line conventional therapy. Samples were sequenced using a panel of hotspots and targeted regions of 22 genes commonly involved in CRC. This revealed 51 patients carrying actionable gene mutations, 22 of which carried druggable alterations. These mutations were frequently associated with additional genetic alterations. To take into account this molecular complexity and assisted by an unbiased bioinformatic analysis, we defined three subgroups of patients carrying distinct molecular patterns. We demonstrated these three molecular subgroups are associated with a different response to first-line conventional combination therapies. The best outcome was achieved in patients exclusively carrying mutations on TP53 and/or RAS genes. By contrast, in patients carrying mutations in any of the other genes, alone or associated with mutations of TP53/RAS, the expected response is much worse compared to patients with exclusive TP53/RAS mutations. Additionally, our data indicate that the standard approach has limited efficacy in patients without any mutations in the genes included in the panel. In conclusion, we identified a reliable and easy-to-use approach for a simplified molecular-based stratification of mCRC patients that predicts the efficacy of the first-line conventional combination therapy.
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Affiliation(s)
- Carlo Capalbo
- Department of Molecular Medicine, University La Sapienza, 00161 Rome, Italy.
- Department of Medical Oncology Sant' Andrea Hospital, I-00189 Rome, Italy.
| | | | - Domenico Raimondo
- Department of Molecular Medicine, University La Sapienza, 00161 Rome, Italy.
| | | | - Umberto Malapelle
- Department of Public Health, University Federico II, 80131 Naples, Italy.
| | - Pasquale Pisapia
- Department of Public Health, University Federico II, 80131 Naples, Italy.
| | - Valentina Magri
- Department of Radiological Oncological and Pathological Sciences, University La Sapienza, 00161 Rome, Italy.
| | - Alessandra Prete
- Department of Radiological Oncological and Pathological Sciences, University La Sapienza, 00161 Rome, Italy.
| | - Silvia Pecorari
- Department of Radiological Oncological and Pathological Sciences, University La Sapienza, 00161 Rome, Italy.
| | | | - Anna Coppa
- Department of Experimental Medicine, University La Sapienza, 00161 Rome, Italy.
| | - Caterina Bonfiglio
- National Institute of Gastroenterology-Research Hospital, IRCCS "S. de Bellis", Castellana Grotte, 70013 Bari, Italy.
| | - Arianna Nicolussi
- Department of Experimental Medicine, University La Sapienza, 00161 Rome, Italy.
| | - Virginia Valentini
- Department of Molecular Medicine, University La Sapienza, 00161 Rome, Italy.
| | - Alessandra Tessitore
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, 67100 L'Aquila, Italy.
| | - Beatrice Cardinali
- Institute of Cell Biology and Neurobiology, National Research Council, Campus A. Buzzati-Traverso, 00015 Monterotondo Scalo, Italy.
| | - Marialaura Petroni
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, 00161 Rome, Italy.
| | - Paola Infante
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, 00161 Rome, Italy.
| | - Matteo Santoni
- Oncology Unit, Macerata Hospital, 62012 Macerata, Italy.
| | - Marco Filetti
- Department of Medical Oncology Sant' Andrea Hospital, I-00189 Rome, Italy.
| | - Valeria Colicchia
- Department of Molecular Medicine, University La Sapienza, 00161 Rome, Italy.
| | - Paola Paci
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, 00185 Rome, Italy.
| | - Silvia Mezi
- Department of Radiological Oncological and Pathological Sciences, University La Sapienza, 00161 Rome, Italy.
| | - Flavia Longo
- Department of Radiological Oncological and Pathological Sciences, University La Sapienza, 00161 Rome, Italy.
| | - Enrico Cortesi
- Department of Radiological Oncological and Pathological Sciences, University La Sapienza, 00161 Rome, Italy.
| | - Paolo Marchetti
- Department of Medical Oncology Sant' Andrea Hospital, I-00189 Rome, Italy.
| | - Giancarlo Troncone
- Department of Public Health, University Federico II, 80131 Naples, Italy.
| | - Diana Bellavia
- Department of Molecular Medicine, University La Sapienza, 00161 Rome, Italy.
| | - Gianluca Canettieri
- Department of Molecular Medicine, University La Sapienza, 00161 Rome, Italy.
- Pasteur Institute-Cenci Bolognetti Foundation, 00161 Rome, Italy.
| | - Giuseppe Giannini
- Department of Molecular Medicine, University La Sapienza, 00161 Rome, Italy.
- Pasteur Institute-Cenci Bolognetti Foundation, 00161 Rome, Italy.
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23
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Pepe F, De Luca C, Smeraglio R, Pisapia P, Sgariglia R, Nacchio M, Russo M, Serra N, Rocco D, Battiloro C, Ambrosio F, Gragnano G, Vigliar E, Bellevicine C, Troncone G, Malapelle U. Performance analysis of SiRe next-generation sequencing panel in diagnostic setting: focus on NSCLC routine samples. J Clin Pathol 2018; 72:38-45. [PMID: 30279174 DOI: 10.1136/jclinpath-2018-205386] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 08/28/2018] [Accepted: 08/29/2018] [Indexed: 01/14/2023]
Abstract
AIMS Following the development for liquid biopsies of the SiRe next-generation sequencing (NGS) panel that covers 568 clinical relevant mutations in EGFR, KRAS, NRAS, BRAF, cKIT and PDGFRa genes, in this current study, we apply this small NGS panel on tissue samples of lung cancer. METHODS A total of 322 specimens were prospectively tested. Technical parameters were analysed on both cytological and histological samples. In a subset of 75 samples, the EGFR SiRe results were compared with those generated by the European Community (CE)-IVD EGFR assay on Idylla platform. Clinical outcomes of 11 patients treated, on the basis of SiRe results, were also evaluated. RESULTS Only 28 (8.7%) specimens failed to produce a library; out of the 294 remaining samples, a total of 168 somatic mutations were found. In nearly all instances (74/75-99%), the EGFR SiRe results were confirmed by Idylla. In general, SiRe analytical parameters were excellent. However, histological and cytological specimens differed in relation to average reads for sample, mean number of mapped reads, median read length and average reads for amplicon. Treatment outcome evaluation in 11 patients showed a partial response in 82 % (9/11) patients with a median progression-free survival of 340 days. CONCLUSIONS The small gene panel SiRe is a clinically relevant tool useful to widespread the adoption of NGS in predictive molecular pathology laboratories.
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Affiliation(s)
- Francesco Pepe
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Caterina De Luca
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Riccardo Smeraglio
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Pasquale Pisapia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Roberta Sgariglia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Mariantonia Nacchio
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Maria Russo
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Nicola Serra
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Danilo Rocco
- Oncology, A.O.R.N. Vincenzo Monaldi, Naples, Italy
| | | | | | - Gianluca Gragnano
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Elena Vigliar
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Claudio Bellevicine
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
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24
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The gene mutational discrepancies between primary and paired metastatic colorectal carcinoma detected by next-generation sequencing. J Cancer Res Clin Oncol 2018; 144:2149-2159. [DOI: 10.1007/s00432-018-2742-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 08/21/2018] [Indexed: 01/22/2023]
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25
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Antoniotti C, Ongaro E, Falcone A, Cremolini C. The Winding Roadmap of Biomarkers toward Clinic: Lessons from Predictors of Resistance to Anti-EGFRs in Metastatic Colorectal Cancer. Int J Mol Sci 2018; 19:E2298. [PMID: 30081606 PMCID: PMC6121538 DOI: 10.3390/ijms19082298] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 07/31/2018] [Accepted: 08/01/2018] [Indexed: 01/06/2023] Open
Abstract
In the evolving molecular landscape of metastatic colorectal cancer, optimizing available tools to select patients to receive anti-epidermal growth factor receptor (anti-EGFR) monoclonal antibodies is a modern challenge of colorectal oncologists. Several molecular biomarkers have been investigated in recent years as potential predictors of resistance to anti-EGFR agents in preclinical and clinical retrospective series. Nevertheless, none of them have been implemented in clinical practice due to the lack of a formal prospective demonstration. Here, we propose a literature review of molecular alterations associated with resistance to anti-EGFRs, underlining the reasons why their roadmap from laboratories to clinics was prematurely halted.
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Affiliation(s)
- Carlotta Antoniotti
- Department of Oncology, University Hospital of Pisa, 56126 Pisa, Italy.
- Department of Translational Research and New Technologies in Medicine, University of Pisa, 56126 Pisa, Italy.
| | - Elena Ongaro
- Department of Oncology, University Hospital of Pisa, 56126 Pisa, Italy.
- Department of Translational Research and New Technologies in Medicine, University of Pisa, 56126 Pisa, Italy.
- Department of Oncology, Azienda Sanitaria Universitaria Integrata S. Maria della Misericordia, 33100 Udine, Italy.
| | - Alfredo Falcone
- Department of Oncology, University Hospital of Pisa, 56126 Pisa, Italy.
- Department of Translational Research and New Technologies in Medicine, University of Pisa, 56126 Pisa, Italy.
| | - Chiara Cremolini
- Department of Oncology, University Hospital of Pisa, 56126 Pisa, Italy.
- Department of Translational Research and New Technologies in Medicine, University of Pisa, 56126 Pisa, Italy.
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26
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Antitumor Efficacy of Dual Blockade of EGFR Signaling by Osimertinib in Combination With Selumetinib or Cetuximab in Activated EGFR Human NCLC Tumor Models. J Thorac Oncol 2018. [DOI: 10.1016/j.jtho.2018.02.025] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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27
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Bruera G, Pepe F, Malapelle U, Pisapia P, Mas AD, Di Giacomo D, Calvisi G, Troncone G, Ricevuto E. KRAS, NRAS and BRAF mutations detected by next generation sequencing, and differential clinical outcome in metastatic colorectal cancer (MCRC) patients treated with first line FIr-B/FOx adding bevacizumab (BEV) to triplet chemotherapy. Oncotarget 2018; 9:26279-26290. [PMID: 29899858 PMCID: PMC5995185 DOI: 10.18632/oncotarget.25180] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 04/05/2018] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND First line triplet chemotherapy/BEV significantly improved clinical outcome of MCRC. KRAS/NRAS/BRAF mutations were evaluated by next generation sequencing (NGS) in MCRC patients treated with first line FIr-B/FOx. METHODS KRAS exons 2-4 (KRAS2-4 ), NRAS2-4 , BRAF15 were evaluated in 67 tumours by ION Torrent platform. Mutation detection criteria: >500×sequence coverage (cov); >1% mutant allelic fraction (AF). Clinical outcomes were compared by log-rank. RESULTS In 63 samples, KRAS2-4 /NRAS2-4 /BRAF15 wild-type (wt) were 14 (22.2%), mutant (mut) 49 (77.8%): KRAS2-4 42 (66.7%); NRAS2-4 11 (16.4%); BRAF15 5 (7.5%). Sixty mutations were detected, range 1-3 mut: 43 (71.7%) >1000×cov/>5% AF; 9 (15%) >500×cov/>5% AF; 8 (13.3%) >1000×cov/<5% AF. Mut distribution in KRAS2-4 /NRAS2-4 /BRAF15 : 40 (63.5%) >1000×cov/>5% AF, 8 (12.7%) >500×cov/>5% AF, 1 (1.6%) >1000×cov/<5% AF; BRAF15 1 (1.5%) >500×cov/>5% AF, 4 (6%) >1000×cov/<5% AF. Prevalence of ≥2 mut samples: KRAS2-4 /NRAS2-4 /BRAF15 8 (12.7%); KRAS2-4 7 (11.1%); NRAS2-4 5 (7.5%). BRAF15 mutant were all ≥2 mut (7.5%), atypical and associated to KRAS and/or NRAS mut: c.1405 G>A; c.1406 G>C; c.1756 G>A, 2 samples; c.1796 C>T. At 21 months (m) follow-up, clinical outcome wt compared to mut was not significantly different: in KRAS2-4 /NRAS2-4 /BRAF15 , progression-free survival (PFS) 18/12 m, overall survival (OS) 28/22 m; 1/≥2 mutations, PFS 14/11, OS 37/22. PFS was trendy worse in RAS/BRAF wt vs ≥2 mut genes (P 0.059). CONCLUSIONS Most MCRC harboured KRAS2-4 /NRAS2-4 /BRAF15 mutations by NGS, often multiple and affecting few tumoral clones; 22% were triple wt. Clinical outcome is not significantly affected by KRAS2-4 /NRAS2-4 /BRAF15 genotype, trendy different in triple wt, compared with KRAS2-4 /NRAS2-4 /BRAF15 ≥2 mut.
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Affiliation(s)
- Gemma Bruera
- Oncology Territorial Care, S. Salvatore Hospital, Oncology Network ASL1 Abruzzo, University of L'Aquila, L'Aquila, Italy
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, Italy
| | - Francesco Pepe
- Department of Public Health, University Federico II, Napoli, Italy
| | | | - Pasquale Pisapia
- Department of Public Health, University Federico II, Napoli, Italy
| | - Antonella Dal Mas
- Pathology, S. Salvatore Hospital, Oncology Network ASL1 Abruzzo, L'Aquila, Italy
| | - Daniela Di Giacomo
- Oncology Territorial Care, S. Salvatore Hospital, Oncology Network ASL1 Abruzzo, University of L'Aquila, L'Aquila, Italy
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, Italy
| | - Giuseppe Calvisi
- Pathology, S. Salvatore Hospital, Oncology Network ASL1 Abruzzo, L'Aquila, Italy
| | | | - Enrico Ricevuto
- Oncology Territorial Care, S. Salvatore Hospital, Oncology Network ASL1 Abruzzo, University of L'Aquila, L'Aquila, Italy
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, L’Aquila, Italy
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28
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Sayagués JM, Del Carmen S, Del Mar Abad M, Corchete LA, Bengoechea O, Anduaga MF, Baldeón MJ, Cruz JJ, Alcazar JA, Angoso M, González M, García J, Muñoz-Bellvis L, Orfao A, Sarasquete ME. Combined assessment of the TNM stage and BRAF mutational status at diagnosis in sporadic colorectal cancer patients. Oncotarget 2018; 9:24081-24096. [PMID: 29844874 PMCID: PMC5963609 DOI: 10.18632/oncotarget.25300] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 04/06/2018] [Indexed: 12/12/2022] Open
Abstract
The prognostic impact of KRAS mutations and other KRAS-related and non-related genes such as BRAF, NRAS and TP53, on sporadic colorectal cancer (sCRC) remain controversial and/or have not been fully established. Here we investigated the frequency of such mutations in primary sCRC tumors and their impact on patient progression-free survival (PFS) and overall survival (OS). Primary tumor tissues from 87 sCRC patients were analysed using a custom-built next generation sequencing (NGS) panel to assess the hotspot mutated regions of KRAS/NRAS (exons 2, 3 and 4), BRAF (exon 15) and TP53 (all exons). Overall, mutations in these genes were detected in 46/87 sCRC tumors analyzed (53%) with the following frequencies per gene: TP53, 33%; KRAS, 28%; BRAF, 7%; and NRAS, 1%. A significant association was found between KRAS mutations and right side colon tumor location (p=0.05), well-differentiated tumors (p=0.04) and absence of lymphovascular invasion (p=0.05). In turn, BRAF-mutated tumors frequently corresponded to poorly- or moderately-differentiated sCRC (p=0.02) and showed a higher frequency of peritoneal carcinomatosis (p=0.006) and microsatellite instability (p=0.007). From the prognostic point of view, the BRAF mutational status together with the TNM stage were the only variables that showed an independent adverse impact on patient outcome in the multivariate analyses for both PFS and OS. Based on these results a scoring system was built and patients were classified into three prognostic subgroups with different PFS rates at 2 years: 91% vs. 77% vs. 0%, respectively (p<0.0001). Additional prospective studies in larger series of sCRC patients where mutations in genes other than those investigated here are required to validate the utility of the proposed predictive model.
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Affiliation(s)
- José María Sayagués
- Cytometry Service-NUCLEUS, Department of Medicine, Cancer Research Center (IBMCC-CSIC/USAL), CIBERONC and IBSAL (University Hospital of Salamanca), Salamanca, Spain
| | - Sofía Del Carmen
- Department of Pathology, University Hospital of Salamanca, Salamanca, Spain
| | - María Del Mar Abad
- Department of Pathology, University Hospital of Salamanca, Salamanca, Spain
| | - Luís Antonio Corchete
- Cáncer Research Center and Service of Hematology (University Hospital of Salamanca), Salamanca, Spain
| | - Oscar Bengoechea
- Department of Pathology, University Hospital of Salamanca, Salamanca, Spain
| | - María Fernanda Anduaga
- Service of General and Gastrointestinal Surgery, University Hospital of Salamanca, Salamanca, Spain
| | - María Jesús Baldeón
- Department of Oncology (University Hospital of Salamanca) and IBSAL (University Hospital of Salamanca), Salamanca, Spain
| | - Juan Jesús Cruz
- Department of Oncology (University Hospital of Salamanca) and IBSAL (University Hospital of Salamanca), Salamanca, Spain
| | - Jose Antonio Alcazar
- Service of General and Gastrointestinal Surgery, University Hospital of Salamanca, Salamanca, Spain
| | - María Angoso
- Service of General and Gastrointestinal Surgery, University Hospital of Salamanca, Salamanca, Spain
| | - Marcos González
- Cáncer Research Center and Service of Hematology (University Hospital of Salamanca), Salamanca, Spain
| | - Jacinto García
- Service of General and Gastrointestinal Surgery, University Hospital of Salamanca, Salamanca, Spain
| | - Luís Muñoz-Bellvis
- Service of General and Gastrointestinal Surgery, University Hospital of Salamanca, Salamanca, Spain
| | - Alberto Orfao
- Cytometry Service-NUCLEUS, Department of Medicine, Cancer Research Center (IBMCC-CSIC/USAL), CIBERONC and IBSAL (University Hospital of Salamanca), Salamanca, Spain
| | - María Eugenia Sarasquete
- Cáncer Research Center and Service of Hematology (University Hospital of Salamanca), Salamanca, Spain
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Simultaneous identification of clinically relevant single nucleotide variants, copy number alterations and gene fusions in solid tumors by targeted next-generation sequencing. Oncotarget 2018; 9:22749-22768. [PMID: 29854313 PMCID: PMC5978263 DOI: 10.18632/oncotarget.25229] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 04/05/2018] [Indexed: 01/19/2023] Open
Abstract
In this study, we have set-up a routine pipeline to evaluate the clinical application of Oncomine™ Focus Assay, a panel that allows the simultaneous detection of single nucleotide hotspot mutations in 35 genes, copy number alterations (CNAs) in 19 genes and gene fusions involving 23 genes in cancer samples. For this study we retrospectively selected 106 patients that were submitted to surgical resection for lung, gastric, colon or rectal cancer. We found that 56 patients out of 106 showed at least one alteration (53%), with 47 patients carrying at least one relevant nucleotide variant, 10 patients carrying at least one CNA and 3 patients carrying one gene fusion. On the basis of the mutational profiles obtained, we have identified 22 patients (20.7%) that were potentially eligible for targeted therapy. The most frequently mutated genes across all tumor types included KRAS (30 patients), PIK3CA (16 patients), BRAF (6 patients), EGFR (5 patients), NRAS (4 patients) and ERBB2 (3 patients) whereas CCND1, ERBB2, EGFR and MYC were the genes most frequently subjected to copy number gain. Finally, gene fusions were identified only in lung cancer patients and involved MET [MET(13)–MET(15) fusion] and FGFR3 [FGFR3(chr 17)–TACC3(chr 11)]. In conclusion, we demonstrate that the analysis with a multi-biomarker panel of cancer patients after surgery, may present several potential advantages in clinical daily practice, including the simultaneous detection of different potentially druggable alterations, reasonable costs, short time of testing and automated interpretation of results.
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D'Haene N, Fontanges Q, De Nève N, Blanchard O, Melendez B, Delos M, Dehou MF, Maris C, Nagy N, Rousseau E, Vandenhove J, Gilles A, De Prez C, Verset L, Van Craynest MP, Demetter P, Van Laethem JL, Salmon I, Le Mercier M. Clinical application of targeted next-generation sequencing for colorectal cancer patients: a multicentric Belgian experience. Oncotarget 2018; 9:20761-20768. [PMID: 29755687 PMCID: PMC5945518 DOI: 10.18632/oncotarget.25099] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 03/17/2018] [Indexed: 01/14/2023] Open
Abstract
International guidelines made RAS (KRAS and NRAS) status a prerequisite for the use of anti-EGFR agents for metastatic colorectal cancer (CRC) patients. Daily, new data emerges on the theranostic and prognostic role of molecular biomarkers; this is a strong incentive for a validated, sensitive, and broadly available molecular screening test. Next-generation sequencing (NGS) has begun to supplant other technologies for genomic profiling. We report here our 2 years of clinical practice using NGS results to guide therapeutic decisions. The Ion Torrent AmpliSeq colon/lung cancer panel, which allows mutation detection in 22 cancer-related genes, was prospectively used in clinical practice (BELAC ISO 15189 accredited method). The DNA of 741 formalin-fixed paraffin-embedded CRC tissues, including primary tumors and metastasis, was obtained from 14 different Belgian institutions and subjected to targeted NGS. Of the tumors tested, 98% (727) were successfully sequenced and 89% (650) harbored at least one mutation. KRAS, BRAF and NRAS mutations were found in 335 (46%), 78 (11%) and 32 (4%) samples, respectively. These mutation frequencies were consistent with those reported in public databases. Moreover, mutations and amplifications in potentially actionable genes were identified in 464 samples (64%), including mutations in PIK3CA (14%), ERBB2 (0.4%), AKT1 (0.6%), and MAP2K1 (0.1%), as well as amplifications of ERBB2 (0.3%) and EGFR (0.3%). The median turnaround time between reception of the sample in the laboratory and report release was 8 calendar days. Overall, the AmpliSeq colon/lung cancer panel was successfully applied in daily practice and provided reliable clinically relevant information for CRC patients.
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Affiliation(s)
- Nicky D'Haene
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Quitterie Fontanges
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Nancy De Nève
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Oriane Blanchard
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Barbara Melendez
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Monique Delos
- Department of Pathology, CHU UCL Namur, Yvoir, Belgium
| | | | - Calliope Maris
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium.,Department of Pathology, Braine l´Alleud Waterloo Hospital, Braine l´Alleud, Belgium
| | - Nathalie Nagy
- Department of Pathology, Charleroi University Hospital, Charleroi, Belgium
| | | | | | - André Gilles
- Department of Pathology, EPICURA Hospital, Frameries, Belgium
| | - Carine De Prez
- Department of Pathology, Brugmann University Hospital, Brussels, Belgium
| | - Laurine Verset
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium.,CurePath, Jumet, Belgium
| | | | - Pieter Demetter
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Jean-Luc Van Laethem
- Department of Oncology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Isabelle Salmon
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Marie Le Mercier
- Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
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Fassan M. Molecular Diagnostics in Pathology: Time for a Next-Generation Pathologist? Arch Pathol Lab Med 2018; 142:313-320. [DOI: 10.5858/arpa.2017-0269-ra] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023]
Abstract
Context.—Comprehensive molecular investigations of mainstream carcinogenic processes have led to the use of effective molecular targeted agents in most cases of solid tumors in clinical settings.Objective.—To update readers regarding the evolving role of the pathologist in the therapeutic decision-making process and the introduction of next-generation technologies into pathology practice.Data Sources.—Current literature on the topic, primarily sourced from the PubMed (National Center for Biotechnology Information, Bethesda, Maryland) database, were reviewed.Conclusions.—Adequate evaluation of cytologic-based and tissue-based predictive diagnostic biomarkers largely depends on both proper pathologic characterization and customized processing of biospecimens. Moreover, increased requests for molecular testing have paralleled the recent, sharp decrease in tumor material to be analyzed—material that currently comprises cytology specimens or, at minimum, small biopsies in most cases of metastatic/advanced disease. Traditional diagnostic pathology has been completely revolutionized by the introduction of next-generation technologies, which provide multigene, targeted mutational profiling, even in the most complex of clinical cases. Combining traditional and molecular knowledge, pathologists integrate the morphological, clinical, and molecular dimensions of a disease, leading to a proper diagnosis and, therefore, the most-appropriate tailored therapy.
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Affiliation(s)
- Matteo Fassan
- From the Department of Medicine, Surgical Pathology and Cytopathology Unit, University of Padua, Padua, Italy
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Mauger F, How-Kit A, Tost J. COLD-PCR Technologies in the Area of Personalized Medicine: Methodology and Applications. Mol Diagn Ther 2018; 21:269-283. [PMID: 28101802 DOI: 10.1007/s40291-016-0254-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Somatic mutations bear great promise for use as biomarkers for personalized medicine, but are often present only in low abundance in biological material and are therefore difficult to detect. Many assays for mutation analysis in cancer-related genes (hotspots) have been developed to improve diagnosis, prognosis, prediction of drug resistance, and monitoring of the response to treatment. Two major approaches have been developed: mutation-specific amplification methods and methods that enrich and detect mutations without prior knowledge on the exact location and identity of the mutation. CO-amplification at Lower Denaturation temperature Polymerase Chain Reaction (COLD-PCR) methods such as full-, fast-, ice- (improved and complete enrichment), enhanced-ice, and temperature-tolerant COLD-PCR make use of a critical temperature in the polymerase chain reaction to selectively denature wild-type-mutant heteroduplexes, allowing the enrichment of rare mutations. Mutations can subsequently be identified using a variety of laboratory technologies such as high-resolution melting, digital polymerase chain reaction, pyrosequencing, Sanger sequencing, or next-generation sequencing. COLD-PCR methods are sensitive, specific, and accurate if appropriately optimized and have a short time to results. A large variety of clinical samples (tumor DNA, circulating cell-free DNA, circulating cell-free fetal DNA, and circulating tumor cells) have been studied using COLD-PCR in many different applications including the detection of genetic changes in cancer and infectious diseases, non-invasive prenatal diagnosis, detection of microorganisms, or DNA methylation analysis. In this review, we describe in detail the different COLD-PCR approaches, highlighting their specificities, advantages, and inconveniences and demonstrating their use in different fields of biological and biomedical research.
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Affiliation(s)
- Florence Mauger
- Laboratory for Epigenetics and Environment, Centre National de Génotypage, CEA-Institut de Génomique, Batiment G2, 2 rue Gaston Crémieux, 91000, Evry, France
| | - Alexandre How-Kit
- Laboratory for Genomics, Fondation Jean Dausset-CEPH, 75010, Paris, France
| | - Jörg Tost
- Laboratory for Epigenetics and Environment, Centre National de Génotypage, CEA-Institut de Génomique, Batiment G2, 2 rue Gaston Crémieux, 91000, Evry, France.
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Abraham J, Singh S, Joshi S. Liquid biopsy - emergence of a new era in personalized cancer care. ACTA ACUST UNITED AC 2018. [DOI: 10.1186/s41241-018-0053-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Hou H, Liu D, Zhang C, Jiang Y, Lu G, Zhou N, Yang X, Zhang X, Li Z, Zhu H, Qian Z, Zhang X. Targeted next generation sequencing in Chinese colorectal cancer patients guided anti-EGFR treatment and facilitated precision cancer medicine. Oncotarget 2017; 8:105072-105080. [PMID: 29285234 PMCID: PMC5739621 DOI: 10.18632/oncotarget.21349] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Accepted: 08/28/2017] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVE Colorectal cancer (CRC) patients with both RAS and BRAF wild-type tumors determined by non-next generation sequencing (NGS) testing may still not respond due to the presence of additional mutated genes such as PIK3CA or PTEN. In this study, a broad, hybrid capture-based NGS assay was used to identify RAS, BRAF and additional targetable genetic alterations from Chinese CRC tissues. METHODS Fifty-seven cases of CRC were enrolled, and all the patients signed the informed consent. In total, 7708 exons of 508 tumor-related genes and 78 introns of 19 frequently rearranged genes were assessed for base substitutions, INDELs, copy number alterations, and gene fusions. RESULTS The study found that 50.9% (29/57) of the tumors harbored KRAS mutations, 3.5% (2/57) harbored NRAS mutations and 3.5% (2/57) harbored BRAF mutations. More specifically, 89.7% (26/29) of RAS mutations were located in codon 12. Except for RAS and RAF, anti-EGFR therapy response genetic mutations in PTEN (n=2) and PIK3CA (n=1) were found in 4.7% (3/64) of the samples. Actionable alterations were found in HER2 (n = 7), CCND2 (n = 2), NF1 (n = 1), and BRCA1 (n = 1). CONCLUSIONS Our results illustrated that 82.5% (47/57) of the samples harbored at least one actionable genetic alteration identified by NGS. HER2 amplifications or mutations, which were identified in 12.3% of the tissues, defined a unique molecular subtype of CRC. The study suggests that high-throughput NGS testing in CRC tissues is a comprehensive and efficient genomic profiling assay to guide personalized therapy.
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Affiliation(s)
- Helei Hou
- Department of Medical Oncology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266005, China
| | - Dong Liu
- Department of Medical Oncology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266005, China
| | - Chuantao Zhang
- Department of Medical Oncology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266005, China
| | - Yanxia Jiang
- Department of Pathology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266005, China
| | - Guifang Lu
- Department of Gastroenterology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Na Zhou
- Department of Medical Oncology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266005, China
| | - Xiaonan Yang
- BGI-Qingdao Institute, Qingdao SINO-GERMAN Ecopark, Qingdao, 266555, China
| | - Xiaoping Zhang
- Department of Clinical Laboratory, BGI-Shenzhen, Shenzhen, 518083, China
| | - Zhuokun Li
- BGI-Qingdao Institute, Qingdao SINO-GERMAN Ecopark, Qingdao, 266555, China
| | - Hongmei Zhu
- Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China
| | - Zhaoyang Qian
- Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China
| | - Xiaochun Zhang
- Department of Medical Oncology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266005, China
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Discordance in RAS Mutations between Primary Colon Tumor and Metastases: A Real Event or a Matter of Methodology? Int J Biol Markers 2017; 32:e474-e477. [DOI: 10.5301/ijbm.5000273] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/19/2017] [Indexed: 11/20/2022]
Abstract
Background Analysis of K- and N-RAS mutations is mandatory before planning treatment of metastatic colorectal cancer, because only RAS wild-type (WT) patients can benefit from treatment with anti-EGFR monoclonal antibodies (cetuximab and panitumumab). Case report Here we report the case of a 69-year-old male patient affected by metastatic sigmoid cancer. He underwent left hemicolectomy, and histology diagnosed a well-differentiated, pT4, node-positive adenocarcinoma; KRAS analysis performed with direct sequencing identified a mutation in exon 2 of the KRAS gene (GGT->GTT). After first-line chemotherapy with FOLFOX6 plus bevacizumab, the patient underwent surgical resection of residual liver metastases. Histology showed metastatic deposits from colic adenocarcinoma with extensive coagulative necrosis. Mutational analysis of the KRAS gene was also performed on liver metastases by pyrosequencing assay, and no mutation was identified. Due to the discordant results (GGT->GTT exon 2 KRAS mutation in the primary tumor, and KRAS-WT in the liver metastases), mutational analysis on liver metastasis was repeated using next-generation sequencing and enriching the sample in tumor cells by manual microdissection; the same type of mutation of the primary tumor (GGT->GTT exon 2 KRAS gene) was confirmed. Conclusions Accurate tissue sampling and adequately sensitive assays are essential to correctly identify colorectal cancer patients who can be treated with an anti-EGFR monoclonal antibody.
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Troncone G. Reply to Costs of ALK, ROS1, EGFR, and KRAS testing in non-small cell lung cancer: About different strategies in France. Cancer Cytopathol 2017; 125:877. [PMID: 28892267 DOI: 10.1002/cncy.21918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 08/22/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Giancarlo Troncone
- Section of Anatomic Pathology Department of Public Health, University of Naples, Federico II, Naples, Italy
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Paschke R, Cantara S, Crescenzi A, Jarzab B, Musholt TJ, Sobrinho Simoes M. European Thyroid Association Guidelines regarding Thyroid Nodule Molecular Fine-Needle Aspiration Cytology Diagnostics. Eur Thyroid J 2017; 6:115-129. [PMID: 28785538 PMCID: PMC5527175 DOI: 10.1159/000468519] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 03/02/2017] [Indexed: 01/19/2023] Open
Abstract
Molecular fine-needle aspiration (FNA) cytology diagnostics has the potential to address the inherent limitation of FNA cytology which is an indeterminate (atypia of undetermined significance/follicular lesion of undetermined significance follicular neoplasm) cytology. Because of the emerging role of molecular FNA cytology diagnostics, the European Thyroid Association convened a panel of international experts to review methodological aspects, indications, results, and limitations of molecular FNA cytology diagnostics. The panel reviewed the evidence for the diagnostic value of mutation panel assessment (including at least BRAF, NRAS, HRAS, KRAS, PAX8/PPARG, RET/PTC) of targeted next generation sequencing and of a microarray gene expression classifier (GEC) test in the diagnostic assessment of an indeterminate cytology thyroid nodule. Moreover, possible surgical consequences of molecular FNA diagnostic results of thyroid nodules and the evidence that analysis of a molecular FNA diagnostic panel of somatic mutations or a microarray GEC test can alter the follow-up were reviewed. Molecular tests may help clinicians to drive patient care and the surgical decision if the analysis is performed in specialized laboratories. These molecular tests require standardization of performance characteristics and appropriate calibration as well as analytic validation before clinical interpretation.
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Affiliation(s)
- Ralf Paschke
- Division of Endocrinology and Metabolism, Departments of Medicine, Pathology, Oncology and Arnie Charbonneau Cancer Institute, Calgary, AB, Canada
- *Ralf Paschke, MD, PhD, Division of Endocrinology, Cumming School of Medicine, University of Calgary, HMRB, Room 382B, 3330 Hospital Dr NW, Calgary, AB T2N 4N1 (Canada), E-Mail
| | - Silvia Cantara
- Department of Medical, Surgical, and Neurological Sciences, Endocrinology Section, University of Siena, Siena, Italy
| | - Anna Crescenzi
- Pathology Unit, University Hospital Campus Bio-Medico, Rome, Italy
| | - Barbara Jarzab
- Department of Nuclear Medicine and Endocrine Oncology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Gliwice Branch, Gliwice, Poland
| | - Thomas J. Musholt
- Endocrine Surgery Section, Department of General, Visceral, and Transplantation Surgery, University Medicine of the Johannes Gutenberg-University Mainz, Mainz, Germany
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Targeted sequencing-based analyses of candidate gene variants in ulcerative colitis-associated colorectal neoplasia. Br J Cancer 2017; 117:136-143. [PMID: 28524162 PMCID: PMC5520210 DOI: 10.1038/bjc.2017.148] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 04/25/2017] [Accepted: 04/26/2017] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Long-standing ulcerative colitis (UC) leading to colorectal cancer (CRC) is one of the most serious and life-threatening consequences acknowledged globally. Ulcerative colitis-associated colorectal carcinogenesis showed distinct molecular alterations when compared with sporadic colorectal carcinoma. METHODS Targeted sequencing of 409 genes in tissue samples of 18 long-standing UC subjects at high risk of colorectal carcinoma (UCHR) was performed to identify somatic driver mutations, which may be involved in the molecular changes during the transformation of non-dysplastic mucosa to high-grade dysplasia. Findings from the study are also compared with previously published genome wide and exome sequencing data in inflammatory bowel disease-associated and sporadic colorectal carcinoma. RESULTS Next-generation sequencing analysis identified 1107 mutations in 275 genes in UCHR subjects. In addition to TP53 (17%) and KRAS (22%) mutations, recurrent mutations in APC (33%), ACVR2A (61%), ARID1A (44%), RAF1 (39%) and MTOR (61%) were observed in UCHR subjects. In addition, APC, FGFR3, FGFR2 and PIK3CA driver mutations were identified in UCHR subjects. Recurrent mutations in ARID1A (44%), SMARCA4 (17%), MLL2 (44%), MLL3 (67%), SETD2 (17%) and TET2 (50%) genes involved in histone modification and chromatin remodelling were identified in UCHR subjects. CONCLUSIONS Our study identifies new oncogenic driver mutations which may be involved in the transition of non-dysplastic cells to dysplastic phenotype in the subjects with long-standing UC with high risk of progression into colorectal neoplasia.
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Goodwin S, McPherson JD, McCombie WR. Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet 2017; 17:333-51. [PMID: 27184599 PMCID: PMC10373632 DOI: 10.1038/nrg.2016.49] [Citation(s) in RCA: 2143] [Impact Index Per Article: 306.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Since the completion of the human genome project in 2003, extraordinary progress has been made in genome sequencing technologies, which has led to a decreased cost per megabase and an increase in the number and diversity of sequenced genomes. An astonishing complexity of genome architecture has been revealed, bringing these sequencing technologies to even greater advancements. Some approaches maximize the number of bases sequenced in the least amount of time, generating a wealth of data that can be used to understand increasingly complex phenotypes. Alternatively, other approaches now aim to sequence longer contiguous pieces of DNA, which are essential for resolving structurally complex regions. These and other strategies are providing researchers and clinicians a variety of tools to probe genomes in greater depth, leading to an enhanced understanding of how genome sequence variants underlie phenotype and disease.
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Affiliation(s)
- Sara Goodwin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - John D McPherson
- Department of Biochemistry and Molecular Medicine; and the Comprehensive Cancer Center, University of California, Davis, California 95817, USA
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Chakravorty S, Hegde M. Gene and Variant Annotation for Mendelian Disorders in the Era of Advanced Sequencing Technologies. Annu Rev Genomics Hum Genet 2017; 18:229-256. [PMID: 28415856 DOI: 10.1146/annurev-genom-083115-022545] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Comprehensive annotations of genetic and noncoding regions and corresponding accurate variant classification for Mendelian diseases are the next big challenge in the new genomic era of personalized medicine. Progress in the development of faster and more accurate pipelines for genome annotation and variant classification will lead to the discovery of more novel disease associations and candidate therapeutic targets. This ultimately will facilitate better patient recruitment in clinical trials. In this review, we describe the trends in research at the intersection of basic and clinical genomics that aims to increase understanding of overall genomic complexity, complex inheritance patterns of disease, and patient-phenotype-specific genomic associations. We describe the emerging field of translational functional genomics, which integrates other functional "-omics" approaches that support next-generation sequencing genomic data in order to facilitate personalized diagnostics, disease management, biomarker discovery, and medicine. We also discuss the utility of this integrated approach for diagnostic clinics and medical databases and its role in the future of personalized medicine.
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Affiliation(s)
- Samya Chakravorty
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30322;
| | - Madhuri Hegde
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30322;
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Cantara S, Marzocchi C, Pilli T, Cardinale S, Forleo R, Castagna MG, Pacini F. Molecular Signature of Indeterminate Thyroid Lesions: Current Methods to Improve Fine Needle Aspiration Cytology (FNAC) Diagnosis. Int J Mol Sci 2017; 18:ijms18040775. [PMID: 28383480 PMCID: PMC5412359 DOI: 10.3390/ijms18040775] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 03/29/2017] [Accepted: 04/03/2017] [Indexed: 02/05/2023] Open
Abstract
Fine needle aspiration cytology (FNAC) represents the gold standard for determining the nature of thyroid nodules. It is a reliable method with good sensitivity and specificity. However, indeterminate lesions remain a diagnostic challenge and researchers have contributed molecular markers to search for in cytological material to refine FNAC diagnosis and avoid unnecessary surgeries. Nowadays, several "home-made" methods as well as commercial tests are available to investigate the molecular signature of an aspirate. Moreover, other markers (i.e., microRNA, and circulating tumor cells) have been proposed to discriminate benign from malignant thyroid lesions. Here, we review the literature and provide data from our laboratory on mutational analysis of FNAC material and circulating microRNA expression obtained in the last 6 years.
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Affiliation(s)
- Silvia Cantara
- Department of Medical, Surgical and Neurological Sciences, University of Siena, 53100 Siena, Italy.
| | - Carlotta Marzocchi
- Department of Medical, Surgical and Neurological Sciences, University of Siena, 53100 Siena, Italy.
| | - Tania Pilli
- Department of Medical, Surgical and Neurological Sciences, University of Siena, 53100 Siena, Italy.
| | - Sandro Cardinale
- Department of Medical, Surgical and Neurological Sciences, University of Siena, 53100 Siena, Italy.
| | - Raffaella Forleo
- Department of Medical, Surgical and Neurological Sciences, University of Siena, 53100 Siena, Italy.
| | - Maria Grazia Castagna
- Department of Medical, Surgical and Neurological Sciences, University of Siena, 53100 Siena, Italy.
| | - Furio Pacini
- Department of Medical, Surgical and Neurological Sciences, University of Siena, 53100 Siena, Italy.
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Loree JM, Kopetz S, Raghav KPS. Current companion diagnostics in advanced colorectal cancer; getting a bigger and better piece of the pie. J Gastrointest Oncol 2017; 8:199-212. [PMID: 28280626 PMCID: PMC5334060 DOI: 10.21037/jgo.2017.01.01] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 11/18/2016] [Indexed: 12/19/2022] Open
Abstract
While the treatment of colorectal cancer continues to rely heavily on conventional cytotoxic therapy, an increasing number of targeted agents are under development. Many of these treatments require companion diagnostic tests in order to define an appropriate population that will derive benefit. In addition, a growing number of biomarkers provide prognostic information about a patient's malignancy. As we learn more about these biomarkers and their assays, selecting the appropriate companion diagnostic becomes increasingly important. In the case of many biomarkers, there are numerous assays which could provide the same information to a treating physician, however each assay has strengths and weaknesses. Institutions must balance cost, assay sensitivity, turn-around time, and labor resources when selecting which assay to offer. In this review we will discuss the current state of companion diagnostics available in metastatic colorectal cancer and explore emerging biomarkers and their assays. We will focus on KRAS, BRAF, HER2, and PIK3CA testing, as well as microsatellite stability assessment and multigene panels.
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Affiliation(s)
- Jonathan M Loree
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kanwal P S Raghav
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Kamps R, Brandão RD, Bosch BJVD, Paulussen ADC, Xanthoulea S, Blok MJ, Romano A. Next-Generation Sequencing in Oncology: Genetic Diagnosis, Risk Prediction and Cancer Classification. Int J Mol Sci 2017; 18:ijms18020308. [PMID: 28146134 PMCID: PMC5343844 DOI: 10.3390/ijms18020308] [Citation(s) in RCA: 282] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 01/19/2017] [Indexed: 12/17/2022] Open
Abstract
Next-generation sequencing (NGS) technology has expanded in the last decades with significant improvements in the reliability, sequencing chemistry, pipeline analyses, data interpretation and costs. Such advances make the use of NGS feasible in clinical practice today. This review describes the recent technological developments in NGS applied to the field of oncology. A number of clinical applications are reviewed, i.e., mutation detection in inherited cancer syndromes based on DNA-sequencing, detection of spliceogenic variants based on RNA-sequencing, DNA-sequencing to identify risk modifiers and application for pre-implantation genetic diagnosis, cancer somatic mutation analysis, pharmacogenetics and liquid biopsy. Conclusive remarks, clinical limitations, implications and ethical considerations that relate to the different applications are provided.
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Affiliation(s)
- Rick Kamps
- Department of Clinical Genetics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Rita D Brandão
- Department of Clinical Genetics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Bianca J van den Bosch
- Department of Clinical Genetics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Aimee D C Paulussen
- Department of Clinical Genetics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Sofia Xanthoulea
- Department of Gynaecology and Obstetrics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Marinus J Blok
- Department of Clinical Genetics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Andrea Romano
- Department of Gynaecology and Obstetrics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
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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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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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Bellevicine C, Sgariglia R, Malapelle U, Vigliar E, Nacchio M, Ciancia G, Eszlinger M, Paschke R, Troncone G. Young investigator challenge: Can the Ion AmpliSeq Cancer Hotspot Panel v2 be used for next-generation sequencing of thyroid FNA samples? Cancer Cytopathol 2016; 124:776-784. [DOI: 10.1002/cncy.21780] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 08/30/2016] [Accepted: 09/01/2016] [Indexed: 01/21/2023]
Affiliation(s)
- Claudio Bellevicine
- Department of Public Health; University of Naples “Federico II,”; Naples Italy
| | - Roberta Sgariglia
- Department of Public Health; University of Naples “Federico II,”; Naples Italy
| | - Umberto Malapelle
- Department of Public Health; University of Naples “Federico II,”; Naples Italy
| | - Elena Vigliar
- Department of Public Health; University of Naples “Federico II,”; Naples Italy
| | - Mariantonia Nacchio
- Department of Public Health; University of Naples “Federico II,”; Naples Italy
| | - Giuseppe Ciancia
- Department of Advanced Biomedical Sciences; University of Naples “Federico II,”; Naples Italy
| | - Markus Eszlinger
- Department of Oncology, Cumming School of Medicine; University of Calgary; Calgary Alberta Canada
| | - Ralf Paschke
- Department of Endocrinology, Cumming School of Medicine; University of Calgary; Calgary Alberta Canada
- Department of Oncology, Cumming School of Medicine; University of Calgary; Calgary Alberta Canada
| | - Giancarlo Troncone
- Department of Public Health; University of Naples “Federico II,”; Naples Italy
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De Luca C, Gragnano G, Pisapia P, Vigliar E, Malapelle U, Bellevicine C, Troncone G. EGFR mutation detection on lung cancer cytological specimens by the novel fully automated PCR-based Idylla EGFR Mutation Assay. J Clin Pathol 2016; 70:295-300. [PMID: 27543600 DOI: 10.1136/jclinpath-2016-203989] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 07/28/2016] [Accepted: 07/31/2016] [Indexed: 11/03/2022]
Abstract
AIMS In everyday practice, epidermal growth factor receptor (EGFR) testing is centralised in referral laboratories that receive paucicellular cytological specimens. Ideally, EGFR testing should be carried out in the centre where the patient is diagnosed such that the most cellular slide can be selected from in-house collected cytological material. However, available techniques are little standardised and difficult to be implemented in settings with little expertise in molecular testing. The Idylla EGFR prototype assay is a rapid and fully automated test which may easily be adopted by a wider number of pathological centres. This study assessed whether an Idylla EGFR prototype assay can be reliably applied to cytological lung cancer specimens. METHODS The limit of detection (LOD) of the Idylla EGFR prototype assay was assessed by cell line dilution studies. A total of 10 ng was directly placed inside an Idylla EGFR prototype assay cartridge. Idylla results were compared with fragment length (exon 19 del) and Taqman assays. RESULTS The Idylla EGFR prototype assay showed an LOD of 1% mutant allele and yielded valid results in 74/76 (97.3%) samples, detecting all the mutant cases (n=32) identified by standard techniques; in addition, Idylla detected two low abundance EGFR exon 19 deletions and two G719X exon 18 point mutations, not covered by our standard reference method. CONCLUSIONS Idylla EGFR prototype assay is sensitive on extracted DNA and can reliably be applied on cytological samples, enabling implementation of EGFR testing even in less experienced diagnostic units.
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Affiliation(s)
- Caterina De Luca
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Gianluca Gragnano
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Pasquale Pisapia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Elena Vigliar
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Claudio Bellevicine
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
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Mack E, Stabla K, Riera-Knorrenschild J, Moll R, Neubauer A, Brendel C. A rational two-step approach to KRAS mutation testing in colorectal cancer using high resolution melting analysis and pyrosequencing. BMC Cancer 2016; 16:585. [PMID: 27485514 PMCID: PMC4971616 DOI: 10.1186/s12885-016-2589-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 07/20/2016] [Indexed: 01/03/2023] Open
Abstract
Background KRAS mutation testing is mandatory in the management of metastatic colorectal cancer prior to treatment with anti-EGFR antibodies as patients whose tumors express mutant KRAS do not benefit from these agents. Although the U.S. Food and Drug Administration has recently approved two in-vitro diagnostics kits for determination of KRAS status, there is generally no consensus on the preferred method and new tests are continuously being developed. Most of these techniques focus on the hotspot mutations at codons 12 and 13 of the KRAS gene. Methods We describe a two-step approach to KRAS codon 12/13 mutation testing involving high resolution melting analysis (HRM) followed by pyrosequencing using the Therascreen KRAS Pyro kit (Qiagen) of only those samples that are not clearly identified as KRAS wildtype or mutant by HRM. First, we determined KRAS status in a panel of 61 colorectal cancer samples using both methods to compare technical performance and concordance of results. Subsequently, we evaluated practicability and costs of our concept in an independent set of 120 colorectal cancer samples in a routine diagnostic setting. Results HRM and pyrosequencing appeared to be equally sensitive, allowing for clear detection of mutant alleles at a mutant allele frequency ≥12.5 %. Pyrosequencing yielded more exploitable results due to lower input requirements and a lower rate of analysis failures. KRAS codon 12/13 status was called concordantly for 98.2 % (56/57) of all samples that could be successfully analysed by both methods and 100 % (19/19) of samples that were identified mutant by HRM. Reviewing the actual effort and expenses for KRAS mutation testing in our laboratory revealed, that the selective use of pyrosequencing for only those samples that could not be analysed by HRM increased the fraction of valid results from 87.5 % for HRM alone to 99.2 % (119/120) while allowing for a net reduction of operational costs of >75 % compared to pyrosequencing alone. Conclusions Combination of HRM and pyrosequencing in a two-step diagnostic procedure constitutes a reliable and economic analysis platform for KRAS mutation testing in colorectal cancer in a clinical setting. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2589-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elisabeth Mack
- Klinik für Hämatologie, Onkologie und Immunologie, Universitätsklinikum Gießen und Marburg, Standort Marburg, Philipps-Universität Marburg, Baldingerstraße, Marburg, Germany
| | - Kathleen Stabla
- Klinik für Hämatologie, Onkologie und Immunologie, Universitätsklinikum Gießen und Marburg, Standort Marburg, Philipps-Universität Marburg, Baldingerstraße, Marburg, Germany
| | - Jorge Riera-Knorrenschild
- Klinik für Hämatologie, Onkologie und Immunologie, Universitätsklinikum Gießen und Marburg, Standort Marburg, Philipps-Universität Marburg, Baldingerstraße, Marburg, Germany
| | - Roland Moll
- Institut für Pathologie, Universitätsklinikum Gießen und Marburg, Standort Marburg, Philipps-Universität Marburg, Baldingerstraße, Marburg, Germany
| | - Andreas Neubauer
- Klinik für Hämatologie, Onkologie und Immunologie, Universitätsklinikum Gießen und Marburg, Standort Marburg, Philipps-Universität Marburg, Baldingerstraße, Marburg, Germany
| | - Cornelia Brendel
- Klinik für Hämatologie, Onkologie und Immunologie, Universitätsklinikum Gießen und Marburg, Standort Marburg, Philipps-Universität Marburg, Baldingerstraße, Marburg, Germany.
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Sahm F, Schrimpf D, Jones DTW, Meyer J, Kratz A, Reuss D, Capper D, Koelsche C, Korshunov A, Wiestler B, Buchhalter I, Milde T, Selt F, Sturm D, Kool M, Hummel M, Bewerunge-Hudler M, Mawrin C, Schüller U, Jungk C, Wick A, Witt O, Platten M, Herold-Mende C, Unterberg A, Pfister SM, Wick W, von Deimling A. Next-generation sequencing in routine brain tumor diagnostics enables an integrated diagnosis and identifies actionable targets. Acta Neuropathol 2016; 131:903-10. [PMID: 26671409 DOI: 10.1007/s00401-015-1519-8] [Citation(s) in RCA: 185] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 12/04/2015] [Accepted: 12/04/2015] [Indexed: 12/13/2022]
Abstract
With the number of prognostic and predictive genetic markers in neuro-oncology steadily growing, the need for comprehensive molecular analysis of neuropathology samples has vastly increased. We therefore developed a customized enrichment/hybrid-capture-based next-generation sequencing (NGS) gene panel comprising the entire coding and selected intronic and promoter regions of 130 genes recurrently altered in brain tumors, allowing for the detection of single nucleotide variations, fusions, and copy number aberrations. Optimization of probe design, library generation and sequencing conditions on 150 samples resulted in a 5-workday routine workflow from the formalin-fixed paraffin-embedded sample to neuropathological report. This protocol was applied to 79 retrospective cases with established molecular aberrations for validation and 71 prospective cases for discovery of potential therapeutic targets. Concordance of NGS compared to established, single biomarker methods was 98.0 %, with discrepancies resulting from one case where a TERT promoter mutation was not called by NGS and three ATRX mutations not being detected by Sanger sequencing. Importantly, in samples with low tumor cell content, NGS was able to identify mutant alleles that were not detectable by traditional methods. Information derived from NGS data identified potential targets for experimental therapy in 37/47 (79 %) glioblastomas, 9/10 (90 %) pilocytic astrocytomas, and 5/14 (36 %) medulloblastomas in the prospective target discovery cohort. In conclusion, we present the settings for high-throughput, adaptive next-generation sequencing in routine neuropathology diagnostics. Such an approach will likely become highly valuable in the near future for treatment decision making, as more therapeutic targets emerge and genetic information enters the classification of brain tumors.
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50
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Abstract
Next-generation sequencing (NGS) has been rapidly integrated into molecular pathology, dramatically increasing the breadth genomic of information available to oncologists and their patients. This review will explore the ways in which this new technology is currently applied to bolster care for patients with solid tumors and hematological malignancies, focusing on practices and guidelines for assessing the technical validity and clinical utility of DNA variants identified during clinical NGS oncology testing.
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Affiliation(s)
- Samuel P Strom
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
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