1
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Kondapuram SK, Coumar MS. Pan-cancer gene expression analysis: Identification of deregulated autophagy genes and drugs to target them. Gene X 2022; 844:146821. [PMID: 35985410 DOI: 10.1016/j.gene.2022.146821] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 07/07/2022] [Accepted: 08/12/2022] [Indexed: 12/24/2022] Open
Abstract
Identifying suitable deregulated targets in autophagy pathway is essential for developing autophagy modulating cancer therapies. With this aim, we systematically analyzed the expression levels of genes that contribute to the execution of autophagy in 21 cancers. Deregulated genes for 21 cancers were analyzed using the level 3 mRNA data from TCGAbiolinks. A total of 574 autophagy genes were mapped to the deregulated genes across 21 cancers. PPI network, cluster analysis, gene enrichment, gene ontology, KEGG pathway, patient survival, protein expression and cMap analysis were performed. Among the autophagy genes, 260 were upregulated, and 43 were downregulated across pan-cancer. The upregulated autophagy genes - CDKN2A and BIRC5 - were the most frequent signatures in cancers and could be universal cancer biomarkers. Significant involvement of autophagy process was found in 8 cancers (CHOL, HNSC, GBM, KICH, KIRC, KIRP, LIHC and SARC). Fifteen autophagy hub genes (ATP6V0C, BIRC5, HDAC1, IL4, ITGB1, ITGB4, MAPK3, mTOR, cMYC, PTK2, SRC, TCIRG1, TP63, TP73 and ULK1) were found to be linked with patients survival and also expressed in cancer patients tissue samples, making them as potential drug targets for these cancers. The deregulated autophagy genes were further used to identify drugs Losartan, BMS-345541, Embelin, Abexinostat, Panobinostat, Vorinostat, PD-184352, PP-1, XMD-1150, Triplotide, Doxorubicin and Ouabain, which could target one or more autophagy hub genes. Overall, our findings shed light on the most frequent cancer-associated autophagy genes, potential autophagy targets and molecules for cancer treatment. These findings can accelerate autophagy modulation in cancer therapy.
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Affiliation(s)
- Sree Karani Kondapuram
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry- 605014, India
| | - Mohane Selvaraj Coumar
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry- 605014, India.
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Brennan P, Davey-Smith G. Identifying Novel Causes of Cancers to Enhance Cancer Prevention: New Strategies Are Needed. J Natl Cancer Inst 2022; 114:353-360. [PMID: 34743211 PMCID: PMC8902436 DOI: 10.1093/jnci/djab204] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 08/30/2021] [Accepted: 10/29/2021] [Indexed: 12/09/2022] Open
Abstract
The burden of cancer from a clinical, societal, and economic viewpoint continues to increase in all parts of the world, along with much debate regarding how to confront this. Projected increases in cancer indicate a 50% increase in the number of cases over the next 2 decades, with the greatest proportional increase in low- and medium-income settings. In contrast to the historic high cancer burden due to viral and bacterial infections in these regions, future increases are expected to be due to cancers linked to westernization including breast, colorectum, lung, and prostate cancer. Identifying the reasons underlying these increases will be paramount to informing prevention efforts. Evidence from epidemiological and laboratory studies conducted in high-income countries over the last 70 years has led to the conclusion that approximately 40% of the cancer burden is explained by known risk factors-the 2 most important being tobacco and obesity in that order-raising the question of what is driving the rest of the cancer burden. International cancer statistics continue to show that approximately 80% of the cancer burden in high-income countries could be preventable in principle, implying that there are important environmental or lifestyle risk factors for cancer that have not yet been discovered. Emerging genomic evidence from population and experimental studies points to an important role for nonmutagenic promoters in driving cancer incidence rates. New research strategies and infrastructures that combine population-based and laboratory research at a global level are required to break this deadlock.
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Affiliation(s)
- Paul Brennan
- International Agency for Research on Cancer (IARC/WHO), Genomic Epidemiology Branch, Lyon, France
| | - George Davey-Smith
- Medical Research Council Integrative Epidemiology Unit (IEU), University of Bristol, Clifton, Bristol, UK
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3
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Hawranek C, Hajdarevic S, Rosén A. A Focus Group Study of Perceptions of Genetic Risk Disclosure in Members of the Public in Sweden: "I'll Phone the Five Closest Ones, but What Happens to the Other Ten?". J Pers Med 2021; 11:jpm11111191. [PMID: 34834542 PMCID: PMC8622605 DOI: 10.3390/jpm11111191] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 12/14/2022] Open
Abstract
This study explores perceptions and preferences on receiving genetic risk information about hereditary cancer risk in members of the Swedish public. We conducted qualitative content analysis of five focus group discussions with participants (n = 18) aged between 24 and 71 years, recruited from various social contexts. Two prominent phenomena surfaced around the interplay between the three stakeholders involved in risk disclosure: the individual, healthcare, and the relative at risk. First, there is a genuine will to share risk information that can benefit others, even if this is difficult and causes discomfort. Second, when the duty to inform becomes overwhelming, compromises are made, such as limiting one’s own responsibility of disclosure or projecting the main responsibility onto another party. In conclusion, our results reveal a discrepancy between public expectations and the actual services offered by clinical genetics. These expectations paired with desire for a more personalized process and shared decision-making highlight a missing link in today’s risk communication and suggest a need for developed clinical routines with stronger healthcare–patient collaboration. Future research needs to investigate the views of genetic professionals on how to address these expectations to co-create a transparent risk disclosure process which can realize the full potential of personalized prevention.
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Affiliation(s)
- Carolina Hawranek
- Department of Radiation Sciences, Oncology, Umeå University, 901 87 Umeå, Sweden;
- Correspondence: ; Tel.: +46-76-89-34-504
| | - Senada Hajdarevic
- Department of Nursing, Umeå University, 901 87 Umeå, Sweden;
- Department of Public Health and Clinical Medicine, Family Medicine, Umeå University, 901 87 Umeå, Sweden
| | - Anna Rosén
- Department of Radiation Sciences, Oncology, Umeå University, 901 87 Umeå, Sweden;
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Family Health History-Based Cancer Prevention Training for Community Health Workers. Am J Prev Med 2021; 60:e159-e167. [PMID: 33358550 DOI: 10.1016/j.amepre.2020.09.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 09/15/2020] [Accepted: 09/17/2020] [Indexed: 11/21/2022]
Abstract
Cancer is the second leading cause of death in the U.S. Utilizing family health history in cancer prevention holds promise in lessening the burden of cancer. Nevertheless, family health history is underutilized in public health and preventive medicine. Community health workers, also known as lay health educators, are ideal candidates to offer basic cancer family history-based education and services to the general public. The authors developed the first cancer family history-based genomics training program in cancer prevention tailored for community health workers. This paper details the development and pilot testing findings of the training. Specifically, a multidisciplinary research team of geneticists, genetic counselors, health educators, community health workers, and community health worker instructors developed a 7-module, 6-hour, bilingual (English and Spanish) cancer family history-based training focusing on cancer family history-based risk assessment, lifestyle recommendations, and genetic evaluation and testing. The curriculum was based on an integrated theoretical framework, the National Comprehensive Cancer Network guidelines, the community health worker core competencies, and the 4MAT instructional model. The Texas Department of State Health Services approved and certified the curriculum with 2 delivery formats: in-person/face-to-face workshops and online training. A total of 34 community health workers completed the pilot training in person (n=17) and online (n=17) in 2018 and 2019. Participating community health workers' knowledge, attitudes, self-efficacy, and intention in delivering basic cancer family history-based genomics education and services significantly increased on the immediate post-test measures compared with their pretest data. Positive ratings and feedback were also reported by the community health workers. Findings from this pilot study suggest that wider training is warranted for educating more community health workers in the U.S.
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Ginsburg O, Ashton-Prolla P, Cantor A, Mariosa D, Brennan P. The role of genomics in global cancer prevention. Nat Rev Clin Oncol 2021; 18:116-128. [PMID: 32973296 DOI: 10.1038/s41571-020-0428-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/07/2020] [Indexed: 02/07/2023]
Abstract
Despite improvements in the understanding of cancer causation, much remains unknown regarding the mechanisms by which genomic and non-genomic factors initiate carcinogenesis, drive cell invasion and metastasis, and enable cancer to develop. Technological advances have enabled the analysis of whole genomes, comprising thousands of tumours across populations worldwide, with the aim of identifying mutation signatures associated with particular tumour types. Large collaborative efforts have resulted in the identification and improved understanding of causal factors, and have shed light on new opportunities to prevent cancer. In this new era in cancer genomics, discoveries from studies conducted on an international scale can inform evidence-based strategies in cancer control along the cancer care continuum, from prevention to treatment. In this Review, we present the relevant history and emerging frontiers of cancer genetics and genomics from the perspective of global cancer prevention. We highlight the importance of local context in the adoption of new technologies and emergent evidence, with illustrative examples from worldwide. We emphasize the challenges in implementing important genomic findings in clinical settings with disparate resource availability and present a conceptual framework for the translation of such findings into clinical practice, and evidence-based policies in order to maximize the utility for a population.
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Affiliation(s)
- Ophira Ginsburg
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA.
- Section for Global Health, Division of Health and Behavior, Department of Population Health, NYU Grossman School of Medicine, New York, NY, USA.
| | - Patricia Ashton-Prolla
- Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre and Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Anna Cantor
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | | | - Paul Brennan
- International Agency for Research on Cancer, Lyon, France
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6
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Seo H, Cho DH. Feature selection algorithm based on dual correlation filters for cancer-associated somatic variants. BMC Bioinformatics 2020; 21:486. [PMID: 33121438 PMCID: PMC7596964 DOI: 10.1186/s12859-020-03767-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 09/18/2020] [Indexed: 12/30/2022] Open
Abstract
Background Since the development of sequencing technology, an enormous amount of genetic information has been generated, and human cancer analysis using this information is drawing attention. As the effects of variants on human cancer become known, it is important to find cancer-associated variants among countless variants. Results We propose a new filter-based feature selection method applicable for extracting cancer-associated somatic variants considering correlations of data. Both variants associated with the activation and deactivation of cancer’s characteristics are analyzed using dual correlation filters. The multiobjective optimization is utilized to consider two types of variants simultaneously without redundancy. To overcome high computational complexity problem, we calculate the correlation-based weight to select significant variants instead of directly searching for the optimal subset of variants. The proposed algorithm is applied to the identification of melanoma metastasis or breast cancer stage, and the classification results of the proposed method are compared with those of conventional single correlation filter-based method. Conclusions We verified that the proposed dual correlation filter-based method can extract cancer-associated variants related to the characteristics of human cancer.
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Affiliation(s)
- Hyein Seo
- School of Electrical Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, 34141, Daejeon, Republic of Korea
| | - Dong-Ho Cho
- School of Electrical Engineering, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, 34141, Daejeon, Republic of Korea.
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7
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Bélisle-Pipon JC, Vayena E, Green RC, Cohen IG. Genetic testing, insurance discrimination and medical research: what the United States can learn from peer countries. Nat Med 2019; 25:1198-1204. [PMID: 31388181 DOI: 10.1038/s41591-019-0534-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 06/25/2019] [Indexed: 12/29/2022]
Abstract
While genetic testing may be the gateway to the future of medicine, it also poses challenges for individuals, especially in terms of differentiated treatments on the basis of their genetic characteristics. The fear of unwanted disclosure to insurers and the possibility of genetic discrimination can hamper the recruitment of individuals for clinical research that involves genetic testing. Precision medicine initiatives, such as All of Us, are proliferating in the United States. In order to succeed, however, they must ensure that the millions of Americans recruited to share their genetic data are not penalized with regard to life, disability and long-term insurance coverage. In this Perspective, we discuss several initiatives adopted by countries around the world, such as the United Kingdom and France, that better balance the interests of insurers and research subjects, and explain how the United States might learn from them. We call for regulatory and industry leadership to come together to establish a voluntary moratorium on insurance pricing with the aim of protecting research participants.
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Affiliation(s)
| | - Effy Vayena
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Robert C Green
- Brigham and Women's Hospital, Broad Institute and Harvard Medical School, Boston, MA, USA
| | - I Glenn Cohen
- Petrie-Flom Center for Health Law Policy, Biotechnology, and Bioethics, Harvard Law School, Cambridge, MA, USA.
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8
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Mariosa D, Carreras-Torres R, Martin RM, Johansson M, Brennan P. Commentary: What can Mendelian randomization tell us about causes of cancer? Int J Epidemiol 2019; 48:816-821. [PMID: 31503317 PMCID: PMC6659369 DOI: 10.1093/ije/dyz151] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2019] [Indexed: 12/16/2022] Open
Affiliation(s)
- Daniela Mariosa
- Section of Genetics, International Agency for Research on Cancer (IARC), Lyon, France
| | - Robert Carreras-Torres
- Section of Genetics, International Agency for Research on Cancer (IARC), Lyon, France
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Spain
| | - Richard M Martin
- MRC Integrative Epidemiology Unit, Nutrition Biomedical Research Unit, University of Bristol, Bristol, UK
- Department of Population Health Sciences, Bristol Medical School, Nutrition Biomedical Research Unit, University of Bristol, Bristol, UK
- University Hospitals Bristol NHS Foundation Trust National Institute for Health Research Bristol, Nutrition Biomedical Research Unit, University of Bristol, Bristol, UK
| | - Mattias Johansson
- Section of Genetics, International Agency for Research on Cancer (IARC), Lyon, France
| | - Paul Brennan
- Section of Genetics, International Agency for Research on Cancer (IARC), Lyon, France
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9
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Mandal RK, Mittal RD. Glutathione S-Transferase P1 313 (A > G) Ile105Val Polymorphism Contributes to Cancer Susceptibility in Indian Population: A Meta-analysis of 39 Case-Control Studies. Indian J Clin Biochem 2018; 35:8-19. [PMID: 32071492 DOI: 10.1007/s12291-018-0787-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 09/08/2018] [Indexed: 12/17/2022]
Abstract
GSTP1 involved in the metabolism of carcinogens and toxins, reduces damage of DNA and act as a suppressor of carcinogenesis. Many studies have reported that 313 A > G polymorphism is associated with different cancer in Indian population, but the results remain conflicting rather than conclusive. Therefore, we have performed meta-analysis to clarify the more precise association of GSPT1 313 A > G polymorphism with cancer risk in Indian population. We retrieved all relevant published literature from PubMed (Medline) and Google scholar web database and included those study only based on the established inclusion criteria. Pooled ORs and 95% CIs were used to appraise the strength of association. Publication bias and sensitivity analysis was also evaluated. A total of 6581 confirmed cancer cases and 8218 controls were included from eligible thirty nine case-controls studies. Pooled analysis suggested that the variant genotypes significantly increased the risk of cancer in allele (G vs. A: OR 1.266, 95% CI 1.129-1.418, p = 0.001), heterozygous (AG vs. AA: OR 1.191, 95% CI 1.047-1.355, p = 0.008), homozygous (GG vs. AA: OR 1.811, 95% CI 1.428-2.297, p = 0.001), dominant (GG + AG vs. AA: OR 1.276, 95% CI 1.110-1.466, p = 0.001) and recessive (GG vs. AG + AA: OR 1.638, 95% CI 1.340-2.002, p = 0.001) genetic models. The stability of these observations was confirmed by a sensitivity analysis. Begger's funnel plot and Egger's test did not reveal any publication bias. This meta-analysis suggests that the GSTP1 313 A > G polymorphism may contribute to genetic susceptibility to cancer in Indian population. However, larger studies and randomized clinical trial will be required to elucidate the biological and molecular mechanism of GSTP1 gene in cancer.
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Affiliation(s)
- Raju K Mandal
- 1Research and Scientific Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Kingdom of Saudi Arabia.,2Department of Urology and Renal Transplantation, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
| | - Rama D Mittal
- 2Department of Urology and Renal Transplantation, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
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10
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Wu N, Zhang X, Tian J, Yu S, Qiao Y. Association of GEMIN4 gene polymorphism and the risk of cancer: a meta-analysis. Onco Targets Ther 2017; 10:5263-5271. [PMID: 29138579 PMCID: PMC5679687 DOI: 10.2147/ott.s147204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Gem-associated protein 4 (GEMIN4) gene is a key regulator for the miRNA biogenesis processes. Recent studies have demonstrated that some single-nucleotide polymorphisms (SNPs) in GEMIN4 gene are associated with the risk of cancer, but the results are still controversial. Therefore, we conducted a meta-analysis to analyze the association between three major SNPs (rs2740348, rs7813, and rs3744741) in the GEMIN4 gene and the risk of cancer. Relevant articles were searched in Web of Science, PubMed, Cochrane Library, Chinese Wan Fang, and Chinese National Knowledge Infrastructure databases. Pooled odds ratio (OR) with 95% confidence interval (CI) was calculated to quantitatively estimate the association. Publication bias and sensitivity analyses were undertaken to evaluate the stability of the results. Overall, the pooled results showed that rs2740348 involving 3,604 cases and 3,770 controls was significantly associated with increased cancer risk (GG vs GC/CC: OR =1.16, 95% CI =1.05-1.29, P=0.004) and rs7813 involving 4,729 cases and 4,562 controls was also related to increased cancer risk (TT vs TC/CC: OR =1.12, 95% CI =1.03-1.22, P=0.009). However, there was no significant association between rs3744741 and cancer risk under overall genetic models. In conclusion, our study has demonstrated that rs2740348 and rs7813 are associated with increased risk of cancer, and they may be new biomarkers for predicting cancer risk.
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Affiliation(s)
- Nan Wu
- The Core Laboratory for Public Health Science and Practice, The First Affiliated Hospital of China Medical University, Shenyang, People's Republic of China
| | - Xiaowei Zhang
- The Core Laboratory for Public Health Science and Practice, The First Affiliated Hospital of China Medical University, Shenyang, People's Republic of China
| | - Jinlong Tian
- The Core Laboratory for Public Health Science and Practice, The First Affiliated Hospital of China Medical University, Shenyang, People's Republic of China
| | - Shuang Yu
- The Core Laboratory for Public Health Science and Practice, The First Affiliated Hospital of China Medical University, Shenyang, People's Republic of China
| | - Ying Qiao
- The Core Laboratory for Public Health Science and Practice, The First Affiliated Hospital of China Medical University, Shenyang, People's Republic of China
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11
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Brennan P, Perola M, van Ommen GJ, Riboli E. Chronic disease research in Europe and the need for integrated population cohorts. Eur J Epidemiol 2017; 32:741-749. [PMID: 28986739 PMCID: PMC5662668 DOI: 10.1007/s10654-017-0315-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 09/11/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Paul Brennan
- Genetics Section, International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69372, Lyon Cedex 08, France.
| | - Markus Perola
- National Institute for Health and Welfare, Helsinki, Finland
| | - Gert-Jan van Ommen
- Department of Human Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
- Biobanking and Biomolecular Research Resources Infrastructure (BBMRI-ERIC), Graz, Austria
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12
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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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13
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Manolio TA. Implementing genomics and pharmacogenomics in the clinic: The National Human Genome Research Institute's genomic medicine portfolio. Atherosclerosis 2016; 253:225-236. [PMID: 27612677 PMCID: PMC5064852 DOI: 10.1016/j.atherosclerosis.2016.08.034] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 08/19/2016] [Accepted: 08/23/2016] [Indexed: 01/08/2023]
Abstract
Increasing knowledge about the influence of genetic variation on human health and growing availability of reliable, cost-effective genetic testing have spurred the implementation of genomic medicine in the clinic. As defined by the National Human Genome Research Institute (NHGRI), genomic medicine uses an individual's genetic information in his or her clinical care, and has begun to be applied effectively in areas such as cancer genomics, pharmacogenomics, and rare and undiagnosed diseases. In 2011 NHGRI published its strategic vision for the future of genomic research, including an ambitious research agenda to facilitate and promote the implementation of genomic medicine. To realize this agenda, NHGRI is consulting and facilitating collaborations with the external research community through a series of "Genomic Medicine Meetings," under the guidance and leadership of the National Advisory Council on Human Genome Research. These meetings have identified and begun to address significant obstacles to implementation, such as lack of evidence of efficacy, limited availability of genomics expertise and testing, lack of standards, and difficulties in integrating genomic results into electronic medical records. The six research and dissemination initiatives comprising NHGRI's genomic research portfolio are designed to speed the evaluation and incorporation, where appropriate, of genomic technologies and findings into routine clinical care. Actual adoption of successful approaches in clinical care will depend upon the willingness, interest, and energy of professional societies, practitioners, patients, and payers to promote their responsible use and share their experiences in doing so.
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Affiliation(s)
- Teri A Manolio
- Division of Genomic Medicine, National Human Genome Research Institute, 5635 Fishers Lane, Room 4113, MSC 9305, Bethesda MD, USA.
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14
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Byers T, Wender RC, Jemal A, Baskies AM, Ward EE, Brawley OW. The American Cancer Society challenge goal to reduce US cancer mortality by 50% between 1990 and 2015: Results and reflections. CA Cancer J Clin 2016; 66:359-69. [PMID: 27175568 DOI: 10.3322/caac.21348] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 03/31/2016] [Accepted: 04/01/2016] [Indexed: 12/19/2022] Open
Abstract
In 1996, the Board of Directors of the American Cancer Society (ACS) challenged the United States to reduce what looked to be possible peak cancer mortality in 1990 by 50% by the year 2015. This analysis examines the trends in cancer mortality across this 25-year challenge period from 1990 to 2015. In 2015, cancer death rates were 26% lower than in 1990 (32% lower among men and 22% lower among women). The 50% reduction goal was more fully met for the cancer sites for which there was enactment of effective approaches for prevention, early detection, and/or treatment. Among men, mortality rates dropped for lung cancer by 45%, for colorectal cancer by 47%, and for prostate cancer by 53%. Among women, mortality rates dropped for lung cancer by 8%, for colorectal cancer by 44%, and for breast cancer by 39%. Declines in the death rates of all other cancer sites were substantially smaller (13% among men and 17% among women). The major factors that accounted for these favorable trends were progress in tobacco control and improvements in early detection and treatment. As we embark on new national cancer goals, this recent past experience should teach us that curing the cancer problem will require 2 sets of actions: making new discoveries in cancer therapeutics and more completely applying those discoveries in cancer prevention we have already made. CA Cancer J Clin 2016;66:359-369. © 2016 American Cancer Society.
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Affiliation(s)
- Tim Byers
- Professor of Epidemiology, Colorado School of Public Health, University of Colorado, Aurora, CO
| | - Richard C Wender
- Chief Cancer Control Officer, American Cancer Society, Atlanta, GA
| | - Ahmedin Jemal
- Vice President,Surveillance and Health Services Research Program, American Cancer Society, Atlanta, GA
| | - Arnold M Baskies
- Surgical Oncologist, Virtua Surgical Specialists, Hainesport, NJ and Vice-President of the American Cancer Society Board of Directors, Atlanta, GA
| | - Elizabeth E Ward
- National Vice-President for Intramural Research, American Cancer Society, Atlanta, GA
| | - Otis W Brawley
- Chief Medical Officer, American Cancer Society, Atlanta, GA
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Fernandez-Cuesta L, Perdomo S, Avogbe PH, Leblay N, Delhomme TM, Gaborieau V, Abedi-Ardekani B, Chanudet E, Olivier M, Zaridze D, Mukeria A, Vilensky M, Holcatova I, Polesel J, Simonato L, Canova C, Lagiou P, Brambilla C, Brambilla E, Byrnes G, Scelo G, Le Calvez-Kelm F, Foll M, McKay JD, Brennan P. Identification of Circulating Tumor DNA for the Early Detection of Small-cell Lung Cancer. EBioMedicine 2016; 10:117-23. [PMID: 27377626 PMCID: PMC5036515 DOI: 10.1016/j.ebiom.2016.06.032] [Citation(s) in RCA: 137] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 06/20/2016] [Accepted: 06/23/2016] [Indexed: 12/18/2022] Open
Abstract
Circulating tumor DNA (ctDNA) is emerging as a key potential biomarker for post-diagnosis surveillance but it may also play a crucial role in the detection of pre-clinical cancer. Small-cell lung cancer (SCLC) is an excellent candidate for early detection given there are no successful therapeutic options for late-stage disease, and it displays almost universal inactivation of TP53. We assessed the presence of TP53 mutations in the cell-free DNA (cfDNA) extracted from the plasma of 51 SCLC cases and 123 non-cancer controls. We identified mutations using a pipeline specifically designed to accurately detect variants at very low fractions. We detected TP53 mutations in the cfDNA of 49% SCLC patients and 11.4% of non-cancer controls. When stratifying the 51 initial SCLC cases by stage, TP53 mutations were detected in the cfDNA of 35.7% early-stage and 54.1% late-stage SCLC patients. The results in the controls were further replicated in 10.8% of an independent series of 102 non-cancer controls. The detection of TP53 mutations in 11% of the 225 non-cancer controls suggests that somatic mutations in cfDNA among individuals without any cancer diagnosis is a common occurrence, and poses serious challenges for the development of ctDNA screening tests.
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Affiliation(s)
- Lynnette Fernandez-Cuesta
- International Agency for Research on Cancer (IARC-WHO), 150 cours Albert Thomas, 69008 Lyons, France
| | - Sandra Perdomo
- International Agency for Research on Cancer (IARC-WHO), 150 cours Albert Thomas, 69008 Lyons, France; Institute of Nutrition, Genetics and Metabolism Research, Universidad El Bosque, Bogotá, Colombia
| | - Patrice H Avogbe
- International Agency for Research on Cancer (IARC-WHO), 150 cours Albert Thomas, 69008 Lyons, France
| | - Noemie Leblay
- International Agency for Research on Cancer (IARC-WHO), 150 cours Albert Thomas, 69008 Lyons, France
| | - Tiffany M Delhomme
- International Agency for Research on Cancer (IARC-WHO), 150 cours Albert Thomas, 69008 Lyons, France
| | - Valerie Gaborieau
- International Agency for Research on Cancer (IARC-WHO), 150 cours Albert Thomas, 69008 Lyons, France
| | - Behnoush Abedi-Ardekani
- International Agency for Research on Cancer (IARC-WHO), 150 cours Albert Thomas, 69008 Lyons, France
| | - Estelle Chanudet
- International Agency for Research on Cancer (IARC-WHO), 150 cours Albert Thomas, 69008 Lyons, France
| | - Magali Olivier
- International Agency for Research on Cancer (IARC-WHO), 150 cours Albert Thomas, 69008 Lyons, France
| | - David Zaridze
- Russian N.N. Blokhin Cancer Research Centre, Moscow, Russian Federation
| | - Anush Mukeria
- Russian N.N. Blokhin Cancer Research Centre, Moscow, Russian Federation
| | | | - Ivana Holcatova
- 1st Faculty of Medicine, Charles University, Prague, Czech Republic
| | | | - Lorenzo Simonato
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Cristina Canova
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | | | | | | | - Graham Byrnes
- International Agency for Research on Cancer (IARC-WHO), 150 cours Albert Thomas, 69008 Lyons, France
| | - Ghislaine Scelo
- International Agency for Research on Cancer (IARC-WHO), 150 cours Albert Thomas, 69008 Lyons, France
| | - Florence Le Calvez-Kelm
- International Agency for Research on Cancer (IARC-WHO), 150 cours Albert Thomas, 69008 Lyons, France
| | - Matthieu Foll
- International Agency for Research on Cancer (IARC-WHO), 150 cours Albert Thomas, 69008 Lyons, France
| | - James D McKay
- International Agency for Research on Cancer (IARC-WHO), 150 cours Albert Thomas, 69008 Lyons, France.
| | - Paul Brennan
- International Agency for Research on Cancer (IARC-WHO), 150 cours Albert Thomas, 69008 Lyons, France.
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Hollstein M, Alexandrov LB, Wild CP, Ardin M, Zavadil J. Base changes in tumour DNA have the power to reveal the causes and evolution of cancer. Oncogene 2016; 36:158-167. [PMID: 27270430 PMCID: PMC5241425 DOI: 10.1038/onc.2016.192] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 03/31/2016] [Accepted: 03/31/2016] [Indexed: 12/19/2022]
Abstract
Next-generation sequencing (NGS) technology has demonstrated that the cancer genomes are peppered with mutations. Although most somatic tumour mutations are unlikely to have any role in the cancer process per se, the spectra of DNA sequence changes in tumour mutation catalogues have the potential to identify the mutagens, and to reveal the mutagenic processes responsible for human cancer. Very recently, a novel approach for data mining of the vast compilations of tumour NGS data succeeded in separating and precisely defining at least 30 distinct patterns of sequence change hidden in mutation databases. At least half of these mutational signatures can be readily assigned to known human carcinogenic exposures or endogenous mechanisms of mutagenesis. A quantum leap in our knowledge of mutagenesis in human cancers has resulted, stimulating a flurry of research activity. We trace here the major findings leading first to the hypothesis that carcinogenic insults leave characteristic imprints on the DNA sequence of tumours, and culminating in empirical evidence from NGS data that well-defined carcinogen mutational signatures are indeed present in tumour genomic DNA from a variety of cancer types. The notion that tumour DNAs can divulge environmental sources of mutation is now a well-accepted fact. This approach to cancer aetiology has also incriminated various endogenous, enzyme-driven processes that increase the somatic mutation load in sporadic cancers. The tasks now confronting the field of molecular epidemiology are to assign mutagenic processes to orphan and newly discovered tumour mutation patterns, and to determine whether avoidable cancer risk factors influence signatures produced by endogenous enzymatic mechanisms. Innovative research with experimental models and exploitation of the geographical heterogeneity in cancer incidence can address these challenges.
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Affiliation(s)
- M Hollstein
- Molecular Mechanisms and Biomarkers, International Agency for Research on Cancer, World Health Organization, Lyon, France.,Faculty of Medicine and Health, University of Leeds, Leeds, UK
| | - L B Alexandrov
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos, NM, USA.,Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - C P Wild
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - M Ardin
- Molecular Mechanisms and Biomarkers, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - J Zavadil
- Molecular Mechanisms and Biomarkers, International Agency for Research on Cancer, World Health Organization, Lyon, France
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