1
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Dalfovo D, Scandino R, Paoli M, Valentini S, Romanel A. Germline determinants of aberrant signaling pathways in cancer. NPJ Precis Oncol 2024; 8:57. [PMID: 38429380 PMCID: PMC10907629 DOI: 10.1038/s41698-024-00546-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 02/16/2024] [Indexed: 03/03/2024] Open
Abstract
Cancer is a complex disease influenced by a heterogeneous landscape of both germline genetic variants and somatic aberrations. While there is growing evidence suggesting an interplay between germline and somatic variants, and a substantial number of somatic aberrations in specific pathways are now recognized as hallmarks in many well-known forms of cancer, the interaction landscape between germline variants and the aberration of those pathways in cancer remains largely unexplored. Utilizing over 8500 human samples across 33 cancer types characterized by TCGA and considering binary traits defined using a large collection of somatic aberration profiles across ten well-known oncogenic signaling pathways, we conducted a series of GWAS and identified genome-wide and suggestive associations involving 276 SNPs. Among these, 94 SNPs revealed cis-eQTL links with cancer-related genes or with genes functionally correlated with the corresponding traits' oncogenic pathways. GWAS summary statistics for all tested traits were then used to construct a set of polygenic scores employing a customized computational strategy. Polygenic scores for 24 traits demonstrated significant performance and were validated using data from PCAWG and CCLE datasets. These scores showed prognostic value for clinical variables and exhibited significant effectiveness in classifying patients into specific cancer subtypes or stratifying patients with cancer-specific aggressive phenotypes. Overall, we demonstrate that germline genetics can describe patients' genetic liability to develop specific cancer molecular and clinical profiles.
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Affiliation(s)
- Davide Dalfovo
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123, Trento, (TN), Italy
| | - Riccardo Scandino
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123, Trento, (TN), Italy
| | - Marta Paoli
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123, Trento, (TN), Italy
| | - Samuel Valentini
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123, Trento, (TN), Italy
| | - Alessandro Romanel
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123, Trento, (TN), Italy.
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2
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Ahmad O, Försti A. The complementary roles of genome-wide approaches in identifying genes linked to an inherited risk of colorectal cancer. Hered Cancer Clin Pract 2023; 21:1. [PMID: 36707860 PMCID: PMC9883872 DOI: 10.1186/s13053-023-00245-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 01/18/2023] [Indexed: 01/29/2023] Open
Abstract
The current understanding of the inherited risk of colorectal cancer (CRC) started with an observational clinical era in the late 19th century, which was followed by a genetic era starting in the late 20th century. Genome-wide linkage analysis allowed mapping several high-risk genes, which marked the beginning of the genetic era. The current high-throughput genomic phase includes genome-wide association study (GWAS) and genome-wide sequencing approaches which have revolutionized the conception of the inherited risk of CRC. On the one hand, GWAS has allowed the identification of multiple low risk loci correlated with CRC. On the other, genome-wide sequencing has led to the discovery of a second batch of high-to-moderate-risk genes that correlate to atypical familial CRC and polyposis syndromes. In contrast to other common cancers, which are usually dominated by a polygenic background, CRC risk is believed to be equally explained by monogenic and polygenic architectures, which jointly contribute to a quarter of familial clustering. Despite the fact that genome-wide approaches have allowed the identification of a continuum of responsible high-to-moderate-to-low-risk variants, much of the predisposition and familial clustering of CRC has not yet been explained. Other genetic, epigenetic and environmental factors might be playing important roles as well. In this review we aim to provide insights on the complementary roles played by different genomic approaches in allowing the current understanding of the genetic architecture of inherited CRC.
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Affiliation(s)
- Olfat Ahmad
- grid.510964.fHopp Children’s Cancer Center (KiTZ), Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany ,grid.5253.10000 0001 0328 4908Institute of Human Genetics, University Hospital Heidelberg, Heidelberg, Germany ,grid.4991.50000 0004 1936 8948University of Oxford, Oxford, UK ,grid.419782.10000 0001 1847 1773King Hussein Cancer Center (KHCC), Amman, Jordan
| | - Asta Försti
- grid.510964.fHopp Children’s Cancer Center (KiTZ), Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
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3
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Liu S, Liu W, Zhao D, Zhang Y, Zhao Z, Luo B. The Glypican-4 Gene Polymorphism rs1048369 and Susceptibility to Epstein-Barr Virus-Positive and -Negative Nasopharyngeal Carcinoma in Northern China. Oncol Res Treat 2019; 42:572-579. [PMID: 31522169 DOI: 10.1159/000502753] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 08/14/2019] [Indexed: 11/19/2022]
Abstract
BACKGROUND Gene polymorphism rs1048369 of glypican-4 (GPC4) gene has been reported to be significantly different between Epstein-Barr virus (EBV)-associated gastric carcinoma (GC) and EBV-negative GC. However, little is known about the polymorphism in nasopharyngeal carcinoma (NPC), which is a malignant tumor with a high prevalence of EBV. OBJECTIVE The distribution of GPC4 polymorphism rs1048369 was investigated in NPC patients, especially in those with EBV infection. The association between the polymorphism of GPC4 and the susceptibility to EBV-positive and EBV-negative NPC was also explored. PATIENTS AND METHODS The GPC4 gene polymorphism rs1048369 was detected in 143 cases of EBV-positive NPC and in 19 cases of EBV-negative NPC using polymerase chain reaction. One hundred and seven peripheral blood samples from healthy individuals were also measured as a control group. RESULTS The difference in genotype CC between EBV-positive NPC patients and healthy individuals was significant (χ2 = 15.273, p < 0.01). No significant difference was observed between EBV-positive and EBV-negative NPC cases. Between EBV-negative NPC cases and healthy individuals, there was no significant difference in GPC4 gene polymorphism in both genotypic and allelic frequencies. CONCLUSIONS The GPC4 gene polymorphism is associated with susceptibility to EBV-positive NPC. The CC genotype of GPC4 may represent a risk factor for NPC in Northern China.
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Affiliation(s)
- Shuzhen Liu
- Department of Transfusion Medicine, The Affiliated Hospital of Qingdao University, Qingdao, China.,Department of Medical Microbiology, Qingdao University Medical College, Qingdao, China
| | - Wen Liu
- Department of Medical Microbiology, Qingdao University Medical College, Qingdao, China
| | - Danrui Zhao
- Department of Medical Microbiology, Qingdao University Medical College, Qingdao, China
| | - Yan Zhang
- Department of Medical Microbiology, Qingdao University Medical College, Qingdao, China.,Department of Clinical Laboratory, Zibo Central Hospital, Zibo, China
| | - Zhenzhen Zhao
- Department of Medical Microbiology, Qingdao University Medical College, Qingdao, China
| | - Bing Luo
- Department of Medical Microbiology, Qingdao University Medical College, Qingdao, China,
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4
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Kolberg HC, Schneeweiss A, Fehm TN, Wöckel A, Huober J, Pontones C, Titzmann A, Belleville E, Lux MP, Janni W, Hartkopf AD, Taran FA, Wallwiener M, Overkamp F, Tesch H, Ettl J, Lüftner D, Müller V, Schütz F, Fasching PA, Brucker SY. Update Breast Cancer 2019 Part 3 - Current Developments in Early Breast Cancer: Review and Critical Assessment by an International Expert Panel. Geburtshilfe Frauenheilkd 2019; 79:470-482. [PMID: 31148847 PMCID: PMC6529230 DOI: 10.1055/a-0887-0861] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 04/01/2019] [Indexed: 12/13/2022] Open
Abstract
The treatment of breast cancer patients in a curative situation is special in many ways. The local therapy with surgery and radiation therapy is a central aspect of the treatment. The complete elimination of tumour cells at the site of the primary disease must be ensured while simultaneously striving to keep the long-term effects as minor as possible. There is still focus on the continued reduction of the invasiveness of local therapy. With regard to systemic therapy, chemotherapies with taxanes, anthracyclines and, in some cases, platinum-based chemotherapies have become established in the past couple of decades. The context for use is being continually further defined. Likewise, there are questions in the case of antihormonal therapy which also still need to be further defined following the introduction of aromatase inhibitors, such as the length of therapy or ovarian suppression in premenopausal patients. Finally, personalisation of the treatment of early breast cancer patients is also being increasingly used. Prognostic tests could potentially support therapeutic decisions. It must also be considered how the possible use of new therapies, such as checkpoint inhibitors and CDK4/6 inhibitors could look in practice once study results in this regard are available. This overview addresses the backgrounds on the current votes taken by the international St. Gallen panel of experts in Vienna in 2019 for current questions in the treatment of breast cancer patients in a curative situation.
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Affiliation(s)
| | - Andreas Schneeweiss
- National Center for Tumor Diseases, Division Gynecologic Oncology, University Hospital and German Cancer Research Center Heidelberg, Heidelberg, Germany
| | - Tanja N Fehm
- Department of Gynecology and Obstetrics, University Hospital Düsseldorf, Düsseldorf, Germany
| | - Achim Wöckel
- Department of Gynecology and Obstetrics, University Hospital Würzburg, Würzburg, Germany
| | - Jens Huober
- Department of Gynecology and Obstetrics, Ulm University Hospital, Ulm, Germany
| | - Constanza Pontones
- Erlangen University Hospital, Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Adriana Titzmann
- Erlangen University Hospital, Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | | | - Michael P Lux
- Kooperatives Brustzentrum Paderborn, Klinik für Gynäkologie und Geburtshilfe, Frauenklinik St. Louise, Paderborn, St. Josefs-Krankenhaus, Salzkotten, Germany
| | - Wolfgang Janni
- Department of Gynecology and Obstetrics, Ulm University Hospital, Ulm, Germany
| | - Andreas D Hartkopf
- Department of Obstetrics and Gynecology, University of Tübingen, Tübingen, Germany
| | - Florin-Andrei Taran
- Department of Obstetrics and Gynecology, University of Tübingen, Tübingen, Germany
| | - Markus Wallwiener
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
| | | | - Hans Tesch
- Oncology Practice at Bethanien Hospital Frankfurt, Frankfurt, Germany
| | - Johannes Ettl
- Department of Obstetrics and Gynecology, Technical University of Munich, School of Medicine, Klinikum rechts der Isar, Munich, Germany
| | - Diana Lüftner
- Charité University Hospital, Campus Benjamin Franklin, Department of Hematology, Oncology and Tumour Immunology, Berlin, Germany
| | - Volkmar Müller
- Department of Gynecology, Hamburg-Eppendorf University Medical Center, Hamburg, Germany
| | - Florian Schütz
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
| | - Peter A Fasching
- Erlangen University Hospital, Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Sara Y Brucker
- Department of Obstetrics and Gynecology, University of Tübingen, Tübingen, Germany
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5
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Correlation between prostate stem cell antigen gene expression and oral squamous cell carcinoma. Oncol Lett 2018; 15:9151-9161. [PMID: 29844822 PMCID: PMC5958807 DOI: 10.3892/ol.2018.8468] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Accepted: 01/16/2018] [Indexed: 02/05/2023] Open
Abstract
The aetiology of oral squamous cell carcinoma (OSCC) remains unclear. Numerous single nucleotide polymorphisms (SNPs) associated with cancer have been identified using genome-wide association studies (GWAS). The present study was designed to identify common SNPs associated with cancer susceptibility and to evaluate their involvement in OSCC. Susceptible loci were identified by analysing a cancer GWAS catalogue. A multicentre case-control study using an OSCC and control population was performed for selected SNPs. The function of the selected locus and its associated gene was explored using a reverse transcription-polymerase chain reaction, enzyme linked immunosorbent assay and immunohistochemistry. The association between genotypes and clinical parameters was assessed in 76 patients with OSCC. Rs2294008 located in the prostate stem cell antigen gene (PSCA) was selected. It was identified that the rs2294008 polymorphism was associated with OSCC susceptibility and PSCA may be involved in the development, progression and prognosis of OSCC.
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6
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Heidenreich B, Kumar R. Altered TERT promoter and other genomic regulatory elements: occurrence and impact. Int J Cancer 2017; 141:867-876. [PMID: 28407294 DOI: 10.1002/ijc.30735] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 03/28/2017] [Accepted: 03/31/2017] [Indexed: 12/19/2022]
Abstract
Study of genetic alterations, inherited or acquired, that increase the risk or drive cancers and many other diseases had remained mostly confined to coding sequences of the human genome. Data from genome wide associations studies, development of the Encyclopedia of DNA Elements (ENCODE), and a spurt in detection of driver somatic mutations have shifted focus towards noncoding regions of the human genome. The majority of genetic variants robustly associated with cancers and other syndromes identified through genome wide studies are located within noncoding regulatory regions of the genome. Genome wide techniques have put an emphasis on the role of three-dimensional chromosomal structures and cis-acting elements in regulations of different genes. The variants within noncoding genomic regions can potentially alter a number of regulatory elements including promoters, enhancers, insulators, noncoding long RNAs and others that affect cancers and various diseases through altered expression of critical genes. With effect of genetic alterations within regulatory elements dependent on other partner molecules like transcription factors and histone marks, an understanding of such modifications can potentially identify extended therapeutic targets. That concept has been augmented by the detection of driver somatic noncoding mutations within the promoter region of the telomerase reverse transcriptase (TERT) gene in different cancers. The acquired somatic noncoding mutations within different regulatory elements are now being reported in different cancers with an increased regularity. In this review we discuss the occurrence and impact of germline and somatic alterations within the TERT promoter and other genomic regulatory elements.
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Affiliation(s)
- Barbara Heidenreich
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Rajiv Kumar
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany.,German Consortium for Translational Research (DKTK), German Cancer Research Center, Heidelberg, Germany
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7
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Lynch SM, Mitra N, Ross M, Newcomb C, Dailey K, Jackson T, Zeigler-Johnson CM, Riethman H, Branas CC, Rebbeck TR. A Neighborhood-Wide Association Study (NWAS): Example of prostate cancer aggressiveness. PLoS One 2017; 12:e0174548. [PMID: 28346484 PMCID: PMC5367705 DOI: 10.1371/journal.pone.0174548] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 03/11/2017] [Indexed: 12/31/2022] Open
Abstract
PURPOSE Cancer results from complex interactions of multiple variables at the biologic, individual, and social levels. Compared to other levels, social effects that occur geospatially in neighborhoods are not as well-studied, and empiric methods to assess these effects are limited. We propose a novel Neighborhood-Wide Association Study(NWAS), analogous to genome-wide association studies(GWAS), that utilizes high-dimensional computing approaches from biology to comprehensively and empirically identify neighborhood factors associated with disease. METHODS Pennsylvania Cancer Registry data were linked to U.S. Census data. In a successively more stringent multiphase approach, we evaluated the association between neighborhood (n = 14,663 census variables) and prostate cancer aggressiveness(PCA) with n = 6,416 aggressive (Stage≥3/Gleason grade≥7 cases) vs. n = 70,670 non-aggressive (Stage<3/Gleason grade<7) cases in White men. Analyses accounted for age, year of diagnosis, spatial correlation, and multiple-testing. We used generalized estimating equations in Phase 1 and Bayesian mixed effects models in Phase 2 to calculate odds ratios(OR) and confidence/credible intervals(CI). In Phase 3, principal components analysis grouped correlated variables. RESULTS We identified 17 new neighborhood variables associated with PCA. These variables represented income, housing, employment, immigration, access to care, and social support. The top hits or most significant variables related to transportation (OR = 1.05;CI = 1.001-1.09) and poverty (OR = 1.07;CI = 1.01-1.12). CONCLUSIONS This study introduces the application of high-dimensional, computational methods to large-scale, publically-available geospatial data. Although NWAS requires further testing, it is hypothesis-generating and addresses gaps in geospatial analysis related to empiric assessment. Further, NWAS could have broad implications for many diseases and future precision medicine studies focused on multilevel risk factors of disease.
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Affiliation(s)
- Shannon M. Lynch
- Fox Chase Cancer Center, Cancer Prevention and Control, Philadelphia, Pennsylvania, United States of America
- * E-mail:
| | - Nandita Mitra
- University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Michelle Ross
- University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Craig Newcomb
- University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Karl Dailey
- University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Tara Jackson
- University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | | | - Harold Riethman
- Old Dominion University, Norfolk, Virginia, United States of America
| | - Charles C. Branas
- University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
- Columbia University, Mailman School of Public Health, New York, New York, United States of America
| | - Timothy R. Rebbeck
- Dana Farber Cancer Institute and Harvard TH Chan School of Public Health, Boston, Massachusetts, United States of America
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8
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Carter H, Marty R, Hofree M, Gross AM, Jensen J, Fisch KM, Wu X, DeBoever C, Van Nostrand EL, Song Y, Wheeler E, Kreisberg JF, Lippman SM, Yeo GW, Gutkind JS, Ideker T. Interaction Landscape of Inherited Polymorphisms with Somatic Events in Cancer. Cancer Discov 2017; 7:410-423. [PMID: 28188128 DOI: 10.1158/2159-8290.cd-16-1045] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 02/06/2017] [Accepted: 02/08/2017] [Indexed: 02/06/2023]
Abstract
Recent studies have characterized the extensive somatic alterations that arise during cancer. However, the somatic evolution of a tumor may be significantly affected by inherited polymorphisms carried in the germline. Here, we analyze genomic data for 5,954 tumors to reveal and systematically validate 412 genetic interactions between germline polymorphisms and major somatic events, including tumor formation in specific tissues and alteration of specific cancer genes. Among germline-somatic interactions, we found germline variants in RBFOX1 that increased incidence of SF3B1 somatic mutation by 8-fold via functional alterations in RNA splicing. Similarly, 19p13.3 variants were associated with a 4-fold increased likelihood of somatic mutations in PTEN. In support of this association, we found that PTEN knockdown sensitizes the MTOR pathway to high expression of the 19p13.3 gene GNA11 Finally, we observed that stratifying patients by germline polymorphisms exposed distinct somatic mutation landscapes, implicating new cancer genes. This study creates a validated resource of inherited variants that govern where and how cancer develops, opening avenues for prevention research.Significance: This study systematically identifies germline variants that directly affect tumor evolution, either by dramatically increasing alteration frequency of specific cancer genes or by influencing the site where a tumor develops. Cancer Discovery; 7(4); 410-23. ©2017 AACR.See related commentary by Geeleher and Huang, p. 354This article is highlighted in the In This Issue feature, p. 339.
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Affiliation(s)
- Hannah Carter
- Department of Medicine, Division of Medical Genetics, University of California, San Diego, La Jolla, California. .,Moores Cancer Center, University of California, San Diego, La Jolla, California.,Cancer Cell Map Initiative (CCMI), La Jolla and San Francisco, California.,Institute for Genomic Medicine, University of California, San Diego, La Jolla, California
| | - Rachel Marty
- Bioinformatics Program, University of California, San Diego, La Jolla, California
| | - Matan Hofree
- Department of Computer Science, University of California, San Diego, La Jolla, California
| | - Andrew M Gross
- Bioinformatics Program, University of California, San Diego, La Jolla, California
| | - James Jensen
- Bioinformatics Program, University of California, San Diego, La Jolla, California
| | - Kathleen M Fisch
- Department of Medicine, Division of Medical Genetics, University of California, San Diego, La Jolla, California.,Moores Cancer Center, University of California, San Diego, La Jolla, California.,Cancer Cell Map Initiative (CCMI), La Jolla and San Francisco, California.,Department of Medicine, Center for Computational Biology and Bioinformatics, University of California, San Diego, La Jolla, California
| | - Xingyu Wu
- Moores Cancer Center, University of California, San Diego, La Jolla, California
| | - Christopher DeBoever
- Bioinformatics Program, University of California, San Diego, La Jolla, California
| | - Eric L Van Nostrand
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, California.,Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California
| | - Yan Song
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, California.,Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California
| | - Emily Wheeler
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, California.,Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California
| | - Jason F Kreisberg
- Department of Medicine, Division of Medical Genetics, University of California, San Diego, La Jolla, California.,Cancer Cell Map Initiative (CCMI), La Jolla and San Francisco, California
| | - Scott M Lippman
- Moores Cancer Center, University of California, San Diego, La Jolla, California
| | - Gene W Yeo
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, California.,Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California
| | - J Silvio Gutkind
- Moores Cancer Center, University of California, San Diego, La Jolla, California.,Cancer Cell Map Initiative (CCMI), La Jolla and San Francisco, California
| | - Trey Ideker
- Department of Medicine, Division of Medical Genetics, University of California, San Diego, La Jolla, California.,Moores Cancer Center, University of California, San Diego, La Jolla, California.,Cancer Cell Map Initiative (CCMI), La Jolla and San Francisco, California.,Institute for Genomic Medicine, University of California, San Diego, La Jolla, California.,Bioinformatics Program, University of California, San Diego, La Jolla, California.,Department of Computer Science, University of California, San Diego, La Jolla, California
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9
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Abstract
Enhancer elements function as the logic gates of the genetic regulatory circuitry. One of their most important functions is the integration of extracellular signals with intracellular cell fate information to generate cell type-specific transcriptional responses. Mutations occurring in cancer often misregulate enhancers that normally control the signal-dependent expression of growth-related genes. This misregulation can result from trans-acting mechanisms, such as activation of the transcription factors or epigenetic regulators that control enhancer activity, or can be caused in cis by direct mutations that alter the activity of the enhancer or its target gene specificity. These processes can generate tumour type-specific super-enhancers and establish a 'locked' gene regulatory state that drives the uncontrolled proliferation of cancer cells. Here, we review the role of enhancers in cancer, and their potential as therapeutic targets.
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Affiliation(s)
- Inderpreet Sur
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, and Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Jussi Taipale
- Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, and Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm SE-171 77, Sweden
- Genome-Scale Biology Program, University of Helsinki, Biomedicum, PO Box 63, Helsinki 00014, Finland
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10
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Zhong JH, Zhao Z, Liu J, Yu HL, Zhou JY, Shi R. Association between APE1 Asp148Glu polymorphism and the risk of urinary cancers: a meta-analysis of 18 case-control studies. Onco Targets Ther 2016; 9:1499-510. [PMID: 27042118 PMCID: PMC4801150 DOI: 10.2147/ott.s101456] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background Several observational studies suggested that APE1 Asp148Glu was significantly associated with urinary cancers; however, the results of published studies are inconsistent. Materials and methods The PubMed and EMBASE were searched for case–control studies regarding the association between Asp148Glu and the risk of urinary cancers with a time limit of September 12, 2015. Pooled odds ratios (ORs) and 95% confidence intervals (CIs) were used to assess the strength of the association between Asp148Glu and the risk of developing prostate cancer, kidney cancer, bladder cancer, as well as all urinary cancers combined. Results A total of 18 case–control studies were included in the analysis. Our meta-analysis revealed that the inheritance of at least one APE1 148Glu among Asian men was associated with a 1.26-fold increase in the risk of developing urinary cancers. Meanwhile, APE1 Asp148Glu was significantly associated with the risk of prostate cancer. However, there were no significant relationships between the APE1 SNP (single nucleotide polymorphism) and all urinary cancers combined and bladder cancer and kidney cancer among the men of Caucasian/Asian/African descent or all racial/ethnic groups combined. When stratified by the quality score, no significant association was found in high-quality studies (score ≥7), but a significant increased risk of urinary cancers was observed in lower quality studies (score <7) (dominant model: OR=1.27, 95% CI=1.11–1.45). Conclusion Our meta-analysis suggests that APE1 Asp148Glu was not associated with the risk of urinary cancers but might increase the risk of urinary cancers among Asians. Stratification by cancer type identified a significant association of Asp148Glu with prostate cancer.
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Affiliation(s)
- Jie-Hui Zhong
- Department of Clinical Medicine, The First Clinical Medical College, Southern Medical University, Guangzhou, People's Republic of China; Institute of Genetic Engineering, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
| | - Zhen Zhao
- Department of Urinary Surgery, Southern Medical University, Guangzhou, People's Republic of China
| | - Jie Liu
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Hai-Lang Yu
- Institute of Genetic Engineering, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
| | - Jue-Yu Zhou
- Institute of Genetic Engineering, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
| | - Rong Shi
- Institute of Genetic Engineering, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
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11
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Baker SG. The latent class twin method. Biometrics 2016; 72:827-34. [PMID: 26753781 DOI: 10.1111/biom.12460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Revised: 09/01/2015] [Accepted: 10/01/2015] [Indexed: 01/20/2023]
Abstract
The twin method refers to the use of data from same-sex identical and fraternal twins to estimate the genetic and environmental contributions to a trait or outcome. The standard twin method is the variance component twin method that estimates heritability, the fraction of variance attributed to additive genetic inheritance. The latent class twin method estimates two quantities that are easier to interpret than heritability: the genetic prevalence, which is the fraction of persons in the genetic susceptibility latent class, and the heritability fraction, which is the fraction of persons in the genetic susceptibility latent class with the trait or outcome. We extend the latent class twin method in three important ways. First, we incorporate an additive genetic model to broaden the sensitivity analysis beyond the original autosomal dominant and recessive genetic models. Second, we specify a separate survival model to simplify computations and improve convergence. Third, we show how to easily adjust for covariates by extending the method of propensity scores from a treatment difference to zygosity. Applying the latent class twin method to data on breast cancer among Nordic twins, we estimated a genetic prevalence of 1%, a result with important implications for breast cancer prevention research.
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Affiliation(s)
- Stuart G Baker
- Biometry Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, Maryland 20892-7354, U.S.A..
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12
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Boccellino M, Alaia C, Misso G, Cossu AM, Facchini G, Piscitelli R, Quagliuolo L, Caraglia M. Gene interference strategies as a new tool for the treatment of prostate cancer. Endocrine 2015; 49:588-605. [PMID: 26049369 DOI: 10.1007/s12020-015-0629-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 05/11/2015] [Indexed: 12/14/2022]
Abstract
Prostate cancer (PCa) is one of the most common cancer in men. It affects older men and the incidence increases with age; the median age at diagnosis is 67 years. The diagnosis of PCa is essentially based on three tools: digital rectal exam, serum concentration of prostate specific antigen, and transrectal ultrasound-guided biopsy. Currently, the therapeutic treatments of this cancer are different and range from the prostatectomy to hormonal therapy, to radiation therapy, to immunotherapy, and to chemotherapy. However, additional efforts are required in order to find new weapons for the treatment of metastatic setting of disease. The purpose of this review is to highlight new therapeutic strategies based on gene interference; in fact, numerous siRNA and miRNA in the therapeutic treatment of PCa are reported below.
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Affiliation(s)
- Mariarosaria Boccellino
- Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, Via L. De Crecchio, 7, 80138, Naples, Italy
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13
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Fischer D, Wahlfors T, Mattila H, Oja H, Tammela TLJ, Schleutker J. MiRNA Profiles in Lymphoblastoid Cell Lines of Finnish Prostate Cancer Families. PLoS One 2015; 10:e0127427. [PMID: 26020509 PMCID: PMC4447459 DOI: 10.1371/journal.pone.0127427] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 04/15/2015] [Indexed: 12/31/2022] Open
Abstract
Background Heritable factors are evidently involved in prostate cancer (PrCa) carcinogenesis, but currently, genetic markers are not routinely used in screening or diagnostics of the disease. More precise information is needed for making treatment decisions to distinguish aggressive cases from indolent disease, for which heritable factors could be a useful tool. The genetic makeup of PrCa has only recently begun to be unravelled through large-scale genome-wide association studies (GWAS). The thus far identified Single Nucleotide Polymorphisms (SNPs) explain, however, only a fraction of familial clustering. Moreover, the known risk SNPs are not associated with the clinical outcome of the disease, such as aggressive or metastasised disease, and therefore cannot be used to predict the prognosis. Annotating the SNPs with deep clinical data together with miRNA expression profiles can improve the understanding of the underlying mechanisms of different phenotypes of prostate cancer. Results In this study microRNA (miRNA) profiles were studied as potential biomarkers to predict the disease outcome. The study subjects were from Finnish high risk prostate cancer families. To identify potential biomarkers we combined a novel non-parametrical test with an importance measure provided from a Random Forest classifier. This combination delivered a set of nine miRNAs that was able to separate cases from controls. The detected miRNA expression profiles could predict the development of the disease years before the actual PrCa diagnosis or detect the existence of other cancers in the studied individuals. Furthermore, using an expression Quantitative Trait Loci (eQTL) analysis, regulatory SNPs for miRNA miR-483-3p that were also directly associated with PrCa were found. Conclusion Based on our findings, we suggest that blood-based miRNA expression profiling can be used in the diagnosis and maybe even prognosis of the disease. In the future, miRNA profiling could possibly be used in targeted screening, together with Prostate Specific Antigene (PSA) testing, to identify men with an elevated PrCa risk.
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Affiliation(s)
- Daniel Fischer
- School of Health Sciences, University of Tampere, 33014 Tampere, Finland
| | - Tiina Wahlfors
- BioMediTech, University of Tampere, and Fimlab Laboratories, Tampere, Finland
| | - Henna Mattila
- BioMediTech, University of Tampere, and Fimlab Laboratories, Tampere, Finland
| | - Hannu Oja
- Department of Mathematics and Statistics, University of Turku, 20014 Turku, Finland
| | - Teuvo L. J. Tammela
- Department of Urology, Tampere University Hospital and Medical School, University of Tampere, Tampere, Finland
| | - Johanna Schleutker
- Medical Biochemistry and Genetics, Institute of Biomedicine, University of Turku, Turku, Finland
- * E-mail:
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Aloraifi F, Boland MR, Green AJ, Geraghty JG. Gene analysis techniques and susceptibility gene discovery in non-BRCA1/BRCA2 familial breast cancer. Surg Oncol 2015; 24:100-9. [PMID: 25936246 DOI: 10.1016/j.suronc.2015.04.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 03/11/2015] [Accepted: 04/04/2015] [Indexed: 02/06/2023]
Abstract
Breast cancer is the leading cause of cancer deaths in females worldwide occurring in both hereditary and sporadic forms. Women with inherited pathogenic mutations in the BRCA1 or BRCA2 genes have up to an 85% risk of developing breast cancer in their lifetimes. These patients are candidates for risk-reduction measures such as intensive radiological screening, prophylactic surgery or chemoprevention. However, only about 20% of familial breast cancer cases are attributed to mutations in BRCA1 and BRCA2, while a further 5-10% are attributed to mutations in other rare susceptibility genes such as TP53, STK11, PTEN, ATM and CHEK2. A multitude of genome wide association studies (GWAS) have been conducted confirming low-risk common variants associated with breast cancer in excess of 90 loci, which may contribute to a further 23% of the heritability. We currently find ourselves in "the next generation", with technologies offering deep sequencing at a fraction of the cost. Starting off primarily in a research setting, multi-gene panel testing is now utilized in the clinic to sequence multiple predisposing genes simultaneously (otherwise known as multi-gene panel testing). In this review, we focus on the hereditary breast cancer discoveries, techniques and the challenges we face in this complex disease, especially in the light of the vast amount of data we now have at hand. It has been 20 years since the first breast cancer susceptibility gene has been discovered and there has been substantial progress in unraveling the genetic component of the disease. However, hereditary breast cancer remains a challenging topic subject to common debate.
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Affiliation(s)
- Fatima Aloraifi
- Smurfit Institute of Genetics, Trinity College, Dublin 2, Ireland.
| | - Michael R Boland
- Department of Breast Surgery, St Vincent's University Hospital, Dublin 4, Ireland
| | | | - James G Geraghty
- Department of Breast Surgery, St Vincent's University Hospital, Dublin 4, Ireland
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15
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Cremers RG, Galesloot TE, Aben KK, van Oort IM, Vasen HF, Vermeulen SH, Kiemeney LA. Known susceptibility SNPs for sporadic prostate cancer show a similar association with "hereditary" prostate cancer. Prostate 2015; 75:474-83. [PMID: 25560306 PMCID: PMC6680338 DOI: 10.1002/pros.22933] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 10/23/2014] [Indexed: 11/25/2022]
Abstract
BACKGROUND More than 70 single nucleotide polymorphisms (SNPs) have been reported to be associated with prostate cancer (PC) risk; these were mainly identified in the general population with predominantly sporadic PC (SPC). Previous studies have suggested similar associations between a selection of these SNPs and hereditary PC (HPC). Our aim was to evaluate the effect of all known PC risk SNPs and their discriminative value for SPC and HPC. METHODS Seventy-four PC susceptibility SNPs (reported in literature up to June 2014) were genotyped in a population-based series of 620 SPC patients, 312 HPC patients from the national Dutch registry and 1819 population-based referents. Association analyses were performed using logistic regression, focusing on directional consistency of the odds ratios (ORs) with those in the original reports, that is, whether the OR was in the same direction as in the original report. Discriminative performance was evaluated by a genetic risk score used in logistic regression and receiver operating characteristic (ROC) curve analyses. RESULTS Directional consistency was seen for 62 SNPs in SPC and 64 SNPs in HPC, 56 of which overlapped. ORs were mostly higher for HPC with 22 ORs >1.25 versus 5 for SPC. Discriminative performance was better for HPC with an area under the ROC curve of 0.73 versus 0.64 for SPC. CONCLUSIONS A large overlap was found for the associations between low-penetrance susceptibility SNPs and SPC and HPC, suggesting a similarity in genetic etiology. This warrants a reconsideration of "HPC" and a restrictive policy toward prostate-specific antigen testing in men with a positive family history. Genetic risk scores might be used for PC risk stratification on the population level.
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Affiliation(s)
- Ruben G. Cremers
- Department for Health EvidenceRadboud university medical centerNijmegenThe Netherlands
- Department of UrologyRadboud university medical centerNijmegenThe Netherlands
- The Netherlands Foundation for the Detection of Hereditary TumoursLeidenThe Netherlands
| | - Tessel E. Galesloot
- Department for Health EvidenceRadboud university medical centerNijmegenThe Netherlands
| | - Katja K. Aben
- Department for Health EvidenceRadboud university medical centerNijmegenThe Netherlands
- Comprehensive Cancer Centre the NetherlandsUtrechtThe Netherlands
| | - Inge M. van Oort
- Department of UrologyRadboud university medical centerNijmegenThe Netherlands
| | - Hans F. Vasen
- The Netherlands Foundation for the Detection of Hereditary TumoursLeidenThe Netherlands
| | - Sita H. Vermeulen
- Department for Health EvidenceRadboud university medical centerNijmegenThe Netherlands
| | - Lambertus A. Kiemeney
- Department for Health EvidenceRadboud university medical centerNijmegenThe Netherlands
- Department of UrologyRadboud university medical centerNijmegenThe Netherlands
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16
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Fachal L, Dunning AM. From candidate gene studies to GWAS and post-GWAS analyses in breast cancer. Curr Opin Genet Dev 2015; 30:32-41. [PMID: 25727315 DOI: 10.1016/j.gde.2015.01.004] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 12/16/2014] [Accepted: 01/21/2015] [Indexed: 12/31/2022]
Abstract
There are now more than 90 established breast cancer risk loci, with 57 new ones, revealed through genome-wide-association studies (GWAS) during the last two years. Established high, moderate and low penetrance genetic variants currently explain ∼49% of familial breast cancer risk. GWAS-discovered variants account for 14%, and it is estimated that another 1000 yet-to-be-discovered loci could contribute an additional ∼14% of familial risk. Polygenic risk scores can already be used to stratify breast cancer risk in the female population and could improve the targeting of mammographic screening programmes, which are at present largely based on age-specific risks. Fine-scale mapping and functional analyses are revealing candidate causal variants and the molecular mechanisms by which GWAS-hits may act. Better-powered GWAS and genome-wide sequencing projects are likely to continue identifying new breast cancer causal variants.
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Affiliation(s)
- Laura Fachal
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK; Genomic Medicine Group, CIBERER, University of Santiago de Compostela, 15706 Santiago de Compostela, Spain
| | - Alison M Dunning
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge CB1 8RN, UK.
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Abstract
Recent advances in whole-genome technologies have supplied the field of cancer research with an overwhelming amount of molecular data. Improvements in massively parallel sequencing approaches have led to logarithmic decreases in costs, and so these methods are becoming almost commonplace in the analysis of clinical trials and other cohorts of interest. Furthermore, whole-transcriptome quantification by RNA sequencing is quickly replacing microarrays. However, older chip-based methodologies such as comparative genomic hybridization and single-nucleotide polymorphism arrays have benefited from this technological explosion and are now so accessible that they can be employed in increasingly larger cohorts of patients. The study of breast cancer lends itself particularly well to these technologies. It is the most commonly diagnosed neoplasm in women, giving rise to nearly 230,000 new cases each year. Many patients are given a diagnosis of early-stage disease, for which surgery is the standard of care. These attributes result in excellent availability of tissues for whole-genome/transcriptome analysis. The Cancer Genome Atlas project has generated comprehensive catalogs of publically available genomic breast cancer data. In addition, other studies employing the power of genomic technologies in medium to large cohorts were recently published. These data are now publically available for the generation of novel hypotheses. However, these studies differed in the methods, patient cohorts, and analytical techniques employed and represent complementary snapshots of the molecular underpinnings of breast cancer. Here, we will discuss the convergences and divergences of these reports as well as the scientific and clinical implications of their findings.
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18
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Hale V, Weischer M, Park JY. CHEK2 (∗) 1100delC Mutation and Risk of Prostate Cancer. Prostate Cancer 2014; 2014:294575. [PMID: 25431674 PMCID: PMC4241328 DOI: 10.1155/2014/294575] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 10/12/2014] [Indexed: 01/20/2023] Open
Abstract
Although the causes of prostate cancer are largely unknown, previous studies support the role of genetic factors in the development of prostate cancer. CHEK2 plays a critical role in DNA replication by responding to double-stranded breaks. In this review, we provide an overview of the current knowledge of the role of a genetic variant, 1100delC, of CHEK2 on prostate cancer risk and discuss the implication for potential translation of this knowledge into clinical practice. Currently, twelve articles that discussed CHEK2 (∗)1100delC and its association with prostate cancer were identified. Of the twelve prostate cancer studies, five studies had independent data to draw conclusive evidence from. The pooled results of OR and 95% CI were 1.98 (1.23-3.18) for unselected cases and 3.39 (1.78-6.47) for familial cases, indicating that CHEK2 (∗)1100delC mutation is associated with increased risk of prostate cancer. Screening for CHEK2(∗)1100delC should be considered in men with a familial history of prostate cancer.
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Affiliation(s)
- Victoria Hale
- Department of Cancer Epidemiology, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA
| | - Maren Weischer
- Department of Clinical Biochemistry, Herlev Hospital, 2730 Herlev, Denmark
| | - Jong Y. Park
- Department of Cancer Epidemiology, Moffitt Cancer Center, 12902 Magnolia Drive, Tampa, FL 33612, USA
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19
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Abstract
For the past 30 years, improvements in the survival of patients with osteosarcoma have been mostly incremental. Despite evidence of genomic instability and a high frequency of chromothripsis and kataegis, osteosarcomas carry few recurrent targetable mutations, and trials of targeted agents have been generally disappointing. Bone has a highly specialized immune environment and many immune signalling pathways are important in bone homeostasis. The success of the innate immune stimulant mifamurtide in the adjuvant treatment of non-metastatic osteosarcoma suggests that newer immune-based treatments, such as immune checkpoint inhibitors, may substantially improve disease outcome.
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Affiliation(s)
- Maya Kansara
- 1] Research Division, Peter MacCallum Cancer Centre, Melbourne, 3002, Victoria, Australia. [2] Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, 3010, Victoria, Australia
| | - Michele W Teng
- 1] Immunology in Cancer and Infection Laboratory and Cancer Immunoregulation and Immunotherapy Laboratory, QIMR Berghofer Medical Research Institute, Herston, 4006, Queensland, Australia. [2] School of Medicine, University of Queensland, Herston, 4006, Queensland, Australia
| | - Mark J Smyth
- 1] Immunology in Cancer and Infection Laboratory and Cancer Immunoregulation and Immunotherapy Laboratory, QIMR Berghofer Medical Research Institute, Herston, 4006, Queensland, Australia. [2] School of Medicine, University of Queensland, Herston, 4006, Queensland, Australia
| | - David M Thomas
- 1] Research Division, Peter MacCallum Cancer Centre, Melbourne, 3002, Victoria, Australia. [2] Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, 3010, Victoria, Australia. [3] The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, 2010, New South Wales, Australia
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20
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Cerebellar degeneration-related autoantigen 1 (CDR1) gene expression in prostate cancer cell lines. Int J Biol Markers 2014; 29:e288-90. [PMID: 24366849 DOI: 10.5301/jbm.5000062] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/05/2013] [Indexed: 01/02/2023]
Abstract
Prostate cancer (PCa) is the most frequent cancer among men in many developing countries, and the second leading cause of cancer-related death in men. A genetic component has been implicated in PCa onset and development. The cerebellar degeneration-related autoantigen 1 (CDR1) gene, mapping in Xq26-q27.2, is expressed in cerebrum, cerebellum, heart, lung, liver, and kidney. In addition, CDR1 expression has been detected in neuroblastoma, renal carcinoma cell lines, and other cancer cell lines. In this study, we investigated the expression of the CDR1 gene in the LNCaP and PC-3 PCa cell lines, and in the PNT1A normal prostate cell line. CDR1 mRNA expression was evaluated by qRT-PCR. We found that the CDR1 gene was overexpressed in the LNCaP and PC-3 PCa cell lines as compared with the PNT1A normal prostate cell line. These data suggest that CDR1 could be a new biomarker for PCa identification.
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21
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Pujana MA. Integrating germline and somatic data towards a personalized cancer medicine. Trends Mol Med 2014; 20:413-5. [DOI: 10.1016/j.molmed.2014.05.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 05/10/2014] [Accepted: 05/14/2014] [Indexed: 12/27/2022]
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22
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Demichelis F, Stanford JL. Genetic predisposition to prostate cancer: Update and future perspectives. Urol Oncol 2014; 33:75-84. [PMID: 24996773 DOI: 10.1016/j.urolonc.2014.04.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 04/27/2014] [Accepted: 04/28/2014] [Indexed: 02/08/2023]
Abstract
OBJECTIVE Prostate cancer is the second most frequent cancer in men worldwide and kills over 250,000 men worldwide every year. Prostate cancer is a heterogeneous disease at the clinical and the molecular level. The Scandinavian Twin Registry Study demonstrated that in contrast to most malignancies where environment was the overriding influence, heritable factors account for more than fifty percent of prostate cancers. METHODS AND MATERIALS We review the literature on prostate cancer risk variants (rare and common) including SNPs and Copy Number Variants (CNVs) and discuss the potential implications of significant variants for prostate cancer patient care. RESULTS The search for prostate cancer susceptibility genes has included both family-based studies and case-control studies utilizing a variety of approaches from array-based to sequencing-based studies. A major challenge is to identify genetic variants associated with more aggressive, potentially lethal prostate cancer and to understand their role in the progression of the disease. CONCLUSION Future risk models useful in the clinical setting will likely incorporate several risk loci rather than single variants and may be dependent on an individual patient's ethnic background.
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Affiliation(s)
- Francesca Demichelis
- Centre for Integrative Biology, University of Trento, Trento, Italy; Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, NY; Institute for Precision Medicine, Weill Medical College of Cornell University and New York Presbyterian Hospital, New York, NY.
| | - Janet L Stanford
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA; Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA
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23
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Nagel ZD, Chaim IA, Samson LD. Inter-individual variation in DNA repair capacity: a need for multi-pathway functional assays to promote translational DNA repair research. DNA Repair (Amst) 2014; 19:199-213. [PMID: 24780560 DOI: 10.1016/j.dnarep.2014.03.009] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Why does a constant barrage of DNA damage lead to disease in some individuals, while others remain healthy? This article surveys current work addressing the implications of inter-individual variation in DNA repair capacity for human health, and discusses the status of DNA repair assays as potential clinical tools for personalized prevention or treatment of disease. In particular, we highlight research showing that there are significant inter-individual variations in DNA repair capacity (DRC), and that measuring these differences provides important biological insight regarding disease susceptibility and cancer treatment efficacy. We emphasize work showing that it is important to measure repair capacity in multiple pathways, and that functional assays are required to fill a gap left by genome wide association studies, global gene expression and proteomics. Finally, we discuss research that will be needed to overcome barriers that currently limit the use of DNA repair assays in the clinic.
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Affiliation(s)
- Zachary D Nagel
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Isaac A Chaim
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Leona D Samson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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24
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Wu JH, Yang K, Ma HS, Xu Y. Association of endothelia nitric oxide synthase gene rs1799983 polymorphism with susceptibility to prostate cancer: a meta-analysis. Tumour Biol 2014; 35:7057-62. [DOI: 10.1007/s13277-014-1870-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 03/18/2014] [Indexed: 12/16/2022] Open
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25
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Realizing the promise of cancer predisposition genes. Nature 2014; 505:302-8. [PMID: 24429628 DOI: 10.1038/nature12981] [Citation(s) in RCA: 394] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 11/21/2013] [Indexed: 12/14/2022]
Abstract
Genes in which germline mutations confer highly or moderately increased risks of cancer are called cancer predisposition genes. More than 100 of these genes have been identified, providing important scientific insights in many areas, particularly the mechanisms of cancer causation. Moreover, clinical utilization of cancer predisposition genes has had a substantial impact on diagnosis, optimized management and prevention of cancer. The recent transformative advances in DNA sequencing hold the promise of many more cancer predisposition gene discoveries, and greater and broader clinical applications. However, there is also considerable potential for incorrect inferences and inappropriate clinical applications. Realizing the promise of cancer predisposition genes for science and medicine will thus require careful navigation.
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Imaging and Markers as Novel Diagnostic Tools in Detecting Insignificant Prostate Cancer: A Critical Overview. INTERNATIONAL SCHOLARLY RESEARCH NOTICES 2014; 2014:243080. [PMID: 27351008 PMCID: PMC4897503 DOI: 10.1155/2014/243080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 05/19/2014] [Indexed: 11/22/2022]
Abstract
Recent therapeutic advances for managing low-risk prostate cancer include the active surveillance and focal treatment. However, locating a tumor and detecting its volume by adequate sampling is still problematic. Development of predictive biomarkers guiding individual therapeutic choices remains an ongoing challenge. At the same time, prostate cancer magnetic resonance imaging is gaining increasing importance for prostate diagnostics. The high morphological resolution of T2-weighted imaging and functional MRI methods may increase the specificity and sensitivity of diagnostics. Also, recent studies founded an ability of novel biomarkers to identify clinically insignificant prostate cancer, risk of progression, and association with poor differentiation and, therefore, with clinical significance. Probably, the above mentioned methods would improve tumor characterization in terms of its volume, aggressiveness, and focality. In this review, we attempted to evaluate the applications of novel imaging techniques and biomarkers in assessing the significance of the prostate cancer.
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Labbé DP, Nowak DG, Deblois G, Lessard L, Giguère V, Trotman LC, Tremblay ML. Prostate cancer genetic-susceptibility locus on chromosome 20q13 is amplified and coupled to androgen receptor-regulation in metastatic tumors. Mol Cancer Res 2013; 12:184-9. [PMID: 24379448 DOI: 10.1158/1541-7786.mcr-13-0477] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
UNLABELLED The 20q13 chromosomal region has been previously identified as the hereditary prostate cancer genetic-susceptibility locus on chromosome 20 (HPC20). In this study, the 20q13 region was shown to be frequently co-amplified with the androgen receptor (AR) in metastatic prostate cancer. Furthermore, the AR signaling axis, which plays an essential role in the pathogenesis of prostate cancer, was demonstrated to be central to the regulation of the 20q13 common amplified region (CAR). High-resolution mapping analyses revealed hot spots of AR recruitment to response elements in the vicinity of most genes located on the 20q13 CAR. Moreover, amplification of AR significantly co-occurred with CAR amplification on 20q13 and it was confirmed that the majority of AR-bound genes on the 20q13 CAR were indeed regulated by androgens. These data reveal that amplification of the AR is tightly linked to amplification of the AR-regulated CAR region on 20q13. These results suggest that the cross-talk between gene amplification and gene transcription is an important step in the development of castration-resistant metastatic disease. IMPLICATIONS These novel results are a noteworthy example of the cross-talk between gene amplification and gene transcription in the development of advanced prostate cancer.
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Affiliation(s)
- David P Labbé
- Goodman Cancer Research Centre, McGill University, 1160 Pine Avenue, Room 617, Montréal, QC, Canada H3A 1A3.
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28
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Monteiro ANA, Freedman ML. Lessons from postgenome-wide association studies: functional analysis of cancer predisposition loci. J Intern Med 2013; 274:414-24. [PMID: 24127939 PMCID: PMC3801430 DOI: 10.1111/joim.12085] [Citation(s) in RCA: 22] [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] [Indexed: 11/29/2022]
Abstract
In the last few years, genome-wide association studies (GWASs) have identified hundreds of predisposition loci for several types of human cancers. Recent progress has been made in determining the underlying mechanisms through which different single-nucleotide polymorphisms (SNPs) affect predisposition to cancer. Although there has been much debate about the clinical utility of GWASs, less attention has been paid to how GWASs and post-GWASs functional analysis have contributed to understanding the aetiology of cancer. Most common variants associated with cancer risk are localized in nonprotein-coding regions highlighting transcriptional regulation as a common theme in the mechanism of cancer predisposition. Here, we outline strategies to functionally dissect predisposition loci and discuss their limitations as well as challenges for future studies.
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Affiliation(s)
- A N A Monteiro
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
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29
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Antognelli C, Mezzasoma L, Mearini E, Talesa VN. Glyoxalase 1-419C>A variant is associated with oxidative stress: implications in prostate cancer progression. PLoS One 2013; 8:e74014. [PMID: 24040147 PMCID: PMC3769356 DOI: 10.1371/journal.pone.0074014] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 07/26/2013] [Indexed: 11/19/2022] Open
Abstract
Glyoxalase 1 is a scavenging enzyme of potent precursors in reactive oxygen species formation and is involved in the occurrence and progression of human malignancies. Glyoxalase I A111E polymorphism has been suggested to influence its enzymatic activity. The present study was aimed at investigating the association of this polymorphism with oxidative stress and its implications in prostate cancer progression or survival. The polymorphism was genotyped in human differently aggressive and invasive prostate cancer cell lines, in 571 prostate cancer or 588 benign prostatic hyperplasia patients, and 580 healthy subjects by Polymerase Chain Reaction/Restriction Fragment Length Polymorphism. Glyoxalase 1 activity, the pro-oxidant Glyoxalase 1-related Argpyrimidine and oxidative stress biomarkers were evaluated by biochemical analyses. Glyoxalase 1 polymorphism was associated with an increase in Glyoxalase 1-related pro-oxidant Argpyrimidine and oxidative stress levels and cancer progression. The mutant A allele conferred a modest risk of prostate cancer, a marked risk of prostate cancer progression and a lower survival time, compared to the wild C allele. The results of our exploratory study point out a significant role for Glyoxalase 1 in prostate cancer progression, providing an additional candidate for risk assessment in prostate cancer patients and an independent prognostic factor for survival. Finally, we provided evidence of the biological plausibility of Glyoxalase 1 polymorphism, either alone or in combination with other ones, all related to oxidative stress control that represents a key event in PCa development and progression.
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Affiliation(s)
- Cinzia Antognelli
- Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy
| | - Letizia Mezzasoma
- Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy
| | - Ettore Mearini
- Department of Medical-Surgical Specialties and Public Health, University of Perugia, Perugia, Italy
| | - Vincenzo Nicola Talesa
- Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy
- * E-mail:
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Birmingham WC, Agarwal N, Kohlmann W, Aspinwall LG, Wang M, Bishoff J, Dechet C, Kinney AY. Patient and provider attitudes toward genomic testing for prostate cancer susceptibility: a mixed method study. BMC Health Serv Res 2013; 13:279. [PMID: 23870420 PMCID: PMC3750463 DOI: 10.1186/1472-6963-13-279] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 06/27/2013] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The strong association between family history and prostate cancer (PCa) suggests a significant genetic contribution, yet specific highly penetrant PCa susceptibility genes have not been identified. Certain single-nucleotide-polymorphisms have been found to correlate with PCa risk; however uncertainty remains regarding their clinical utility and how to best incorporate this information into clinical decision-making. Genetic testing is available directly to consumers and both patients and healthcare providers are becoming more aware of this technology. Purchasing online allows patients to bypass their healthcare provider yet patients may have difficulty interpreting test results and providers may be called upon to interpret results. Determining optimal ways to educate both patients and providers, and strategies for appropriately incorporating this information into clinical decision-making are needed. METHODS A mixed-method study was conducted in Utah between October 2011 and December 2011. Eleven focus group discussions were held and surveys were administered to 23 first-degree relatives of PCa patients living in Utah and 24 primary-care physicians and urologists practicing in Utah to present specific information about these assessments and determine knowledge and attitudes regarding health implications of using these assessments. RESULTS Data was independently coded by two researchers (relative Kappa = .88; provider Kappa = .77) and analyzed using a grounded theory approach. Results indicated differences in attitudes and behavioral intentions between patient and provider. Despite the test's limitations relatives indicated interest in genetic testing (52%) while most providers indicated they would not recommend the test for their patients (79%). Relatives expected providers to interpret genetic test results and use results to provide personalized healthcare recommendations while the majority of providers did not think the information would be useful in patient care (92%) and indicated low-levels of genetic self-efficacy. CONCLUSIONS Although similarities exist, discordance between provider and patient attitudes may influence the effective translation of novel genomic tests into clinical practice suggesting both patient and provider perceptions and expectations be considered in development of clinical decision-support tools.
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Affiliation(s)
- Wendy C Birmingham
- Department of Psychology, Brigham Young University, 1054 SWKT, Provo, UT 84602, USA
| | - Neeraj Agarwal
- Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope, Salt Lake City, UT 84112, USA
- Department of Internal Medicine, University of Utah, 30 North 1900 East, Room 4C104, Salt Lake City, UT 84132, USA
| | - Wendy Kohlmann
- Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope, Salt Lake City, UT 84112, USA
| | - Lisa G Aspinwall
- Department of Psychology, University of Utah, 380 South 1530 East, BEHS 502, Salt Lake City, UT 84112, USA
| | - Mary Wang
- Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope, Salt Lake City, UT 84112, USA
| | - Jay Bishoff
- Intermountain Health Care, 5169 Cottonwood St Ste 420, Murray, UT 84107, USA
| | - Christopher Dechet
- Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope, Salt Lake City, UT 84112, USA
- Department of Urology, University of Utah, 30 North 1900 East, Salt Lake City, 84132 UT, USA
| | - Anita Y Kinney
- Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope, Salt Lake City, UT 84112, USA
- Department of Internal Medicine, University of Utah, 30 North 1900 East, Room 4C104, Salt Lake City, UT 84132, USA
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Southey MC. The Role of New Sequencing Technology in Identifying Rare Mutations in New Susceptibility Genes for Cancer. CURRENT GENETIC MEDICINE REPORTS 2013. [DOI: 10.1007/s40142-013-0021-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Lynch H, Wen H, Kim YC, Snyder C, Kinarsky Y, Chen PX, Xiao F, Goldgar D, Cowan KH, Wang SM. Can unknown predisposition in familial breast cancer be family-specific? Breast J 2013; 19:520-8. [PMID: 23800003 DOI: 10.1111/tbj.12145] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Genetic predisposition plays a key role in the development of familial breast cancer. In spite of strong familial clustering of the disease and extensive efforts made during the past decade; however, progress has been slow in identifying genetic predisposition for the majority of familial breast cancer families. The question arises therefore as to whether current approaches are adequate in identifying the unknown genetic predisposition. We analyzed eight members of a BRCA1-, BRCA2-, p53-, and PTEN-negative breast cancer family, of which five had breast cancer, one is an obligate gene carrier, and two were unaffected. We sequenced the entire coding region of the genome for each member using exome sequencing to identify nonsynonymous variants. We identified 55 nonsynonymous germline variants affecting 49 genes in multiple members of the family, of which 22 are predicted to have damaging effects. We validated 20 of the 22 selected variants in the family by Sanger sequencing. Two variants in KAT6B, an acetal transferase gene, were identified in six family members of which five were affected with breast cancer and one is the unaffected obligate carrier. We further examined the presence of the identified variants in a cohort of 40 additional breast cancer cases from 22 familial breast cancer families, but none of the 22 variants was detected in these cases. Sequencing the entire coding exons in KAT6B detects no variants in these cases. Our results show that genetic predisposition for familial breast cancer can be rich in an affected family, but the predisposition can be family-specific. As such, it will be difficult to detect them by applying population-based approach. Our study supports the concept that focusing on each affected family will be required to determine the genetic predisposition for many familial breast cancer families whose genetic dispositions remain unknown.
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Affiliation(s)
- Henry Lynch
- Hereditary Cancer Center, Department of Preventive Medicine, Creighton University, Omaha, Nebraska
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Lynch SM, Rebbeck TR. Bridging the gap between biologic, individual, and macroenvironmental factors in cancer: a multilevel approach. Cancer Epidemiol Biomarkers Prev 2013; 22:485-95. [PMID: 23462925 DOI: 10.1158/1055-9965.epi-13-0010] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
To address the complex nature of cancer occurrence and outcomes, approaches have been developed to simultaneously assess the role of two or more etiologic agents within hierarchical levels including the: (i) macroenvironment level (e.g., health care policy, neighborhood, or family structure); (ii) individual level (e.g., behaviors, carcinogenic exposures, socioeconomic factors, and psychologic responses); and (iii) biologic level (e.g., cellular biomarkers and inherited susceptibility variants). Prior multilevel approaches tend to focus on social and environmental hypotheses, and are thus limited in their ability to integrate biologic factors into a multilevel framework. This limited integration may be related to the limited translation of research findings into the clinic. We propose a "Multi-level Biologic and Social Integrative Construct" (MBASIC) to integrate macroenvironment and individual factors with biology. The goal of this framework is to help researchers identify relationships among factors that may be involved in the multifactorial, complex nature of cancer etiology, to aid in appropriate study design, to guide the development of statistical or mechanistic models to study these relationships, and to position the results of these studies for improved intervention, translation, and implementation. MBASIC allows researchers from diverse fields to develop hypotheses of interest under a common conceptual framework, to guide transdisciplinary collaborations, and to optimize the value of multilevel studies for clinical and public health activities.
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Affiliation(s)
- Shannon M Lynch
- Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, 243 Blockley Hall, 423 Guardian Drive, Philadelphia, PA 19104, USA.
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Kamm L, Bogdanov D, Laur S, Vilo J. A new way to protect privacy in large-scale genome-wide association studies. ACTA ACUST UNITED AC 2013; 29:886-93. [PMID: 23413435 PMCID: PMC3605601 DOI: 10.1093/bioinformatics/btt066] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Motivation: Increased availability of various genotyping techniques has initiated a race for finding genetic markers that can be used in diagnostics and personalized medicine. Although many genetic risk factors are known, key causes of common diseases with complex heritage patterns are still unknown. Identification of such complex traits requires a targeted study over a large collection of data. Ideally, such studies bring together data from many biobanks. However, data aggregation on such a large scale raises many privacy issues. Results: We show how to conduct such studies without violating privacy of individual donors and without leaking the data to third parties. The presented solution has provable security guarantees. Contact:jaak.vilo@ut.ee Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Liina Kamm
- Institute of Computer Science, University of Tartu, Liivi 2, Tartu 50409, Estonia
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Taherian N, Hamel N, Bégin LR, Bismar TA, Goldgar DE, Feng BJ, Foulkes WD. Familial prostate cancer: the damage done and lessons learnt. Nat Rev Urol 2013; 10:116-22. [PMID: 23318356 DOI: 10.1038/nrurol.2012.257] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
BACKGROUND A 51-year-old French Canadian man presented to his family physician owing to an extensive family history of prostate cancer in five brothers, his father and two paternal uncles. His serum PSA level was 4.9 ng/ml and a six-core biopsy revealed the presence of a prostate adenocarcinoma with a Gleason score of 7 (3+4). He was treated with radical prostatectomy. Repeat PSA tests revealed a gradual rise in PSA levels despite androgen deprivation therapy with bicalutamide and goserelin over the course of 3 years. Genetic evaluation was undertaken in view of his personal and family history. The proband died at the age of 58 years of widespread metastasis. INVESTIGATIONS PSA testing, six-core biopsy, genetic counselling and mutation analysis for French Canadian founder mutations in the BRCA1 and BRCA2 genes, histopathological review of tumour tissue from family members, examination of loss of heterozygosity at the BRCA2 gene locus, immunohistochemistry to determine the expression of the ERG nuclear oncoprotein in prostate tumours, genotyping with eight selected risk-associated single nucleotide polymorphisms, Doppler ultrasonography of the leg, CT of the abdomen and pelvis with intravenous and oral contrast, chest CT with intravenous contrast for the assessment of metastatic prostate cancer, genetic testing for the G84E variant in the HOXB13 gene. DIAGNOSIS Early-onset and aggressive prostate cancer associated with a nonsense French Canadian BRCA2 founder mutation, c.5857G>T (p.Glu1953(*)). MANAGEMENT Radical prostatectomy, hormone therapy with bicalutamide and goserelin, palliative chemotherapy initially with docetaxel plus prednisone then with mitoxantrone plus prednisone, as well as genetic counselling and testing for the proband and his family members.
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Affiliation(s)
- Nassim Taherian
- Department of Medical Genetics, Research Institute of McGill University Health Centre, Montreal, QC H3G 1A4, Canada
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Laitinen VH, Wahlfors T, Saaristo L, Rantapero T, Pelttari LM, Kilpivaara O, Laasanen SL, Kallioniemi A, Nevanlinna H, Aaltonen L, Vessella RL, Auvinen A, Visakorpi T, Tammela TLJ, Schleutker J. HOXB13 G84E mutation in Finland: population-based analysis of prostate, breast, and colorectal cancer risk. Cancer Epidemiol Biomarkers Prev 2013; 22:452-60. [PMID: 23292082 DOI: 10.1158/1055-9965.epi-12-1000-t] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND A recently identified germline mutation G84E in HOXB13 was shown to increase the risk of prostate cancer. In a family-based analysis by The International Consortium for Prostate Cancer Genetics (ICPCG), the G84E mutation was most prevalent in families from the Nordic countries of Finland (22.4%) and Sweden (8.2%). METHODS To further investigate the importance of G84E in the Finns, we determined its frequency in more than 4,000 prostate cancer cases and 5,000 controls. In addition, 986 breast cancer and 442 colorectal cancer (CRC) cases were studied. Genotyping was conducted using TaqMan, MassARRAY iPLEX, and sequencing. Statistical analyses were conducted using Fisher exact test, and overall survival was analyzed using Cox modeling. RESULTS The frequency of the G84E mutation was significantly higher among patients with prostate cancer and highest among patients with a family history of the disease, hereditary prostate cancer [8.4% vs. 1.0% in controls; OR 8.8; 95% confidence interval (CI), 4.9-15.7]. The mutation contributed significantly to younger age (≤55 years) at onset and high prostate-specific antigen (PSA; ≥20 ng/mL) at diagnosis. An association with increased prostate cancer risk in patients with prior benign prostate hyperplasia (BPH) diagnosis was also revealed. No statistically significant evidence for a contribution in CRC risk was detected, but a suggestive role for the mutation was observed in familial BRCA1/2-negative breast cancer. CONCLUSIONS These findings confirm an increased cancer risk associated with the G84E mutation in the Finnish population, particularly for early-onset prostate cancer and cases with substantially elevated PSA. IMPACT This study confirms the overall importance of the HOXB13 G84E mutation in prostate cancer susceptibility.
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Affiliation(s)
- Virpi H Laitinen
- Johanna Schleutker, Medical Biochemistry and Genetics, Institute of Biomedicine, Kiinamyllynkatu 10, FI-20014 University of Turku, Finland.
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Abstract
Screening for prostate cancer is a controversial topic within the field of urology. The US Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial did not demonstrate any difference in prostate-cancer-related mortality rates between men screened annually rather than on an 'opportunistic' basis. However, in the world's largest trial to date--the European Randomised Study of Screening for Prostate Cancer--screening every 2-4 years was associated with a 21% reduction in prostate-cancer-related mortality rate after 11 years. Citing the uncertain ratio between potential harm and potential benefit, the US Preventive Services Task Force recently recommended against serum PSA screening. Although this ratio has yet to be elucidated, PSA testing--and early tumour detection--is undoubtedly beneficial for some individuals. Instead of adopting a 'one size fits all' approach, physicians are likely to perform personalized risk assessment to minimize the risk of negative consequences, such as anxiety, unnecessary testing and biopsies, overdiagnosis, and overtreatment. The PSA test needs to be combined with other predictive factors or be used in a more thoughtful way to identify men at risk of symptomatic or life-threatening cancer, without overdiagnosing indolent disease. A risk-adapted approach is needed, whereby PSA testing is tailored to individual risk.
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Jiang Y, Qin Z, Hu Z, Guan X, Wang Y, He Y, Xue J, Liu X, Chen J, Dai J, Jin G, Ma H, Wang S, Shen H. Genetic variation in a hsa-let-7 binding site in RAD52 is associated with breast cancer susceptibility. Carcinogenesis 2012. [PMID: 23188672 DOI: 10.1093/carcin/bgs373] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Genetic variants may influence miRNA-mRNA interaction through modulate binding affinity, creating or destroying miRNA-binding sites. Twenty-four single nucleotide polymorphisms (SNPs) that were predicted to affect the binding affinity of breast cancer-related miRNAs to 3'-untranslated regions (UTR) of known genes were genotyped in 878 breast cancer cases and 900 controls in Chinese women. Three promising SNPs (rs10494836, rs10857748 and rs7963551) were further validated in additional 914 breast cancer cases and 967 controls. The variant allele (C) of rs7963551 at 3'-UTR of RAD52 showed a consistently reduced breast cancer risk in two stages with a combined odds ratio (OR) of 0.84 [95% confidence interval (CI) = 0.75-0.95], which was more prominent among women with early age at first live birth (OR = 0.71, 95% CI = 0.58-0.87). A significant interaction was observed between rs7963551 and age at first live birth on breast cancer risk (P for interaction = 0.04). Luciferase activity assay showed a higher expression level for rs7963551 C allele as compared with A allele (P = 5.19 × 10(-3) for MCF-7 cell lines), which might be due to a reduced inhibition from a weakened binding capacity of miRNA to 3'-UTR of RAD52 harboring C allele. These findings indicate that rs7963551 located at hsa-let-7 binding site may alter expression of RAD52 through modulating miRNA-mRNA interaction and contribute to the development of breast cancer in Chinese women.
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Affiliation(s)
- Yue Jiang
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing 210029, China
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Pelttari LM, Nurminen R, Gylfe A, Aaltonen LA, Schleutker J, Nevanlinna H. Screening of Finnish RAD51C founder mutations in prostate and colorectal cancer patients. BMC Cancer 2012; 12:552. [PMID: 23176254 PMCID: PMC3522023 DOI: 10.1186/1471-2407-12-552] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 11/13/2012] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Rare, heterozygous germline mutations in the RAD51C gene have been found in breast and ovarian cancer families. In the Finnish population, we have identified two founder mutations in RAD51C that increase the risk of ovarian cancer but not breast cancer in the absence of ovarian cancer. Risk for other cancers has not been studied. METHODS To study the role of RAD51C mutations in other common cancer types, we genotyped the Finnish RAD51C founder mutations c.837 + 1G > A and c.93delG in 1083 prostate cancer patients and 802 colorectal cancer patients using TaqMan Real-Time PCR. RESULTS No RAD51C mutations c.837 + 1G > A or c.93delG were detected among the prostate or colorectal cancer patients. CONCLUSIONS The results suggest that the RAD51C mutations do not predispose to prostate or colorectal cancer.
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Affiliation(s)
- Liisa M Pelttari
- Departments of Obstetrics and Gynecology, Helsinki University Central Hospital and University of Helsinki, Helsinki, Finland
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Abstract
A wide variety of diseases have a significant genetic component, including major causes of morbidity and mortality in the western world. Many of these diseases are also angiogenesis dependent. In humans, common polymorphisms, although more subtle in effect than rare mutations that cause Mendelian disease, are expected to have greater overall effects on human disease. Thus, common polymorphisms in angiogenesis-regulating genes may affect the response to an angiogenic stimulus and thereby affect susceptibility to or progression of such diseases. Candidate gene studies have identified several associations between angiogenesis gene polymorphisms and disease. Similarly, emerging pharmacogenomic evidence indicates that several angiogenesis-regulating polymorphisms may predict response to therapy. In contrast, genome-wide association studies have identified only a few risk alleles in obvious angiogenesis genes. As in other traits, regulatory polymorphisms appear to dominate the landscape of angiogenic responsiveness. Rodent assays, including the mouse corneal micropocket assay, tumor models, and a macular degeneration model have allowed the identification and comparison of loci that directly affect the trait. Complementarity between human and animal approaches will allow increased understanding of the genetic basis for angiogenesis-dependent disease.
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Affiliation(s)
- Michael S Rogers
- Vascular Biology Program, Children's Hospital, Boston, Massachusettes, USA.
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Betts JA, French JD, Brown MA, Edwards SL. Long-range transcriptional regulation of breast cancer genes. Genes Chromosomes Cancer 2012; 52:113-25. [PMID: 23077082 DOI: 10.1002/gcc.22020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Revised: 09/19/2012] [Accepted: 09/19/2012] [Indexed: 12/11/2022] Open
Abstract
Breast cancer is a major health problem and understanding the genetic basis of this disease is crucial for predicting risk and developing effective targeted therapeutics. Several breast cancer predisposing genes have been identified, but mutations in the coding regions of these genes only accounts for a small proportion of risk. Research now suggests that combinations of multiple non-coding changes in breast cancer susceptibility genes, which cause moderate alterations in gene expression, will be responsible for the remaining inherited risk. These non-coding changes will include variants in proximal and distal transcriptional and post-transcriptional regulatory elements and may affect the levels and function of trans-acting factors, including proteins and RNAs, which act on these elements. Somatic changes in such elements and factors have also been associated with breast cancer progression. With the recent advent of techniques allowing the detection of long-range DNA interactions spanning the human genome, it has become increasingly clear that long-range regulatory elements constitute an important mechanism for gene regulation. Recent studies have identified several such elements that are important for regulating genes involved in breast cancer, raising the possibility that defects in these sequences may contribute to breast cancer predisposition and progression. In this review, we discuss the emerging functions of cis-regulatory elements and a subset of trans-acting factors in breast tumorigenesis. We also discuss some recent progress in our understanding of how dysregulation in these transcriptional components may contribute to breast cancer, and the potential implications for molecular diagnosis, prognosis prediction, and the treatment of this disease.
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Affiliation(s)
- Joshua A Betts
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland, Australia
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Schleutker J. Polymorphisms in androgen signaling pathway predisposing to prostate cancer. Mol Cell Endocrinol 2012; 360:25-37. [PMID: 21782882 DOI: 10.1016/j.mce.2011.07.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Revised: 06/30/2011] [Accepted: 07/01/2011] [Indexed: 11/30/2022]
Abstract
Prostate cancer is the most frequent male malignancy diagnosed in western countries and androgens are known to mediate key physiological processes in prostate tissue. Since endogenous androgens have long been considered to be risk factors for prostate cancer, genes involved in androgen biosynthesis and metabolism have been extensively studied. In this review, association of androgen pathway genes, their polymorphic sites and risk of prostate cancer in different ethnic backgrounds is addressed together with their use to predict susceptibility and clinical outcomes of prostate cancer patients. The effect of the polymorphisms seems vary in different patients, populations and ethnic backgrounds. To date it is evident that the association between androgen pathway gene polymorphisms and prostate cancer risk is complex and many of the results are characterized by irreproducibility, which can be attributed to a variety of biological, statistical and technical reasons. In the future, with increasing knowledge, developing technologies and new genomic biomarkers it likely becomes possible to better estimate the risk of prostate cancer, and distinguish indolent disease from aggressive based on molecular profiling, and the analysis of gene-gene and gene-environment interactions.
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Affiliation(s)
- Johanna Schleutker
- Institute of Biomedical Technology, University of Tampere, and Centre for Laboratory Medicine, Tampere University Hospital, Biokatu 8, 33520 Tampere, Finland.
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Ku CS, Cooper DN, Wu M, Roukos DH, Pawitan Y, Soong R, Iacopetta B. Gene discovery in familial cancer syndromes by exome sequencing: prospects for the elucidation of familial colorectal cancer type X. Mod Pathol 2012; 25:1055-68. [PMID: 22522846 DOI: 10.1038/modpathol.2012.62] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Recent advances in genotyping and sequencing technologies have provided powerful tools with which to explore the genetic basis of both Mendelian (monogenic) and sporadic (polygenic) diseases. Several hundred genome-wide association studies have so far been performed to explore the genetics of various polygenic or complex diseases including those cancers with a genetic predisposition. Exome sequencing has also proven very successful in elucidating the etiology of a range of hitherto poorly understood Mendelian disorders caused by high-penetrance mutations. Despite such progress, the genetic etiology of several familial cancers, such as familial colorectal cancer type X, has remained elusive. Familial colorectal cancer type X and Lynch syndrome are similar in terms of their fulfilling certain clinical criteria, but the former group is not characterized by germline mutations in DNA mismatch-repair genes. On the other hand, the genetics of sporadic colorectal cancer have been investigated by genome-wide association studies, leading to the identification of multiple new susceptibility loci. In addition, there is increasing evidence to suggest that familial and sporadic cancers exhibit similarities in terms of their genetic etiologies. In this review, we have summarized our current knowledge of familial colorectal cancer type X, discussed current approaches to probing its genetic etiology through the application of new sequencing technologies and the recruitment of the results of colorectal cancer genome-wide association studies, and explore the challenges that remain to be overcome given the uncertainty of the current genetic model (ie, monogenic vs polygenic) of familial colorectal cancer type X.
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Affiliation(s)
- Chee-Seng Ku
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
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Genome-wide association study for ovarian cancer susceptibility using pooled DNA. Twin Res Hum Genet 2012; 15:615-623. [PMID: 22794196 DOI: 10.1017/thg.2012.38] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Recent Genome-Wide Association Studies (GWAS) have identified four low-penetrance ovarian cancer susceptibility loci. We hypothesized that further moderate- or low-penetrance variants exist among the subset of single-nucleotide polymorphisms (SNPs) not well tagged by the genotyping arrays used in the previous studies, which would account for some of the remaining risk. We therefore conducted a time- and cost-effective stage 1 GWAS on 342 invasive serous cases and 643 controls genotyped on pooled DNA using the high-density Illumina 1M-Duo array. We followed up 20 of the most significantly associated SNPs, which are not well tagged by the lower density arrays used by the published GWAS, and genotyping them on individual DNA. Most of the top 20 SNPs were clearly validated by individually genotyping the samples used in the pools. However, none of the 20 SNPs replicated when tested for association in a much larger stage 2 set of 4,651 cases and 6,966 controls from the Ovarian Cancer Association Consortium. Given that most of the top 20 SNPs from pooling were validated in the same samples by individual genotyping, the lack of replication is likely to be due to the relatively small sample size in our stage 1 GWAS rather than due to problems with the pooling approach. We conclude that there are unlikely to be any moderate or large effects on ovarian cancer risk untagged by less dense arrays. However, our study lacked power to make clear statements on the existence of hitherto untagged small-effect variants.
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Kouprina N, Lee NCO, Pavlicek A, Samoshkin A, Kim JH, Lee HS, Varma S, Reinhold WC, Otstot J, Solomon G, Davis S, Meltzer PS, Schleutker J, Larionov V. Exclusion of the 750-kb genetically unstable region at Xq27 as a candidate locus for prostate malignancy in HPCX1-linked families. Genes Chromosomes Cancer 2012; 51:933-48. [PMID: 22733720 DOI: 10.1002/gcc.21977] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Accepted: 05/08/2012] [Indexed: 12/14/2022] Open
Abstract
Several linkage studies provided evidence for the presence of the hereditary prostate cancer locus, HPCX1, at Xq27-q28. The strongest linkage peak of prostate cancer overlies a variable region of ~750 kb at Xq27 enriched by segmental duplications (SDs), suggesting that the predisposition to prostate cancer may be a genomic disorder caused by recombinational interaction between SDs. The large size of SDs and their sequence similarity make it difficult to examine this region for possible rearrangements using standard methods. To overcome this problem, direct isolation of a set of genomic segments by in vivo recombination in yeast (a TAR cloning technique) was used to perform a mutational analysis of the 750 kb region in X-linked families. We did not detect disease-specific rearrangements within this region. In addition, transcriptome and computational analyses were performed to search for nonannotated genes within the Xq27 region, which may be associated with genetic predisposition to prostate cancer. Two candidate genes were identified, one of which is a novel gene termed SPANXL that represents a highly diverged member of the SPANX gene family, and the previously described CDR1 gene that is expressed at a high level in both normal and malignant prostate cells, and mapped 210 kb of upstream the SPANX gene cluster. No disease-specific alterations were identified in these genes. Our results exclude the 750-kb genetically unstable region at Xq27 as a candidate locus for prostate malignancy. Adjacent regions appear to be the most likely candidates to identify the elusive HPCX1 locus.
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Affiliation(s)
- Natalay Kouprina
- Laboratory of Molecular Pharmacology, NCI, NIH, Bethesda, MD, USA.
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Bailey-Wilson JE, Childs EJ, Cropp CD, Schaid DJ, Xu J, Camp NJ, Cannon-Albright LA, Farnham JM, George A, Powell I, Carpten JD, Giles GG, Hopper JL, Severi G, English DR, Foulkes WD, Mæhle L, Møller P, Eeles R, Easton D, Guy M, Edwards S, Badzioch MD, Whittemore AS, Oakley-Girvan I, Hsieh CL, Dimitrov L, Stanford JL, Karyadi DM, Deutsch K, McIntosh L, Ostrander EA, Wiley KE, Isaacs SD, Walsh PC, Thibodeau SN, McDonnell SK, Hebbring S, Lange EM, Cooney KA, Tammela TLJ, Schleutker J, Maier C, Bochum S, Hoegel J, Grönberg H, Wiklund F, Emanuelsson M, Cancel-Tassin G, Valeri A, Cussenot O, Isaacs WB. Analysis of Xq27-28 linkage in the international consortium for prostate cancer genetics (ICPCG) families. BMC MEDICAL GENETICS 2012; 13:46. [PMID: 22712434 PMCID: PMC3495053 DOI: 10.1186/1471-2350-13-46] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Accepted: 04/30/2012] [Indexed: 11/20/2022]
Abstract
BACKGROUND Genetic variants are likely to contribute to a portion of prostate cancer risk. Full elucidation of the genetic etiology of prostate cancer is difficult because of incomplete penetrance and genetic and phenotypic heterogeneity. Current evidence suggests that genetic linkage to prostate cancer has been found on several chromosomes including the X; however, identification of causative genes has been elusive. METHODS Parametric and non-parametric linkage analyses were performed using 26 microsatellite markers in each of 11 groups of multiple-case prostate cancer families from the International Consortium for Prostate Cancer Genetics (ICPCG). Meta-analyses of the resultant family-specific linkage statistics across the entire 1,323 families and in several predefined subsets were then performed. RESULTS Meta-analyses of linkage statistics resulted in a maximum parametric heterogeneity lod score (HLOD) of 1.28, and an allele-sharing lod score (LOD) of 2.0 in favor of linkage to Xq27-q28 at 138 cM. In subset analyses, families with average age at onset less than 65 years exhibited a maximum HLOD of 1.8 (at 138 cM) versus a maximum regional HLOD of only 0.32 in families with average age at onset of 65 years or older. Surprisingly, the subset of families with only 2-3 affected men and some evidence of male-to-male transmission of prostate cancer gave the strongest evidence of linkage to the region (HLOD = 3.24, 134 cM). For this subset, the HLOD was slightly increased (HLOD = 3.47 at 134 cM) when families used in the original published report of linkage to Xq27-28 were excluded. CONCLUSIONS Although there was not strong support for linkage to the Xq27-28 region in the complete set of families, the subset of families with earlier age at onset exhibited more evidence of linkage than families with later onset of disease. A subset of families with 2-3 affected individuals and with some evidence of male to male disease transmission showed stronger linkage signals. Our results suggest that the genetic basis for prostate cancer in our families is much more complex than a single susceptibility locus on the X chromosome, and that future explorations of the Xq27-28 region should focus on the subset of families identified here with the strongest evidence of linkage to this region.
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Affiliation(s)
- Joan E Bailey-Wilson
- Inherited Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD, 21224, USA
- African American Hereditary Prostate Cancer ICPCG Group, Phoenix, AZ, USA
- University of Tampere ICPCG Group, Tampere, Finland
| | - Erica J Childs
- Inherited Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD, 21224, USA
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Cheryl D Cropp
- Inherited Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Daniel J Schaid
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, 55905, USA
| | - Jianfeng Xu
- Data Coordinating Center for the ICPCG and Center for Human Genomics, Wake Forest University School of Medicine, Winston-Salem, NC, 27157, USA
| | - Nicola J Camp
- University of Utah ICPCG Group and Division of Genetic Epidemiology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Lisa A Cannon-Albright
- University of Utah ICPCG Group and Division of Genetic Epidemiology, University of Utah School of Medicine, Salt Lake City, UT, USA
- George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, UT, USA
| | - James M Farnham
- University of Utah ICPCG Group and Division of Genetic Epidemiology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Asha George
- Inherited Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, MD, 21224, USA
- African American Hereditary Prostate Cancer ICPCG Group, Phoenix, AZ, USA
- Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Isaac Powell
- African American Hereditary Prostate Cancer ICPCG Group, Phoenix, AZ, USA
- Karmanos Cancer Institute, Wayne State University, Detroit, MI, USA
| | - John D Carpten
- African American Hereditary Prostate Cancer ICPCG Group, Phoenix, AZ, USA
- Translational Genomics Research Institute, Genetic Basis of Human Disease Research Division, Phoenix, AZ, USA
| | - Graham G Giles
- ACTANE consortium
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, School of Population Health, The University of Melbourne, Melbourne, Australia
| | - John L Hopper
- ACTANE consortium
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, School of Population Health, The University of Melbourne, Melbourne, Australia
| | - Gianluca Severi
- ACTANE consortium
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, School of Population Health, The University of Melbourne, Melbourne, Australia
| | - Dallas R English
- ACTANE consortium
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, School of Population Health, The University of Melbourne, Melbourne, Australia
| | - William D Foulkes
- ACTANE consortium
- Program in Cancer Genetics, McGill University, Montreal, QC, Canada
| | - Lovise Mæhle
- ACTANE consortium
- Department of Medical Genetics, Oslo University Hospital, The Norwegian Radium Hospital, Oslo,Norway
| | - Pål Møller
- ACTANE consortium
- Department of Medical Genetics, Oslo University Hospital, The Norwegian Radium Hospital, Oslo,Norway
| | - Rosalind Eeles
- ACTANE consortium
- Institute of Cancer Research and Royal Marsden NHS Foundation Trust, Surrey, UK
| | - Douglas Easton
- ACTANE consortium
- Cancer Research UK Genetic Epidemiology Unit, Cambridge, UK
| | - Michelle Guy
- ACTANE consortium
- Institute of Cancer Research and Royal Marsden NHS Foundation Trust, Surrey, UK
| | - Steve Edwards
- ACTANE consortium
- Institute of Cancer Research and Royal Marsden NHS Foundation Trust, Surrey, UK
| | - Michael D Badzioch
- ACTANE consortium
- Division of Medical Genetics, University of Washington Medical Center, Seattle, WA, USA
| | - Alice S Whittemore
- BC/CA/HI ICPCG Group, Stanford, CA, USA
- Department of Health Research and Policy, Stanford School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Ingrid Oakley-Girvan
- BC/CA/HI ICPCG Group, Stanford, CA, USA
- Department of Health Research and Policy, Stanford School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
- Cancer Prevention Institute of California
| | - Chih-Lin Hsieh
- BC/CA/HI ICPCG Group, Stanford, CA, USA
- Department of Urology and Department of Biochemistry and Molecular Biology, University of Southern California, Los Ageles, CA, USA
| | - Latchezar Dimitrov
- Data Coordinating Center for the ICPCG and Center for Human Genomics, Wake Forest University School of Medicine, Winston-Salem, NC, 27157, USA
| | - Janet L Stanford
- FHCRC ICPCG Group, Seattle, WA, USA
- Fred Hutchinson Cancer Research Center, Division of Public Health Sciences, Seattle, WA, USA
| | - Danielle M Karyadi
- FHCRC ICPCG Group, Seattle, WA, USA
- Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kerry Deutsch
- FHCRC ICPCG Group, Seattle, WA, USA
- Institute for Systems Biology, Seattle, WA, USA
| | - Laura McIntosh
- FHCRC ICPCG Group, Seattle, WA, USA
- Fred Hutchinson Cancer Research Center, Division of Public Health Sciences, Seattle, WA, USA
| | - Elaine A Ostrander
- FHCRC ICPCG Group, Seattle, WA, USA
- Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kathleen E Wiley
- Johns Hopkins University ICPCG Group and Department of Urology, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Sarah D Isaacs
- Johns Hopkins University ICPCG Group and Department of Urology, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Patrick C Walsh
- Johns Hopkins University ICPCG Group and Department of Urology, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | | | | | | | - Ethan M Lange
- University of Michigan ICPCG Group, Ann Arbor, MI, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Kathleen A Cooney
- University of Michigan ICPCG Group, Ann Arbor, MI, USA
- University of Michigan, Ann Arbor, MI, USA
| | - Teuvo LJ Tammela
- University of Tampere ICPCG Group, Tampere, Finland
- Institute of Biomedical Technology, University of Tampere, Tampere, Finland
- Centre for Laboratory Medicine and Department of Urology, Tampere University Hospital, Tampere, Finland
| | - Johanna Schleutker
- University of Tampere ICPCG Group, Tampere, Finland
- Institute of Biomedical Technology, University of Tampere, Tampere, Finland
- Centre for Laboratory Medicine and Department of Urology, Tampere University Hospital, Tampere, Finland
| | - Christiane Maier
- University of Ulm ICPCG Group, Ulm, Germany
- Dept of Urology, University of Ulm, Ulm, Germany
- Institute of Human Genetics, University of Ulm, Ulm, Germany
| | - Sylvia Bochum
- University of Ulm ICPCG Group, Ulm, Germany
- Institute of Human Genetics, University of Ulm, Ulm, Germany
| | - Josef Hoegel
- University of Ulm ICPCG Group, Ulm, Germany
- Institute of Human Genetics, University of Ulm, Ulm, Germany
| | - Henrik Grönberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Fredrik Wiklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | | | | | | | - Olivier Cussenot
- CeRePP ICPCG Group, 75020, Paris, France
- Hopital Tenon, Assistance Publique-Hopitaux de Paris, 75020, Paris, France
| | - William B Isaacs
- Johns Hopkins University ICPCG Group and Department of Urology, Johns Hopkins Medical Institutions, Baltimore, MD, USA
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Cremers R, van Asperen C, Kil P, Vasen H, Wiersma T, van Oort I, Kiemeney L. Urologists' and GPs' knowledge of hereditary prostate cancer is suboptimal for prostate cancer counseling: a nation-wide survey in The Netherlands. Fam Cancer 2012; 11:195-200. [PMID: 22160565 PMCID: PMC3365231 DOI: 10.1007/s10689-011-9500-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
A family history of prostate cancer (PCa) is an established risk factor for PCa. In case of a positive family history, the balance between positive and adverse effects of prostate-specific antigen (PSA) testing might be different from the general population, for which the European Randomized Study of Screening for Prostate Cancer (ERSPC) showed a beneficial effect on mortality. This, however, went at the cost of considerable overtreatment. This study assessed Dutch physicians' knowledge of heredity and PCa and their 'post-ERSPC' attitude towards PCa testing, including consideration of family history. In January 2010, all Dutch urologists and clinical geneticists (CGs) and 300 general practitioners (GPs) were invited by email to complete an anonymous online survey, which contained questions about hereditary PCa and their attitudes towards PCa case-finding and screening. 109 urologists (31%), 69 GPs (23%) and 46 CGs (31%) completed the survey. CGs had the most accurate knowledge of hereditary PCa. All but 1 CG mentioned at least one inherited trait with PCa, compared to only 25% of urologists and 9% of GPs. CGs hardly ever counseled men about PCa testing. Most urologists and GPs discuss possible risks and benefits before testing for PCa with PSA. Remarkably, 35-40% of them do not take family history into consideration. Knowledge of urologists and GPs about heredity and PCa is suboptimal. Hence, PCa counseling might not be optimal for men with a positive family history. Multidisciplinary guidelines on this topic should be developed to optimize personalized counseling.
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Affiliation(s)
- Ruben Cremers
- Department of Epidemiology, Biostatistics and HTA (133), Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
- Netherlands Foundation for the Detection of Hereditary Tumors, Leiden, The Netherlands
| | - Christi van Asperen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Paul Kil
- Department of Urology, St. Elisabeth Hospital, Tilburg, The Netherlands
| | - Hans Vasen
- Netherlands Foundation for the Detection of Hereditary Tumors, Leiden, The Netherlands
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Tjerk Wiersma
- Dutch College of General Practitioners, Utrecht, The Netherlands
| | - Inge van Oort
- Department of Urology, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Lambertus Kiemeney
- Department of Epidemiology, Biostatistics and HTA (133), Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
- Department of Urology, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands
- Comprehensive Cancer Centre The Netherlands, Nijmegen, The Netherlands
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49
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Stephens PJ, Tarpey PS, Davies H, Van Loo P, Greenman C, Wedge DC, Nik-Zainal S, Martin S, Varela I, Bignell GR, Yates LR, Papaemmanuil E, Beare D, Butler A, Cheverton A, Gamble J, Hinton J, Jia M, Jayakumar A, Jones D, Latimer C, Lau KW, McLaren S, McBride DJ, Menzies A, Mudie L, Raine K, Rad R, Chapman MS, Teague J, Easton D, Langerød A, Lee MTM, Shen CY, Tee BTK, Huimin BW, Broeks A, Vargas AC, Turashvili G, Martens J, Fatima A, Miron P, Chin SF, Thomas G, Boyault S, Mariani O, Lakhani SR, van de Vijver M, van 't Veer L, Foekens J, Desmedt C, Sotiriou C, Tutt A, Caldas C, Reis-Filho JS, Aparicio SAJR, Salomon AV, Børresen-Dale AL, Richardson AL, Campbell PJ, Futreal PA, Stratton MR. The landscape of cancer genes and mutational processes in breast cancer. Nature 2012; 486:400-4. [PMID: 22722201 PMCID: PMC3428862 DOI: 10.1038/nature11017] [Citation(s) in RCA: 1273] [Impact Index Per Article: 106.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Accepted: 03/06/2012] [Indexed: 12/17/2022]
Abstract
All cancers carry somatic mutations in their genomes. A subset, known as driver mutations, confer clonal selective advantage on cancer cells and are causally implicated in oncogenesis, and the remainder are passenger mutations. The driver mutations and mutational processes operative in breast cancer have not yet been comprehensively explored. Here we examine the genomes of 100 tumours for somatic copy number changes and mutations in the coding exons of protein-coding genes. The number of somatic mutations varied markedly between individual tumours. We found strong correlations between mutation number, age at which cancer was diagnosed and cancer histological grade, and observed multiple mutational signatures, including one present in about ten per cent of tumours characterized by numerous mutations of cytosine at TpC dinucleotides. Driver mutations were identified in several new cancer genes including AKT2, ARID1B, CASP8, CDKN1B, MAP3K1, MAP3K13, NCOR1, SMARCD1 and TBX3. Among the 100 tumours, we found driver mutations in at least 40 cancer genes and 73 different combinations of mutated cancer genes. The results highlight the substantial genetic diversity underlying this common disease.
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Affiliation(s)
- Philip J Stephens
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
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50
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Leedham S, Tomlinson I. The continuum model of selection in human tumors: general paradigm or niche product? Cancer Res 2012; 72:3131-4. [PMID: 22552286 DOI: 10.1158/0008-5472.can-12-1052] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Berger and colleagues recently proposed a continuum model of how somatic mutations cause tumors to grow, thus supplementing the established binary models, such as oncogene activation and "two hits" at tumor suppressor loci. In the basic continuum model, decreases or increases in gene function, short of full inactivation or activation, impact linearly on cancer development. An extension, called the fail-safe model, envisaged an optimum level of gene derangement for tumor growth, but proposed that the cell gained protection from tumorigenesis because additional mutations caused excessive derangement. Most of the evidence in support of the continuum model came from Pten mutant mice rather than humans. In this article, we assess the validity and applicability of the continuum and fail-safe models. We suggest that the latter is of limited use: In part, it restates the existing "just right" of optimum intermediate gene derangement in tumorigenesis, and in part it is inherently implausible that a cell should avoid becoming cancerous only when it is some way down the road to that state. In contrast, the basic continuum model is a very useful addition to the other genetic models of tumorigenesis, especially in certain scenarios. Fittingly for a quantitative model, we propose that the continuum model is most likely to apply where multiple, cancer-promoting mutations have relatively small, additive effects, either through the well-established case of additive germline predisposition alleles or in a largely hypothetical situation where cancers may have acquired several somatic "mini-driver" mutations, each with weaker effects than classical tumor suppressors or fully activated oncogenes.
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Affiliation(s)
- Simon Leedham
- Molecular and Population Genetics Laboratory, Nuffield Department of Medicine, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
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