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Meiser B, Butow P, Davies G, Napier CE, Schlub TE, Bartley N, Juraskova I, Ballinger ML, Thomas DM, Best MC. Psychological predictors of cancer patients' and their relatives' attitudes towards the return of genomic sequencing results. Eur J Med Genet 2022; 65:104516. [PMID: 35487418 DOI: 10.1016/j.ejmg.2022.104516] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 03/02/2022] [Accepted: 04/23/2022] [Indexed: 11/03/2022]
Abstract
This study assessed the psychological predictors of attitudes toward the return of germline genomic sequencing results in cancer patients and their biological relatives with a likely genetic basis for their cancer diagnosis, who completed a questionnaire prior to undergoing genomic sequencing. Of 602 probands and relatives, 94% of probands and 89% of relatives thought people would like to be informed about single-gene conditions for which there is prevention or treatment. Amongst relatives, this view was associated with higher perceived susceptibility and self-efficacy. Probands (66%) and relatives (59%) thought people would be interested in learning about single-gene conditions for which there is no prevention or treatment. Amongst probands, this view was associated with lower tolerance of uncertainty and amongst relatives with higher self-efficacy. Probands (92%) and relatives (90%) thought people would like to be informed about polygenic conditions that can have a major impact on health. Amongst probands this view was associated with lower perceived susceptibility of cancer recurrence, and amongst relatives, with higher perceived susceptibility and self-efficacy. Probands (86%) and relatives (86%) thought that people would like to be informed about polygenic conditions that can have a lower impact on health, and this view was associated with a lower perceived susceptibility of recurrence amongst probands. Inconclusion, these findings show that individuals' attitudes about the return of results depend on the perceived utility of different types of tests. Therefore, individuals need to gain a clear understanding of test utility, and appropriate consent processes are required to achieve informed choices.
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Affiliation(s)
- Bettina Meiser
- Psychosocial Research Group, Prince of Wales Clinical School, University of NSW, Kensington, NSW, 2032, Australia.
| | - Phyllis Butow
- Psycho-Oncology Co-operative Research Group (PoCoG), School of Psychology, University of Sydney, Sydney NSW, 2006, Australia
| | - Grace Davies
- Psycho-Oncology Co-operative Research Group (PoCoG), School of Psychology, University of Sydney, Sydney NSW, 2006, Australia
| | - Christine E Napier
- Cancer Theme, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
| | - Timothy E Schlub
- Sydney School of Public Health, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, 2006, Australia
| | - Nicci Bartley
- Psycho-Oncology Co-operative Research Group (PoCoG), School of Psychology, University of Sydney, Sydney NSW, 2006, Australia
| | - Ilona Juraskova
- Psycho-Oncology Co-operative Research Group (PoCoG), School of Psychology, University of Sydney, Sydney NSW, 2006, Australia
| | - Mandy L Ballinger
- Cancer Theme, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia; St Vincent's Clinical School, University of NSW, Kensington, NSW, 2032, Australia
| | - David M Thomas
- Cancer Theme, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia; St Vincent's Clinical School, University of NSW, Kensington, NSW, 2032, Australia
| | - Megan C Best
- Psycho-Oncology Co-operative Research Group (PoCoG), School of Psychology, University of Sydney, Sydney NSW, 2006, Australia
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Pavanello M, Chan IHY, Ariff A, Pharoah PDP, Gayther SA, Ramus SJ. Rare Germline Genetic Variants and the Risks of Epithelial Ovarian Cancer. Cancers (Basel) 2020; 12:E3046. [PMID: 33086730 PMCID: PMC7589980 DOI: 10.3390/cancers12103046] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 02/06/2023] Open
Abstract
A family history of ovarian or breast cancer is the strongest risk factor for epithelial ovarian cancer (EOC). Germline deleterious variants in the BRCA1 and BRCA2 genes confer EOC risks by age 80, of 44% and 17% respectively. The mismatch repair genes, particularly MSH2 and MSH6, are also EOC susceptibility genes. Several other DNA repair genes, BRIP1, RAD51C, RAD51D, and PALB2, have been identified as moderate risk EOC genes. EOC has five main histotypes; high-grade serous (HGS), low-grade serous (LGS), clear cell (CCC), endometrioid (END), and mucinous (MUC). This review examines the current understanding of the contribution of rare genetic variants to EOC, focussing on providing frequency data for each histotype. We provide an overview of frequency and risk for pathogenic variants in the known susceptibility genes as well as other proposed genes. We also describe the progress to-date to understand the role of missense variants and the different breast and ovarian cancer risks for each gene. Identification of susceptibility genes have clinical impact by reducing disease-associated mortality through improving risk prediction, with the possibility of prevention strategies, and developing new targeted treatments and these clinical implications are also discussed.
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Affiliation(s)
- Marina Pavanello
- School of Women’s and Children’s Health, Faculty of Medicine, University of New South Wales, Sydney 2052, Australia; (M.P.); (I.H.C.); (A.A.)
- Adult Cancer Program, Lowy Cancer Research Centre, University of New South Wales, Sydney 2052, Australia
| | - Isaac HY Chan
- School of Women’s and Children’s Health, Faculty of Medicine, University of New South Wales, Sydney 2052, Australia; (M.P.); (I.H.C.); (A.A.)
| | - Amir Ariff
- School of Women’s and Children’s Health, Faculty of Medicine, University of New South Wales, Sydney 2052, Australia; (M.P.); (I.H.C.); (A.A.)
- Adult Cancer Program, Lowy Cancer Research Centre, University of New South Wales, Sydney 2052, Australia
| | - Paul DP Pharoah
- Strangeways Research Laboratory, University of Cambridge, Cambridge CB1 8RN, UK;
| | - Simon A. Gayther
- Center for Cancer Prevention and Translational Genomics, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA;
- Applied Genomics, Computation and Translational Core, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Susan J. Ramus
- School of Women’s and Children’s Health, Faculty of Medicine, University of New South Wales, Sydney 2052, Australia; (M.P.); (I.H.C.); (A.A.)
- Adult Cancer Program, Lowy Cancer Research Centre, University of New South Wales, Sydney 2052, Australia
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Yanes T, Young MA, Meiser B, James PA. Clinical applications of polygenic breast cancer risk: a critical review and perspectives of an emerging field. Breast Cancer Res 2020; 22:21. [PMID: 32066492 PMCID: PMC7026946 DOI: 10.1186/s13058-020-01260-3] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 02/07/2020] [Indexed: 01/04/2023] Open
Abstract
Polygenic factors are estimated to account for an additional 18% of the familial relative risk of breast cancer, with those at the highest level of polygenic risk distribution having a least a twofold increased risk of the disease. Polygenic testing promises to revolutionize health services by providing personalized risk assessments to women at high-risk of breast cancer and within population breast screening programs. However, implementation of polygenic testing needs to be considered in light of its current limitations, such as limited risk prediction for women of non-European ancestry. This article aims to provide a comprehensive review of the evidence for polygenic breast cancer risk, including the discovery of variants associated with breast cancer at the genome-wide level of significance and the use of polygenic risk scores to estimate breast cancer risk. We also review the different applications of this technology including testing of women from high-risk breast cancer families with uninformative genetic testing results, as a moderator of monogenic risk, and for population screening programs. Finally, a potential framework for introducing testing for polygenic risk in familial cancer clinics and the potential challenges with implementing this technology in clinical practice are discussed.
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Affiliation(s)
- Tatiane Yanes
- Psychosocial Research Group, Prince of Wales Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia. .,The University of Queensland Diamantina Institute, Dermatology Research Centre, University of Queensland, Brisbane, QLD, 4102, Australia.
| | - Mary-Anne Young
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Bettina Meiser
- Psychosocial Research Group, Prince of Wales Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Paul A James
- Parkville Integrated Familial Cancer Centre, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
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Kerr A, Broer T, Ross E, Cunningham Burley S. Polygenic risk-stratified screening for cancer: Responsibilization in public health genomics. SOCIAL STUDIES OF SCIENCE 2019; 49:605-626. [PMID: 31230567 PMCID: PMC6688132 DOI: 10.1177/0306312719858404] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
In this article, we examine professional discourse around the development of polygenic risk-stratified screening (PRSS) for cancer. Analyzing a range of contemporary professional literatures from Europe, North America and Australia, we explore how the drive to screen for molecular markers of cancer risk makes professionals, screening recipients and publics responsible, in different ways, for acquiring, curating and analyzing molecular data. Investigating how these responsibilities are invoked in discussions of new data practices, technologies, organizational arrangements, engagement, education and protocols for participation, we argue that agendas for PRSS for cancer are both expanding and stratifying responsibilities. Data collection is to be achieved by intensified responsibilities for including, reassuring and recruiting populations, as well as by opening and enriching the datasets on which models and preventative screening arrangements are based. Enhanced responsibilities for screening recipients and publics are also invoked, not just in relation to personal health but for population health more generally, via research participation and consenting to data re-use in the public interest. Professionals, screening recipients and publics are also to become responsible for moderating expectations of screening according to genomic designations. Together these discourses go beyond individual risk management to extend and diversify the responsibilities of practitioners, screening recipients and publics as public health genomics develops.
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Affiliation(s)
- Anne Kerr
- School of Sociology and Social Policy, University of Leeds, Leeds, UK
| | - Tineke Broer
- Tilburg Institute for Law, Technology, and Society (TILT), Tilburg University, Tilburg, The Netherlands
| | | | - Sarah Cunningham Burley
- Usher Institute of Population Health Sciences and Informatics, Edinburgh Medical School, The University of Edinburgh, Edinburgh, UK
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Genetic diagnosis of a Chinese multiple endocrine neoplasia type 2A family through whole genome sequencing. J Biosci 2018; 42:209-218. [PMID: 28569245 DOI: 10.1007/s12038-017-9686-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Approximately 98% of patients with multiple endocrine neoplasia type 2A (MEN 2A) have an identifiable RET mutation. Prophylactic or early total thyroidectomy or pheochromocytoma/parathyroid removal in patients can be preventative or curative and has become standard management. The general strategy for RET screening on family members at risk is to sequence the most commonly affected exons and, if negative, to extend sequencing to additional exons. However, different families with MEN 2A due to the same RET mutation often have significant variability in the clinical exhibition of disease and aggressiveness of the MTC, which implies additional genetic loci exsit beyond RET coding region. Whole genome sequencing (WGS) greatly expands the breadth of screening from genes associated with a particular disease to the whole genome and, potentially, all the information that the genome contains about diseases or traits. This is presumably due to additive effect of disease modifying factors. In this study, we performed WGS on a typical Chinese MEN 2A proband and identified the pathogenic RET p.C634R mutation. We also identified several neutral variants within RET and pheochromocytoma-related genes. Moreover, we found several interesting structural variants including genetic deletions (RSPO1, OVCH2 and AP3S1, etc.) and fusion transcripts (FSIP1-BAZ2A, etc.).
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Abstract
Next-generation or massively parallel sequencing has transformed the landscape of genetic testing for cancer susceptibility. Panel-based genetic tests evaluate multiple genes simultaneously and rapidly. Because these tests are frequently offered in clinical settings, understanding their clinical validity and utility is critical. When evaluating the inherited risk of breast and ovarian cancers, panel-based tests provide incremental benefit compared with BRCA1/2 genetic testing. For inherited risk of other cancers, such as colon cancer and pheochromocytoma-paraganglioma, the clinical utility and yield of panel-based testing are higher; in fact, simultaneous evaluation of multiple genes has been the historical standard for these diseases. Evaluating inherited risk with panel-based testing has recently entered clinical practice for prostate and pancreatic cancers, with potential therapeutic implications. The resulting variants of uncertain significance and mutations with unclear actionability pose challenges to service providers and patients, underscoring the importance of genetic counseling and data-sharing initiatives. This review explores the evolving merits, challenges, and nuances of panel-based testing for cancer susceptibility.
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Affiliation(s)
- Payal D Shah
- Division of Hematology and Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104;
| | - Katherine L Nathanson
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104; .,Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104
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Integrating personalized genomics into Turkish healthcare system: A cancer-oriented pilot activity of Istanbul Northern Anatolian Public Hospitals with GLAB. North Clin Istanb 2017; 4:1-3. [PMID: 28752136 PMCID: PMC5530150 DOI: 10.14744/nci.2017.38980] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 04/19/2017] [Indexed: 11/20/2022] Open
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Abouelhoda M, Faquih T, El-Kalioby M, Alkuraya FS. Revisiting the morbid genome of Mendelian disorders. Genome Biol 2016; 17:235. [PMID: 27884173 PMCID: PMC5123336 DOI: 10.1186/s13059-016-1102-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 11/08/2016] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The pathogenicity of many Mendelian variants has been challenged by large-scale sequencing efforts. However, many rare and benign "disease mutations" are difficult to analyze due to their rarity. The Saudi Arabian variome is enriched for homozygosity due to inbreeding, a key advantage that can be exploited for the critical examination of previously published variants. RESULTS We collated all "disease-related mutations" listed in the Human Gene Mutation Database (HGMD) and ClinVar, including "variants of uncertain significance" (VOUS). We find that the use of public databases including 1000 Genomes, ExAC, and Kaviar can reclassify many of these variants as likely benign. Our Saudi Human Genome Program (SHGP) can reclassify many variants that are rare in public databases. Furthermore, SGPD allows us to observe many previously reported variants in the homozygous state and our extensive phenotyping of participants makes it possible to demonstrate the lack of phenotype for these variants, thus challenging their pathogenicity despite their rarity. We also find that 18 VOUS BRCA1 and BRCA2 variants that are listed in BRCA Exchange are present at least once in the homozygous state in patients who lack features of Fanconi anemia. Reassuringly, we could reciprocally demonstrate that none of those labeled as "pathogenic" were observed in the homozygous statue in individuals who lack Fanconi phenotype in our database. CONCLUSION Our study shows the importance of revisiting disease-related databases using public resources as well as of population-specific resources to improve the specificity of the morbid genome of Mendelian diseases in humans.
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Affiliation(s)
- Mohamed Abouelhoda
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
- Saudi Human Genome Program, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia.
| | - Tariq Faquih
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
- Saudi Human Genome Program, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | - Mohamed El-Kalioby
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
- Saudi Human Genome Program, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
- Saudi Human Genome Program, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia.
- Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.
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Clinical Decision Making: Integrating Advances in the Molecular Understanding of Spine Tumors. Spine (Phila Pa 1976) 2016; 41 Suppl 20:S171-S177. [PMID: 27488298 DOI: 10.1097/brs.0000000000001836] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
STUDY DESIGN Literature review. OBJECTIVE To describe advancements in molecular techniques, biomarkers, technology, and targeted therapeutics and the potential these modalities hold to predict treatment paradigms, clinical outcomes, and/or survival in patients diagnosed with primary spinal column tumors. SUMMARY OF BACKGROUND DATA Advances in molecular technologies and techniques have influenced the prevention, diagnosis, and overall management of patients diagnosed with cancer. Assessment of genomic, proteomic alterations, epigenetic, and posttranslational modifications as well as developments in diagnostic modalities and targeted therapeutics, although the best studied in nonspinal metastatic disease, have led to increased understanding of spine oncology that is expected to improve patient outcomes. In this manuscript, the technological advancements that are expected to change the landscape of spinal oncology are discussed with a focus on how these technologies will aid in clinical decision-making for patients diagnosed with primary spinal tumors. METHODS A review of the literature was performed focusing on studies that integrated next-generation sequencing, circulating tumor cells/circulating tumor DNA, advances in imaging modalities and/or radiotherapy in the diagnosis and treatment of cancer. RESULTS We discuss genetic and epigenetic drivers, aberrations in receptor tyrosine kinase signaling, and emerging therapeutic strategies that include receptor tyrosine kinase inhibitors, immunotherapy strategies, and vaccine-based cancer prevention strategies. CONCLUSION The wide range of approaches currently in use and the emerging technologies yet to be fully realized will allow for better development of rationale therapeutics to improve patient outcomes. LEVEL OF EVIDENCE N/A.
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Chatterjee N, Shi J, García-Closas M. Developing and evaluating polygenic risk prediction models for stratified disease prevention. Nat Rev Genet 2016; 17:392-406. [PMID: 27140283 DOI: 10.1038/nrg.2016.27] [Citation(s) in RCA: 437] [Impact Index Per Article: 54.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Knowledge of genetics and its implications for human health is rapidly evolving in accordance with recent events, such as discoveries of large numbers of disease susceptibility loci from genome-wide association studies, the US Supreme Court ruling of the non-patentability of human genes, and the development of a regulatory framework for commercial genetic tests. In anticipation of the increasing relevance of genetic testing for the assessment of disease risks, this Review provides a summary of the methodologies used for building, evaluating and applying risk prediction models that include information from genetic testing and environmental risk factors. Potential applications of models for primary and secondary disease prevention are illustrated through several case studies, and future challenges and opportunities are discussed.
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Affiliation(s)
- Nilanjan Chatterjee
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University.,Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA.,Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland 20892, USA
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland 20892, USA
| | - Montserrat García-Closas
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland 20892, USA
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Fallin MD, Duggal P, Beaty TH. Genetic Epidemiology and Public Health: The Evolution From Theory to Technology. Am J Epidemiol 2016; 183:387-93. [PMID: 26905340 DOI: 10.1093/aje/kww001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 01/04/2016] [Indexed: 12/28/2022] Open
Abstract
Genetic epidemiology represents a hybrid of epidemiologic designs and statistical models that explicitly consider both genetic and environmental risk factors for disease. It is a relatively new field in public health; the term was first coined only 35 years ago. In this short time, the field has been through a major evolution, changing from a field driven by theory, without the technology for genetic measurement or computational capacity to apply much of the designs and methods developed, to a field driven by rapidly expanding technology in genomic measurement and computational analyses while epidemiologic theory struggles to keep up. In this commentary, we describe 4 different eras of genetic epidemiology, spanning this evolution from theory to technology, what we have learned, what we have added to the broader field of public health, and what remains to be done.
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Abstract
Sarcomas are rare and heterogeneous diseases that affect a younger population than most epithelial cancers. Epidemiologic studies suggest a strong genetic component to sarcomas, and many familial cancer syndromes have been described, in which sarcomas are a feature. The best known of these are the Li-Fraumeni and retinoblastoma syndromes, study of which has been pivotal to elucidating the molecular basis for the cell response to DNA damage and the cell division. Although much has been learnt about cancer biology from the study of sarcoma families, in general clinical management of increased sarcoma risk has lagged behind other cancer predisposition syndromes. With the advent of genomic tools for genetic testing, it is likely that a substantial fraction of sarcoma patients will be identified as carriers of known risk alleles. The translation of this knowledge into effective risk management programs and cancer treatments will be essential to changes in routine clinical practice.
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Affiliation(s)
- David M Thomas
- The Kinghorn Cancer Centre & Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.
| | - Mandy L Ballinger
- The Kinghorn Cancer Centre & Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
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Distinguishing activity from progress. Lancet Oncol 2015; 16:1586-8. [PMID: 26678186 DOI: 10.1016/s1470-2045(15)00466-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 10/27/2015] [Indexed: 11/20/2022]
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