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Ricker C. DE LAS FAMILIAS CON SÍNDROMES A LOS GENES. LAS PRIMERAS CARACTERIZACIONES CLÍNICAS Y GENÉTICAS DE DOS SÍNDROMES HEREDITARIOS CON PREDISPOSICIÓN AL CÁNCER: ¿CUÁL FUE EL COMIENZO? REVISTA MÉDICA CLÍNICA LAS CONDES 2017. [DOI: 10.1016/j.rmclc.2017.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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López F, Hurtado BQC, Álvarez BQK, Kronberg U, Pinto EE, Peralta O, Adaniel C, Salinas EF, Letelier C. ¿CÓMO ORGANIZAR Y ESTRUCTURAR UN PROGRAMA DE SÍNDROMES HEREDITARIOS QUE PREDISPONEN AL DESARROLLO DEL CÁNCER? REVISTA MÉDICA CLÍNICA LAS CONDES 2017. [DOI: 10.1016/j.rmclc.2017.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Ricker C. FROM FAMILIES SYNDROMES TO GENES… THE FIRST CLINICAL AND GENETIC CHARACTERIZATIONS OF HEREDITARY SYNDROMES PREDISPOSING TO CANCER: WHAT WAS THE BEGINNING? REVISTA MÉDICA CLÍNICA LAS CONDES 2017. [DOI: 10.1016/j.rmclc.2017.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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Lynch PM. HISTORY OF HEREDITARY NONPOLYPOSIS COLORECTAL CANCER OR “LYNCH SYNDROME”. REVISTA MÉDICA CLÍNICA LAS CONDES 2017. [DOI: 10.1016/j.rmclc.2017.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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Lynch PM. HISTORIA DEL CÁNCER COLORRECTAL HEREDITARIO NO POLIPÓSICO (HNPCC). REVISTA MÉDICA CLÍNICA LAS CONDES 2017. [DOI: 10.1016/j.rmclc.2017.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Recent Discoveries in the Genetics of Familial Colorectal Cancer and Polyposis. Clin Gastroenterol Hepatol 2017; 15:809-819. [PMID: 27712984 DOI: 10.1016/j.cgh.2016.09.148] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 09/26/2016] [Accepted: 09/27/2016] [Indexed: 02/07/2023]
Abstract
The development of genome-wide massively parallel sequencing, ie, whole-genome and whole-exome sequencing, and copy number approaches has raised high expectations for the identification of novel hereditary colorectal cancer genes. Although relatively successful for genes causing adenomatous polyposis syndromes, both autosomal dominant and recessive, the identification of genes associated with hereditary non-polyposis colorectal cancer has proven extremely challenging, mainly because of the absence of major high-penetrance genes and the difficulty in demonstrating the functional impact of the identified variants and their causal association with tumor development. Indeed, most, if not all, novel candidate non-polyposis colorectal cancer genes identified so far lack corroborative data in independent studies. Here we review the novel hereditary colorectal cancer genes and syndromes identified and the candidate genes proposed in recent years as well as discuss the challenges we face.
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The current value of determining the mismatch repair status of colorectal cancer: A rationale for routine testing. Crit Rev Oncol Hematol 2017; 116:38-57. [PMID: 28693799 DOI: 10.1016/j.critrevonc.2017.05.006] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 03/02/2017] [Accepted: 05/15/2017] [Indexed: 02/08/2023] Open
Abstract
Colorectal Cancer (CRC) is the third most prevalent cancer in men and women. Up to 15% of CRCs display microsatellite instability (MSI). MSI is reflective of a deficient mismatch repair (MMR) system and is most commonly caused by hypermethylation of the MLH1 promoter. However, it may also be due to autosomal dominant constitutional mutations in DNA MMR, termed Lynch Syndrome. MSI may be diagnosed via polymerase chain reaction (PCR) or alternatively, immunohistochemistry (IHC) can identify MMR deficiency (dMMR). Many institutions now advocate universal tumor screening of CRC via either PCR for MSI or IHC for dMMR to guide Lynch Syndrome testing. The association of sporadic MSI with methylation of the MLH1 promoter and an activating BRAF mutation may offer further exclusion criteria for genetic testing. Aside from screening for Lynch syndrome, MMR testing is important because of its prognostic and therapeutic implications. Several studies have shown MSI CRCs exhibit different clinicopathological features and prognosis compared to microsatellite-stable (MSS) CRCs. For example, response to conventional chemotherapy has been reported to be less in MSI tumours. More recently, MSI tumours have been shown to be responsive to immune-checkpoint inhibition providing a novel therapeutic strategy. This provides a rationale for routine testing for MSI or dMMR in CRC.
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Espenschied CR, LaDuca H, Li S, McFarland R, Gau CL, Hampel H. Multigene Panel Testing Provides a New Perspective on Lynch Syndrome. J Clin Oncol 2017; 35:2568-2575. [PMID: 28514183 DOI: 10.1200/jco.2016.71.9260] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Purpose Most existing literature describes Lynch syndrome (LS) as a hereditary syndrome leading to high risks of colorectal cancer (CRC) and endometrial cancer mainly as a result of mutations in MLH1 and MSH2. Most of these studies were performed on cohorts with disease suggestive of hereditary CRC and population-based CRC and endometrial cancer cohorts, possibly biasing results. We aimed to describe a large cohort of mismatch repair (MMR) mutation carriers ascertained through multigene panel testing, evaluate their phenotype, and compare the results with those of previous studies. Methods We retrospectively reviewed clinical histories of patients who had multigene panel testing, including the MMR and EPCAM genes, between March 2012 and June 2015 (N = 34,981) and performed a series of statistical comparisons. Results Overall, MSH6 mutations were most frequent, followed by PMS2, MSH2, MLH1, and EPCAM mutations, respectively. Of 528 patients who had MMR mutations, 63 (11.9%) had breast cancer only and 144 (27.3%) had CRC only. When comparing those with breast cancer only to those with CRC only, MSH6 and PMS2 mutations were more frequent than MLH1 and MSH2 mutations ( P = 2.3 × 10-5). Of the 528 patients, 22.2% met BRCA1 and BRCA2 ( BRCA1/2) testing criteria and not LS criteria, and 5.1% met neither BRCA1/2 nor LS testing criteria. MSH6 and PMS2 mutations were more frequent than MLH1 and MSH2 mutations among patients who met BRCA1/2 testing criteria but did not meet LS testing criteria ( P = 4.3 × 10-7). Conclusion These results provide a new perspective on LS and suggest that individuals with MSH6 and PMS2 mutations may present with a hereditary breast and ovarian cancer phenotype. These data also highlight the limitations of current testing criteria in identifying these patients, as well as the need for further investigation of cancer risks in patients with MMR mutations.
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Affiliation(s)
- Carin R Espenschied
- Carin R. Espenschied, Holly LaDuca, Shuwei Li, Rachel McFarland, and Chia-Ling Gau, Ambry Genetics, Clinical Diagnostics, Aliso Viejo, CA; and Heather Hampel, The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Holly LaDuca
- Carin R. Espenschied, Holly LaDuca, Shuwei Li, Rachel McFarland, and Chia-Ling Gau, Ambry Genetics, Clinical Diagnostics, Aliso Viejo, CA; and Heather Hampel, The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Shuwei Li
- Carin R. Espenschied, Holly LaDuca, Shuwei Li, Rachel McFarland, and Chia-Ling Gau, Ambry Genetics, Clinical Diagnostics, Aliso Viejo, CA; and Heather Hampel, The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Rachel McFarland
- Carin R. Espenschied, Holly LaDuca, Shuwei Li, Rachel McFarland, and Chia-Ling Gau, Ambry Genetics, Clinical Diagnostics, Aliso Viejo, CA; and Heather Hampel, The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Chia-Ling Gau
- Carin R. Espenschied, Holly LaDuca, Shuwei Li, Rachel McFarland, and Chia-Ling Gau, Ambry Genetics, Clinical Diagnostics, Aliso Viejo, CA; and Heather Hampel, The Ohio State University Comprehensive Cancer Center, Columbus, OH
| | - Heather Hampel
- Carin R. Espenschied, Holly LaDuca, Shuwei Li, Rachel McFarland, and Chia-Ling Gau, Ambry Genetics, Clinical Diagnostics, Aliso Viejo, CA; and Heather Hampel, The Ohio State University Comprehensive Cancer Center, Columbus, OH
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Abstract
Next-generation or massively parallel sequencing has transformed the landscape of genetic testing for cancer susceptibility. Panel-based genetic tests evaluate multiple genes simultaneously and rapidly. Because these tests are frequently offered in clinical settings, understanding their clinical validity and utility is critical. When evaluating the inherited risk of breast and ovarian cancers, panel-based tests provide incremental benefit compared with BRCA1/2 genetic testing. For inherited risk of other cancers, such as colon cancer and pheochromocytoma-paraganglioma, the clinical utility and yield of panel-based testing are higher; in fact, simultaneous evaluation of multiple genes has been the historical standard for these diseases. Evaluating inherited risk with panel-based testing has recently entered clinical practice for prostate and pancreatic cancers, with potential therapeutic implications. The resulting variants of uncertain significance and mutations with unclear actionability pose challenges to service providers and patients, underscoring the importance of genetic counseling and data-sharing initiatives. This review explores the evolving merits, challenges, and nuances of panel-based testing for cancer susceptibility.
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Affiliation(s)
- Payal D Shah
- Division of Hematology and Oncology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104;
| | - Katherine L Nathanson
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104; .,Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104
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Kastrinos F, Uno H, Ukaegbu C, Alvero C, McFarland A, Yurgelun MB, Kulke MH, Schrag D, Meyerhardt JA, Fuchs CS, Mayer RJ, Ng K, Steyerberg EW, Syngal S. Development and Validation of the PREMM 5 Model for Comprehensive Risk Assessment of Lynch Syndrome. J Clin Oncol 2017; 35:2165-2172. [PMID: 28489507 DOI: 10.1200/jco.2016.69.6120] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Purpose Current Lynch syndrome (LS) prediction models quantify the risk to an individual of carrying a pathogenic germline mutation in three mismatch repair (MMR) genes: MLH1, MSH2, and MSH6. We developed a new prediction model, PREMM5, that incorporates the genes PMS2 and EPCAM to provide comprehensive LS risk assessment. Patients and Methods PREMM5 was developed to predict the likelihood of a mutation in any of the LS genes by using polytomous logistic regression analysis of clinical and germline data from 18,734 individuals who were tested for all five genes. Predictors of mutation status included sex, age at genetic testing, and proband and family cancer histories. Discrimination was evaluated by the area under the receiver operating characteristic curve (AUC), and clinical impact was determined by decision curve analysis; comparisons were made to the existing PREMM1,2,6 model. External validation of PREMM5 was performed in a clinic-based cohort of 1,058 patients with colorectal cancer. Results Pathogenic mutations were detected in 1,000 (5%) of 18,734 patients in the development cohort; mutations included MLH1 (n = 306), MSH2 (n = 354), MSH6 (n = 177), PMS2 (n = 141), and EPCAM (n = 22). PREMM5 distinguished carriers from noncarriers with an AUC of 0.81 (95% CI, 0.79 to 0.82), and performance was similar in the validation cohort (AUC, 0.83; 95% CI, 0.75 to 0.92). Prediction was more difficult for PMS2 mutations (AUC, 0.64; 95% CI, 0.60 to 0.68) than for other genes. Performance characteristics of PREMM5 exceeded those of PREMM1,2,6. Decision curve analysis supported germline LS testing for PREMM5 scores ≥ 2.5%. Conclusion PREMM5 provides comprehensive risk estimation of all five LS genes and supports LS genetic testing for individuals with scores ≥ 2.5%. At this threshold, PREMM5 provides performance that is superior to the existing PREMM1,2,6 model in the identification of carriers of LS, including those with weaker phenotypes and individuals unaffected by cancer.
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Affiliation(s)
- Fay Kastrinos
- Fay Kastrinos and Ashley McFarland, Columbia University Medical Center, New York, NY; Hajime Uno, Chinedu Ukaegbu, Matthew B. Yurgelun, Matthew H. Kulke, Deborah Schrag, Jeffrey A. Meyerhardt, Charles S. Fuchs, Robert J. Mayer, Kimmie Ng, and Sapna Syngal, Dana-Farber Cancer Institute; Carmelita Alvero, Harvard T.H. Chan School of Public Health; Matthew B. Yurgelun, Matthew H. Kulke, Deborah Schrag, Jeffrey A. Meyerhardt, Charles S. Fuchs, Robert J. Mayer, Kimmie Ng, and Sapna Syngal, Harvard Medical School; Sapna Syngal, Brigham and Women's Hospital, Boston, MA; and Ewout W. Steyerberg, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Hajime Uno
- Fay Kastrinos and Ashley McFarland, Columbia University Medical Center, New York, NY; Hajime Uno, Chinedu Ukaegbu, Matthew B. Yurgelun, Matthew H. Kulke, Deborah Schrag, Jeffrey A. Meyerhardt, Charles S. Fuchs, Robert J. Mayer, Kimmie Ng, and Sapna Syngal, Dana-Farber Cancer Institute; Carmelita Alvero, Harvard T.H. Chan School of Public Health; Matthew B. Yurgelun, Matthew H. Kulke, Deborah Schrag, Jeffrey A. Meyerhardt, Charles S. Fuchs, Robert J. Mayer, Kimmie Ng, and Sapna Syngal, Harvard Medical School; Sapna Syngal, Brigham and Women's Hospital, Boston, MA; and Ewout W. Steyerberg, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Chinedu Ukaegbu
- Fay Kastrinos and Ashley McFarland, Columbia University Medical Center, New York, NY; Hajime Uno, Chinedu Ukaegbu, Matthew B. Yurgelun, Matthew H. Kulke, Deborah Schrag, Jeffrey A. Meyerhardt, Charles S. Fuchs, Robert J. Mayer, Kimmie Ng, and Sapna Syngal, Dana-Farber Cancer Institute; Carmelita Alvero, Harvard T.H. Chan School of Public Health; Matthew B. Yurgelun, Matthew H. Kulke, Deborah Schrag, Jeffrey A. Meyerhardt, Charles S. Fuchs, Robert J. Mayer, Kimmie Ng, and Sapna Syngal, Harvard Medical School; Sapna Syngal, Brigham and Women's Hospital, Boston, MA; and Ewout W. Steyerberg, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Carmelita Alvero
- Fay Kastrinos and Ashley McFarland, Columbia University Medical Center, New York, NY; Hajime Uno, Chinedu Ukaegbu, Matthew B. Yurgelun, Matthew H. Kulke, Deborah Schrag, Jeffrey A. Meyerhardt, Charles S. Fuchs, Robert J. Mayer, Kimmie Ng, and Sapna Syngal, Dana-Farber Cancer Institute; Carmelita Alvero, Harvard T.H. Chan School of Public Health; Matthew B. Yurgelun, Matthew H. Kulke, Deborah Schrag, Jeffrey A. Meyerhardt, Charles S. Fuchs, Robert J. Mayer, Kimmie Ng, and Sapna Syngal, Harvard Medical School; Sapna Syngal, Brigham and Women's Hospital, Boston, MA; and Ewout W. Steyerberg, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Ashley McFarland
- Fay Kastrinos and Ashley McFarland, Columbia University Medical Center, New York, NY; Hajime Uno, Chinedu Ukaegbu, Matthew B. Yurgelun, Matthew H. Kulke, Deborah Schrag, Jeffrey A. Meyerhardt, Charles S. Fuchs, Robert J. Mayer, Kimmie Ng, and Sapna Syngal, Dana-Farber Cancer Institute; Carmelita Alvero, Harvard T.H. Chan School of Public Health; Matthew B. Yurgelun, Matthew H. Kulke, Deborah Schrag, Jeffrey A. Meyerhardt, Charles S. Fuchs, Robert J. Mayer, Kimmie Ng, and Sapna Syngal, Harvard Medical School; Sapna Syngal, Brigham and Women's Hospital, Boston, MA; and Ewout W. Steyerberg, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Matthew B Yurgelun
- Fay Kastrinos and Ashley McFarland, Columbia University Medical Center, New York, NY; Hajime Uno, Chinedu Ukaegbu, Matthew B. Yurgelun, Matthew H. Kulke, Deborah Schrag, Jeffrey A. Meyerhardt, Charles S. Fuchs, Robert J. Mayer, Kimmie Ng, and Sapna Syngal, Dana-Farber Cancer Institute; Carmelita Alvero, Harvard T.H. Chan School of Public Health; Matthew B. Yurgelun, Matthew H. Kulke, Deborah Schrag, Jeffrey A. Meyerhardt, Charles S. Fuchs, Robert J. Mayer, Kimmie Ng, and Sapna Syngal, Harvard Medical School; Sapna Syngal, Brigham and Women's Hospital, Boston, MA; and Ewout W. Steyerberg, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Matthew H Kulke
- Fay Kastrinos and Ashley McFarland, Columbia University Medical Center, New York, NY; Hajime Uno, Chinedu Ukaegbu, Matthew B. Yurgelun, Matthew H. Kulke, Deborah Schrag, Jeffrey A. Meyerhardt, Charles S. Fuchs, Robert J. Mayer, Kimmie Ng, and Sapna Syngal, Dana-Farber Cancer Institute; Carmelita Alvero, Harvard T.H. Chan School of Public Health; Matthew B. Yurgelun, Matthew H. Kulke, Deborah Schrag, Jeffrey A. Meyerhardt, Charles S. Fuchs, Robert J. Mayer, Kimmie Ng, and Sapna Syngal, Harvard Medical School; Sapna Syngal, Brigham and Women's Hospital, Boston, MA; and Ewout W. Steyerberg, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Deborah Schrag
- Fay Kastrinos and Ashley McFarland, Columbia University Medical Center, New York, NY; Hajime Uno, Chinedu Ukaegbu, Matthew B. Yurgelun, Matthew H. Kulke, Deborah Schrag, Jeffrey A. Meyerhardt, Charles S. Fuchs, Robert J. Mayer, Kimmie Ng, and Sapna Syngal, Dana-Farber Cancer Institute; Carmelita Alvero, Harvard T.H. Chan School of Public Health; Matthew B. Yurgelun, Matthew H. Kulke, Deborah Schrag, Jeffrey A. Meyerhardt, Charles S. Fuchs, Robert J. Mayer, Kimmie Ng, and Sapna Syngal, Harvard Medical School; Sapna Syngal, Brigham and Women's Hospital, Boston, MA; and Ewout W. Steyerberg, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Jeffrey A Meyerhardt
- Fay Kastrinos and Ashley McFarland, Columbia University Medical Center, New York, NY; Hajime Uno, Chinedu Ukaegbu, Matthew B. Yurgelun, Matthew H. Kulke, Deborah Schrag, Jeffrey A. Meyerhardt, Charles S. Fuchs, Robert J. Mayer, Kimmie Ng, and Sapna Syngal, Dana-Farber Cancer Institute; Carmelita Alvero, Harvard T.H. Chan School of Public Health; Matthew B. Yurgelun, Matthew H. Kulke, Deborah Schrag, Jeffrey A. Meyerhardt, Charles S. Fuchs, Robert J. Mayer, Kimmie Ng, and Sapna Syngal, Harvard Medical School; Sapna Syngal, Brigham and Women's Hospital, Boston, MA; and Ewout W. Steyerberg, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Charles S Fuchs
- Fay Kastrinos and Ashley McFarland, Columbia University Medical Center, New York, NY; Hajime Uno, Chinedu Ukaegbu, Matthew B. Yurgelun, Matthew H. Kulke, Deborah Schrag, Jeffrey A. Meyerhardt, Charles S. Fuchs, Robert J. Mayer, Kimmie Ng, and Sapna Syngal, Dana-Farber Cancer Institute; Carmelita Alvero, Harvard T.H. Chan School of Public Health; Matthew B. Yurgelun, Matthew H. Kulke, Deborah Schrag, Jeffrey A. Meyerhardt, Charles S. Fuchs, Robert J. Mayer, Kimmie Ng, and Sapna Syngal, Harvard Medical School; Sapna Syngal, Brigham and Women's Hospital, Boston, MA; and Ewout W. Steyerberg, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Robert J Mayer
- Fay Kastrinos and Ashley McFarland, Columbia University Medical Center, New York, NY; Hajime Uno, Chinedu Ukaegbu, Matthew B. Yurgelun, Matthew H. Kulke, Deborah Schrag, Jeffrey A. Meyerhardt, Charles S. Fuchs, Robert J. Mayer, Kimmie Ng, and Sapna Syngal, Dana-Farber Cancer Institute; Carmelita Alvero, Harvard T.H. Chan School of Public Health; Matthew B. Yurgelun, Matthew H. Kulke, Deborah Schrag, Jeffrey A. Meyerhardt, Charles S. Fuchs, Robert J. Mayer, Kimmie Ng, and Sapna Syngal, Harvard Medical School; Sapna Syngal, Brigham and Women's Hospital, Boston, MA; and Ewout W. Steyerberg, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Kimmie Ng
- Fay Kastrinos and Ashley McFarland, Columbia University Medical Center, New York, NY; Hajime Uno, Chinedu Ukaegbu, Matthew B. Yurgelun, Matthew H. Kulke, Deborah Schrag, Jeffrey A. Meyerhardt, Charles S. Fuchs, Robert J. Mayer, Kimmie Ng, and Sapna Syngal, Dana-Farber Cancer Institute; Carmelita Alvero, Harvard T.H. Chan School of Public Health; Matthew B. Yurgelun, Matthew H. Kulke, Deborah Schrag, Jeffrey A. Meyerhardt, Charles S. Fuchs, Robert J. Mayer, Kimmie Ng, and Sapna Syngal, Harvard Medical School; Sapna Syngal, Brigham and Women's Hospital, Boston, MA; and Ewout W. Steyerberg, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Ewout W Steyerberg
- Fay Kastrinos and Ashley McFarland, Columbia University Medical Center, New York, NY; Hajime Uno, Chinedu Ukaegbu, Matthew B. Yurgelun, Matthew H. Kulke, Deborah Schrag, Jeffrey A. Meyerhardt, Charles S. Fuchs, Robert J. Mayer, Kimmie Ng, and Sapna Syngal, Dana-Farber Cancer Institute; Carmelita Alvero, Harvard T.H. Chan School of Public Health; Matthew B. Yurgelun, Matthew H. Kulke, Deborah Schrag, Jeffrey A. Meyerhardt, Charles S. Fuchs, Robert J. Mayer, Kimmie Ng, and Sapna Syngal, Harvard Medical School; Sapna Syngal, Brigham and Women's Hospital, Boston, MA; and Ewout W. Steyerberg, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Sapna Syngal
- Fay Kastrinos and Ashley McFarland, Columbia University Medical Center, New York, NY; Hajime Uno, Chinedu Ukaegbu, Matthew B. Yurgelun, Matthew H. Kulke, Deborah Schrag, Jeffrey A. Meyerhardt, Charles S. Fuchs, Robert J. Mayer, Kimmie Ng, and Sapna Syngal, Dana-Farber Cancer Institute; Carmelita Alvero, Harvard T.H. Chan School of Public Health; Matthew B. Yurgelun, Matthew H. Kulke, Deborah Schrag, Jeffrey A. Meyerhardt, Charles S. Fuchs, Robert J. Mayer, Kimmie Ng, and Sapna Syngal, Harvard Medical School; Sapna Syngal, Brigham and Women's Hospital, Boston, MA; and Ewout W. Steyerberg, University Medical Center Rotterdam, Rotterdam, the Netherlands
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Stephens MC, Boardman LA, Lazaridis KN. Individualized Medicine in Gastroenterology and Hepatology. Mayo Clin Proc 2017; 92:810-825. [PMID: 28473040 DOI: 10.1016/j.mayocp.2017.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 02/23/2017] [Accepted: 03/02/2017] [Indexed: 02/08/2023]
Abstract
After the completion of the Human Genome Project, there has been an acceleration in methodologies on sequencing nucleic acids (DNA and RNA) at a high precision and with ever-decreasing turnaround time and cost. Collectively, these approaches are termed next-generation sequencing and are already affecting the transformation of medical practice. In this symposium article, we highlight the current knowledge of the genetics of selected gastrointestinal tract and liver diseases, namely, inflammatory bowel disease, hereditary cholestatic liver disease, and familial colon cancer syndromes. In addition, we provide a stepwise approach to use next-generation sequencing methodologies for clinical practice with the goal to improve the diagnosis as well as management of and/or therapy of the chosen digestive diseases. This early experience of applying next-generation sequencing in the practice of gastroenterology and hepatology will delineate future best practices in the field, ultimately for the benefit of our patients.
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Affiliation(s)
- Michael C Stephens
- Division of Gastroenterology and Hepatology, College of Medicine, Mayo Clinic, Rochester, MN
| | - Lisa A Boardman
- Division of Gastroenterology and Hepatology, College of Medicine, Mayo Clinic, Rochester, MN
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Pearlman R, Frankel WL, Swanson B, Zhao W, Yilmaz A, Miller K, Bacher J, Bigley C, Nelsen L, Goodfellow PJ, Goldberg RM, Paskett E, Shields PG, Freudenheim JL, Stanich PP, Lattimer I, Arnold M, Liyanarachchi S, Kalady M, Heald B, Greenwood C, Paquette I, Prues M, Draper DJ, Lindeman C, Kuebler JP, Reynolds K, Brell JM, Shaper AA, Mahesh S, Buie N, Weeman K, Shine K, Haut M, Edwards J, Bastola S, Wickham K, Khanduja KS, Zacks R, Pritchard CC, Shirts BH, Jacobson A, Allen B, de la Chapelle A, Hampel H. Prevalence and Spectrum of Germline Cancer Susceptibility Gene Mutations Among Patients With Early-Onset Colorectal Cancer. JAMA Oncol 2017; 3:464-471. [PMID: 27978560 DOI: 10.1001/jamaoncol.2016.5194] [Citation(s) in RCA: 458] [Impact Index Per Article: 65.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Importance Hereditary cancer syndromes infer high cancer risks and require intensive cancer surveillance, yet the prevalence and spectrum of these conditions among unselected patients with early-onset colorectal cancer (CRC) is largely undetermined. Objective To determine the frequency and spectrum of cancer susceptibility gene mutations among patients with early-onset CRC. Design, Setting, and Participants Overall, 450 patients diagnosed with colorectal cancer younger than 50 years were prospectively accrued from 51 hospitals into the Ohio Colorectal Cancer Prevention Initiative from January 1, 2013, to June 20, 2016. Mismatch repair (MMR) deficiency was determined by microsatellite instability and/or immunohistochemistry. Germline DNA was tested for mutations in 25 cancer susceptibility genes using next-generation sequencing. Main Outcomes and Measures Mutation prevalence and spectrum in patients with early-onset CRC was determined. Clinical characteristics were assessed by mutation status. Results In total 450 patients younger than 50 years were included in the study, and 75 gene mutations were found in 72 patients (16%). Forty-eight patients (10.7%) had MMR-deficient tumors, and 40 patients (83.3%) had at least 1 gene mutation: 37 had Lynch syndrome (13, MLH1 [including one with constitutional MLH1 methylation]; 16, MSH2; 1, MSH2/monoallelic MUTYH; 2, MSH6; 5, PMS2); 1 patient had the APC c.3920T>A, p.I1307K mutation and a PMS2 variant; 9 patients (18.8%) had double somatic MMR mutations (including 2 with germline biallelic MUTYH mutations); and 1 patient had somatic MLH1 methylation. Four hundred two patients (89.3%) had MMR-proficient tumors, and 32 patients (8%) had at least 1 gene mutation: 9 had mutations in high-penetrance CRC genes (5, APC; 1, APC/PMS2; 2, biallelic MUTYH; 1, SMAD4); 13 patients had mutations in high- or moderate-penetrance genes not traditionally associated with CRC (3, ATM; 1, ATM/CHEK2; 2, BRCA1; 4, BRCA2; 1, CDKN2A; 2, PALB2); 10 patients had mutations in low-penetrance CRC genes (3, APC c.3920T>A, p.I1307K; 7, monoallelic MUTYH). Importantly, 24 of 72 patients (33.3%) who were mutation positive did not meet established genetic testing criteria for the gene(s) in which they had a mutation. Conclusions and Relevance Of 450 patients with early-onset CRC, 72 (16%) had gene mutations. Given the high frequency and wide spectrum of mutations, genetic counseling and testing with a multigene panel could be considered for all patients with early-onset CRC.
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Affiliation(s)
- Rachel Pearlman
- The Ohio State University Comprehensive Cancer Center, Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus
| | - Wendy L Frankel
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus
| | - Benjamin Swanson
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus
| | - Weiqiang Zhao
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus
| | - Ahmet Yilmaz
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus
| | - Kristin Miller
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus
| | - Jason Bacher
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus
| | - Christopher Bigley
- The Ohio State University Comprehensive Cancer Center, Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus
| | - Lori Nelsen
- The Ohio State University Comprehensive Cancer Center, Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus
| | - Paul J Goodfellow
- The Ohio State University Comprehensive Cancer Center, Department of Obstetrics and Gynecology, The Ohio State University Wexner Medical Center, Columbus
| | - Richard M Goldberg
- The Ohio State University Comprehensive Cancer Center, Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus
| | - Electra Paskett
- The Ohio State University Comprehensive Cancer Center, Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus
| | - Peter G Shields
- The Ohio State University Comprehensive Cancer Center, Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus
| | - Jo L Freudenheim
- Department of Epidemiology and Environmental Health, University at Buffalo, Buffalo, New York
| | - Peter P Stanich
- Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus
| | - Ilene Lattimer
- The Ohio State University Comprehensive Cancer Center, Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus
| | - Mark Arnold
- Department of Surgery, The Ohio State University Wexner Medical Center, Columbus
| | - Sandya Liyanarachchi
- The Ohio State University Comprehensive Cancer Center, Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus
| | - Matthew Kalady
- Department of Colorectal Surgery, Cleveland Clinic, Cleveland, Ohio
| | - Brandie Heald
- Department of Colorectal Surgery, Cleveland Clinic, Cleveland, Ohio
| | - Carla Greenwood
- Department of Digestive Diseases and Surgery, Cleveland Clinic, Cleveland, Ohio
| | - Ian Paquette
- Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Marla Prues
- Cancer Center Research, The Christ Hospital Health Network, Cincinnati, Ohio
| | - David J Draper
- TriHealth Cancer Institute, Good Samaritan Hospital, Cincinnati, Ohio
| | - Carolyn Lindeman
- TriHealth Cancer Institute, Good Samaritan Hospital, Cincinnati, Ohio
| | | | - Kelly Reynolds
- Department of Cancer Services, Riverside Methodist Hospital, Columbus, Ohio
| | - Joanna M Brell
- Department of Medicine, MetroHealth Medical Center, Cleveland, Ohio
| | - Amy A Shaper
- Research Institute, MetroHealth Medical Center, Cleveland, Ohio
| | - Sameer Mahesh
- Department of Internal Medicine, Summa Cancer Institute, Summa Akron City Hospital, Akron, Ohio
| | - Nicole Buie
- Summa Center for Clinical Trials, Summa Akron City Hospital, Akron, Ohio
| | - Kisa Weeman
- Department of Hematology/Oncology, Aultman Hospital, Canton, Ohio
| | - Kristin Shine
- Department of Oncology Clinical Trials, Aultman Hospital, Canton, Ohio
| | | | | | - Shyamal Bastola
- Department of Oncology and Hematology, Genesis HealthCare System, Zanesville, Ohio
| | - Karen Wickham
- Department of Oncology and Hematology, Genesis HealthCare System, Zanesville, Ohio
| | - Karamjit S Khanduja
- Division of Colon and Rectal Surgery, Mount Carmel East Hospital, Columbus, Ohio
| | - Rosemary Zacks
- Department of Clinical Trials, Mount Carmel East Hospital, Columbus, Ohio
| | - Colin C Pritchard
- Department of Laboratory Medicine, University of Washington, Seattle
| | - Brian H Shirts
- Department of Laboratory Medicine, University of Washington, Seattle
| | - Angela Jacobson
- Department of Laboratory Medicine, University of Washington, Seattle
| | | | - Albert de la Chapelle
- The Ohio State University Comprehensive Cancer Center, Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus
| | - Heather Hampel
- The Ohio State University Comprehensive Cancer Center, Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus
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Spira A, Yurgelun MB, Alexandrov L, Rao A, Bejar R, Polyak K, Giannakis M, Shilatifard A, Finn OJ, Dhodapkar M, Kay NE, Braggio E, Vilar E, Mazzilli SA, Rebbeck TR, Garber JE, Velculescu VE, Disis ML, Wallace DC, Lippman SM. Precancer Atlas to Drive Precision Prevention Trials. Cancer Res 2017; 77:1510-1541. [PMID: 28373404 PMCID: PMC6681830 DOI: 10.1158/0008-5472.can-16-2346] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 01/20/2017] [Accepted: 01/20/2017] [Indexed: 02/07/2023]
Abstract
Cancer development is a complex process driven by inherited and acquired molecular and cellular alterations. Prevention is the holy grail of cancer elimination, but making this a reality will take a fundamental rethinking and deep understanding of premalignant biology. In this Perspective, we propose a national concerted effort to create a Precancer Atlas (PCA), integrating multi-omics and immunity - basic tenets of the neoplastic process. The biology of neoplasia caused by germline mutations has led to paradigm-changing precision prevention efforts, including: tumor testing for mismatch repair (MMR) deficiency in Lynch syndrome establishing a new paradigm, combinatorial chemoprevention efficacy in familial adenomatous polyposis (FAP), signal of benefit from imaging-based early detection research in high-germline risk for pancreatic neoplasia, elucidating early ontogeny in BRCA1-mutation carriers leading to an international breast cancer prevention trial, and insights into the intricate germline-somatic-immunity interaction landscape. Emerging genetic and pharmacologic (metformin) disruption of mitochondrial (mt) respiration increased autophagy to prevent cancer in a Li-Fraumeni mouse model (biology reproduced in clinical pilot) and revealed profound influences of subtle changes in mt DNA background variation on obesity, aging, and cancer risk. The elaborate communication between the immune system and neoplasia includes an increasingly complex cellular microenvironment and dynamic interactions between host genetics, environmental factors, and microbes in shaping the immune response. Cancer vaccines are in early murine and clinical precancer studies, building on the recent successes of immunotherapy and HPV vaccine immune prevention. Molecular monitoring in Barrett's esophagus to avoid overdiagnosis/treatment highlights an important PCA theme. Next generation sequencing (NGS) discovered age-related clonal hematopoiesis of indeterminate potential (CHIP). Ultra-deep NGS reports over the past year have redefined the premalignant landscape remarkably identifying tiny clones in the blood of up to 95% of women in their 50s, suggesting that potentially premalignant clones are ubiquitous. Similar data from eyelid skin and peritoneal and uterine lavage fluid provide unprecedented opportunities to dissect the earliest phases of stem/progenitor clonal (and microenvironment) evolution/diversity with new single-cell and liquid biopsy technologies. Cancer mutational signatures reflect exogenous or endogenous processes imprinted over time in precursors. Accelerating the prevention of cancer will require a large-scale, longitudinal effort, leveraging diverse disciplines (from genetics, biochemistry, and immunology to mathematics, computational biology, and engineering), initiatives, technologies, and models in developing an integrated multi-omics and immunity PCA - an immense national resource to interrogate, target, and intercept events that drive oncogenesis. Cancer Res; 77(7); 1510-41. ©2017 AACR.
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Affiliation(s)
- Avrum Spira
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
- Department of Pathology and Bioinformatics, Boston University School of Medicine, Boston, Massachusetts
| | - Matthew B Yurgelun
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ludmil Alexandrov
- Theoretical Division, Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Anjana Rao
- Division of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, California
| | - Rafael Bejar
- Department of Medicine, Moores Cancer Center, University of California San Diego, La Jolla, California
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Marios Giannakis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Olivera J Finn
- Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Madhav Dhodapkar
- Department of Hematology and Immunology, Yale Cancer Center, New Haven, Connecticut
| | - Neil E Kay
- Department of Hematology, Mayo Clinic Hospital, Rochester, Minnesota
| | - Esteban Braggio
- Department of Hematology, Mayo Clinic Hospital, Phoenix, Arizona
| | - Eduardo Vilar
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sarah A Mazzilli
- Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
- Department of Pathology and Bioinformatics, Boston University School of Medicine, Boston, Massachusetts
| | - Timothy R Rebbeck
- Division of Hematology and Oncology, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Judy E Garber
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Victor E Velculescu
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland
- Department of Pathology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland
| | - Mary L Disis
- Department of Medicine, Center for Translational Medicine in Women's Health, University of Washington, Seattle, Washington
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Scott M Lippman
- Department of Medicine, Moores Cancer Center, University of California San Diego, La Jolla, California.
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164
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Kamps R, Brandão RD, Bosch BJVD, Paulussen ADC, Xanthoulea S, Blok MJ, Romano A. Next-Generation Sequencing in Oncology: Genetic Diagnosis, Risk Prediction and Cancer Classification. Int J Mol Sci 2017; 18:ijms18020308. [PMID: 28146134 PMCID: PMC5343844 DOI: 10.3390/ijms18020308] [Citation(s) in RCA: 284] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 01/19/2017] [Indexed: 12/17/2022] Open
Abstract
Next-generation sequencing (NGS) technology has expanded in the last decades with significant improvements in the reliability, sequencing chemistry, pipeline analyses, data interpretation and costs. Such advances make the use of NGS feasible in clinical practice today. This review describes the recent technological developments in NGS applied to the field of oncology. A number of clinical applications are reviewed, i.e., mutation detection in inherited cancer syndromes based on DNA-sequencing, detection of spliceogenic variants based on RNA-sequencing, DNA-sequencing to identify risk modifiers and application for pre-implantation genetic diagnosis, cancer somatic mutation analysis, pharmacogenetics and liquid biopsy. Conclusive remarks, clinical limitations, implications and ethical considerations that relate to the different applications are provided.
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Affiliation(s)
- Rick Kamps
- Department of Clinical Genetics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Rita D Brandão
- Department of Clinical Genetics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Bianca J van den Bosch
- Department of Clinical Genetics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Aimee D C Paulussen
- Department of Clinical Genetics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Sofia Xanthoulea
- Department of Gynaecology and Obstetrics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Marinus J Blok
- Department of Clinical Genetics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Andrea Romano
- Department of Gynaecology and Obstetrics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
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165
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Yurgelun MB, Kulke MH, Fuchs CS, Allen BA, Uno H, Hornick JL, Ukaegbu CI, Brais LK, McNamara PG, Mayer RJ, Schrag D, Meyerhardt JA, Ng K, Kidd J, Singh N, Hartman AR, Wenstrup RJ, Syngal S. Cancer Susceptibility Gene Mutations in Individuals With Colorectal Cancer. J Clin Oncol 2017; 35:1086-1095. [PMID: 28135145 DOI: 10.1200/jco.2016.71.0012] [Citation(s) in RCA: 317] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Purpose Hereditary factors play an important role in colorectal cancer (CRC) risk, yet the prevalence of germline cancer susceptibility gene mutations in patients with CRC unselected for high-risk features (eg, early age at diagnosis, personal/family history of cancer or polyps, tumor microsatellite instability [MSI], mismatch repair [MMR] deficiency) is unknown. Patients and Methods We recruited 1,058 participants who received CRC care in a clinic-based setting without preselection for age at diagnosis, personal/family history, or MSI/MMR results. All participants underwent germline testing for mutations in 25 genes associated with inherited cancer risk. Each gene was categorized as high penetrance or moderate penetrance on the basis of published estimates of the lifetime cancer risks conferred by pathogenic germline mutations in that gene. Results One hundred five (9.9%; 95% CI, 8.2% to 11.9%) of 1,058 participants carried one or more pathogenic mutations, including 33 (3.1%) with Lynch syndrome (LS). Twenty-eight (96.6%) of 29 available LS CRCs demonstrated abnormal MSI/MMR results. Seventy-four (7.0%) of 1,058 participants carried non-LS gene mutations, including 23 (2.2%) with mutations in high-penetrance genes (five APC, three biallelic MUTYH, 11 BRCA1/2, two PALB2, one CDKN2A, and one TP53), 15 of whom lacked clinical histories suggestive of their underlying mutation. Thirty-eight (3.6%) participants had moderate-penetrance CRC risk gene mutations (19 monoallelic MUTYH, 17 APC*I1307K, two CHEK2). Neither proband age at CRC diagnosis, family history of CRC, nor personal history of other cancers significantly predicted the presence of pathogenic mutations in non-LS genes. Conclusion Germline cancer susceptibility gene mutations are carried by 9.9% of patients with CRC. MSI/MMR testing reliably identifies LS probands, although 7.0% of patients with CRC carry non-LS mutations, including 1.0% with BRCA1/2 mutations.
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Affiliation(s)
- Matthew B Yurgelun
- Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Hajime Uno, Chinedu I. Ukaegbu, Lauren K. Brais, Philip G. McNamara, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Dana-Farber Cancer Institute; Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Hajime Uno, Jason L. Hornick, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Harvard Medical School; Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Jason L. Hornick, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Brigham and Women's Hospital, Boston, MA; and Brian A. Allen, John Kidd, Nanda Singh, Anne-Renee Hartman, and Richard J. Wenstrup, Myriad Genetics, Salt Lake City, UT
| | - Matthew H Kulke
- Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Hajime Uno, Chinedu I. Ukaegbu, Lauren K. Brais, Philip G. McNamara, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Dana-Farber Cancer Institute; Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Hajime Uno, Jason L. Hornick, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Harvard Medical School; Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Jason L. Hornick, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Brigham and Women's Hospital, Boston, MA; and Brian A. Allen, John Kidd, Nanda Singh, Anne-Renee Hartman, and Richard J. Wenstrup, Myriad Genetics, Salt Lake City, UT
| | - Charles S Fuchs
- Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Hajime Uno, Chinedu I. Ukaegbu, Lauren K. Brais, Philip G. McNamara, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Dana-Farber Cancer Institute; Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Hajime Uno, Jason L. Hornick, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Harvard Medical School; Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Jason L. Hornick, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Brigham and Women's Hospital, Boston, MA; and Brian A. Allen, John Kidd, Nanda Singh, Anne-Renee Hartman, and Richard J. Wenstrup, Myriad Genetics, Salt Lake City, UT
| | - Brian A Allen
- Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Hajime Uno, Chinedu I. Ukaegbu, Lauren K. Brais, Philip G. McNamara, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Dana-Farber Cancer Institute; Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Hajime Uno, Jason L. Hornick, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Harvard Medical School; Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Jason L. Hornick, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Brigham and Women's Hospital, Boston, MA; and Brian A. Allen, John Kidd, Nanda Singh, Anne-Renee Hartman, and Richard J. Wenstrup, Myriad Genetics, Salt Lake City, UT
| | - Hajime Uno
- Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Hajime Uno, Chinedu I. Ukaegbu, Lauren K. Brais, Philip G. McNamara, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Dana-Farber Cancer Institute; Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Hajime Uno, Jason L. Hornick, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Harvard Medical School; Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Jason L. Hornick, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Brigham and Women's Hospital, Boston, MA; and Brian A. Allen, John Kidd, Nanda Singh, Anne-Renee Hartman, and Richard J. Wenstrup, Myriad Genetics, Salt Lake City, UT
| | - Jason L Hornick
- Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Hajime Uno, Chinedu I. Ukaegbu, Lauren K. Brais, Philip G. McNamara, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Dana-Farber Cancer Institute; Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Hajime Uno, Jason L. Hornick, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Harvard Medical School; Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Jason L. Hornick, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Brigham and Women's Hospital, Boston, MA; and Brian A. Allen, John Kidd, Nanda Singh, Anne-Renee Hartman, and Richard J. Wenstrup, Myriad Genetics, Salt Lake City, UT
| | - Chinedu I Ukaegbu
- Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Hajime Uno, Chinedu I. Ukaegbu, Lauren K. Brais, Philip G. McNamara, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Dana-Farber Cancer Institute; Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Hajime Uno, Jason L. Hornick, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Harvard Medical School; Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Jason L. Hornick, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Brigham and Women's Hospital, Boston, MA; and Brian A. Allen, John Kidd, Nanda Singh, Anne-Renee Hartman, and Richard J. Wenstrup, Myriad Genetics, Salt Lake City, UT
| | - Lauren K Brais
- Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Hajime Uno, Chinedu I. Ukaegbu, Lauren K. Brais, Philip G. McNamara, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Dana-Farber Cancer Institute; Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Hajime Uno, Jason L. Hornick, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Harvard Medical School; Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Jason L. Hornick, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Brigham and Women's Hospital, Boston, MA; and Brian A. Allen, John Kidd, Nanda Singh, Anne-Renee Hartman, and Richard J. Wenstrup, Myriad Genetics, Salt Lake City, UT
| | - Philip G McNamara
- Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Hajime Uno, Chinedu I. Ukaegbu, Lauren K. Brais, Philip G. McNamara, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Dana-Farber Cancer Institute; Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Hajime Uno, Jason L. Hornick, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Harvard Medical School; Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Jason L. Hornick, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Brigham and Women's Hospital, Boston, MA; and Brian A. Allen, John Kidd, Nanda Singh, Anne-Renee Hartman, and Richard J. Wenstrup, Myriad Genetics, Salt Lake City, UT
| | - Robert J Mayer
- Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Hajime Uno, Chinedu I. Ukaegbu, Lauren K. Brais, Philip G. McNamara, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Dana-Farber Cancer Institute; Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Hajime Uno, Jason L. Hornick, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Harvard Medical School; Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Jason L. Hornick, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Brigham and Women's Hospital, Boston, MA; and Brian A. Allen, John Kidd, Nanda Singh, Anne-Renee Hartman, and Richard J. Wenstrup, Myriad Genetics, Salt Lake City, UT
| | - Deborah Schrag
- Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Hajime Uno, Chinedu I. Ukaegbu, Lauren K. Brais, Philip G. McNamara, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Dana-Farber Cancer Institute; Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Hajime Uno, Jason L. Hornick, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Harvard Medical School; Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Jason L. Hornick, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Brigham and Women's Hospital, Boston, MA; and Brian A. Allen, John Kidd, Nanda Singh, Anne-Renee Hartman, and Richard J. Wenstrup, Myriad Genetics, Salt Lake City, UT
| | - Jeffrey A Meyerhardt
- Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Hajime Uno, Chinedu I. Ukaegbu, Lauren K. Brais, Philip G. McNamara, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Dana-Farber Cancer Institute; Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Hajime Uno, Jason L. Hornick, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Harvard Medical School; Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Jason L. Hornick, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Brigham and Women's Hospital, Boston, MA; and Brian A. Allen, John Kidd, Nanda Singh, Anne-Renee Hartman, and Richard J. Wenstrup, Myriad Genetics, Salt Lake City, UT
| | - Kimmie Ng
- Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Hajime Uno, Chinedu I. Ukaegbu, Lauren K. Brais, Philip G. McNamara, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Dana-Farber Cancer Institute; Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Hajime Uno, Jason L. Hornick, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Harvard Medical School; Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Jason L. Hornick, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Brigham and Women's Hospital, Boston, MA; and Brian A. Allen, John Kidd, Nanda Singh, Anne-Renee Hartman, and Richard J. Wenstrup, Myriad Genetics, Salt Lake City, UT
| | - John Kidd
- Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Hajime Uno, Chinedu I. Ukaegbu, Lauren K. Brais, Philip G. McNamara, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Dana-Farber Cancer Institute; Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Hajime Uno, Jason L. Hornick, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Harvard Medical School; Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Jason L. Hornick, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Brigham and Women's Hospital, Boston, MA; and Brian A. Allen, John Kidd, Nanda Singh, Anne-Renee Hartman, and Richard J. Wenstrup, Myriad Genetics, Salt Lake City, UT
| | - Nanda Singh
- Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Hajime Uno, Chinedu I. Ukaegbu, Lauren K. Brais, Philip G. McNamara, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Dana-Farber Cancer Institute; Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Hajime Uno, Jason L. Hornick, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Harvard Medical School; Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Jason L. Hornick, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Brigham and Women's Hospital, Boston, MA; and Brian A. Allen, John Kidd, Nanda Singh, Anne-Renee Hartman, and Richard J. Wenstrup, Myriad Genetics, Salt Lake City, UT
| | - Anne-Renee Hartman
- Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Hajime Uno, Chinedu I. Ukaegbu, Lauren K. Brais, Philip G. McNamara, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Dana-Farber Cancer Institute; Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Hajime Uno, Jason L. Hornick, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Harvard Medical School; Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Jason L. Hornick, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Brigham and Women's Hospital, Boston, MA; and Brian A. Allen, John Kidd, Nanda Singh, Anne-Renee Hartman, and Richard J. Wenstrup, Myriad Genetics, Salt Lake City, UT
| | - Richard J Wenstrup
- Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Hajime Uno, Chinedu I. Ukaegbu, Lauren K. Brais, Philip G. McNamara, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Dana-Farber Cancer Institute; Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Hajime Uno, Jason L. Hornick, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Harvard Medical School; Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Jason L. Hornick, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Brigham and Women's Hospital, Boston, MA; and Brian A. Allen, John Kidd, Nanda Singh, Anne-Renee Hartman, and Richard J. Wenstrup, Myriad Genetics, Salt Lake City, UT
| | - Sapna Syngal
- Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Hajime Uno, Chinedu I. Ukaegbu, Lauren K. Brais, Philip G. McNamara, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Dana-Farber Cancer Institute; Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Hajime Uno, Jason L. Hornick, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Harvard Medical School; Matthew B. Yurgelun, Matthew H. Kulke, Charles S. Fuchs, Jason L. Hornick, Robert J. Mayer, Deborah Schrag, Jeffrey A. Meyerhardt, Kimmie Ng, and Sapna Syngal, Brigham and Women's Hospital, Boston, MA; and Brian A. Allen, John Kidd, Nanda Singh, Anne-Renee Hartman, and Richard J. Wenstrup, Myriad Genetics, Salt Lake City, UT
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Coffee B, Cox HC, Kidd J, Sizemore S, Brown K, Manley S, Mancini-DiNardo D. Detection of somatic variants in peripheral blood lymphocytes using a next generation sequencing multigene pan cancer panel. Cancer Genet 2017; 211:5-8. [PMID: 28279308 DOI: 10.1016/j.cancergen.2017.01.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 12/21/2016] [Accepted: 01/06/2017] [Indexed: 12/13/2022]
Abstract
Next Generation Sequencing (NGS) multigene panels, which are routinely used to assess hereditary cancer risk, can detect both inherited germline variants and somatic variants in cancer-risk genes. We evaluated the frequency and distribution of likely somatic Pathogenic and Likely Pathogenic variants (PVs) detected in >220,000 individuals who underwent clinical testing with a 25-gene panel between September 2013 and March 2016. Likely somatic PVs are defined as variants with NGS read frequencies from 10% to 30%. Overall, 137 (0.06%) individuals were identified as carrying likely somatic PVs, most commonly in TP53 (73), CHEK2 (27), and ATM (20). Among this group, a second PV with a NGS read frequency consistent with a germline variant within the same gene or a different gene on the panel was detected in 21 individuals (15.3%), which is similar to the detection rate in our general testing population. Likely somatic PVs accounted for 38.8% of all PVs in TP53. In comparison, likely somatic PVs accounted for <1% of PVs in most other genes. Likely somatic PVs were more frequently identified in older individuals (p < 0.001). Additional studies are ongoing to further investigate the incidence and clinical implications of somatic variants, enabling the appropriate medical management for these patients.
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Affiliation(s)
- Bradford Coffee
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT, USA.
| | - Hannah C Cox
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT, USA
| | - John Kidd
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT, USA
| | - Scott Sizemore
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT, USA
| | - Krystal Brown
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT, USA
| | - Susan Manley
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT, USA
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167
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Feliubadaló L, Tonda R, Gausachs M, Trotta JR, Castellanos E, López-Doriga A, Teulé À, Tornero E, Del Valle J, Gel B, Gut M, Pineda M, González S, Menéndez M, Navarro M, Capellá G, Gut I, Serra E, Brunet J, Beltran S, Lázaro C. Benchmarking of Whole Exome Sequencing and Ad Hoc Designed Panels for Genetic Testing of Hereditary Cancer. Sci Rep 2017; 7:37984. [PMID: 28050010 PMCID: PMC5209723 DOI: 10.1038/srep37984] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 11/02/2016] [Indexed: 12/14/2022] Open
Abstract
Next generation sequencing panels have been developed for hereditary cancer, although there is some debate about their cost-effectiveness compared to exome sequencing. The performance of two panels is compared to exome sequencing. Twenty-four patients were selected: ten with identified mutations (control set) and fourteen suspicious of hereditary cancer but with no mutation (discovery set). TruSight Cancer (94 genes) and a custom panel (122 genes) were assessed alongside exome sequencing. Eighty-three genes were targeted by the two panels and exome sequencing. More than 99% of bases had a read depth of over 30x in the panels, whereas exome sequencing covered 94%. Variant calling with standard settings identified the 10 mutations in the control set, with the exception of MSH6 c.255dupC using TruSight Cancer. In the discovery set, 240 unique non-silent coding and canonic splice-site variants were identified in the panel genes, 7 of them putatively pathogenic (in ATM, BARD1, CHEK2, ERCC3, FANCL, FANCM, MSH2). The three approaches identified a similar number of variants in the shared genes. Exomes were more expensive than panels but provided additional data. In terms of cost and depth, panels are a suitable option for genetic diagnostics, although exomes also identify variants in non-targeted genes.
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Affiliation(s)
- Lídia Feliubadaló
- Hereditary Cancer Program, Joint Program on Hereditary Cancer, Catalan Institute of Oncology, IDIBELL campus in Hospitalet de Llobregat, Catalonia, Spain
| | - Raúl Tonda
- Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Catalonia, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain
| | - Mireia Gausachs
- Hereditary Cancer Program, Joint Program on Hereditary Cancer, Catalan Institute of Oncology, IDIBELL campus in Hospitalet de Llobregat, Catalonia, Spain
| | - Jean-Rémi Trotta
- Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Catalonia, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain
| | - Elisabeth Castellanos
- Genetic Variation in Cancer Group, Joint Program on Hereditary Cancer, Institut de Medicina Predictiva i Personalitzada del Càncer, Badalona, Catalonia, Spain
| | - Adriana López-Doriga
- Hereditary Cancer Program, Joint Program on Hereditary Cancer, Catalan Institute of Oncology, IDIBELL campus in Hospitalet de Llobregat, Catalonia, Spain
| | - Àlex Teulé
- Hereditary Cancer Program, Joint Program on Hereditary Cancer, Catalan Institute of Oncology, IDIBELL campus in Hospitalet de Llobregat, Catalonia, Spain
| | - Eva Tornero
- Hereditary Cancer Program, Joint Program on Hereditary Cancer, Catalan Institute of Oncology, IDIBELL campus in Hospitalet de Llobregat, Catalonia, Spain
| | - Jesús Del Valle
- Hereditary Cancer Program, Joint Program on Hereditary Cancer, Catalan Institute of Oncology, IDIBELL campus in Hospitalet de Llobregat, Catalonia, Spain
| | - Bernat Gel
- Genetic Variation in Cancer Group, Joint Program on Hereditary Cancer, Institut de Medicina Predictiva i Personalitzada del Càncer, Badalona, Catalonia, Spain
| | - Marta Gut
- Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Catalonia, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain
| | - Marta Pineda
- Hereditary Cancer Program, Joint Program on Hereditary Cancer, Catalan Institute of Oncology, IDIBELL campus in Hospitalet de Llobregat, Catalonia, Spain
| | - Sara González
- Hereditary Cancer Program, Joint Program on Hereditary Cancer, Catalan Institute of Oncology, IDIBELL campus in Hospitalet de Llobregat, Catalonia, Spain
| | - Mireia Menéndez
- Hereditary Cancer Program, Joint Program on Hereditary Cancer, Catalan Institute of Oncology, IDIBELL campus in Hospitalet de Llobregat, Catalonia, Spain
| | - Matilde Navarro
- Hereditary Cancer Program, Joint Program on Hereditary Cancer, Catalan Institute of Oncology, IDIBELL campus in Hospitalet de Llobregat, Catalonia, Spain
| | - Gabriel Capellá
- Hereditary Cancer Program, Joint Program on Hereditary Cancer, Catalan Institute of Oncology, IDIBELL campus in Hospitalet de Llobregat, Catalonia, Spain
| | - Ivo Gut
- Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Catalonia, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain
| | - Eduard Serra
- Genetic Variation in Cancer Group, Joint Program on Hereditary Cancer, Institut de Medicina Predictiva i Personalitzada del Càncer, Badalona, Catalonia, Spain
| | - Joan Brunet
- Hereditary Cancer Program, Joint Program on Hereditary Cancer, Catalan Institute of Oncology, IdibGi in Girona, Catalonia, Spain
| | - Sergi Beltran
- Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Catalonia, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain
| | - Conxi Lázaro
- Hereditary Cancer Program, Joint Program on Hereditary Cancer, Catalan Institute of Oncology, IDIBELL campus in Hospitalet de Llobregat, Catalonia, Spain
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168
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de Gouvea ACRC, Garber JE. Breast Cancer Genetics. Breast Cancer 2017. [DOI: 10.1007/978-3-319-48848-6_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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169
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Cragun D, Kinney AY, Pal T. Care delivery considerations for widespread and equitable implementation of inherited cancer predisposition testing. Expert Rev Mol Diagn 2017; 17:57-70. [PMID: 27910721 PMCID: PMC5642111 DOI: 10.1080/14737159.2017.1267567] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
INTRODUCTION DNA sequencing advances through next-generation sequencing (NGS) and several practice changing events, have led to shifting paradigms for inherited cancer predisposition testing. These changes necessitated a means by which to maximize health benefits without unnecessarily inflating healthcare costs and exacerbating health disparities. Areas covered: NGS-based tests encompass multi-gene panel tests, whole exome sequencing, and whole genome sequencing, all of which test for multiple genes simultaneously, compared to prior sequencing practices through which testing was performed sequentially for one or two genes. Taking an ecological approach, this article synthesizes the current literature to consider the broad impact of these advances from the individual patient-, interpersonal-, organizational-, community- and policy-levels. Furthermore, the authors describe how multi-level factors that impact genetic testing and follow-up care reveal great potential to widen existing health disparities if these issues are not addressed. Expert commentary: As we consider ways to maximize patient benefit from testing in a cost effective manner, it is important to consider perspectives from multiple levels. This information is needed to guide the development of interventions such that the promise of genomic testing may be realized by all populations, regardless of race, ethnicity and ability to pay.
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Affiliation(s)
- Deborah Cragun
- University of South Florida, Department of Global Health, College of Public Health
| | - Anita Y Kinney
- University of New Mexico Comprehensive Cancer Center
- Department of Internal Medicine, University of New Mexico
| | - Tuya Pal
- Department of Cancer Epidemiology, Population Sciences, Moffitt Cancer Center
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170
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Abstract
Mutations linked to hereditary cancer syndromes may increase an individual's risk of developing cancer, as well as its recurrence. New genes that may also carry pathogenic mutations associated with cancer risk have been identified; as a result, individuals previously tested should consider additional testing. This article provides a case study illustrating the importance of such testing.
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171
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Ring KL, Bruegl AS, Allen BA, Elkin EP, Singh N, Hartman AR, Daniels MS, Broaddus RR. Germline multi-gene hereditary cancer panel testing in an unselected endometrial cancer cohort. Mod Pathol 2016; 29:1381-1389. [PMID: 27443514 PMCID: PMC5541389 DOI: 10.1038/modpathol.2016.135] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 06/03/2016] [Accepted: 06/04/2016] [Indexed: 01/06/2023]
Abstract
Hereditary endometrial carcinoma is associated with germline mutations in Lynch syndrome genes. The role of other cancer predisposition genes is unclear. We aimed to determine the prevalence of cancer predisposition gene mutations in an unselected endometrial carcinoma patient cohort. Mutations in 25 genes were identified using a next-generation sequencing-based panel applied in 381 endometrial carcinoma patients who had undergone tumor testing to screen for Lynch syndrome. Thirty-five patients (9.2%) had a deleterious mutation: 22 (5.8%) in Lynch syndrome genes (three MLH1, five MSH2, two EPCAM-MSH2, six MSH6, and six PMS2) and 13 (3.4%) in 10 non-Lynch syndrome genes (four CHEK2, one each in APC, ATM, BARD1, BRCA1, BRCA2, BRIP1, NBN, PTEN, and RAD51C). Of 21 patients with deleterious mutations in Lynch syndrome genes with tumor testing, 2 (9.5%) had tumor testing results suggestive of sporadic cancer. Of 12 patients with deleterious mutations in MSH6 and PMS2, 10 were diagnosed at age >50 and 8 did not have a family history of Lynch syndrome-associated cancers. Patients with deleterious mutations in non-Lynch syndrome genes were more likely to have serous tumor histology (23.1 vs 6.4%, P=0.02). The three patients with non-Lynch syndrome deleterious mutations and serous histology had mutations in BRCA2, BRIP1, and RAD51C. Current clinical criteria fail to identify a portion of actionable mutations in Lynch syndrome and other hereditary cancer syndromes. Performance characteristics of tumor testing are sufficiently robust to implement universal tumor testing to identify patients with Lynch syndrome. Germline multi-gene panel testing is feasible and informative, leading to the identification of additional actionable mutations.
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Affiliation(s)
- Kari L. Ring
- The University of Texas MD Anderson Cancer Center, Houston, TX, Department of Gynecologic Oncology and Reproductive Medicine
| | - Amanda S. Bruegl
- Oregon Health & Science University, Portland, OR, Department of Obstetrics and Gynecology
| | | | | | | | | | - Molly S. Daniels
- The University of Texas MD Anderson Cancer Center, Houston, TX, Department of Gynecologic Oncology and Reproductive Medicine
| | - Russell R. Broaddus
- The University of Texas MD Anderson Cancer Center, Houston, TX, Department of Pathology
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172
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Hall MJ, Obeid E, Daly MB. Multigene Panels to Evaluate Hereditary Cancer Risk: Reckless or Relevant? J Clin Oncol 2016; 34:4186-4187. [PMID: 27551136 DOI: 10.1200/jco.2016.68.6725] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Michael J Hall
- Michael J. Hall, Elias Obeid, and Mary B. Daly, Fox Chase Cancer Center, Philadelphia, PA
| | - Elias Obeid
- Michael J. Hall, Elias Obeid, and Mary B. Daly, Fox Chase Cancer Center, Philadelphia, PA
| | - Mary B Daly
- Michael J. Hall, Elias Obeid, and Mary B. Daly, Fox Chase Cancer Center, Philadelphia, PA
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173
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Graffeo R, Livraghi L, Pagani O, Goldhirsch A, Partridge AH, Garber JE. Time to incorporate germline multigene panel testing into breast and ovarian cancer patient care. Breast Cancer Res Treat 2016; 160:393-410. [DOI: 10.1007/s10549-016-4003-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 09/23/2016] [Indexed: 02/07/2023]
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174
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Marabelli M, Molinaro V, Abou Khouzam R, Berrino E, Panero M, Balsamo A, Venesio T, Ranzani GN. Colorectal Adenomatous Polyposis: Heterogeneity of Susceptibility Gene Mutations and Phenotypes in a Cohort of Italian Patients. Genet Test Mol Biomarkers 2016; 20:777-785. [PMID: 27705013 DOI: 10.1089/gtmb.2016.0198] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
AIMS Colorectal adenomatous polyposis entailing cancer predisposition is caused by constitutional mutations in different genes. APC is associated with the familial adenomatous polyposis (FAP/AFAP) and MUTYH with the MUTYH-associated polyposis (MAP), while POLE and POLD1 mutations cause the polymerase proofreading-associated polyposis (PPAP). METHODS We screened for mutations in patients with multiple adenomas/FAP: 121 patients were analyzed for APC and MUTYH mutations, and 36 patients were also evaluated for POLE and POLD1 gene mutations. RESULTS We found 20 FAP/AFAP, 15 MAP, and no PPAP subjects: pathogenic mutations proved to be heterogeneous, and included 5 APC and 1 MUTYH novel mutations. The mutation detection rate was significantly different between patients with 5-100 polyps and those with >100 polyps (p = 8.154 × 10-7), with APC mutations being associated with an aggressive phenotype (p = 1.279 × 10-9). Mean age at diagnosis was lower in FAP/AFAP compared to MAP (p = 3.055 × 10-4). Mutation-negative probands showed a mean age at diagnosis that was significantly higher than FAP/AFAP (p = 3.46986 × 10-7) and included 45.3% of patients with <30 polyps and 70.9% of patients with no family history. CONCLUSIONS This study enlarges the APC and MUTYH mutational spectra, and also evaluated variants of uncertain significance, including the MUTYH p.Gln338His mutation. Moreover this study underscores the phenotypic heterogeneity and genotype-phenotype correlations in a cohort of Italian patients.
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Affiliation(s)
- Monica Marabelli
- 1 Department of Biology and Biotechnology, University of Pavia , Pavia, Italy
| | - Valeria Molinaro
- 1 Department of Biology and Biotechnology, University of Pavia , Pavia, Italy
| | - Raefa Abou Khouzam
- 1 Department of Biology and Biotechnology, University of Pavia , Pavia, Italy
| | | | - Mara Panero
- 2 Candiolo Cancer Institute , FPO-IRCCS, Torino, Italy
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175
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Universal Versus Targeted Screening for Lynch Syndrome: Comparing Ascertainment and Costs Based on Clinical Experience. Dig Dis Sci 2016; 61:2887-2895. [PMID: 27384051 DOI: 10.1007/s10620-016-4218-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Accepted: 05/27/2016] [Indexed: 12/09/2022]
Abstract
BACKGROUND Strategies to screen colorectal cancers (CRCs) for Lynch syndrome are evolving rapidly; the optimal strategy remains uncertain. AIM We compared targeted versus universal screening of CRCs for Lynch syndrome. METHODS In 2010-2011, we employed targeted screening (age < 60 and/or Bethesda criteria). From 2012 to 2014, we screened all CRCs. Immunohistochemistry for the four mismatch repair proteins was done in all cases, followed by other diagnostic studies as indicated. We modeled the diagnostic costs of detecting Lynch syndrome and estimated the 5-year costs of preventing CRC by colonoscopy screening, using a system dynamics model. RESULTS Using targeted screening, 51/175 (29 %) cancers fit criteria and were tested by immunohistochemistry; 15/51 (29 %, or 8.6 % of all CRCs) showed suspicious loss of ≥1 mismatch repair protein. Germline mismatch repair gene mutations were found in 4/4 cases sequenced (11 suspected cases did not have germline testing). Using universal screening, 17/292 (5.8 %) screened cancers had abnormal immunohistochemistry suspicious for Lynch syndrome. Germline mismatch repair mutations were found in only 3/10 cases sequenced (7 suspected cases did not have germline testing). The mean cost to identify Lynch syndrome probands was ~$23,333/case for targeted screening and ~$175,916/case for universal screening at our institution. Estimated costs to identify and screen probands and relatives were: targeted, $9798/case and universal, $38,452/case. CONCLUSIONS In real-world Lynch syndrome management, incomplete clinical follow-up was the major barrier to do genetic testing. Targeted screening costs 2- to 7.5-fold less than universal and rarely misses Lynch syndrome cases. Future changes in testing costs will likely change the optimal algorithm.
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176
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Abstract
Prevention is an essential component of cancer eradication. Next-generation sequencing of cancer genomes and epigenomes has defined large numbers of driver mutations and molecular subgroups, leading to therapeutic advances. By comparison, there is a relative paucity of such knowledge in premalignant neoplasia, which inherently limits the potential to develop precision prevention strategies. Studies on the interplay between germ-line and somatic events have elucidated genetic processes underlying premalignant progression and preventive targets. Emerging data hint at the immune system's ability to intercept premalignancy and prevent cancer. Genetically engineered mouse models have identified mechanisms by which genetic drivers and other somatic alterations recruit inflammatory cells and induce changes in normal cells to create and interact with the premalignant tumor microenvironment to promote oncogenesis and immune evasion. These studies are currently limited to only a few lesion types and patients. In this Perspective, we advocate a large-scale collaborative effort to systematically map the biology of premalignancy and the surrounding cellular response. By bringing together scientists from diverse disciplines (e.g., biochemistry, omics, and computational biology; microbiology, immunology, and medical genetics; engineering, imaging, and synthetic chemistry; and implementation science), we can drive a concerted effort focused on cancer vaccines to reprogram the immune response to prevent, detect, and reject premalignancy. Lynch syndrome, clonal hematopoiesis, and cervical intraepithelial neoplasia which also serve as models for inherited syndromes, blood, and viral premalignancies, are ideal scenarios in which to launch this initiative.
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177
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Stoffel EM, Yurgelun MB. Genetic predisposition to colorectal cancer: Implications for treatment and prevention. Semin Oncol 2016; 43:536-542. [PMID: 27899184 DOI: 10.1053/j.seminoncol.2016.08.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 08/17/2016] [Indexed: 12/24/2022]
Abstract
Colorectal cancer (CRC) is the third most common cancer diagnosed in men and women and approximately 5% of cases are associated with identifiable germline mutations associated with hereditary cancer syndromes. Lifetime risks for CRC can approach 50%-80% for mutation carriers in the absence of endoscopic and/or surgical intervention, and early identification of at-risk individuals can guide clinical interventions for cancer prevention and treatment. Personal and family history and molecular phenotype of CRC tumors are used in determining which patients should be referred for clinical genetic evaluation. Outcomes of genetic testing performed using next-generation sequencing (NGS) multigene panels suggest there can be significant overlap in clinical features among the various hereditary cancer syndromes. This review summarizes new developments in diagnosis and management of patients with genetic predisposition to CRC.
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178
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Tung N, Domchek SM, Stadler Z, Nathanson KL, Couch F, Garber JE, Offit K, Robson ME. Counselling framework for moderate-penetrance cancer-susceptibility mutations. Nat Rev Clin Oncol 2016; 13:581-8. [PMID: 27296296 PMCID: PMC5513673 DOI: 10.1038/nrclinonc.2016.90] [Citation(s) in RCA: 218] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The use of multigene panels for the assessment of cancer susceptibility is expanding rapidly in clinical practice, particularly in the USA, despite concerns regarding the uncertain clinical validity for some gene variants and the uncertain clinical utility of most multigene panels. So-called 'moderate-penetrance' gene mutations associated with cancer susceptibility are identified in approximately 2-5% of individuals referred for clinical testing; some of these mutations are potentially actionable. Nevertheless, the appropriate management of individuals harbouring such moderate-penetrance genetic variants is unclear. The cancer risks associated with mutations in moderate-penetrance genes are lower and different than those reported for high-penetrance gene mutations (such as mutations in BRCA1 and BRCA2, and those associated with Lynch syndrome). The extrapolation of guidelines for the management of individuals with high-penetrance variants of cancer-susceptibility genes to the clinical care of patients with moderate-penetrance gene mutations could result in substantial harm. Thus, we provide a framework for clinical decision-making pending the development of a sufficient evidence base to document the clinical utility of the interventions for individuals with inherited moderate-penetrance gene mutations associated with an increased risk of cancer.
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Affiliation(s)
- Nadine Tung
- Division of Hematology-Oncology, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, Massachusetts 02215, USA
| | - Susan M Domchek
- Abramson Cancer Center, 3400 Spruce Street, Philadelphia, Pennsylvania 19104, USA, and the Department of Medicine, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, Pennsylvania 19104, USA
| | - Zsofia Stadler
- Clinical Genetics Service, Memorial Sloan Kettering Cancer Center, 1275 York Avenue; and the Weill Cornell Medical College, 1300 York Avenue, New York, New York 10065, USA
| | - Katherine L Nathanson
- Abramson Cancer Center, 3400 Spruce Street, Philadelphia, Pennsylvania 19104, USA, and the Department of Medicine, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, Pennsylvania 19104, USA
| | - Fergus Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street South West, Rochester, Minnesota 55905, USA
| | - Judy E Garber
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, USA
| | - Kenneth Offit
- Clinical Genetics Service, Memorial Sloan Kettering Cancer Center, 1275 York Avenue; and the Weill Cornell Medical College, 1300 York Avenue, New York, New York 10065, USA
| | - Mark E Robson
- Clinical Genetics Service, Memorial Sloan Kettering Cancer Center, 1275 York Avenue; and the Weill Cornell Medical College, 1300 York Avenue, New York, New York 10065, USA
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179
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Abstract
Although almost all gastrointestinal cancers develop from sporadic genomic events, approximately 5% arise from germline mutations in genes associated with cancer predisposition. The number of these genes continues to increase. Tumor phenotypes and family history provide the framework for identifying at-risk individuals. The diagnosis of a hereditary cancer syndrome has implications for management of patients and their families. Systematic approaches that integrate family history and molecular characterization of tumors and polyps facilitate identification of individuals with this genetic predisposition. This article summarizes diagnosis and management of hereditary cancer syndromes associated with gastrointestinal cancers.
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Affiliation(s)
- Elena M Stoffel
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan Health System, 2150A Cancer Center, Ann Arbor, MI 48109, USA.
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180
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Abstract
Cancer is fundamentally a genetic disease caused by mutational or epigenetic alterations in DNA. There has been a remarkable expansion of the molecular understanding of colonic carcinogenesis in the last 30 years and that understanding is changing many aspects of colorectal cancer care. It is becoming increasingly clear that there are genetic subsets of colorectal cancer that have different risk factors, prognosis, and response to treatment. This article provides a general update on colorectal cancer and highlights the ways that genetics is changing clinical care.
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Affiliation(s)
- Joshua C Obuch
- Division of Gastroenterology & Hepatology, Department of Medicine, University of Colorado, School of Medicine, 12631 E. 17th Avenue, MS B-158, Aurora, CO 80045, USA
| | - Dennis J Ahnen
- University of Colorado, School of Medicine, 12631 E. 17th Avenue, MS B-158, Aurora, CO 80045, USA.
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181
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Dragani TA, Castells A, Kulasingam V, Diamandis EP, Earl H, Iams WT, Lovly CM, Sedelaar JPM, Schalken JA. Major milestones in translational oncology. BMC Med 2016; 14:110. [PMID: 27469586 PMCID: PMC4964079 DOI: 10.1186/s12916-016-0654-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 07/13/2016] [Indexed: 11/16/2022] Open
Abstract
Translational oncology represents a bridge between basic research and clinical practice in cancer medicine. Today, translational research in oncology benefits from an abundance of knowledge resulting from genome-scale studies regarding the molecular pathways involved in tumorigenesis. In this Forum article, we highlight the state of the art of translational oncology in five major cancer types. We illustrate the use of molecular profiling to subtype colorectal cancer for both diagnosis and treatment, and summarize the results of a nationwide screening program for ovarian cancer based on detection of a tumor biomarker in serum. Additionally, we discuss how circulating tumor DNA can be assayed to safely monitor breast cancer over the course of treatment, and report on how therapy with immune checkpoint inhibitors is proving effective in advanced lung cancer. Finally, we summarize efforts to use molecular profiling of prostate cancer biopsy specimens to support treatment decisions. Despite encouraging early successes, we cannot disregard the complex genetics of individual susceptibility to cancer nor the enormous complexity of the somatic changes observed in tumors, which urge particular attention to the development of personalized therapies.
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Affiliation(s)
- Tommaso A. Dragani
- Fondazione IRCCS Istituto Nazionale dei Tumori, Via G.A. Amadeo 42, I-20133 Milan, Italy
| | - Antoni Castells
- Department of Gastroenterology, Hospital Clinic, University of Barcelona, IDIBAPS, CIBERehd, Barcelona, Catalonia Spain
| | - Vathany Kulasingam
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario Canada
- Department of Clinical Biochemistry, University Health Network, Toronto, Ontario Canada
| | - Eleftherios P. Diamandis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario Canada
- Department of Clinical Biochemistry, University Health Network, Toronto, Ontario Canada
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario Canada
| | - Helena Earl
- Deptartment of Oncology, University of Cambridge, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre, Addenbrooke’s Hospital, Cambridge Biomedical Campus, Cambridge, UK
| | - Wade T. Iams
- Department of Medicine Vanderbilt University Medical Center, Nashville, TN USA
| | - Christine M. Lovly
- Department of Medicine Vanderbilt University Medical Center, Nashville, TN USA
- Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, TN USA
- Vanderbilt-Ingram Cancer Center, Nashville, TN USA
| | | | - Jack A. Schalken
- Department of Urology, Radboud University Medical Center, Nijmegen, The Netherlands
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182
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Kennelly RP, Gryfe R, Winter DC. Familial colorectal cancer: Patient assessment, surveillance and surgical management. Eur J Surg Oncol 2016; 43:294-302. [PMID: 27546013 DOI: 10.1016/j.ejso.2016.07.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 07/12/2016] [Indexed: 02/06/2023] Open
Abstract
Germline mutations account for 5-10% of colorectal cancer. Most mutations are autosomal dominant with high penetrance and affected patients benefit greatly from appropriate treatment. This review presents the current knowledge regarding familial colorectal cancer and provides practical information based on international guidelines and the best available evidence regarding patient assessment, surveillance and surgical management. Surgeons are often the first point of contact and frequently, the main provider of care for families with cancer syndromes or patients with familial cancer. Patients with a polyposis phenotype should undergo appropriate genetic testing. In non-polyposis patients with a cancer diagnosis, tumor testing for Lynch syndrome can guide the use of genetic testing. In patients without a personal history of cancer or polyposis, a carefully obtained family history with testing of available tumor tissue or of a living relative affected by colorectal cancer informs the need for genetic testing. Surveillance and surgical management should be planned following thorough assessment of familial cancer risk. Evidence exists to provide guidance as to the surveillance strategies required, the specific indications of genetic testing and the appropriate timing of operative intervention. A carefully obtained family history with selective genetic testing should inform surveillance and surgical management in patients who have a genetic predisposition for the development of colorectal cancer.
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Affiliation(s)
- R P Kennelly
- Mount Sinai Hospital, Toronto, Ontario, Canada; St. Vincent's University Hospital, Dublin, Ireland.
| | - R Gryfe
- Mount Sinai Hospital, Toronto, Ontario, Canada
| | - D C Winter
- St. Vincent's University Hospital, Dublin, Ireland
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183
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Classification of genetic variants in genes associated with Lynch syndrome using a clinical history weighting algorithm. BMC Genet 2016; 17:99. [PMID: 27363726 PMCID: PMC4929734 DOI: 10.1186/s12863-016-0407-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 06/23/2016] [Indexed: 11/15/2022] Open
Abstract
Background Lynch syndrome is a hereditary cancer syndrome associated with high risks of colorectal and endometrial cancer that is caused by pathogenic variants in the mismatch repair genes (MLH1, MSH2, MSH6, PMS2, EPCAM). Accurate classification of variants identified in these genes as pathogenic or benign enables informed medical management decisions. Previously, we developed a clinical History Weighting Algorithm (HWA) for the classification of variants of uncertain significance (VUSs) in BRCA1 and BRCA2. The BRCA1/2 HWA is based on the premise that pathogenic variants in these genes will be identified more often in individuals with strong personal and/or family histories of breast and/or ovarian cancer, while the identification of benign variants should be independent of cancer history. Here we report the development of a similar HWA to allow for classification of VUSs in genes associated with Lynch syndrome using data collected through both syndrome-specific and pan-cancer panel testing. Methods Upon completion of algorithm development, the HWA was tested using simulated variants constructed from 79,214 probands, as well as 379 true variants. Positive (PPV) and negative predictive values (NPV) were calculated on a per gene basis. Results 25,500 pathogenic and 50,500 benign simulated variants were analyzed using the HWA and the PPVs and NPVs for each gene were greater than 0.997 and 0.999, respectively. The HWA was also evaluated using 100 trials for each of the 379 true variants. PPVs of >0.998 and NPVs of >0.999 were obtained for all genes. Conclusions We have developed and implemented a HWA to aid in the classification of VUSs in genes associated with Lynch syndrome. The work presented here demonstrates that this HWA is able to classify MLH1, MSH2, and MSH6 VUSs as either benign or pathogenic with high accuracy.
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184
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Whole Gene Capture Analysis of 15 CRC Susceptibility Genes in Suspected Lynch Syndrome Patients. PLoS One 2016; 11:e0157381. [PMID: 27300758 PMCID: PMC4907507 DOI: 10.1371/journal.pone.0157381] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 05/27/2016] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND AND AIMS Lynch Syndrome (LS) is caused by pathogenic germline variants in one of the mismatch repair (MMR) genes. However, up to 60% of MMR-deficient colorectal cancer cases are categorized as suspected Lynch Syndrome (sLS) because no pathogenic MMR germline variant can be identified, which leads to difficulties in clinical management. We therefore analyzed the genomic regions of 15 CRC susceptibility genes in leukocyte DNA of 34 unrelated sLS patients and 11 patients with MLH1 hypermethylated tumors with a clear family history. METHODS Using targeted next-generation sequencing, we analyzed the entire non-repetitive genomic sequence, including intronic and regulatory sequences, of 15 CRC susceptibility genes. In addition, tumor DNA from 28 sLS patients was analyzed for somatic MMR variants. RESULTS Of 1979 germline variants found in the leukocyte DNA of 34 sLS patients, one was a pathogenic variant (MLH1 c.1667+1delG). Leukocyte DNA of 11 patients with MLH1 hypermethylated tumors was negative for pathogenic germline variants in the tested CRC susceptibility genes and for germline MLH1 hypermethylation. Somatic DNA analysis of 28 sLS tumors identified eight (29%) cases with two pathogenic somatic variants, one with a VUS predicted to pathogenic and LOH, and nine cases (32%) with one pathogenic somatic variant (n = 8) or one VUS predicted to be pathogenic (n = 1). CONCLUSIONS This is the first study in sLS patients to include the entire genomic sequence of CRC susceptibility genes. An underlying somatic or germline MMR gene defect was identified in ten of 34 sLS patients (29%). In the remaining sLS patients, the underlying genetic defect explaining the MMRdeficiency in their tumors might be found outside the genomic regions harboring the MMR and other known CRC susceptibility genes.
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185
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The Fanconi anemia DNA damage repair pathway in the spotlight for germline predisposition to colorectal cancer. Eur J Hum Genet 2016; 24:1501-5. [PMID: 27165003 PMCID: PMC5027689 DOI: 10.1038/ejhg.2016.44] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 03/29/2016] [Accepted: 04/07/2016] [Indexed: 11/16/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most common neoplasms in the world. Fanconi anemia (FA) is a very rare genetic disease causing bone marrow failure, congenital growth abnormalities and cancer predisposition. The comprehensive FA DNA damage repair pathway requires the collaboration of 53 proteins and it is necessary to restore genome integrity by efficiently repairing damaged DNA. A link between FA genes in breast and ovarian cancer germline predisposition has been previously suggested. We selected 74 CRC patients from 40 unrelated Spanish families with strong CRC aggregation compatible with an autosomal dominant pattern of inheritance and without mutations in known hereditary CRC genes and performed germline DNA whole-exome sequencing with the aim of finding new candidate germline predisposition variants. After sequencing and data analysis, variant prioritization selected only those very rare alterations, producing a putative loss of function and located in genes with a role compatible with cancer. We detected an enrichment for variants in FA DNA damage repair pathway genes in our familial CRC cohort as 6 families carried heterozygous, rare, potentially pathogenic variants located in BRCA2/FANCD1, BRIP1/FANCJ, FANCC, FANCE and REV3L/POLZ. In conclusion, the FA DNA damage repair pathway may play an important role in the inherited predisposition to CRC.
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186
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Mork ME, You YN, Vilar E. Reply to L.B. Saltz. J Clin Oncol 2016; 34:1560-1. [DOI: 10.1200/jco.2015.66.2049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Maureen E. Mork
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Y. Nancy You
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Eduardo Vilar
- The University of Texas MD Anderson Cancer Center, Houston, TX
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187
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Screening for Cancer Genetic Syndromes With a Simple Risk-Assessment Tool in a Community-Based Open-Access Colonoscopy Practice. Am J Gastroenterol 2016; 111:589-93. [PMID: 27021195 DOI: 10.1038/ajg.2016.84] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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188
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Advances in Hereditary Colorectal and Pancreatic Cancers. Clin Ther 2016; 38:1600-21. [PMID: 27045993 DOI: 10.1016/j.clinthera.2016.03.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 03/05/2016] [Accepted: 03/08/2016] [Indexed: 12/19/2022]
Abstract
PURPOSE Innovations in genetic medicine have led to improvements in the early detection, prevention, and treatment of cancer for patients with inherited risks of gastrointestinal cancer, particularly hereditary colorectal cancer and hereditary pancreatic cancer. METHODS This review provides an update on recent data and key advances that have improved the identification, understanding, and management of patients with hereditary colorectal cancer and hereditary pancreatic cancer. FINDINGS This review details recent and emerging data that highlight the developing landscape of genetics in hereditary colorectal and pancreatic cancer risk. A summary is provided of the current state-of-the-art practices for identifying, evaluating, and managing patients with suspected hereditary colorectal cancer and pancreatic cancer risk. The impact of next-generation sequencing technologies in the clinical diagnosis of hereditary gastrointestinal cancer and also in discovery efforts of new genes linked to familial cancer risk are discussed. Emerging targeted therapies that may play a particularly important role in the treatment of patients with hereditary forms of colorectal cancer and pancreatic cancer are also reviewed. Current approaches for pancreatic cancer screening and the psychosocial impact of such procedures are also detailed. IMPLICATIONS Given the availability of new diagnostic, risk-reducing, and therapeutic strategies that exist for patients with hereditary risk of colorectal or pancreatic cancer, it is imperative that clinicians be vigilant about evaluating patients for hereditary cancer syndromes. Continuing to advance genetics research in hereditary gastrointestinal cancers will allow for more progress to be made in personalized medicine and prevention.
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189
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Vindigni SM, Kaz AM. Universal Screening of Colorectal Cancers for Lynch Syndrome: Challenges and Opportunities. Dig Dis Sci 2016; 61:969-76. [PMID: 26602911 DOI: 10.1007/s10620-015-3964-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 11/06/2015] [Indexed: 12/20/2022]
Abstract
Lynch syndrome (LS) is the most common heritable colorectal cancer (CRC) syndrome, accounting for approximately 3 % of CRC cases in the USA each year. LS results from a genetic mutation in one of the four mismatch repair genes, and clinically LS is associated with CRC and other gastrointestinal and extra-gastrointestinal malignancies. In this review, we describe the various clinical criteria utilized for the identification of LS patients and the inherent flaws with these criteria. We discuss the concept of universal testing for LS in all cases of newly diagnosed CRC, along with the potential benefits and challenges of universal testing. Several studies have shown that universal tumor testing is cost-effective and identifies cases of LS that are missed using traditional clinical criteria, which may result in reduced cancer mortality for probands and their families. Yet the full benefits of universal tumor testing may be limited by the availability and patient acceptance of genetic testing, and by logistical obstacles affecting the implementation of universal testing programs. Lastly, we comment on developing technologies such as massively parallel next-generation sequencing, which permits simultaneous sequencing of multiple genes involved in LS and other inherited colon cancer syndromes.
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Affiliation(s)
- Stephen M Vindigni
- Division of Gastroenterology, University of Washington School of Medicine, 1959 NE Pacific Street, Box 356424, Seattle, WA, 98105, USA
| | - Andrew M Kaz
- Division of Gastroenterology, University of Washington School of Medicine, 1959 NE Pacific Street, Box 356424, Seattle, WA, 98105, USA. .,VA Puget Sound Health Care System, 1660 S. Columbian Way, S-111-Gastro, Seattle, WA, 98108, USA.
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190
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Increased yield of actionable mutations using multi-gene panels to assess hereditary cancer susceptibility in an ethnically diverse clinical cohort. Cancer Genet 2016; 209:130-7. [PMID: 26908360 DOI: 10.1016/j.cancergen.2015.12.013] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 11/13/2015] [Accepted: 12/31/2015] [Indexed: 12/26/2022]
Abstract
This study aims to assess multi-gene panel testing in an ethnically diverse clinical cancer genetics practice. We conducted a retrospective study of individuals with a personal or family history of cancer undergoing clinically indicated multi-gene panel tests of 6-110 genes, from six commercial laboratories. The 475 patients in the study included 228 Hispanics (47.6%), 166 non-Hispanic Whites (35.4%), 55 Asians (11.6%), 19 Blacks (4.0%), and seven others (1.5%). Panel testing found that 15.6% (74/475) of patients carried deleterious mutations for a total of 79 mutations identified. This included 7.4% (35/475) of patients who had a mutation identified that would not have been tested with a gene-by-gene approach. The identification of a panel-added mutation impacted clinical management for most of cases (69%, 24/35), and genetic testing was recommended for the first degree relatives of nearly all of them (91%, 32/35). Variants of uncertain significance (VUSs) were identified in a higher proportion of tests performed in ethnic minorities. Multi-gene panel testing increases the yield of mutations detected and adds to the capability of providing individualized cancer risk assessment. VUSs represent an interpretive challenge due to less data available outside of White, non-Hispanic populations. Further studies are necessary to expand understanding of the implementation and utilization of panels across broad clinical settings and patient populations.
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191
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Stoffel EM, Boland CR. Genetics and Genetic Testing in Hereditary Colorectal Cancer. Gastroenterology 2015; 149:1191-1203.e2. [PMID: 26226567 DOI: 10.1053/j.gastro.2015.07.021] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 07/22/2015] [Accepted: 07/23/2015] [Indexed: 02/06/2023]
Abstract
Colorectal cancer (CRC) remains the third most common cancer affecting men and women in the United States. Approximately one-third of CRCs are diagnosed in individuals who have family members also affected with the disease. Although the vast majority of colorectal neoplasms develop as a consequence of somatic genomic alterations arising in individual cells, approximately 5% of all CRCs arise in the setting of germline mutations in genes involved in key cellular processes. To date, multiple genes have been implicated in single-gene hereditary cancer syndromes, many of which are associated with increased risk for CRC, as well as other tumor types. This review outlines the clinical, pathologic, and genetic features of the hereditary cancer syndromes known to be associated with increased risk for CRC and delineates strategies for implementing genetic risk assessments in clinical settings.
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Affiliation(s)
- Elena M Stoffel
- Division of Gastroenterology, University of Michigan Health System, Ann Arbor, Michigan.
| | - C Richard Boland
- Division of Gastroenterology, Baylor University Medical Center, Dallas, Texas
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192
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193
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Stoffel EM. Colorectal Cancer in Young Individuals: Opportunities for Prevention. J Clin Oncol 2015; 33:3525-7. [PMID: 26371141 DOI: 10.1200/jco.2015.62.8446] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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194
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Ballester V, Boardman L. Next Generation Multigene Panel Testing: The Next Step for Identification of Hereditary Colorectal Cancer Syndromes? Gastroenterology 2015; 149:526-8. [PMID: 26226575 DOI: 10.1053/j.gastro.2015.07.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Affiliation(s)
- Veroushka Ballester
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Lisa Boardman
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota.
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195
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Carethers JM, Stoffel EM. Lynch syndrome and Lynch syndrome mimics: The growing complex landscape of hereditary colon cancer. World J Gastroenterol 2015; 21:9253-9261. [PMID: 26309352 PMCID: PMC4541378 DOI: 10.3748/wjg.v21.i31.9253] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Revised: 06/13/2015] [Accepted: 07/08/2015] [Indexed: 02/06/2023] Open
Abstract
Hereditary non-polyposis colorectal cancer (HNPCC) was previously synonymous with Lynch syndrome; however, identification of the role of germline mutations in the DNA mismatch repair (MMR) genes has made it possible to differentiate Lynch syndrome from other conditions associated with familial colorectal cancer (CRC). Broadly, HNPCC may be dichotomized into conditions that demonstrate defective DNA MMR and microsatellite instability (MSI) vs those conditions that demonstrate intact DNA MMR. Conditions characterized by MMR deficient CRCs include Lynch syndrome (germline MMR mutation), Lynch-like syndrome (biallelic somatic MMR mutations), constitutional MMR deficiency syndrome (biallelic germline MMR mutations), and sporadic MSI CRC (somatic biallelic methylation of MLH1). HNPCC conditions with intact DNA MMR associated with familial CRC include polymerase proofreading associated polyposis and familial colorectal cancer type X. Although next generation sequencing technologies have elucidated the genetic cause for some HNPCC conditions, others remain genetically undefined. Differentiating between Lynch syndrome and the other HNPCC disorders has profound implications for cancer risk assessment and surveillance of affected patients and their at-risk relatives. Clinical suspicion coupled with molecular tumor analysis and testing for germline mutations can help differentiate the clinical mimicry within HNPCC and facilitate diagnosis and management.
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196
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Carethers JM. Biomarker-directed Targeted Therapy in Colorectal Cancer. JOURNAL OF DIGESTIVE CANCER REPORTS 2015; 3:5-10. [PMID: 26609516 PMCID: PMC4655967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
With advances in the understanding of the biology and genetics of colorectal cancer (CRC), diagnostic biomarkers that may predict the existence or future presence of cancer or a hereditary condition, and prognostic and treatment biomarkers that may direct the approach to therapy have been developed. Biomarkers can be ascertained and assayed from any tissue that may demonstrate the diagnostic or prognostic value, including from blood cells, epithelial cells via buccal swab, fresh or archival cancer tissue, as well as from cells shed into fecal material. For CRC, current examples of biomarkers for screening and surveillance include germline testing for suspected hereditary CRC syndromes, and stool DNA tests for screening average at-risk patients. Molecular biomarkers for CRC that may alter patient care and treatment include the presence or absence of microsatellite instability, the presence or absence of mutant KRAS, BRAF or PIK3CA, and the level of expression of 15-PGDH in the colorectal mucosa. Molecularly targeted therapies and some general therapeutic approaches rely on biomarker information. Additional novel biomarkers are on the horizon that will undoubtedly further the approach to precision or individualized medicine.
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Affiliation(s)
- John M Carethers
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
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