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Etchegary H, Pike A, Puddester R, Watkins K, Warren M, Francis V, Woods M, Green J, Savas S, Seal M, Gao Z, Avery S, Curtis F, McGrath J, MacDonald D, Burry TN, Dawson L. Cancer prevention in cancer predisposition syndromes: A protocol for testing the feasibility of building a hereditary cancer research registry and nurse navigator follow up model. PLoS One 2022; 17:e0279317. [PMID: 36548287 PMCID: PMC9778977 DOI: 10.1371/journal.pone.0279317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022] Open
Abstract
Monogenic, high penetrance syndromes, conferring an increased risk of malignancies in multiple organs, are important contributors to the hereditary burden of cancer. Early detection and risk reduction strategies in patients with a cancer predisposition syndrome can save their lives. However, despite evidence supporting the benefits of early detection and risk reduction strategies, most Canadian jurisdictions have not implemented programmatic follow up of these patients. In our study site in the province of Newfoundland and Labrador (NL), Canada, there is no centralized, provincial registry of high-risk individuals. There is no continuity or coordination of care providing cancer genetics expertise and no process to ensure that patients are referred to the appropriate specialists or risk management interventions. This paper describes a study protocol to test the feasibility of obtaining and analyzing patient risk management data, specifically patients affected by hereditary breast ovarian cancer syndrome (HBOC; BRCA 1 and BRCA 2 genes) and Lynch syndrome (LS; MLH1, MSH2, MSH6, and PMS2 genes). Through a retrospective cohort study, we will describe these patients' adherence to risk management guidelines and test its relationship to health outcomes, including cancer incidence and stage. Through a qualitative interviews, we will determine the priorities and preferences of patients with any inherited cancer mutation for a follow up navigation model of risk management. Study data will inform a subsequent funding application focused on creating and evaluating a research registry and follow up nurse navigation model. It is not currently known what proportion of cancer mutation carriers are receiving care according to guidelines. Data collected in this study will provide clinical uptake and health outcome information so gaps in care can be identified. Data will also provide patient preference information to inform ongoing and planned research with cancer mutation carriers.
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Affiliation(s)
- Holly Etchegary
- Clinical Epidemiology, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
- * E-mail:
| | - April Pike
- Faculty of Nursing, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Rebecca Puddester
- Faculty of Nursing, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Kathy Watkins
- Centre for Nursing and Health Studies, Eastern Health, St. John’s, Newfoundland, Canada
| | - Mike Warren
- Patient Partner, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Vanessa Francis
- Patient Partner, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Michael Woods
- Division of Biomedical Sciences, Discipline of Oncology, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Jane Green
- Division of Biomedical Sciences, Discipline of Oncology, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Sevtap Savas
- Division of Biomedical Sciences, Discipline of Oncology, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Melanie Seal
- Discipline of Oncology, Faculty of Medicine, Memorial University of Newfoundland, Cancer Care Program, Eastern Health, St. John’s, Newfoundland, Canada
| | - Zhiwei Gao
- Clinical Epidemiology, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Susan Avery
- Family Medicine, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Fiona Curtis
- Provincial Medical Genetics Program, Eastern Health, St. John’s, Newfoundland, Canada
| | - Jerry McGrath
- Gastroenterology, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Donald MacDonald
- Newfoundland and Labrador Centre for Health Information, St. John’s, Newfoundland, Canada
| | - T. Nadine Burry
- Clinical Epidemiology, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Lesa Dawson
- Obstetrics and Gynecology, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
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Kong Y, Shaver LG, Shi F, Mu H, Bu W, Etchegary H, Aubrey-Bassler K, Asghari S, Yi Y, Wang PP. The Effects of Cancer Beliefs and Sociodemographic Factors on Colorectal Cancer Screening Behaviours in Newfoundland and Labrador. Healthcare (Basel) 2022; 10:healthcare10122574. [PMID: 36554096 PMCID: PMC9778754 DOI: 10.3390/healthcare10122574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/25/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
Objectives: This study investigated the beliefs about cancer treatment, outcomes, and screening among adults aged 50−74 in Newfoundland and Labrador and whether these beliefs or sociodemographic factors were associated with differences in colorectal cancer (CRC) screening behaviours. Methods: This analysis uses data collected from an online survey of adults on cancer awareness and prevention in NL. Chi-square tests were used to assess differences in distributions of beliefs based on CRC screening behaviour. Logistic regression was used to identify sociodemographic factors independently associated with CRC screening behaviour. Results: A total of 724 participants were included in the analysis, 57.4% of which had ever had CRC screening. Most held positive beliefs about cancer outcomes and treatment. Only beliefs about screening affected CRC screening behaviour. People who never had CRC screening were more likely to believe their worries about what might be found would prevent them from screening (χ2 = 9.380, p = 0.009); screening is only necessary if they have symptoms (χ2 = 15.680, p < 0.001); and screening has a high risk of leading to unnecessary surgery (χ2 = 6.824, p = 0.032). Regression identified that men had higher likelihood of having had CRC screening than women in our study (OR = 1.689, 95%CI = 1.135−2.515), as did all age groups compared to ages 50−54. No associations were found with the other sociodemographic factors studied. Conclusion: Beliefs about cancer screening appear to play some role in CRC screening behaviour, but the absolute effect was small. The relatively few sociodemographic associations with screening behaviour suggest that NL’s CRC screening program is equitably reaching people from different socioeconomic backgrounds.
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Affiliation(s)
- Yujia Kong
- School of Public Health, Weifang Medical University, Weifang 261053, China
- Division of Community Health and Humanities, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL 1AB 3V6, Canada
| | - Lance Garrett Shaver
- Division of Community Health and Humanities, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL 1AB 3V6, Canada
- Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Fuyan Shi
- School of Public Health, Weifang Medical University, Weifang 261053, China
- Division of Community Health and Humanities, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL 1AB 3V6, Canada
| | - Huaxia Mu
- School of Public Health, Weifang Medical University, Weifang 261053, China
| | - Weixiao Bu
- School of Public Health, Weifang Medical University, Weifang 261053, China
| | - Holly Etchegary
- Division of Community Health and Humanities, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL 1AB 3V6, Canada
| | - Kris Aubrey-Bassler
- Primary Healthcare Research Unit, Discipline of Family Medicine, Memorial University of Newfoundland, St John’s, NL A1B 3V6, Canada
| | - Shabnam Asghari
- Primary Healthcare Research Unit, Discipline of Family Medicine, Memorial University of Newfoundland, St John’s, NL A1B 3V6, Canada
| | - Yanqing Yi
- Division of Community Health and Humanities, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL 1AB 3V6, Canada
- Correspondence: (Y.Y.); (P.P.W.); Tel.: +1-(709)-864-6497 (P.P.W.); Fax: +1-(709)-864-4991 (P.P.W.)
| | - Peizhong Peter Wang
- School of Public Health, Weifang Medical University, Weifang 261053, China
- Division of Community Health and Humanities, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL 1AB 3V6, Canada
- Correspondence: (Y.Y.); (P.P.W.); Tel.: +1-(709)-864-6497 (P.P.W.); Fax: +1-(709)-864-4991 (P.P.W.)
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Shanahan JJ, LeBlanc DM, Courage ER, Benesch MGK, Hickey KE, Hartwig KA, Armstrong CD, Engelbrecht R, Fagan MG, Borgaonkar MR, Pace DE. Characteristics of Interval Colorectal Cancer: A Canadian Retrospective Population-Level Analysis from Newfoundland and Labrador. Curr Oncol 2022; 29:9150-9162. [PMID: 36547130 PMCID: PMC9776431 DOI: 10.3390/curroncol29120716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/15/2022] [Accepted: 11/23/2022] [Indexed: 11/25/2022] Open
Abstract
Interval colorectal cancers (I-CRCs) arise during the interval time period between scheduled colonoscopies. Predicting which patients are at risk of I-CRCs remains an elusive undertaking, but evidence would suggest that most I-CRCs arise from lesions missed on index endoscopy. The procedural factors that lead to missed lesions are numerous and lack consensus in the literature. In Canada, the province of Newfoundland and Labrador has the highest incidence of CRCs. In this study our aim was to examine I-CRCs (3-60 months after last colonoscopy) in NL through a population-level analysis covering 67% of the province from 2001-2018. We estimated the I-CRC rate to be up to 9.3%. Median age of I-CRC diagnosis was 67.1 years with an interval time of 2.9 years. About 57% of these tumors occurred proximal to the splenic flexure, with 53% presenting as local disease. No temporal differences were observed in interval time or tumor distribution. On univariate and multivariable logistical regression, risk of right-sided I-CRC did not correlate to the index colonoscopy indication, bowel preparation quality, size of largest polyp removed, colonoscopy completion rate, or stage at presentation. Improvements in synoptic reporting utilization and national registries are needed to identity risk factors and reduce I-CRC frequency.
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Affiliation(s)
- Jessica J. Shanahan
- Discipline of Surgery, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL A1B 3V6, Canada
| | - Danielle M. LeBlanc
- Discipline of Surgery, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL A1B 3V6, Canada
| | - Emily R. Courage
- Discipline of Surgery, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL A1B 3V6, Canada
| | - Matthew G. K. Benesch
- Discipline of Surgery, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL A1B 3V6, Canada
- Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Kala E. Hickey
- Discipline of Surgery, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL A1B 3V6, Canada
| | - Katia A. Hartwig
- Discipline of Surgery, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL A1B 3V6, Canada
| | - Casey D. Armstrong
- Discipline of Surgery, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL A1B 3V6, Canada
| | - Reniel Engelbrecht
- Discipline of Medicine, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL A1B 3V6, Canada
| | - Mitchell G. Fagan
- Discipline of Surgery, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL A1B 3V6, Canada
| | - Mark R. Borgaonkar
- Discipline of Medicine, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL A1B 3V6, Canada
| | - David E. Pace
- Discipline of Surgery, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL A1B 3V6, Canada
- Correspondence:
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Wang Y, Du M, Vallis J, Shariati M, Parfrey PS, Mclaughlin JR, Wang PP, Zhu Y. The Roles of MTRR and MTHFR Gene Polymorphisms in Colorectal Cancer Survival. Nutrients 2022; 14:nu14214594. [PMID: 36364857 PMCID: PMC9658674 DOI: 10.3390/nu14214594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/25/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022] Open
Abstract
Background: Paradoxically epidemiological data illustrate a negative relationship between dietary folate intake and colorectal cancer (CRC) risk. The occurrence and progression of CRC may be influenced by variants in some key enzyme coding genes in the folate metabolic pathway. We investigated the correlation between genetic variants in methionine synthase reductase (MTRR) and methylenetetrahydrofolate reductase (MTHFR) and CRC survival. Methods: This study used data collected from the Newfoundland Familial Colorectal Cancer Study. A total of 532 patients diagnosed with CRC for the first time from 1999 to 2003 were enrolled, and their mortality were tracked until April 2010. DNA samples were genotyped by Illumina’s integrated quantum 1 million chip. Cox models were established to assess 33 tag single-nucleotide polymorphisms in MTRR and MTHFR in relation to overall survival (OS), disease-free survival (DFS) and CRC-specific survival. Results: The MTRR and MTHFR genes were associated with DFS and CRC-specific survival in CRC patients at the gene level. After multiple comparison adjustment, MTRR rs1801394 A (vs. G) allele was associated with increased DFS (p = 0.024), while MTHRT rs3737966 (G vs. A), rs4846049 (T vs. G), rs1476413 (A vs. G), rs1801131 (C vs. A), rs12121543 (A vs. C), rs1801133 (C vs. T), rs4846052 (T vs. C), rs2066471 (A vs. G) and rs7533315 (T vs. C) were related to worse CRC-specific survival. Additionally, significant interactions were seen among pre-diagnostic alcohol consumption with MTRR rs1801394, rs3776467, rs326124, rs162040, and rs3776455, with superior OS associated with those protective variant alleles limited to patients with alcohol consumption under the median. The MTHFR rs3737966 (G vs. A) allele seemed to be detrimental to CRC survival only among subjects with fruit intake below the median. Conclusions: Polymorphic variants in MTRR and MTHFR genes that code for key enzymes for folate metabolism may be associated with survival in patients with CRC. The gene-CRC outcome association seems modulated by alcohol drinking and fruit intake.
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Affiliation(s)
- Yu Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Tianjin Medical University, Tianjin 300070, China
| | - Meizhi Du
- Department of Epidemiology and Biostatistics, School of Public Health, Tianjin Medical University, Tianjin 300070, China
| | - Jillian Vallis
- Division of Community Health and Humanities, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL A1B 3V6, Canada
| | - Matin Shariati
- Division of Community Health and Humanities, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL A1B 3V6, Canada
| | - Patrick S. Parfrey
- Clinical Epidemiology Unit, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL A1B 3V6, Canada
| | - John R. Mclaughlin
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada
| | - Peizhong Peter Wang
- Division of Community Health and Humanities, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, NL A1B 3V6, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada
- Correspondence: (P.P.W.); (Y.Z.); Tel.: +1-(709)-777-8571 (P.P.W.); +86-(022)-8333-6118 (Y.Z.)
| | - Yun Zhu
- Department of Epidemiology and Biostatistics, School of Public Health, Tianjin Medical University, Tianjin 300070, China
- Correspondence: (P.P.W.); (Y.Z.); Tel.: +1-(709)-777-8571 (P.P.W.); +86-(022)-8333-6118 (Y.Z.)
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Curtis A, Yu Y, Carey M, Parfrey P, Yilmaz YE, Savas S. Examining SNP-SNP interactions and risk of clinical outcomes in colorectal cancer using multifactor dimensionality reduction based methods. Front Genet 2022; 13:902217. [PMID: 35991579 PMCID: PMC9385108 DOI: 10.3389/fgene.2022.902217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 06/30/2022] [Indexed: 12/24/2022] Open
Abstract
Background: SNP interactions may explain the variable outcome risk among colorectal cancer patients. Examining SNP interactions is challenging, especially with large datasets. Multifactor Dimensionality Reduction (MDR)-based programs may address this problem.Objectives: 1) To compare two MDR-based programs for their utility; and 2) to apply these programs to sets of MMP and VEGF-family gene SNPs in order to examine their interactions in relation to colorectal cancer survival outcomes.Methods: This study applied two data reduction methods, Cox-MDR and GMDR 0.9, to study one to three way SNP interactions. Both programs were run using a 5-fold cross validation step and the top models were verified by permutation testing. Prognostic associations of the SNP interactions were verified using multivariable regression methods. Eight datasets, including SNPs from MMP family genes (n = 201) and seven sets of VEGF-family interaction networks (n = 1,517 SNPs) were examined.Results: ∼90 million potential interactions were examined. Analyses in the MMP and VEGF gene family datasets found several novel 1- to 3-way SNP interactions. These interactions were able to distinguish between the patients with different outcome risks (regression p-values 0.03–2.2E-09). The strongest association was detected for a 3-way interaction including CHRM3.rs665159_EPN1.rs6509955_PTGER3.rs1327460 variants.Conclusion: Our work demonstrates the utility of data reduction methods while identifying potential prognostic markers in colorectal cancer.
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Affiliation(s)
- Aaron Curtis
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
- Division of Biomedical Sciences, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
| | - Yajun Yu
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
- Division of Biomedical Sciences, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
| | - Megan Carey
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
| | - Patrick Parfrey
- Discipline of Medicine, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
| | - Yildiz E. Yilmaz
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
- Discipline of Medicine, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
- Department of Mathematics and Statistics, Faculty of Science, Memorial University, St. John’s, NL, Canada
| | - Sevtap Savas
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
- Division of Biomedical Sciences, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
- Discipline of Oncology, Faculty of Medicine, Memorial University, St. John’s, NL, Canada
- *Correspondence: Sevtap Savas,
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Prediagnostic consumption of vitamin D, calcium and dairy products and colorectal cancer survival: results from the Newfoundland Colorectal Cancer Registry Cohort Study. Br J Nutr 2022; 128:290-299. [PMID: 34435555 DOI: 10.1017/s0007114521003299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Vitamin D, Ca and dairy products are negatively associated with colorectal cancer (CRC) incidence, but little is known of their influence on CRC survival. To investigate prediagnostic intakes of vitamin D, Ca and dairy products for their relevance to CRC prognosis, we analysed 504 CRC patients enrolled in the Newfoundland Colorectal Cancer Registry Cohort Study who were diagnosed for the first time with CRC between 1999 and 2003. Follow-up for mortality and cancer recurrence was through April 2010. Data on diet and lifestyle factors were gathered via a validated, semi-quantitative FFQ and a Personal History Questionnaire. Multivariate Cox models estimated hazard ratios (HR) and 95 % CI for the relationship of prediagnostic intakes of vitamin D, Ca and dairy products with all-cause mortality (overall survival, OS) and disease-free survival (DFS) among CRC patients. We found that prediagnostic Ca intake from foods, but not total Ca intake, was negatively associated with all-cause mortality (HR for Q2 v. Q1, 0·44; 95 % CI, 0·26, 0·75). An inverse relationship was also seen in a dose-response fashion for prediagnostic cheese intake (HR for Q4 v. Q1, 0·57, 95 % CI, 0·34, 0·95, Ptrend = 0·029). No evidence for modification by sex, physical activity, alcohol drinking and cigarette smoking was observed. In summary, high prediagnostic intakes of cheese and Ca from foods may be associated with increased survival among CRC patients. By manipulating diet, this study may contribute to the development of novel therapies that add to the armamentarium against CRC. Replication studies are required before any nutritional interventions are made available.
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Paszat L, Sutradhar R, Luo J, Tinmouth J, Rabeneck L, Baxter NN. Uptake and Short-term Outcomes of High-risk Screening Colonoscopy Billing Codes: A Population-based Study Among Young Adults. J Can Assoc Gastroenterol 2022; 5:86-95. [PMID: 35368324 PMCID: PMC8972288 DOI: 10.1093/jcag/gwab014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 05/14/2021] [Indexed: 01/03/2023] Open
Abstract
Background Persons suspected or confirmed with familial colorectal cancer syndrome are recommended to have biennial colonoscopy from late adolescence or early adulthood. Persons without a syndrome but with one or more affected first-degree relatives are recommended to begin colonoscopy 10 years before the age at diagnosis of the youngest affected relative, and every 5 to 10 years. Ontario introduced colonoscopy billing codes for these two indications in 2011. Methods We identified persons in Ontario under 50 years of age, without a prior history of colorectal cancer or inflammatory bowel disease, with one or more of these billing claims between 2013 and 2017. We described the index colonoscopy, and subsequent colonoscopy up-to-date status. We computed average annual rates of colorectal and other cancer diagnoses, and displayed mean cumulative function plots, stratified by billing code, age and sex. Results Billing claims for ‘familial syndrome’ high-risk screening colonoscopy were identified among 14,846 persons; the average annual rate of CRC diagnoses was 38.6 per 100,000 among males and 22.2 among females. Colonoscopy up-to-date status fell to 50% within 7 years. Billing claims for ‘first-degree relative’ screening colonoscopy was identified among 49,505 persons; average annual rates of CRC diagnoses were 16.3 among males and 13.5 per 100,000 among females, respectively. Conclusion Colorectal cancer was more frequent following billing claims for high-risk screening colonoscopy for familial syndromes, as were noncolorectal malignancies potentially associated with these syndromes. This billing claim for familial colorectal cancer syndrome colonoscopy appears to identify a group at elevated short-term risk for cancer.
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Affiliation(s)
- Lawrence Paszat
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Rinku Sutradhar
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Jin Luo
- Cancer Research Programme, Institute for Clinical Evaluative Sciences (ICES), Toronto, Ontario, Canada
| | - Jill Tinmouth
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Linda Rabeneck
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Nancy N Baxter
- School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia
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Hajizadeh M, Charles M, Johnston GM, Urquhart R. Socioeconomic inequalities in colorectal cancer incidence in Canada: trends over two decades. Cancer Causes Control 2021; 33:193-204. [PMID: 34779993 DOI: 10.1007/s10552-021-01518-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 11/02/2021] [Indexed: 11/28/2022]
Abstract
PURPOSE Colorectal cancer is the third most commonly diagnosed cancer in Canada. This study aimed to measure and examine trends in socioeconomic inequalities in the incidence of colorectal cancer in Canada. METHODS This study is a time trend ecological study based on Canadian Census Division level data constructed from the Canadian Cancer Registry, Canadian Census of Population, and National Household Survey. We assessed trends in income and education inequalities in colorectal cancer incidence in Canada from 1992 to 2010. The age-standardized Concentration index ([Formula: see text]), which measures inequality across all socioeconomic groups, was used to quantify socioeconomic inequalities in colorectal cancer incidence in Canada. RESULTS The average crude colorectal cancer incidence was found to be 61.52 per 100,000 population over the study period, with males having a higher incidence rate than females (males: 66.98; females: 56.25 per 100,000 population). The crude incidence increased over time and varied by province. The age-standardized C indicated a higher concentration of colorectal cancer incidence among lower income and less-educated neighborhoods in Canada. Income and education inequalities increased over time among males. CONCLUSION The concentration of colorectal cancer incidence in low socioeconomic neighborhoods in Canada has implications for primary prevention and screening.
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Affiliation(s)
- Mohammad Hajizadeh
- School of Health Administration, Faculty of Health, Dalhousie University, Sir Charles Tupper Medical Building, 5850 College Street, 2nd Floor, Halifax, NS, B3H 4R2, Canada.
| | - Marie Charles
- Faculty of Medicine, Dalhousie University, Halifax, Canada
| | - Grace M Johnston
- Cancer Care Program, Nova Scotia Health, School of Health Administration, Dalhousie University, Halifax, Canada
| | - Robin Urquhart
- Department of Community Health and Epidemiology, Faculty of Medicine, Dalhousie University, Halifax, Canada
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Yu Y, Werdyani S, Carey M, Parfrey P, Yilmaz YE, Savas S. A comprehensive analysis of SNPs and CNVs identifies novel markers associated with disease outcomes in colorectal cancer. Mol Oncol 2021; 15:3329-3347. [PMID: 34309201 PMCID: PMC8637572 DOI: 10.1002/1878-0261.13067] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/29/2021] [Accepted: 07/24/2021] [Indexed: 12/15/2022] Open
Abstract
We aimed to examine the associations of a genome-wide set of single nucleotide polymorphisms (SNPs) and 254 copy number variations (CNVs) and/or insertion/deletions (INDELs) with clinical outcomes in colorectal cancer patients (n = 505). We also aimed to investigate whether their associations changed (e.g., appeared, diminished) over time. Multivariable Cox proportional hazards and piece-wise Cox regression models were used to examine the associations. The Cancer Genome Atlas (TCGA) datasets were used for replication purposes and to examine the gene expression differences between tumor and nontumor tissue samples. A common SNP (WBP11-rs7314075) was associated with disease-specific survival with P-value of 3.2 × 10-8 . Association of this region with disease-specific survival was also detected in the TCGA patient cohort. Two expression quantitative trait loci (eQTLs) were identified in this locus that were implicated in the regulation of ERP27 expression. Interestingly, expression levels of ERP27 and WBP11 were significantly different between colorectal tumors and nontumor tissues. Three SNPs predicted the risk of recurrent disease only after 5 years postdiagnosis. Overall, our study identified novel variants, one of which also showed an association in the TCGA dataset, but no CNVs/INDELs, that associated with outcomes in colorectal cancer. Three SNPs were candidate predictors of long-term recurrence/metastasis risk.
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Affiliation(s)
- Yajun Yu
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, NL, Canada
| | - Salem Werdyani
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, NL, Canada
| | - Megan Carey
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, NL, Canada
| | - Patrick Parfrey
- Discipline of Medicine, Faculty of Medicine, Memorial University, St. John's, NL, Canada
| | - Yildiz E Yilmaz
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, NL, Canada.,Discipline of Medicine, Faculty of Medicine, Memorial University, St. John's, NL, Canada.,Department of Mathematics and Statistics, Faculty of Science, Memorial University, St. John's, NL, Canada
| | - Sevtap Savas
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, NL, Canada.,Discipline of Oncology, Faculty of Medicine, Memorial University, St. John's, NL, Canada
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10
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The correlation between IL-4 polymorphisms and colorectal cancer risk in a population in Northwest China. Eur J Cancer Prev 2021; 29:95-99. [PMID: 31876620 DOI: 10.1097/cej.0000000000000503] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Our aim was to investigate whether polymorphisms in the interleukin-4 (IL-4) gene are associated with the risk of colorectal cancer (CRC) in a Chinese Han population. Six single-nucleotide polymorphisms (SNPs) in the IL-4 were genotyped by Agena MassARRAY in 248 CRC patients and 463 healthy controls. The association of IL-4 polymorphisms with CRC risk was assessed by genetic models, linkage disequilibrium, and haplotype analyses. The results suggested that the CC genotype of rs2243250 confers a lower risk of CRC in the recessive model [odds ratio (OR) = 0.42, 95% confidence interval (CI): 0.19-0.92, P = 0.020]. Similarly, rs2227284 GG was associated with a reduced risk of CRC in the codominant (OR = 0.18, 95% CI: 0.04-0.82, P = 0.027) and recessive (OR = 0.19, 95% CI: 0.04-0.83, P = 0.008) models adjusted for age. Our findings suggested that rs2243250 and rs2227284 in IL-4 are associated significantly with reduced CRC risk, which may facilitate the identification of CRC patients in Chinese populations.
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11
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Subramonian A, Smith D, Dicks E, Dawson L, Borgaonkar M, Etchegary H. Universal tumor screening for lynch syndrome: perspectives of patients regarding willingness and informed consent. Per Med 2020; 17:373-387. [PMID: 32875945 DOI: 10.2217/pme-2020-0026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: Lynch Syndrome is associated with a significant risk of colorectal carcinoma (CRC) and other cancers. Universal tumor screening is a strategy to identify high-risk individuals by testing all CRC tumors for molecular features suggestive of Lynch Syndrome. Patient interest in screening and preferences for consent have been underexplored. Methods: A postal survey was administered to CRC patients in a Canadian province. Results: Most patients (81.4%) were willing to have tumors tested if universal tumor screening were available and were willing to discuss test results with family members and healthcare professionals. The majority (62.6%) preferred informed consent be obtained prior to screening. Conclusion: Patients were supportive of universal screening. They expected consent to be obtained, contrary to current practice across Canada and elsewhere.
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Affiliation(s)
- Anusree Subramonian
- Clinical Epidemiology, Faculty of Medicine, Memorial University, St John's, NL, Canada
| | | | - Elizabeth Dicks
- Clinical Epidemiology, Faculty of Medicine, Memorial University, St John's, NL, Canada
| | - Lesa Dawson
- Gynecologic Oncology, Women's Health & Genetics, Faculty of Medicine, Memorial University, St John's, NL, Canada.,Women's Health and Genetics, Eastern Health, St John's NL, Canada
| | - Mark Borgaonkar
- Gastroenterology, Faculty of Medicine, Memorial University, St John's, NL, Canada
| | - Holly Etchegary
- Clinical Epidemiology, Faculty of Medicine, Memorial University, St John's, NL, Canada
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12
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Evans DR, Green JS, Fahiminiya S, Majewski J, Fernandez BA, Deardorff MA, Johnson GJ, Whelan JH, Hubmacher D, Apte SS, Woods MO. A novel pathogenic missense ADAMTS17 variant that impairs secretion causes Weill-Marchesani Syndrome with variably dysmorphic hand features. Sci Rep 2020; 10:10827. [PMID: 32616716 PMCID: PMC7331723 DOI: 10.1038/s41598-020-66978-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 05/27/2020] [Indexed: 12/15/2022] Open
Abstract
Weill-Marchesani syndrome (WMS) is a rare disorder displaying short stature, brachydactyly and joint stiffness, and ocular features including microspherophakia and ectopia lentis. Brachydactyly and joint stiffness appear less commonly in patients with WMS4 caused by pathogenic ADAMTS17 variants. Here, we investigated a large family with WMS from Newfoundland, Canada. These patients displayed core WMS features, but with proportionate hands that were clinically equivocal for brachydactyly. Whole exome sequencing and autozygosity mapping unveiled a novel pathogenic missense ADAMTS17 variant (c.3068 G > A, p.C1023Y). Sanger sequencing demonstrated variant co-segregation with WMS, and absence in 150 population matched controls. Given ADAMTS17 involvement, we performed deep phenotyping of the patients’ hands. Anthropometrics applied to hand roentgenograms showed that metacarpophalangeal measurements of affected patients were smaller than expected for their age and sex, and when compared to their unaffected sibling. Furthermore, we found a possible sub-clinical phenotype involving markedly shortened metacarpophalangeal bones with intrafamilial variability. Transfection of the variant ADAMTS17 into HEK293T cells revealed significantly reduced secretion into the extracellular medium compared to wild-type. This work expands understanding of the molecular pathogenesis of ADAMTS17, clarifies the variable hand phenotype, and underscores a role for anthropometrics in characterizing sub-clinical brachydactyly in these patients.
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Affiliation(s)
- Daniel R Evans
- Discipline of Genetics, Memorial University of Newfoundland, Faculty of Medicine, St. Johns, NL, A1B 3V6, Canada
| | - Jane S Green
- Discipline of Genetics, Memorial University of Newfoundland, Faculty of Medicine, St. Johns, NL, A1B 3V6, Canada
| | - Somayyeh Fahiminiya
- Department of Human Genetics, McGill University, Montréal, QC, H3A 1B1, Canada.,McGill University and Genome Québec Innovation Centre, Montréal, QC, H3A 0G1, Canada
| | - Jacek Majewski
- Department of Human Genetics, McGill University, Montréal, QC, H3A 1B1, Canada.,McGill University and Genome Québec Innovation Centre, Montréal, QC, H3A 0G1, Canada
| | - Bridget A Fernandez
- Discipline of Genetics, Memorial University of Newfoundland, Faculty of Medicine, St. Johns, NL, A1B 3V6, Canada
| | - Matthew A Deardorff
- Division of Genetics, Children's Hospital of Philadelphia, Department of Pediatrics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania, PA, 19104, USA
| | - Gordon J Johnson
- Care of Dr. Jane Green, Discipline of Genetics, Memorial University of Newfoundland, Faculty of Medicine, St. Johns, NL, A1B 3V6, Canada
| | - James H Whelan
- Memorial University of Newfoundland, Faculty of Medicine, Discipline of Surgery (Ophthalmology), St. Johns, NL, A1B 3V6, Canada
| | - Dirk Hubmacher
- Orthopaedic Research Laboratories, Leni and Peter W. May Department of Orthopaedics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Suneel S Apte
- Department of Biomedical Engineering, Cleveland Clinic Lerner Research Institute, Cleveland, OH, 44195, USA
| | | | - Michael O Woods
- Discipline of Genetics, Memorial University of Newfoundland, Faculty of Medicine, St. Johns, NL, A1B 3V6, Canada.
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13
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Yu Y, Carey M, Pollett W, Green J, Dicks E, Parfrey P, Yilmaz YE, Savas S. The long-term survival characteristics of a cohort of colorectal cancer patients and baseline variables associated with survival outcomes with or without time-varying effects. BMC Med 2019; 17:150. [PMID: 31352904 PMCID: PMC6661748 DOI: 10.1186/s12916-019-1379-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 06/27/2019] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Colorectal cancer is the third most common cancer in the world. In this study, we assessed the long-term survival characteristics and prognostic associations and potential time-varying effects of clinico-demographic variables and two molecular markers (microsatellite instability (MSI) and BRAF Val600Glu mutation) in a population-based patient cohort followed up to ~ 19 years. METHODS The patient cohort included 738 incident cases diagnosed between 1999 and 2003. Cox models were used to analyze the association between the variables and a set of survival outcome measures (overall survival (OS), disease-specific survival (DSS), recurrence-free survival (RFS), metastasis-free survival (MFS), recurrence/metastasis-free survival (RMFS), and event-free survival (EFS)). Cox proportional hazard (PH) assumption was tested for all variables, and Cox models with time-varying effects were used if any departure from the PH assumption was detected. RESULTS During the follow-up, ~ 61% patients died from any cause, ~ 26% died from colorectal cancer, and ~ 10% and ~ 20% experienced recurrences and distant metastases, respectively. Stage IV disease and post-diagnostic recurrence or metastasis were strongly linked to risk of death from colorectal cancer. If a patient had survived the first 6 years without any disease-related event (i.e., recurrence, metastasis, or death from colorectal cancer), their risks became very minimal after this time period. Distinct sets of markers were associated with different outcome measures. In some cases, the effects by variables were constant throughout the follow-up. For example, MSI-high tumor phenotype and older age at diagnosis predicted longer MFS times consistently over the follow-up. However, in some other cases, the effects of the variables varied with time. For example, adjuvant radiotherapy treatment was associated with increased risk of metastasis in patients who received this treatment after 5.5 years post-diagnosis, but not before that. CONCLUSIONS This study describes the long-term survival characteristics of a prospective cohort of colorectal cancer patients, relationships between baseline variables and a detailed set of patient outcomes over a long time, and time-varying effects of a group of variables. The results presented advance our understanding of the long-term prognostic characteristics in colorectal cancer and are expected to inspire future studies and clinical care strategies.
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Affiliation(s)
- Yajun Yu
- Discipline of Genetics, Faculty of Medicine, Memorial University, 300 Prince Philip Drive, New Medical Education Building, St. John's, NL, A1B 3V6, Canada
| | - Megan Carey
- Discipline of Genetics, Faculty of Medicine, Memorial University, 300 Prince Philip Drive, New Medical Education Building, St. John's, NL, A1B 3V6, Canada
| | - William Pollett
- Discipline of Surgery, Faculty of Medicine, Memorial University, St. John's, NL, Canada
| | - Jane Green
- Discipline of Genetics, Faculty of Medicine, Memorial University, 300 Prince Philip Drive, New Medical Education Building, St. John's, NL, A1B 3V6, Canada
| | - Elizabeth Dicks
- Discipline of Medicine, Faculty of Medicine, Memorial University, St. John's, NL, Canada
| | - Patrick Parfrey
- Discipline of Medicine, Faculty of Medicine, Memorial University, St. John's, NL, Canada
| | - Yildiz E Yilmaz
- Discipline of Genetics, Faculty of Medicine, Memorial University, 300 Prince Philip Drive, New Medical Education Building, St. John's, NL, A1B 3V6, Canada.,Discipline of Medicine, Faculty of Medicine, Memorial University, St. John's, NL, Canada.,Department of Mathematics and Statistics, Faculty of Science, Memorial University, St. John's, NL, Canada
| | - Sevtap Savas
- Discipline of Genetics, Faculty of Medicine, Memorial University, 300 Prince Philip Drive, New Medical Education Building, St. John's, NL, A1B 3V6, Canada. .,Discipline of Oncology, Faculty of Medicine, Memorial University, St. John's, NL, Canada.
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14
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Dicks E, Pullman D, Kao K, MacMillan A, Simmonds C, Etchegary H. Universal tumor screening for Lynch syndrome: perspectives of Canadian pathologists and genetic counselors. J Community Genet 2019; 10:335-344. [PMID: 30465127 PMCID: PMC6591350 DOI: 10.1007/s12687-018-0398-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 11/13/2018] [Indexed: 12/31/2022] Open
Abstract
Universal screening of all newly diagnosed colorectal cancer tumors can identify individuals at high risk for Lynch syndrome (LS), a hereditary cancer syndrome predisposing carriers to increased risk of colorectal, endometrial, and other cancers. To inform planning of a universal tumor screening program for LS in our jurisdiction, we undertook online surveys of Canadian pathologists and genetic counselors to describe existing tumor screening programs. Online surveys were hosted on SurveyMonkey between October 2016 and March 2017. Fifty-three pathologists and 66 genetic counselors completed surveys (total n = 119). While attitudes towards tumor screening were positive, considerable variability was observed in the existence of tumor screening, test ordering criteria, and practices. Most respondents indicated consent was not obtained for tumor screening nor were educational materials provided to patients; however, opting out of additional mutation testing in the event of a positive tumor screen was endorsed. Results add to the growing literature on providers' perspectives on population-based tumor screening programs and inform ways to offer these. Findings highlight the need to develop methods of patient education that allow meaningful opt-out decisions. The variability we observed also suggests the need for national standards and guidance on tumor screening for LS.
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Affiliation(s)
- Elizabeth Dicks
- Faculty of Medicine, Memorial University, St. John's, NL, Canada
| | - Daryl Pullman
- Faculty of Medicine, Memorial University, St. John's, NL, Canada
| | - Ken Kao
- Faculty of Medicine, Memorial University, St. John's, NL, Canada
- Immunohistochemistry Laboratory, Eastern Regional Health Authority, St. John's, NL, Canada
| | - Andrée MacMillan
- Provincial Medical Genetics Program, Eastern Regional Health Authority, St. John's, NL, Canada
| | | | - Holly Etchegary
- Faculty of Medicine, Memorial University, St. John's, NL, Canada.
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15
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Penney ME, Parfrey PS, Savas S, Yilmaz YE. A genome-wide association study identifies single nucleotide polymorphisms associated with time-to-metastasis in colorectal cancer. BMC Cancer 2019; 19:133. [PMID: 30738427 PMCID: PMC6368959 DOI: 10.1186/s12885-019-5346-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 02/04/2019] [Indexed: 12/16/2022] Open
Abstract
Background Differentiating between cancer patients who will experience metastasis within a short time and who will be long-term survivors without metastasis is a critical aim in healthcare. The microsatellite instability (MSI)-high tumor phenotype is such a differentiator in colorectal cancer, as patients with these tumors are unlikely to experience metastasis. Our aim in this study was to determine if germline genetic variations could further differentiate colorectal cancer patients based on the long-term risk and timing of metastasis. Methods The patient cohort consisted of 379 stage I-III Caucasian colorectal cancer patients with microsatellite stable or MSI-low tumors. We performed univariable analysis on 810,622 common single nucleotide polymorphisms (SNPs) under different genetic models. Depending on the long-term metastasis-free survival probability estimates, we applied a mixture cure model, Cox proportional hazards regression model, or log-rank test. For SNPs reaching Bonferroni-corrected significance (p < 6.2 × 10− 8) having valid genetic models, multivariable analysis adjusting for significant baseline characteristics was conducted. Results After adjusting for significant baseline characteristics, specific genotypes of ten polymorphisms were significantly associated with time-to-metastasis. These polymorphisms are three intergenic SNPs, rs5749032 (p = 1.28 × 10− 10), rs2327990 (p = 9.59 × 10− 10), rs1145724 (p = 3 × 10− 8), and seven SNPs within the non-coding sequences of three genes: FHIT (p = 2.59 × 10− 9), EPHB1 (p = 8.23 × 10− 9), and MIR7515 (p = 4.87 × 10− 8). Conclusions Our results suggest novel associations of specific genotypes of SNPs with early metastasis in Caucasian colorectal cancer patients. These associations, once replicated in other patient cohorts, could assist in the development of personalized treatment strategies for colorectal cancer patients. Electronic supplementary material The online version of this article (10.1186/s12885-019-5346-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Michelle E Penney
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Canada
| | - Patrick S Parfrey
- Discipline of Medicine, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Canada
| | - Sevtap Savas
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Canada.,Discipline of Oncology, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Canada
| | - Yildiz E Yilmaz
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Canada. .,Discipline of Medicine, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Canada. .,Department of Mathematics and Statistics, Faculty of Science, Memorial University of Newfoundland, St. John's, Canada.
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16
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Screening of BMPR1a for pathogenic mutations in familial colorectal cancer type X families from Newfoundland. Fam Cancer 2019; 17:205-208. [PMID: 28660566 DOI: 10.1007/s10689-017-0016-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The Canadian province of Newfoundland and Labrador (NL) reports one of the highest incidence rates of familial colorectal cancer (CRC) worldwide. The NL population is an invaluable resource for studying genetic disorders because of a unique ancestry, and a willingness to participate in research studies. Familial colorectal cancer type X (FCCTX) describes a cluster of families with strong predisposition for CRC, of unknown etiology. A putative link between FCCTX and BMPR1a mutations has been identified in the Finnish population; however these findings have not been independently replicated. To investigate a potential connection between BMPR1a and FCCTX, we screened a cohort of 22 probands from unrelated NL FCCTX families using Sanger sequencing. This analysis did not independently replicate findings seen in Finland; as no candidate pathogenic BMPR1a mutations were uncovered. Our findings highlight that BMPR1a mutations are not a major contributor of FCCTX incidence in NL. Further investigation of additional FCCTX populations may assist in delineating a role for BMPR1a, if any, in FCCTX globally.
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17
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Penney ME, Parfrey PS, Savas S, Yilmaz YE. Associations of single nucleotide polymorphisms with mucinous colorectal cancer: genome-wide common variant and gene-based rare variant analyses. Biomark Res 2018; 6:17. [PMID: 29942513 PMCID: PMC5998544 DOI: 10.1186/s40364-018-0133-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 05/07/2018] [Indexed: 02/07/2023] Open
Abstract
Background Colorectal cancer has significant impact on individuals and healthcare systems. Many genes have been identified to influence its pathogenesis. However, the genetic basis of mucinous tumor histology, an aggressive subtype of colorectal cancer, is currently not well-known. This study aimed to identify common and rare genetic variations that are associated with the mucinous tumor phenotype. Methods Genome-wide single nucleotide polymorphism (SNP) data was investigated in a colorectal cancer patient cohort (n = 505). Association analyses were performed for 729,373 common SNPs and 275,645 rare SNPs. Common SNP association analysis was performed using univariable and multivariable logistic regression under different genetic models. Rare-variant association analysis was performed using a multi-marker test. Results No associations reached the traditional genome-wide significance. However, promising genetic associations were identified. The identified common SNPs significantly improved the discriminatory accuracy of the model for mucinous tumor phenotype. Specifically, the area under the receiver operating characteristic curve increased from 0.703 (95% CI: 0.634–0.773) to 0.916 (95% CI: 0.873–0.960) when considering the most significant SNPs. Additionally, the rare variant analysis identified a number of genetic regions that potentially contain causal rare variants associated with the mucinous tumor phenotype. Conclusions This is the first study applying both common and rare variant analyses to identify genetic associations with mucinous tumor phenotype using a genome-wide genotype data. Our results suggested novel associations with mucinous tumors. Once confirmed, these results will not only help us understand the biological basis of mucinous histology, but may also help develop targeted treatment options for mucinous tumors. Electronic supplementary material The online version of this article (10.1186/s40364-018-0133-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Michelle E Penney
- 1Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Canada
| | - Patrick S Parfrey
- 2Discipline of Medicine, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Canada
| | - Sevtap Savas
- 1Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Canada.,3Discipline of Oncology, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Canada
| | - Yildiz E Yilmaz
- 1Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Canada.,2Discipline of Medicine, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Canada.,4Department of Mathematics and Statistics, Faculty of Science, Memorial University of Newfoundland, St. John's, Canada
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18
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Yu Y, Cheng D, Parfrey P, Liu G, Savas S. Two functional indel polymorphisms in the promoter region of the Brahma gene (BRM) and disease risk and progression-free survival in colorectal cancer. PLoS One 2018; 13:e0198873. [PMID: 29894502 PMCID: PMC5997361 DOI: 10.1371/journal.pone.0198873] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 05/25/2018] [Indexed: 01/28/2023] Open
Abstract
Background and objective The Brahma gene (BRM) encodes a catalytic ATPase subunit of the Switch/Sucrose non-fermentable (SWI/SNF) complex, which modulates gene expression and many important cellular processes. Two indel polymorphisms in the promoter region of BRM (BRM-741 and BRM-1321) are associated with its reduced expression and the risk of susceptibility or survival outcomes in multiple solid cancers. In this study, we have examined these variants in relation to susceptibility and survival outcomes in colorectal cancer. Methods Genotypes were obtained using TaqMan assays in 427 cases and 408 controls. Multivariate logistic and Cox regression models were fitted to examine the associations of the BRM-741 and BRM-1321 genotypes adjusting for relevant covariates. Sub-group analyses based on tumor location and patient sex were also performed. In all analyses, indels were examined individually as well as in combination. Results Our results showed that there was no association between the BRM polymorphisms and the risk of colorectal cancer. However, genotype combinations of the BRM-741 and BRM-1321 variants were associated with the risk of colon cancer. Particularly, patients having at least one variant allele had increased risk of colon cancer when compared to patients with the double wild-type genotype. In the survival analyses, BRM-741 heterozygosity was associated with longer progression-free survival time in the colorectal cancer patients. A stronger association was detected in the male patients under the recessive genetic model where the homozygosity for the variant allele of BRM-741 was associated with shorter progression-free survival time. Conclusions Our analyses suggest that BRM-741 and BRM-1321 indels are associated with the risk of developing colon cancer and the BRM-741 indel is associated with the disease progression in colorectal cancer patients, especially in the male patients. Although our results show a different relationship between these indels and colorectal cancer compared to other cancer sites, they also suggest that BRM and its promoter variants may have biological roles in susceptibility and survival outcomes in colorectal cancers. Performing further analyses in additional and larger cohorts are needed to confirm our conclusions.
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Affiliation(s)
- Yajun Yu
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John’s, Newfoundland and Labrador, Canada
| | - Dangxiao Cheng
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Patrick Parfrey
- Clinical Epidemiology Unit, Faculty of Medicine, Memorial University, St. John’s, Newfoundland and Labrador, Canada
| | - Geoffrey Liu
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Division of Medical Oncology and Hematology, Department of Medicine, Princess Margaret Cancer Centre and University of Toronto, Toronto, Ontario, Canada
- Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Sevtap Savas
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John’s, Newfoundland and Labrador, Canada
- Discipline of Oncology, Faculty of Medicine, Memorial University, St. John’s, Newfoundland and Labrador, Canada
- * E-mail:
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19
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Evans DR, Venkitachalam S, Revoredo L, Dohey AT, Clarke E, Pennell JJ, Powell AE, Quinn E, Ravi L, Gerken TA, Green JS, Woods MO, Guda K. Evidence for GALNT12 as a moderate penetrance gene for colorectal cancer. Hum Mutat 2018; 39:1092-1101. [PMID: 29749045 DOI: 10.1002/humu.23549] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 05/05/2018] [Accepted: 05/07/2018] [Indexed: 12/29/2022]
Abstract
Characterizing moderate penetrance susceptibility genes is an emerging frontier in colorectal cancer (CRC) research. GALNT12 is a strong candidate CRC-susceptibility gene given previous linkage and association studies, and inactivating somatic and germline alleles in CRC patients. Previously, we found rare segregating germline GALNT12 variants in a clinic-based cohort (N = 118) with predisposition for CRC. Here, we screened a new population-based cohort of incident CRC cases (N = 479) for rare (MAF ≤1%) deleterious germline GALNT12 variants. GALNT12 screening revealed eight rare variants. Two variants were previously described (p.Asp303Asn, p.Arg297Trp), and additionally, we found six other rare variants: five missense (p.His101Gln, p.Ile142Thr, p.Glu239Gln, p.Thr286Met, p.Val290Phe) and one putative splice-altering variant (c.732-8 G>T). Sequencing of population-matched controls (N = 400) revealed higher burden of these variants in CRC cases compared with healthy controls (P = 0.0381). We then functionally characterized the impact of substitutions on GALNT12 enzyme activity using in vitro-derived peptide substrates. Three of the newly identified GALNT12 missense variants (p.His101Gln, p.Ile142Thr, p.Val290Phe) demonstrated a marked loss (>2-fold reduction) of enzymatic activity compared with wild-type (P ≤ 0.05), whereas p.Glu239Gln exhibited a ∼2-fold reduction in activity (P = 0.077). These findings provide strong, independent evidence for the association of GALNT12 defects with CRC-susceptibility; underscoring implications for glycosylation pathway defects in CRC.
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Affiliation(s)
- Daniel R Evans
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Canada
| | - Srividya Venkitachalam
- Division of General Medical Sciences-Oncology, Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Leslie Revoredo
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio
| | - Amanda T Dohey
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Canada
| | - Erica Clarke
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Canada
| | - Julia J Pennell
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Canada
| | - Amy E Powell
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Canada
| | - Erina Quinn
- Division of General Medical Sciences-Oncology, Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Lakshmeswari Ravi
- Division of General Medical Sciences-Oncology, Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Thomas A Gerken
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio.,Department of Pediatrics, Case Western Reserve University School of Medicine, Cleveland, Ohio.,Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Jane S Green
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Canada
| | - Michael O Woods
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Canada
| | - Kishore Guda
- Division of General Medical Sciences-Oncology, Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, Ohio
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20
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Zhu Y, Wang PP, Zhai G, Bapat B, Savas S, Woodrow JR, Campbell PT, Li Y, Yang N, Zhou X, Dicks E, Mclaughlin JR, Parfrey PS. Association of rs2282679 A>C polymorphism in vitamin D binding protein gene with colorectal cancer risk and survival: effect modification by dietary vitamin D intake. BMC Cancer 2018; 18:155. [PMID: 29409465 PMCID: PMC5802053 DOI: 10.1186/s12885-018-4026-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 01/23/2018] [Indexed: 02/14/2023] Open
Abstract
Background The rs2282679 A>C polymorphism in the vitamin D binding protein gene is associated with lower circulating levels of vitamin D. We investigated associations of this SNP with colorectal cancer (CRC) risk and survival and whether the associations vary by dietary vitamin D intake and tumor molecular phenotype. Methods A population-based case-control study identified 637 incident CRC cases (including 489 participants with follow-up data on mortality end-points) and 489 matched controls. Germline DNA samples were genotyped with the Illumina Omni-Quad 1 Million chip in cases and the Affymetrix Axiom® myDesign™ Array in controls. Logistic regression examined the association between the rs2282679 polymorphism and CRC risk with inclusion of potential confounders. Kaplan-Meier curves and multivariable Cox models assessed the polymorphism relative to overall survival (OS) and disease-free survival (DFS). Results The rs2282679 polymorphism was not associated with overall CRC risk; there was evidence, however, of effect modification by total vitamin D intake (Pinteraction = 0.019). Survival analyses showed that the C allele was correlated with poor DFS (per-allele HR, 1.36; 95%CI, 1.05–1.77). The association of rs2282679 on DFS was limited to BRAF wild-type tumors (HR, 1.58; 95%CI, 1.12–2.23). For OS, the C allele was associated with higher all-cause mortality among patients with higher levels of dietary vitamin D (HR, 2.11; 95%CI, 1.29–3.74), calcium (HR, 1.93; 95%CI, 1.08–3.46), milk (HR, 2.36; 95%CI, 1.26–4.44), and total dairy product intakes (HR, 2.03; 95%CI, 1.11–3.72). Conclusion The rs2282679 SNP was not associated with overall CRC risk, but may be associated with survival after cancer diagnosis. The association of this SNP on survival among CRC patients may differ according to dietary vitamin D and calcium intakes and according to tumor BRAF mutation status.
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Affiliation(s)
- Yun Zhu
- Division of Community Health and Humanities, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada.,School of Public Health, Tianjin Medical University, Tianjin, China
| | - Peizhong Peter Wang
- Division of Community Health and Humanities, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada. .,School of Public Health, Tianjin Medical University, Tianjin, China.
| | - Guangju Zhai
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Bharati Bapat
- Department of Laboratory Medicine and Pathobiology, Department of Surgery, University of Toronto, Toronto, ON, Canada
| | - Sevtap Savas
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada.,Discipline of Oncology, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Jennifer R Woodrow
- Division of Community Health and Humanities, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Peter T Campbell
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, USA
| | - Yuming Li
- Tianjin Key Laboratory of Cardiovascular Remodeling and Target Organ Injury, Pingjin Hospital Heart Center, Logistics University of Chinese People's Armed Police Force, Tianjin, China
| | - Ning Yang
- Tianjin Key Laboratory of Cardiovascular Remodeling and Target Organ Injury, Pingjin Hospital Heart Center, Logistics University of Chinese People's Armed Police Force, Tianjin, China
| | - Xin Zhou
- Tianjin Key Laboratory of Cardiovascular Remodeling and Target Organ Injury, Pingjin Hospital Heart Center, Logistics University of Chinese People's Armed Police Force, Tianjin, China
| | - Elizabeth Dicks
- Clinical Epidemiology Unit, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - John R Mclaughlin
- Division of Epidemiology, Public Health Ontario, Toronto, ON, Canada
| | - Patrick S Parfrey
- Clinical Epidemiology Unit, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
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He Y, Penney ME, Negandhi AA, Parfrey PS, Savas S, Yilmaz YE. XRCC3 Thr241Met and TYMS variable number tandem repeat polymorphisms are associated with time-to-metastasis in colorectal cancer. PLoS One 2018; 13:e0192316. [PMID: 29394274 PMCID: PMC5796722 DOI: 10.1371/journal.pone.0192316] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 01/20/2018] [Indexed: 01/13/2023] Open
Abstract
Background Metastasis is a major cause of mortality in cancer. Identifying prognostic factors that distinguish patients who will experience metastasis in the short-term and those that will be free of metastasis in the long-term is of particular interest in current medical research. The objective of this study was to examine if select genetic polymorphisms can differentiate colorectal cancer patients based on timing and long-term risk of metastasis. Methods The patient cohort consisted of 402 stage I-III colorectal cancer patients with microsatellite instability (MSI)-low (MSI-L) or microsatellite stable (MSS) tumors. We applied multivariable mixture cure model, which is the proper model when there is a substantial group of patients who remain free of metastasis in the long-term, to 26 polymorphisms. Time-dependent receiver operator characteristic (ROC) curve analysis was performed to determine the change in discriminatory accuracy of the models when the significant SNPs were included. Results After adjusting for significant baseline characteristics, two polymorphisms were significantly associated with time-to-metastasis: TT and TC genotypes of the XRCC3 Thr241Met (p = 0.042) and the 3R/3R genotype of TYMS 5’-UTR variable number tandem repeat (VNTR) (p = 0.009) were associated with decreased time-to-metastasis. ROC curves showed that the discriminatory accuracy of the model is increased slightly when these polymorphisms were added to the significant baseline characteristics. Conclusions Our results indicate XRCC3 Thr241Met and TYMS 5’-UTR VNTR polymorphisms are associated with time-to-metastasis, and may have potential biological roles in expediting the metastatic process. Once replicated, these associations could contribute to the development of precision medicine for colorectal cancer patients.
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Affiliation(s)
- Yanjing He
- Department of Mathematics and Statistics, Faculty of Science, Memorial University of Newfoundland, St. John's, Canada
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Canada
| | - Michelle E. Penney
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Canada
| | - Amit A. Negandhi
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Canada
| | - Patrick S. Parfrey
- Discipline of Medicine, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Canada
| | - Sevtap Savas
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Canada
- Discipline of Oncology, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Canada
| | - Yildiz E. Yilmaz
- Department of Mathematics and Statistics, Faculty of Science, Memorial University of Newfoundland, St. John's, Canada
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Canada
- Discipline of Medicine, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Canada
- * E-mail:
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22
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Vitamin D receptor and calcium-sensing receptor polymorphisms and colorectal cancer survival in the Newfoundland population. Br J Cancer 2017; 117:898-906. [PMID: 28765616 PMCID: PMC5589991 DOI: 10.1038/bjc.2017.242] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 06/20/2017] [Accepted: 07/03/2017] [Indexed: 02/06/2023] Open
Abstract
Background: Increased serum levels of vitamin D and calcium have been associated with lower risks of colorectal cancer (CRC) incidence and mortality. These inverse associations may be mediated by the vitamin D receptor (VDR) and the calcium-sensing receptor (CASR). We investigated genetic variants in VDR and CASR for their relevance to CRC prognosis. Methods: A population-based cohort of 531 CRC patients diagnosed from 1999 to 2003 in Newfoundland and Labrador, Canada, was followed for mortality and cancer recurrence until April 2010. Germline DNA samples were genotyped with the Illumina Omni-Quad 1 Million chip. Multivariate Cox models assessed 41 tag single-nucleotide polymorphisms and relative haplotypes on VDR and CASR in relation to all-cause mortality (overall survival, OS) and disease-free survival (DFS). Results: Gene-level associations were observed between VDR and the DFS of rectal cancer patients (P=0.037) as well as between CASR and the OS of colon cancer patients (P=0.014). Haplotype analysis within linkage blocks of CASR revealed the G-G-G-G-G-A-C haplotype (rs10222633-rs10934578-rs3804592-rs17250717-A986S-R990G-rs1802757) to be associated with a decreased OS of colon cancer (HR, 3.15; 95% CI, 1.66–5.96). Potential interactions were seen among prediagnostic dietary calcium intake with the CASR R990G (Pint=0.040) and the CASR G-T-G-G-G-G-C haplotype for rs10222633-rs10934578-rs3804592-rs17250717-A986S-R990G-rs1802757 (Pint=0.017), with decreased OS time associated with these variants limited to patients consuming dietary calcium below the median, although the stratified results were not statistically significant after correction for multiple testing. Conclusions: Polymorphic variations in VDR and CASR may be associated with survival after a diagnosis of CRC.
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Sharma I, Zhu Y, Woodrow JR, Mulay S, Parfrey PS, Mclaughlin JR, Hebert JR, Shivappa N, Li Y, Zhou X, Wang PP. Inflammatory diet and risk for colorectal cancer: A population-based case-control study in Newfoundland, Canada. Nutrition 2017; 42:69-74. [PMID: 28870481 DOI: 10.1016/j.nut.2017.05.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/08/2017] [Accepted: 05/17/2017] [Indexed: 12/18/2022]
Abstract
OBJECTIVE Chronic inflammation is implicated in causing cancer. Diet plays an important role in regulating chronic inflammation by altering circulating levels of inflammatory biomarkers. Effect of single food or nutrient on cancer often is inconclusive; perhaps due to dietary interactions and multicolinearity. The aim of this study was to determine prediagnostic inflammatory potential of overall diet in relation to risk for colorectal cancer (CRC). METHODS In all, 547 patients with CRC from Newfoundland Familial Colorectal Cancer Registry and 685 controls from the general population were identified. Data on sociodemographic, medical history, lifestyle, and a 169-item food frequency questionnaire were collected retrospectively from both groups. Energy-adjusted Dietary Inflammatory Index (DII) score was calculated and used as both categorical and continuous variables for analysis. Odds ratio was estimated using multivariable logistic regression after adjusting potential confounders. A linear test for trend was performed using the median value in each quartile. RESULTS Overall energy-adjusted mean DII score was -0.81 (range -5.19 to 6.93). Cases (-0.73 ± 1.5) had slightly higher DII scores than controls (-0.89 ± 1.6; P = 0.04). After adjusting the potential confounders, a statistically significant association was found between DII score and CRC risk. Using DII as a continuous variable (odds ratio [OR]continuous 1.10, 95% confidence interval [CI] 1.01-1.20) and categorical variable (ORquartile 1 versus 4 1.65, 95% CI 1.13-2.42; Ptrend = 0.02). CONCLUSION Our findings indicate that proinflammatory diets are associated with an increased risk for CRC in the Newfoundland population.
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Affiliation(s)
- Ishor Sharma
- Division of Community Health and Humanities, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Yun Zhu
- Division of Community Health and Humanities, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Jennifer R Woodrow
- Division of Community Health and Humanities, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Shree Mulay
- Division of Community Health and Humanities, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Patrick S Parfrey
- Division of Community Health and Humanities, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | | | - James R Hebert
- Department of Epidemiology and Biostatistics, University of South Carolina, Columbia, South Carolina, USA; Cancer Prevention and Control Program, University of South Carolina, Columbia, South Carolina, USA
| | - Nitin Shivappa
- Department of Epidemiology and Biostatistics, University of South Carolina, Columbia, South Carolina, USA; Cancer Prevention and Control Program, University of South Carolina, Columbia, South Carolina, USA
| | - Yuming Li
- Tianjin Key Laboratory of Cardiovascular Remodeling and Target Organ Injury, Pingjin Hospital Heart Center, Logistics University of Chinese People's Armed Police Force, Tianjin, China
| | - Xin Zhou
- Tianjin Key Laboratory of Cardiovascular Remodeling and Target Organ Injury, Pingjin Hospital Heart Center, Logistics University of Chinese People's Armed Police Force, Tianjin, China
| | - Peizhong Peter Wang
- Division of Community Health and Humanities, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada.
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LEHR JOSH, RAHMAN PROTON, O’RIELLY DARREND. High Accuracy and Significant Savings Using Tag-SNP Genotyping to DetermineHLA-B*27Status. J Rheumatol 2017; 44:962-963. [DOI: 10.3899/jrheum.161095] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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25
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Werdyani S, Yu Y, Skardasi G, Xu J, Shestopaloff K, Xu W, Dicks E, Green J, Parfrey P, Yilmaz YE, Savas S. Germline INDELs and CNVs in a cohort of colorectal cancer patients: their characteristics, associations with relapse-free survival time, and potential time-varying effects on the risk of relapse. Cancer Med 2017; 6:1220-1232. [PMID: 28544645 PMCID: PMC5463068 DOI: 10.1002/cam4.1074] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 03/13/2017] [Accepted: 03/16/2017] [Indexed: 12/24/2022] Open
Abstract
INDELs and CNVs are structural variations that may play roles in cancer susceptibility and patient outcomes. Our objectives were a) to computationally detect and examine the genome‐wide INDEL/CNV profiles in a cohort of colorectal cancer patients, and b) to examine the associations of frequent INDELs/CNVs with relapse‐free survival time. We also identified unique variants in 13 Familial Colorectal Cancer Type X (FCCX) cases. The study cohort consisted of 495 colorectal cancer patients. QuantiSNP and PennCNV algorithms were utilized to predict the INDELs/CNVs using genome‐wide signal intensity data. Duplex PCR was used to validate predictions for 10 variants. Multivariable Cox regression models were used to test the associations of 106 common variants with relapse‐free survival time. Score test and the multivariable Cox proportional hazards models with time‐varying coefficients were applied to identify the variants with time‐varying effects on the relapse‐free survival time. A total of 3486 distinct INDELs/CNVs were identified in the patient cohort. The majority of these variants were rare (83%) and deletion variants (81%). The results of the computational predictions and duplex PCR results were highly concordant (93–100%). We identified four promising variants significantly associated with relapse‐free survival time (P < 0.05) in the multivariable Cox proportional hazards regression models after adjustment for clinical factors. More importantly, two additional variants were identified to have time‐varying effects on the risk of relapse. Finally, 58 rare variants were identified unique to the FCCX cases; none of them were detected in more than one patient. This is one of the first genome‐wide analyses that identified the germline INDEL/CNV profiles in colorectal cancer patients. Our analyses identified novel variants and genes that can biologically affect the risk of relapse in colorectal cancer patients. Additionally, for the first time, we identified germline variants that can potentially be early‐relapse markers in colorectal cancer.
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Affiliation(s)
- Salem Werdyani
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, Newfoundland and Labrador, Canada
| | - Yajun Yu
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, Newfoundland and Labrador, Canada
| | - Georgia Skardasi
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, Newfoundland and Labrador, Canada
| | - Jingxiong Xu
- Department of Biostatistics, Princess Margaret Hospital, University of Toronto, Toronto, Ontario, Canada
| | | | - Wei Xu
- Department of Biostatistics, Princess Margaret Hospital, University of Toronto, Toronto, Ontario, Canada.,Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Elizabeth Dicks
- Clinical Epidemiology Unit, Faculty of Medicine, Memorial University, St. John's, Newfoundland and Labrador, Canada
| | - Jane Green
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, Newfoundland and Labrador, Canada.,Discipline of Oncology, Faculty of Medicine, Memorial University, St. John's, Newfoundland and Labrador, Canada
| | - Patrick Parfrey
- Clinical Epidemiology Unit, Faculty of Medicine, Memorial University, St. John's, Newfoundland and Labrador, Canada
| | - Yildiz E Yilmaz
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, Newfoundland and Labrador, Canada.,Clinical Epidemiology Unit, Faculty of Medicine, Memorial University, St. John's, Newfoundland and Labrador, Canada.,Department of Mathematics and Statistics, Faculty of Science, Memorial University, St. John's, Newfoundland and Labrador, Canada
| | - Sevtap Savas
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, Newfoundland and Labrador, Canada.,Discipline of Oncology, Faculty of Medicine, Memorial University, St. John's, Newfoundland and Labrador, Canada
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Parfrey PS, Dicks E, Parfrey O, McNicholas PJ, Noseworthy H, Woods MO, Negriin C, Green J. Evaluation of a population-based approach to familial colorectal cancer. Clin Genet 2016; 91:672-682. [PMID: 27696385 PMCID: PMC5413826 DOI: 10.1111/cge.12877] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 09/19/2016] [Accepted: 09/21/2016] [Indexed: 12/24/2022]
Abstract
As Newfoundland has the highest rate of familial colorectal cancer (CRC) in the world, we started a population‐based clinic to provide colonoscopic and Lynch syndrome (LS) screening recommendations to families of CRC patients based on family risk. Of 1091 incident patients 51% provided a family history. Seventy‐two percent of families were at low or intermediate–low risk of CRC and colonoscopic screening recommendations were provided by letter. Twenty‐eight percent were at high and intermediate–high risk and were referred to the genetic counsellor, but only 30% (N = 48) were interviewed by study end. Colonoscopy was recommended more frequently than every 5 years in 35% of families. Lower family risk was associated with older age of proband but the frequency of screening colonoscopy recommendations varied across all age groups, driven by variability in family history. Twenty‐four percent had a high MMR predict score for a Lynch syndrome mutation, and 23% fulfilled the Provincial Program criteria for LS screening. A population‐based approach in the provision of colonoscopic screening recommendations to families at risk of CRC was limited by the relatively low response rate. A family history first approach to the identification of LS families was inefficient.
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Affiliation(s)
- P S Parfrey
- The Clinical Epidemiology Unit, Memorial University, St Johns, Newfoundland, Canada
| | - E Dicks
- The Clinical Epidemiology Unit, Memorial University, St Johns, Newfoundland, Canada
| | - O Parfrey
- The Clinical Epidemiology Unit, Memorial University, St Johns, Newfoundland, Canada
| | - P J McNicholas
- The Clinical Epidemiology Unit, Memorial University, St Johns, Newfoundland, Canada
| | - H Noseworthy
- The Clinical Epidemiology Unit, Memorial University, St Johns, Newfoundland, Canada
| | - M O Woods
- The Clinical Epidemiology Unit, Memorial University, St Johns, Newfoundland, Canada
| | - C Negriin
- The Clinical Epidemiology Unit, Memorial University, St Johns, Newfoundland, Canada
| | - J Green
- Discipline of Genetics, Health Sciences Centre, Memorial University, St Johns, Newfoundland, Canada
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Dan LA, Werdyani S, Xu J, Shestopaloff K, Hyde A, Dicks E, Younghusband B, Green J, Parfrey P, Xu W, Savas S. No associations of a set of SNPs in the Vascular Endothelial Growth Factor (VEGF) and Matrix Metalloproteinase (MMP) genes with survival of colorectal cancer patients. Cancer Med 2016; 5:2221-31. [PMID: 27334288 PMCID: PMC5055182 DOI: 10.1002/cam4.796] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 05/18/2016] [Accepted: 05/19/2016] [Indexed: 02/06/2023] Open
Abstract
In this study, we aimed to investigate the associations of genetic variations within select genes functioning in angiogenesis, lymph‐angiogenesis, and metastasis pathways and the risk of outcome in colorectal cancer patients. We followed a two‐stage analysis: First, 381 polymorphisms from 30 genes (eight Vascular Endothelial Growth Factor (VEGF) and 22 Matrix Metalloproteinase [MMP] genes) were investigated in the discovery cohort (n = 505). Then, 16 polymorphisms with the lowest P‐value in this analysis were investigated in a separate replication cohort (n = 247). Genotypes were obtained using the Illumina® HumanOmni‐1‐Quad (discovery cohort) and Sequenom MassArray® (replication cohort) platforms. The primary outcome measure was overall survival (OS). Kaplan–Meier, univariate and multivariable Cox regression methods were used to test the associations between genotypes and OS. Four SNPs (rs12365082, rs11225389, rs11225388, and rs2846707) had the univariate analysis P < 0.05 in both the discovery and replication cohorts. These SNPs are in linkage disequilibrium with each other to varying extent and are located in the MMP8 and MMP27 genes. In the multivariable analysis adjusting for age, stage, and microsatellite instability status, three of these SNPs (rs12365082, rs11225389, rs11225388) were independent predictors of OS (P < 0.05) in the discovery cohort. However, the same analysis in the replication cohort did not yield statistically significant results. Overall, while the genetic variations in the VEGF and MMP genes are attractive candidates as prognostic markers, our study showed no evidence of associations of a large set of SNPs in these genes and overall survival of colorectal cancer patients in our study.
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Affiliation(s)
- Lydia A Dan
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, Newfoundland, Canada
| | - Salem Werdyani
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, Newfoundland, Canada
| | - Jingxiong Xu
- Department of Biostatistics, Princess Margaret Hospital, University of Toronto, Toronto, Ontario, Canada
| | | | - Angela Hyde
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, Newfoundland, Canada
| | - Elizabeth Dicks
- Clinical Epidemiology Unit, Faculty of Medicine, Memorial University, St. John's, Newfoundland, Canada
| | - Ban Younghusband
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, Newfoundland, Canada
| | - Jane Green
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, Newfoundland, Canada
| | - Patrick Parfrey
- Clinical Epidemiology Unit, Faculty of Medicine, Memorial University, St. John's, Newfoundland, Canada
| | - Wei Xu
- Department of Biostatistics, Princess Margaret Hospital, University of Toronto, Toronto, Ontario, Canada.,Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Sevtap Savas
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, Newfoundland, Canada. .,Discipline of Oncology, Faculty of Medicine, Memorial University, St. John's, Newfoundland, Canada.
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Savio AJ, Daftary D, Dicks E, Buchanan DD, Parfrey PS, Young JP, Weisenberger D, Green RC, Gallinger S, McLaughlin JR, Knight JA, Bapat B. Promoter methylation of ITF2, but not APC, is associated with microsatellite instability in two populations of colorectal cancer patients. BMC Cancer 2016; 16:113. [PMID: 26884349 PMCID: PMC4756469 DOI: 10.1186/s12885-016-2149-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 02/08/2016] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Aberrant Wnt signaling activation occurs commonly in colorectal carcinogenesis, leading to upregulation of many target genes. APC (adenomatous polyposis coli) is an important component of the β-catenin destruction complex, which regulates Wnt signaling, and is often mutated in colorectal cancer (CRC). In addition to mutational events, epigenetic changes arise frequently in CRC, specifically, promoter hypermethylation which silences tumor suppressor genes. APC and the Wnt signaling target gene ITF2 (immunoglobulin transcription factor 2) incur hypermethylation in various cancers, however, methylation-dependent regulation of these genes in CRC has not been studied in large, well-characterized patient cohorts. The microsatellite instability (MSI) subtype of CRC, featuring DNA mismatch repair deficiency and often promoter hypermethylation of MutL homolog 1 (MLH1), has a favorable outcome and is characterized by different chemotherapeutic responses than microsatellite stable (MSS) tumors. Other epigenetic events distinguishing these subtypes have not yet been fully elucidated. METHODS Here, we quantify promoter methylation of ITF2 and APC by MethyLight in two case-case studies nested in population-based CRC cohorts from the Ontario Familial Colorectal Cancer Registry (n = 330) and the Newfoundland Familial Colorectal Cancer Registry (n = 102) comparing MSI status groups. RESULTS ITF2 and APC methylation are significantly associated with tumor versus normal state (both P < 1.0 × 10(-6)). ITF2 is methylated in 45.8% of MSI cases and 26.9% of MSS cases and is significantly associated with MSI in Ontario (P = 0.002) and Newfoundland (P = 0.005) as well as the MSI-associated feature of MLH1 promoter hypermethylation (P = 6.72 × 10(-4)). APC methylation, although tumor-specific, does not show a significant association with tumor subtype, age, gender, or stage, indicating it is a general tumor-specific CRC biomarker. CONCLUSIONS This study demonstrates, for the first time, MSI-associated ITF2 methylation, and further reveals the subtype-specific epigenetic events modulating Wnt signaling in CRC.
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Affiliation(s)
- Andrea J Savio
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON, Canada.
| | - Darshana Daftary
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON, Canada.
- Ontario Familial Colorectal Cancer Registry, Toronto, ON, Canada.
| | - Elizabeth Dicks
- Faculty of Medicine, Memorial University of Newfoundland, St John's, Newfoundland, Canada.
| | - Daniel D Buchanan
- Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Parkville, VIC, Australia.
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia.
| | - Patrick S Parfrey
- Faculty of Medicine, Memorial University of Newfoundland, St John's, Newfoundland, Canada.
| | - Joanne P Young
- Department of Haematology and Oncology, The Queen Elizabeth Hospital, Woodville, South Australia, Australia.
| | - Daniel Weisenberger
- USC Epigenome Center, University of Southern California, Los Angeles, CA, USA.
| | - Roger C Green
- Faculty of Medicine, Memorial University of Newfoundland, St John's, Newfoundland, Canada.
| | - Steven Gallinger
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON, Canada.
- Ontario Familial Colorectal Cancer Registry, Toronto, ON, Canada.
- Department of Surgery, University of Toronto, Toronto, ON, Canada.
| | - John R McLaughlin
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON, Canada.
- Ontario Familial Colorectal Cancer Registry, Toronto, ON, Canada.
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada.
| | - Julia A Knight
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON, Canada.
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada.
| | - Bharati Bapat
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON, Canada.
- Department of Pathology, University Health Network, Toronto, ON, Canada.
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Zhai G, Zhou J, Woods MO, Green JS, Parfrey P, Rahman P, Green RC. Genetic structure of the Newfoundland and Labrador population: founder effects modulate variability. Eur J Hum Genet 2015; 24:1063-70. [PMID: 26669659 DOI: 10.1038/ejhg.2015.256] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 11/16/2015] [Accepted: 11/18/2015] [Indexed: 01/30/2023] Open
Abstract
The population of the province of Newfoundland and Labrador (NL) has been a resource for genetic studies because of its historical isolation and increased prevalence of several monogenic disorders. Controversy remains regarding the genetic substructure and the extent of genetic homogeneity, which have implications for disease gene mapping. Population substructure has been reported from other isolated populations such as Iceland, Finland and Sardinia. We undertook this study to further our understanding of the genetic architecture of the NL population. We enrolled 494 individuals randomly selected from NL. Genome-wide SNP data were analyzed together with that from 14 other populations including HapMap3, Ireland, Britain and Native American samples from the Human Genome Diversity Project. Using multidimensional scaling and admixture analysis, we observed that the genetic structure of the NL population resembles that of the British population but can be divided into three clusters that correspond to religious/ethnic origins: Protestant English, Roman Catholic Irish and North American aboriginals. We observed reduced heterozygosity and an increased inbreeding coefficient (mean=0.005), which corresponds to that expected in the offspring of third-cousin marriages. We also found that the NL population has a significantly higher number of runs of homozygosity (ROH) and longer lengths of ROH segments. These results are consistent with our understanding of the population history and indicate that the NL population may be ideal for identifying recessive variants for complex diseases that affect populations of European origin.
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Affiliation(s)
- Guangju Zhai
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St John's, Newfoundland and Labrador, Canada
| | - Jiayi Zhou
- Discipline of Medicine, Faculty of Medicine, Memorial University, St John's, Newfoundland and Labrador, Canada
| | - Michael O Woods
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St John's, Newfoundland and Labrador, Canada
| | - Jane S Green
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St John's, Newfoundland and Labrador, Canada
| | - Patrick Parfrey
- Discipline of Medicine, Faculty of Medicine, Memorial University, St John's, Newfoundland and Labrador, Canada
| | - Proton Rahman
- Discipline of Medicine, Faculty of Medicine, Memorial University, St John's, Newfoundland and Labrador, Canada
| | - Roger C Green
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St John's, Newfoundland and Labrador, Canada
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Etchegary H, Green J, Parfrey P, Street C, Pullman D. Community engagement with genetics: public perceptions and expectations about genetics research. Health Expect 2015; 18:1413-25. [PMID: 23968492 PMCID: PMC5060853 DOI: 10.1111/hex.12122] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2013] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Knowledge of molecular biology and genomics continues to expand rapidly, promising numerous opportunities for improving health. However, a key aspect of the success of genomic medicine is related to public understanding and acceptance. DESIGN Using community consultations and an online survey, we explored public attitudes and expectations about genomics research. RESULTS Thirty-three members of the general public in Newfoundland, Canada, took part in the community sessions, while 1024 Atlantic Canadians completed the online survey. Overall, many participants noted they lacked knowledge about genetics and associated research and took the opportunity to ask numerous questions throughout sessions. Participants were largely hopeful about genomics research in its capacity to improve health, not only for current residents, but also for future generations. However, they did not accept such research uncritically, and a variety of complex issues and questions arose during the community consultations and were reflected in survey responses. DISCUSSION With the proliferation of biobanks and the rapid pace of discoveries in genomics research, public support will be crucial to realize health improvements. If researchers can engage the public in regular, transparent dialogue, this two-way communication could allow greater understanding of the research process and the design of efficient and effective genetic health services, informed by the public that will use them.
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Affiliation(s)
| | - Jane Green
- Department of GeneticsMemorial UniversitySt. John'sNLCanada
| | | | - Catherine Street
- Population Therapeutics Research GroupMemorial UniversitySt. John'sNLCanada
| | - Daryl Pullman
- Division of Community HealthMemorial UniversitySt. John'sNLCanada
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Abstract
Despite decades of scientific and clinical research, pancreatic ductal adenocarcinoma (PDAC) remains a lethal malignancy. The clinical and pathologic features of PDAC, specifically the known environmental and genetic risk factors, are reviewed here with special emphasis on the hereditary pancreatic cancer (HPC) syndromes. For these latter conditions, strategies are described for their identification, for primary and secondary prevention in unaffected carriers, and for disease management in affected carriers. Nascent steps have been made toward personalized medicine based on the rational use of screening, tumor subtyping, and targeted therapies; these have been guided by growing knowledge of HPC syndromes in PDAC.
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Affiliation(s)
- Ashton A Connor
- Division of General Surgery, Department of Surgery, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Steven Gallinger
- Division of General Surgery, Department of Surgery, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.
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Mohideen AMSH, Dicks E, Parfrey P, Green R, Savas S. Mitochondrial DNA polymorphisms, its copy number change and outcome in colorectal cancer. BMC Res Notes 2015; 8:272. [PMID: 26116242 PMCID: PMC4482280 DOI: 10.1186/s13104-015-1250-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 06/17/2015] [Indexed: 12/14/2022] Open
Abstract
Background Mitochondrion is a small organelle inside the eukaryotic cells. It has its own genome (mtDNA) and encodes for proteins that are critical for energy production and cellular metabolism. Mitochondrial dysfunctions have been implicated in cancer progression and may be related to poor prognosis in cancer patients. In this study we hypothesized that genetic variations in mtDNA are associated with clinical outcome in colorectal cancer patients. Methods We tested the associations of six mtDNA polymorphisms [MitoT479C, MitoT491C, MitoT10035C, MitoA13781G, 10398 (A/G), and 16189 (T/C)] and the mtDNA copy number change with overall survival (OS) and disease-free survival (DFS) times. Two mtDNA polymorphisms were genotyped using the TaqMan® SNP genotyping technique and the genotypes for the remaining four mtDNA polymorphisms were obtained by the Illumina® HumanOmni1-Quad genome wide SNP genotyping platform in 536 patients. The mtDNA copy number change (in tumor tissues with respect to non-tumor tissues) was estimated using the quantitative real time polymerase chain reaction for 274 patients. Associations of these mtDNA variations with OS and DFS were tested using the Cox regression method. Results In both univariate and multivariable analyses, none of the six mtDNA polymorphisms were associated with OS or DFS. 39.6 and 60.4% of the patients had increased and decreased mtDNA copy number in their tumor tissues when compared to their non-tumor rectum or colon tissues, respectively. However, in contrast to previous findings, the change in the mtDNA copy number was associated with neither OS nor DFS in our patient cohort. Conclusions Our results suggest that the mitochondrial genetic markers investigated in this study are not associated with outcome in colorectal cancer. Electronic supplementary material The online version of this article (doi:10.1186/s13104-015-1250-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Asan Meera Sahib Haja Mohideen
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, 300 Prince Philip Drive, HSC, Room H4333, St. John's, NL, A1B 3V6, Canada.
| | - Elizabeth Dicks
- Clinical Epidemiology Unit, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada.
| | - Patrick Parfrey
- Clinical Epidemiology Unit, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada.
| | - Roger Green
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, 300 Prince Philip Drive, HSC, Room H4333, St. John's, NL, A1B 3V6, Canada.
| | - Sevtap Savas
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, 300 Prince Philip Drive, HSC, Room H4333, St. John's, NL, A1B 3V6, Canada. .,Discipline of Oncology, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada.
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Xu W, Xu J, Shestopaloff K, Dicks E, Green J, Parfrey P, Green R, Savas S. A genome wide association study on Newfoundland colorectal cancer patients' survival outcomes. Biomark Res 2015; 3:6. [PMID: 25866641 PMCID: PMC4393623 DOI: 10.1186/s40364-015-0031-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 02/23/2015] [Indexed: 01/14/2023] Open
Abstract
Background In this study we performed genome-wide association studies to identify candidate SNPs that may predict the risk of disease outcome in colorectal cancer. Methods Patient cohort consisted of 505 unrelated patients with Caucasian ancestry. Germline DNA samples were genotyped using the Illumina® human Omni-1quad SNP chip. Associations of SNPs with overall and disease free survivals were examined primarily for 431 patients with microsatellite instability-low (MSI-L) or stable (MSS) colorectal tumors using Cox proportional hazards method adjusting for clinical covariates. Bootstrap method was applied for internal validation of results. As exploratory analyses, association analyses for the colon (n = 334) and rectal (n = 171) cancer patients were also performed. Results As a result, there was no SNP that reached the genomewide significance levels (p < 5x10−8) in any of the analyses. A small number of genetic markers (n = 10) showed nominal associations (p <10−6) for MSS/MSI-L, colon, or rectal cancer patient groups. These markers were located in two non-coding RNA genes or intergenic regions and none were amino acid substituting polymorphisms. Bootstrap analysis for the MSS/MSI-L cohort data suggested the robustness of the observed nominal associations. Conclusions Likely due to small number of patients, our study did not identify an acceptable level of association of SNPs with outcome in MSS/MSI-L, colon, or rectal cancer patients. A number of SNPs with sub-optimal p-values were, however, identified; these loci may be promising and examined in other larger-sized patient cohorts. Electronic supplementary material The online version of this article (doi:10.1186/s40364-015-0031-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wei Xu
- Department of Biostatistics, Princess Margaret Cancer Centre, Toronto, ON Canada M5G 2 M9 ; Dalla Lana School of Public Health, University of Toronto, Toronto, ON Canada M5T 3M7
| | - Jingxiong Xu
- Department of Biostatistics, Princess Margaret Cancer Centre, Toronto, ON Canada M5G 2 M9 ; Dalla Lana School of Public Health, University of Toronto, Toronto, ON Canada M5T 3M7
| | | | - Elizabeth Dicks
- Clinical Epidemiology Unit, Faculty of Medicine, Memorial University, St. John's, NL Canada A1B 3V6
| | - Jane Green
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, NL Canada A1B 3 V6
| | - Patrick Parfrey
- Clinical Epidemiology Unit, Faculty of Medicine, Memorial University, St. John's, NL Canada A1B 3V6
| | - Roger Green
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, NL Canada A1B 3 V6
| | - Sevtap Savas
- Discipline of Genetics, Faculty of Medicine, Memorial University, St. John's, NL Canada A1B 3 V6 ; Discipline of Oncology, Faculty of Medicine, Memorial University, St. John's, NL Canada A1B 3 V6
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Haja Mohideen AMS, Hyde A, Squires J, Wang J, Dicks E, Younghusband B, Parfrey P, Green R, Savas S. Examining the polymorphisms in the hypoxia pathway genes in relation to outcome in colorectal cancer. PLoS One 2014; 9:e113513. [PMID: 25405996 PMCID: PMC4236175 DOI: 10.1371/journal.pone.0113513] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 10/29/2014] [Indexed: 12/21/2022] Open
Abstract
Introduction Colorectal cancer is a common malignancy. Identification of genetic prognostic markers may help prognostic estimations in colorectal cancer. Genes that regulate response to hypoxia and other genes that are regulated under the hypoxic conditions have been shown to play roles in cancer progression. In this study, we hypothesized that genetic variations in the hypoxia pathway genes were associated with the risk of outcome in colorectal cancer patients. Methods This study was performed in two phases. In the first phase, 49 SNPs from six hypoxia pathway genes (HIF1A, HIF1B, HIF2A, LOX, MIF and CXCL12) in 272 colorectal cancer patients were analyzed. In the second phase, 77 SNPs from seven hypoxia pathway genes (HIF1A, HIF1B, HIF2A, HIF2B, HIF3A, LOX and CXCL12) were analyzed in an additional cohort of 535 patients. Kaplan Meier, Cox univariate and multivariable regression analyses were performed to analyze the relationship between the SNPs and overall survival (OS), disease free survival (DFS) or disease specific survival (DSS). Since this was a hypothesis-generating study, no correction for multiple testing was applied. Results In phase I, one SNP (HIF2A rs11125070) was found to be associated with DFS in multivariable analysis; yet association of a proxy polymorphism (HIF2A rs4953342) was not detected in the phase II patient cohort. In phase II, associations of two SNPs (HIF2A rs4953352 and HIF2B rs12593988) were significant in both OS and DFS multivariable analyses. However, association of HIF2A rs4953352 was not replicated in the phase I cohort using a proxy SNP (HIF2A rs6706003). Conclusion Overall, our study did not find a convincing evidence of association of the investigated polymorphisms with the disease outcomes in colorectal cancer.
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Affiliation(s)
- Asan M. S. Haja Mohideen
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Angela Hyde
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Jessica Squires
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Jing Wang
- Division of Community Health and Humanities, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Elizabeth Dicks
- Clinical Epidemiology Unit, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Ban Younghusband
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Patrick Parfrey
- Clinical Epidemiology Unit, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Roger Green
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Sevtap Savas
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
- Discipline of Oncology, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
- * E-mail:
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Karlitz JJ, Blanton C, Andrews P, Chen VW, Wu XC, Fontham E. Colorectal Cancer Incidence Rates in the Louisiana Acadian Parishes Demonstrated to be Among the Highest in the United States. Clin Transl Gastroenterol 2014; 5:e60. [PMID: 25273154 PMCID: PMC4218930 DOI: 10.1038/ctg.2014.10] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 07/29/2014] [Accepted: 07/30/2014] [Indexed: 01/08/2023] Open
Abstract
OBJECTIVES Determine whether colorectal cancer (CRC) rates are disproportionately high in the French-Acadian region (population 1.2 million) of Louisiana, home of the Cajuns, a founder population. METHODS 2005-2009 cancer incidence rates were stratified by age/race/gender in the 18 Acadian parish region and 9-parish subgroup with higher proportions of French speakers and compared with Louisiana and United States rates. Parishes were identified through language census data. A total of 3,288 CRC cases were identified in the Acadian region and 11,737 in Louisiana. RESULTS CRC rates in whites and white males in the 18 parishes were statistically significantly higher than both Louisiana and US rates. In the 9 parishes, rates increased further; whites had an incidence of 56.1/100,000, 13% higher than Louisiana (P<0.0003) and 23% higher than US rates (P<0.0001). In white males, incidence was 72.6/100,000, 19% higher than Louisiana (P<0.0002) and 37% higher than US rates (P<0.0001). If the 9-parish regions were considered a "state," white males would have the highest CRC incidence in the United States by 11% (P<0.0175) compared with other white male populations. CONCLUSIONS CRC rates are among the highest in the United States, increasing with the proportion of French speakers, a marker for the Cajun population. This appears to be the first study identifying a high rate of cancer in a large, regional, US founder population, raising the possibility of a genetic predisposition. Alternatively, an unidentified, robust environmental risk factor may be present. Future studies are needed to identify genetic and/or other risk factors in this population.
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Affiliation(s)
- Jordan J Karlitz
- Division of Gastroenterology, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Christine Blanton
- Division of Gastroenterology, Tulane University School of Medicine, New Orleans, Louisiana, USA
| | - Patricia Andrews
- Epidemiology Program, Louisiana State University (LSU) Health Sciences Center, School of Public Health, New Orleans, Louisiana, USA
| | - Vivien W Chen
- Epidemiology Program, Louisiana State University (LSU) Health Sciences Center, School of Public Health, New Orleans, Louisiana, USA
| | - Xiao-Cheng Wu
- Epidemiology Program, Louisiana State University (LSU) Health Sciences Center, School of Public Health, New Orleans, Louisiana, USA
| | - Elizabeth Fontham
- Epidemiology Program, Louisiana State University (LSU) Health Sciences Center, School of Public Health, New Orleans, Louisiana, USA
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Etchegary H, Green J, Dicks E, Pullman D, Street C, Parfrey P. Consulting the community: public expectations and attitudes about genetics research. Eur J Hum Genet 2013; 21:1338-43. [PMID: 23591403 PMCID: PMC3831079 DOI: 10.1038/ejhg.2013.64] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Revised: 03/11/2013] [Accepted: 03/13/2013] [Indexed: 11/09/2022] Open
Abstract
Genomic discoveries and technologies promise numerous opportunities for improving health. Key to these potential health improvements, however, are health-care consumers' understanding and acceptance of these new developments. We identified community groups and invited them to a public information-consultation session in order to explore public awareness, perception and expectations about genetics and genomics research. One hundred and four members of seven community groups in Newfoundland, Canada took part in the community sessions. Content analysis of participant comments revealed they were largely hopeful about genetics research in its capacity to improve health; however, they did not accept such research uncritically. Complex issues arose during the community consultations, including the place of genetics in primary care, the value of genetics for personal health, and concerns about access to and uses of genetic information. Participants unequivocally endorsed the value of public engagement with these issues. The rapid pace of discoveries in genomics research offers exciting opportunities to improve population health. However, public support will be crucial to realize health improvements. Our findings suggest that regular, transparent dialog between researchers and the public could allow a greater understanding of the research process, as well as assist in the design of efficient and effective genetic health services, informed by the public that will use them.
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Affiliation(s)
- Holly Etchegary
- Clinical Epidemiology, Faculty of Medicine, Memorial University, St John's, Newfoundland and Labrador, Canada
- Eastern Health, St John's, Newfoundland and Labrador, Canada
| | - Jane Green
- Discipline of Genetics, Memorial University, St John's, Newfoundland and Labrador, Canada
| | - Elizabeth Dicks
- Clinical Epidemiology, Memorial University, St John's, Newfoundland and Labrador, Canada
| | - Daryl Pullman
- Community Health and Humanities, Memorial University, St John's, Newfoundland and Labrador, Canada
| | - Catherine Street
- Population Therapeutics Research Group, Memorial University, St John's, Newfoundland and Labrador, Canada
| | - Patrick Parfrey
- Clinical Epidemiology, Memorial University, St John's, Newfoundland and Labrador, Canada
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Rothenmund H, Singh H, Candas B, Chodirker BN, Serfas K, Aronson M, Holter S, Volenik A, Green J, Dicks E, Woods MO, Gilchrist D, Gryfe R, Cohen Z, Foulkes WD. Hereditary colorectal cancer registries in Canada: report from the Colorectal Cancer Association of Canada consensus meeting; Montreal, Quebec; October 28, 2011. ACTA ACUST UNITED AC 2013; 20:273-8. [PMID: 24155632 DOI: 10.3747/co.20.1566] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
At a consensus meeting held in Montreal, October 28, 2011, a multidisciplinary group of Canadian experts in the fields of genetics, gastroenterology, surgery, oncology, pathology, and health care services participated in presentation and discussion sessions for the purpose of developing consensus statements pertaining to the development and maintenance of hereditary colorectal cancer registries in Canada. Five statements were approved by all participants.
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Affiliation(s)
- H Rothenmund
- Hereditary Colorectal Cancer Registry, Cancer Prevention Centre, Jewish General Hospital, Montreal, QC
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Nicholls SG, Wilson BJ, Craigie SM, Etchegary H, Castle D, Carroll JC, Potter BK, Lemyre L, Little J. Public attitudes towards genomic risk profiling as a component of routine population screening. Genome 2013; 56:626-33. [PMID: 24237344 DOI: 10.1139/gen-2013-0070] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Including low penetrance genomic variants in population-based screening might enable personalization of screening intensity and follow up. The application of genomics in this way requires formal evaluation. Even if clinically beneficial, uptake would still depend on the attitudes of target populations. We developed a deliberative workshop on two hypothetical applications (in colorectal cancer and newborn screening) in which we applied stepped, neutrally-framed, information sets. Data were collected using nonparticipant observation, free-text comments by individual participants, and a structured survey. Qualitative data were transcribed and analyzed using thematic content analysis. Eight workshops were conducted with 170 individuals (120 colorectal cancer screening and 50 newborn screening for type 1 diabetes). The use of information sets promoted informed deliberation. In both contexts, attitudes appeared to be heavily informed by assessments of the likely validity of the test results and its personal and health care utility. Perceived benefits included the potential for early intervention, prevention, and closer monitoring while concerns related to costs, education needs regarding the probabilistic nature of risk, the potential for worry, and control of access to personal genomic information. Differences between the colorectal cancer and newborn screening groups appeared to reflect different assessments of potential personal utility, particularly regarding prevention.
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Affiliation(s)
- S G Nicholls
- a Department of Epidemiology & Community Medicine, University of Ottawa, Ottawa, ON, Canada
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DeRycke MS, Gunawardena SR, Middha S, Asmann YW, Schaid DJ, McDonnell SK, Riska SM, Eckloff BW, Cunningham JM, Fridley BL, Serie DJ, Bamlet WR, Cicek MS, Jenkins MA, Duggan DJ, Buchanan D, Clendenning M, Haile RW, Woods MO, Gallinger SN, Casey G, Potter JD, Newcomb PA, Le Marchand L, Lindor NM, Thibodeau SN, Goode EL. Identification of novel variants in colorectal cancer families by high-throughput exome sequencing. Cancer Epidemiol Biomarkers Prev 2013; 22:1239-51. [PMID: 23637064 PMCID: PMC3704223 DOI: 10.1158/1055-9965.epi-12-1226] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) in densely affected families without Lynch Syndrome may be due to mutations in undiscovered genetic loci. Familial linkage analyses have yielded disparate results; the use of exome sequencing in coding regions may identify novel segregating variants. METHODS We completed exome sequencing on 40 affected cases from 16 multicase pedigrees to identify novel loci. Variants shared among all sequenced cases within each family were identified and filtered to exclude common variants and single-nucleotide variants (SNV) predicted to be benign. RESULTS We identified 32 nonsense or splice-site SNVs, 375 missense SNVs, 1,394 synonymous or noncoding SNVs, and 50 indels in the 16 families. Of particular interest are two validated and replicated missense variants in CENPE and KIF23, which are both located within previously reported CRC linkage regions, on chromosomes 1 and 15, respectively. CONCLUSIONS Whole-exome sequencing identified DNA variants in multiple genes. Additional sequencing of these genes in additional samples will further elucidate the role of variants in these regions in CRC susceptibility. IMPACT Exome sequencing of familial CRC cases can identify novel rare variants that may influence disease risk.
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Affiliation(s)
- Melissa S. DeRycke
- Departments of Health Sciences Research, Biomedical Statistics and Informatics, Laboratory Medicine and Pathology, Medical Genetics, Medical Genomics Technology and Advanced Genomics Technology Center, Mayo Clinic College of Medicine, Rochester, MN, 55905, USA
| | - Shanaka R. Gunawardena
- Departments of Health Sciences Research, Biomedical Statistics and Informatics, Laboratory Medicine and Pathology, Medical Genetics, Medical Genomics Technology and Advanced Genomics Technology Center, Mayo Clinic College of Medicine, Rochester, MN, 55905, USA
| | - Sumit Middha
- Departments of Health Sciences Research, Biomedical Statistics and Informatics, Laboratory Medicine and Pathology, Medical Genetics, Medical Genomics Technology and Advanced Genomics Technology Center, Mayo Clinic College of Medicine, Rochester, MN, 55905, USA
| | - Yan W Asmann
- Departments of Health Sciences Research, Biomedical Statistics and Informatics, Laboratory Medicine and Pathology, Medical Genetics, Medical Genomics Technology and Advanced Genomics Technology Center, Mayo Clinic College of Medicine, Rochester, MN, 55905, USA
| | - Daniel J. Schaid
- Departments of Health Sciences Research, Biomedical Statistics and Informatics, Laboratory Medicine and Pathology, Medical Genetics, Medical Genomics Technology and Advanced Genomics Technology Center, Mayo Clinic College of Medicine, Rochester, MN, 55905, USA
| | - Shannon K. McDonnell
- Departments of Health Sciences Research, Biomedical Statistics and Informatics, Laboratory Medicine and Pathology, Medical Genetics, Medical Genomics Technology and Advanced Genomics Technology Center, Mayo Clinic College of Medicine, Rochester, MN, 55905, USA
| | - Shaun M. Riska
- Departments of Health Sciences Research, Biomedical Statistics and Informatics, Laboratory Medicine and Pathology, Medical Genetics, Medical Genomics Technology and Advanced Genomics Technology Center, Mayo Clinic College of Medicine, Rochester, MN, 55905, USA
| | - Bruce W Eckloff
- Departments of Health Sciences Research, Biomedical Statistics and Informatics, Laboratory Medicine and Pathology, Medical Genetics, Medical Genomics Technology and Advanced Genomics Technology Center, Mayo Clinic College of Medicine, Rochester, MN, 55905, USA
| | - Julie M. Cunningham
- Departments of Health Sciences Research, Biomedical Statistics and Informatics, Laboratory Medicine and Pathology, Medical Genetics, Medical Genomics Technology and Advanced Genomics Technology Center, Mayo Clinic College of Medicine, Rochester, MN, 55905, USA
| | - Brooke L. Fridley
- Department of Biostatistics, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Daniel J. Serie
- Departments of Health Sciences Research, Biomedical Statistics and Informatics, Laboratory Medicine and Pathology, Medical Genetics, Medical Genomics Technology and Advanced Genomics Technology Center, Mayo Clinic College of Medicine, Rochester, MN, 55905, USA
| | - William R. Bamlet
- Departments of Health Sciences Research, Biomedical Statistics and Informatics, Laboratory Medicine and Pathology, Medical Genetics, Medical Genomics Technology and Advanced Genomics Technology Center, Mayo Clinic College of Medicine, Rochester, MN, 55905, USA
| | - Mine S. Cicek
- Departments of Health Sciences Research, Biomedical Statistics and Informatics, Laboratory Medicine and Pathology, Medical Genetics, Medical Genomics Technology and Advanced Genomics Technology Center, Mayo Clinic College of Medicine, Rochester, MN, 55905, USA
| | - Mark A. Jenkins
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, University of Melbourne, Victoria 3010, Australia
| | - David J. Duggan
- Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Daniel Buchanan
- Cancer and Population Studies Group, Queensland Institute of Medical Research, Queensland, Australia
| | - Mark Clendenning
- Cancer and Population Studies Group, Queensland Institute of Medical Research, Queensland, Australia
| | - Robert W. Haile
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Michael O. Woods
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. Johns, NL, Canada
| | | | - Graham Casey
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - John D. Potter
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Polly A. Newcomb
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Loic Le Marchand
- Department of Epidemiology, University of Hawaii, Honolulu, HI, USA
| | - Noralane M. Lindor
- Department of Health Sciences Research, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Stephen N. Thibodeau
- Departments of Health Sciences Research, Biomedical Statistics and Informatics, Laboratory Medicine and Pathology, Medical Genetics, Medical Genomics Technology and Advanced Genomics Technology Center, Mayo Clinic College of Medicine, Rochester, MN, 55905, USA
| | - Ellen L. Goode
- Departments of Health Sciences Research, Biomedical Statistics and Informatics, Laboratory Medicine and Pathology, Medical Genetics, Medical Genomics Technology and Advanced Genomics Technology Center, Mayo Clinic College of Medicine, Rochester, MN, 55905, USA
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Negandhi AA, Hyde A, Dicks E, Pollett W, Younghusband BH, Parfrey P, Green RC, Savas S. MTHFR Glu429Ala and ERCC5 His46His polymorphisms are associated with prognosis in colorectal cancer patients: analysis of two independent cohorts from Newfoundland. PLoS One 2013; 8:e61469. [PMID: 23626689 PMCID: PMC3634085 DOI: 10.1371/journal.pone.0061469] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 03/08/2013] [Indexed: 01/28/2023] Open
Abstract
Introduction In this study, 27 genetic polymorphisms that were previously reported to be associated with clinical outcomes in colorectal cancer patients were investigated in relation to overall survival (OS) and disease free survival (DFS) in colorectal cancer patients from Newfoundland. Methods The discovery and validation cohorts comprised of 532 and 252 patients, respectively. Genotypes of 27 polymorphisms were first obtained in the discovery cohort and survival analyses were performed assuming the co-dominant genetic model. Polymorphisms associated with disease outcomes in the discovery cohort were then investigated in the validation cohort. Results When adjusted for sex, age, tumor stage and microsatellite instability (MSI) status, four polymorphisms were independent predictors of OS in the discovery cohort MTHFR Glu429Ala (HR: 1.72, 95%CI: 1.04–2.84, p = 0.036), ERCC5 His46His (HR: 1.78, 95%CI: 1.15–2.76, p = 0.01), SERPINE1 −675indelG (HR: 0.52, 95%CI: 0.32–0.84, p = 0.008), and the homozygous deletion of GSTM1 gene (HR: 1.4, 95%CI: 1.03–1.92, p = 0.033). In the validation cohort, the MTHFR Glu429Ala polymorphism was associated with shorter OS (HR: 1.71, 95%CI: 1.18–2.49, p = 0.005), although with a different genotype than the discovery cohort (CC genotype in the discovery cohort and AC genotype in the validation cohort). When stratified based on treatment with 5-Fluorouracil (5-FU)-based regimens, this polymorphism was associated with reduced OS only in patients not treated with 5-FU. In the DFS analysis, when adjusted for other variables, the TT genotype of the ERCC5 His46His polymorphism was associated with shorter DFS in both cohorts (discovery cohort: HR: 1.54, 95%CI: 1.04–2.29, p = 0.032 and replication cohort: HR: 1.81, 95%CI: 1.11–2.94, p = 0.018). Conclusions In this study, associations of the MTHFR Glu429Ala polymorphism with OS and the ERCC5 His46His polymorphism with DFS were identified in two colorectal cancer patient cohorts. Our results also suggest that the MTHFR Glu429Ala polymorphism may be an adverse prognostic marker in patients not treated with 5-FU.
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Affiliation(s)
- Amit A. Negandhi
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Angela Hyde
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Elizabeth Dicks
- Clinical Epidemiology Unit, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - William Pollett
- Discipline of Surgery, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Banfield H. Younghusband
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Patrick Parfrey
- Clinical Epidemiology Unit, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Roger C. Green
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
| | - Sevtap Savas
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
- Discipline of Oncology, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada
- * E-mail:
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Warden G, Harnett D, Green J, Wish T, Woods MO, Green R, Dicks E, Rahman P, Zhai G, Parfrey P. A population-based study of hereditary non-polyposis colorectal cancer: evidence of pathologic and genetic heterogeneity. Clin Genet 2013; 84:522-30. [PMID: 23278430 DOI: 10.1111/cge.12080] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Revised: 12/13/2012] [Accepted: 12/13/2012] [Indexed: 01/30/2023]
Abstract
Hereditary non-polyposis colorectal cancer (HNPCC) may be the result of Lynch syndrome (LS) caused by mutations in mismatch repair (MMR) genes, a syndrome of unknown etiology called familial colorectal cancer type-X (FCCTX), or familial serrated neoplasia associated with the colorectal cancer (CRC) somatic BRAF mutation. To determine the cause of HNPCC in the founder population of the island of Newfoundland, we studied 37 families with LS and 29 families without LS who fulfilled the Amsterdam I criteria. In non-LS, four index CRCs were BRAF mutation positive, one of which was microsatellite instable. Geographic clustering of LS families caused by three different founder mutations in MSH2 was observed. Nine unique MMR mutations in four MMR genes were identified in single families distributed in different geographic isolates. The geographic distribution of non-LS was similar to LS. The coefficient of relatedness using genotype data was significantly higher for non-LS than for all CRC. Extensive genealogic investigation failed to connect non-LS families and in some clusters pathologic CRC heterogeneity was observed. We conclude that non-LS HNPCC may be a heterogeneous disorder with different pathogenic pathways, and that the geographic distribution is consistent with multiple different mutations in unknown CRC susceptibility gene(s).
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Zhu Y, Wu H, Wang PP, Savas S, Woodrow J, Wish T, Jin R, Green R, Woods M, Roebothan B, Buehler S, Dicks E, Mclaughlin JR, Campbell PT, Parfrey PS. Dietary patterns and colorectal cancer recurrence and survival: a cohort study. BMJ Open 2013; 3:bmjopen-2012-002270. [PMID: 23396503 PMCID: PMC3586110 DOI: 10.1136/bmjopen-2012-002270] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
OBJECTIVE To examine the association between dietary patterns and colorectal cancer (CRC) survival. DESIGN Cohort study. SETTING A familial CRC registry in Newfoundland. PARTICIPANTS 529 newly diagnosed CRC patients from Newfoundland. They were recruited from 1999 to 2003 and followed up until April 2010. OUTCOME MEASURE Participants reported their dietary intake using a food frequency questionnaire. Dietary patterns were identified with factor analysis. Multivariable Cox proportional hazards models were employed to estimate HR and 95% CI for association of dietary patterns with CRC recurrence and death from all causes, after controlling for covariates. RESULTS Disease-free survival (DFS) among CRC patients was significantly worsened among patients with a high processed meat dietary pattern (the highest vs the lowest quartile HR 1.82, 95% CI 1.07 to 3.09). No associations were observed with the prudent vegetable or the high-sugar patterns and DFS. The association between the processed meat pattern and DFS was restricted to patients diagnosed with colon cancer (the highest vs the lowest quartile: HR 2.29, 95% CI 1.19 to 4.40) whereas the relationship between overall survival (OS) and this pattern was observed among patients with colon cancer only (the highest vs the lowest quartile: HR 2.13, 95% CI 1.03 to 4.43). Potential effect modification was noted for sex (p value for interaction 0.04, HR 3.85 for women and 1.22 for men). CONCLUSIONS The processed meat dietary pattern prior to diagnosis is associated with higher risk of tumour recurrence, metastasis and death among patients with CRC.
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Affiliation(s)
- Yun Zhu
- Division of Community Health and Humanities, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
- Department of Epidemiology, School of Public Health, Tianjin Medical University, Tianjin, China
| | - Hao Wu
- Division of Community Health and Humanities, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Peizhong Peter Wang
- Division of Community Health and Humanities, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
- Department of Epidemiology, School of Public Health, Tianjin Medical University, Tianjin, China
| | - Sevtap Savas
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
- Discipline of Oncology, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Jennifer Woodrow
- Division of Community Health and Humanities, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Tyler Wish
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Rong Jin
- Department of Epidemiology, The First Affiliated Hospital of Wenzhou Medical College, Wenzhou, China
| | - Roger Green
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Michael Woods
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Barbara Roebothan
- Division of Community Health and Humanities, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Sharon Buehler
- Division of Community Health and Humanities, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Elizabeth Dicks
- Clinical Epidemiology Unit, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - John R Mclaughlin
- Prosserman Centre for Health Research, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Peter T Campbell
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia, USA
| | - Patrick S Parfrey
- Clinical Epidemiology Unit, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
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Rawson JB, Sun Z, Dicks E, Daftary D, Parfrey PS, Green RC, Gallinger S, McLaughlin JR, Wang PP, Knight JA, Bapat B. Vitamin D intake is negatively associated with promoter methylation of the Wnt antagonist gene DKK1 in a large group of colorectal cancer patients. Nutr Cancer 2012; 64:919-28. [PMID: 22966878 DOI: 10.1080/01635581.2012.711418] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Diet and lifestyle influence colorectal cancer (CRC) risk but the molecular events that mediate these effects are poorly characterized. Several dietary and lifestyle factors can modulate DNA methylation suggesting that they may influence CRC risk through epigenetic regulation of cancer-related genes. The Wnt regulatory genes DKK1 and Wnt5a are important contributors to colonic carcinogenesis and are often silenced by promoter hypermethylation in CRC; however, the dietary contributions to these events have not been explored. To investigate the link between dietary/lifestyle factors and epigenetic regulation of these Wnt signaling genes, we assessed promoter methylation of these genes in a large cohort of Canadian CRC patients from Ontario (n = 549) and Newfoundland (n = 443) and examined associations to dietary/lifestyle factors implicated in CRC risk and/or DNA methylation including intake of vitamins, fats, cholesterol, fiber, and alcohol as well as body mass index (BMI), and smoking status. Several factors were associated with methylation status including alcohol intake, BMI, and cigarette smoking. Most significantly, however, dietary vitamin D intake was strongly negatively associated with DKK1 methylation in Newfoundland (P = 0.001) and a similar trend was observed in Ontario. These results suggest that vitamin D and other dietary/lifestyle factors may alter CRC risk by mediating extracellular Wnt inhibition.
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Affiliation(s)
- James B Rawson
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
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VAMP1 mutation causes dominant hereditary spastic ataxia in Newfoundland families. Am J Hum Genet 2012; 91:548-52. [PMID: 22958904 DOI: 10.1016/j.ajhg.2012.07.018] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Revised: 06/22/2012] [Accepted: 07/17/2012] [Indexed: 11/20/2022] Open
Abstract
Our group previously described and mapped to chromosomal region 12p13 a form of dominantly inherited hereditary spastic ataxia (HSA) in three large Newfoundland (Canada) families. This report identifies vesicle-associated membrane protein 1 (VAMP1), which encodes a critical protein for synaptic exocytosis, as the responsible gene. In total, 50 affected individuals from these families and three independent probands from Ontario (Canada) share the disease phenotype together with a disruptive VAMP1 mutation that affects a critical donor site for the splicing of VAMP1 isoforms. This mutation leads to the loss of the only VAMP1 isoform (VAMP1A) expressed in the nervous system, thus highlighting an association between the well-studied VAMP1 and a neurological disorder. Given the variable phenotype seen in the affected individuals examined here, we believe that VAMP1 should be tested for mutations in patients with either ataxia or spastic paraplegia.
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Savas S, Hyde A, Stuckless SN, Parfrey P, Younghusband HB, Green R. Serotonin transporter gene (SLC6A4) variations are associated with poor survival in colorectal cancer patients. PLoS One 2012; 7:e38953. [PMID: 22911682 PMCID: PMC3404081 DOI: 10.1371/journal.pone.0038953] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Accepted: 05/14/2012] [Indexed: 12/02/2022] Open
Abstract
Prognosis in colorectal cancer patients is quite variable, even after adjustment for clinical parameters such as disease stage and microsatellite instability status. It is possible that the psychological distress experienced by patients, including anxiety and depression, may be correlated with poor prognosis. In the present study, we hypothesize that genetic variations within three genes biologically linked to the stress response, namely serotonin transporter (SLC6A4), brain-derived neurotrophic factor (BDNF), and arginine vasopressin receptor (AVPR1B) genes are associated with prognosis in colorectal cancer patients. We used a population-based cohort of 280 patients who were followed for up to 12.5 years after diagnosis. Our multivariate analysis showed that a tagSNP in the SLC6A4 gene (rs12150214) was a predictor of shorter overall survival (HR: 1.572, 95%CI: 1.142–2.164, p = 0.005) independent of stage, age, grade and MSI status. Additionally, a multivariate analysis using the combined genotypes of three polymorphisms in this gene demonstrated that the presence of any of the minor alleles at these polymorphic loci was an independent predictor of both shorter overall survival (HR: 1.631, 95%CI: 1.190–2.236, p = 0.002) and shorter disease specific survival (HR: 1.691, 95%CI: 1.138–2.512, p = 0.009). The 5-HTT protein coded by the SLC6A4 gene has also been implicated in inflammation. While our results remain to be replicated in other patient cohorts, we suggest that the genetic variations in the SLC6A4 gene contribute to poor survival in colorectal cancer patients.
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Affiliation(s)
- Sevtap Savas
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada.
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Maceachern J, Mathews M, Green J, Pullman D. Specialists' perceptions of hereditary colorectal cancer screening in Newfoundland and Labrador. Curr Oncol 2012; 19:e123-8. [PMID: 22670101 DOI: 10.3747/co.19.932] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
PURPOSE Colorectal cancer (CRC) screening is particularly valuable in Newfoundland and Labrador (NL), where a substantial proportion of CRC cases have a hereditary link. We examined the perceptions of gastroenterologists and general surgeons with respect to screening practices for patients with hereditary crc. METHODS We surveyed all gastroenterologists and general surgeons in NL to determine demographic and professional practice characteristics and screening knowledge, practices, and attitudes for four groups of patients with hereditary CRC. RESULTS Of the 43 eligible physicians, 36 (83.7%) responded. Most of the physicians surveyed knew the correct age to start screening, preferred screening by colonoscopy, had a systematic means in their own practice of prioritizing patients for screening, and felt that family doctors or patients (or both) should be responsible for monitoring screening compliance. Most physicians reported that patients with hereditary nonpolyposis CRC and familial adenomatous polyposis waited 3 months for screening; patients with a family history of CRC or adenomatous polyp waited 6 months or longer. Although respondents agreed on the need for a province-wide CRC registry [4.36 on a 5-point Likert scale (1 = strongly disagree; 5 = strongly agree)], they disagreed that wait times were reasonable (2.81) and that other health professionals should perform colonoscopies (2.86). They were equivocal about the need for centralized bookings (3.25) and about whether genetic testing is useful for prioritizing patients (3.25). CONCLUSIONS Gastroenterologists and general surgeons in NL were knowledgeable about screening, but had varying opinions about individual roles in screening, wait times, and the means for prioritizing and providing screening for patients with hereditary CRC.
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Affiliation(s)
- J Maceachern
- Division of Community Health and Humanities, Memorial University of Newfoundland, St. John's, NL
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Cicek MS, Cunningham JM, Fridley BL, Serie DJ, Bamlet WR, Diergaarde B, Haile RW, Le Marchand L, Krontiris TG, Younghusband HB, Gallinger S, Newcomb PA, Hopper JL, Jenkins MA, Casey G, Schumacher F, Chen Z, DeRycke MS, Templeton AS, Winship I, Green RC, Green JS, Macrae FA, Parry S, Young GP, Young JP, Buchanan D, Thomas DC, Bishop DT, Lindor NM, Thibodeau SN, Potter JD, Goode EL. Colorectal cancer linkage on chromosomes 4q21, 8q13, 12q24, and 15q22. PLoS One 2012; 7:e38175. [PMID: 22675446 PMCID: PMC3364975 DOI: 10.1371/journal.pone.0038175] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Accepted: 05/01/2012] [Indexed: 12/19/2022] Open
Abstract
A substantial proportion of familial colorectal cancer (CRC) is not a consequence of known susceptibility loci, such as mismatch repair (MMR) genes, supporting the existence of additional loci. To identify novel CRC loci, we conducted a genome-wide linkage scan in 356 white families with no evidence of defective MMR (i.e., no loss of tumor expression of MMR proteins, no microsatellite instability (MSI)-high tumors, or no evidence of linkage to MMR genes). Families were ascertained via the Colon Cancer Family Registry multi-site NCI-supported consortium (Colon CFR), the City of Hope Comprehensive Cancer Center, and Memorial University of Newfoundland. A total of 1,612 individuals (average 5.0 per family including 2.2 affected) were genotyped using genome-wide single nucleotide polymorphism linkage arrays; parametric and non-parametric linkage analysis used MERLIN in a priori-defined family groups. Five lod scores greater than 3.0 were observed assuming heterogeneity. The greatest were among families with mean age of diagnosis less than 50 years at 4q21.1 (dominant HLOD = 4.51, α = 0.84, 145.40 cM, rs10518142) and among all families at 12q24.32 (dominant HLOD = 3.60, α = 0.48, 285.15 cM, rs952093). Among families with four or more affected individuals and among clinic-based families, a common peak was observed at 15q22.31 (101.40 cM, rs1477798; dominant HLOD = 3.07, α = 0.29; dominant HLOD = 3.03, α = 0.32, respectively). Analysis of families with only two affected individuals yielded a peak at 8q13.2 (recessive HLOD = 3.02, α = 0.51, 132.52 cM, rs1319036). These previously unreported linkage peaks demonstrate the continued utility of family-based data in complex traits and suggest that new CRC risk alleles remain to be elucidated.
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Affiliation(s)
- Mine S. Cicek
- Departments of Health Sciences Research, Laboratory Medicine and Pathology, and Medical Genetics, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Julie M. Cunningham
- Departments of Health Sciences Research, Laboratory Medicine and Pathology, and Medical Genetics, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Brooke L. Fridley
- Departments of Health Sciences Research, Laboratory Medicine and Pathology, and Medical Genetics, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Daniel J. Serie
- Departments of Health Sciences Research, Laboratory Medicine and Pathology, and Medical Genetics, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - William R. Bamlet
- Departments of Health Sciences Research, Laboratory Medicine and Pathology, and Medical Genetics, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Brenda Diergaarde
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Robert W. Haile
- Department of Preventive Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Loic Le Marchand
- University of Hawaii Cancer Center, Honolulu, Hawaii, United States of America
| | - Theodore G. Krontiris
- Department of Molecular Medicine, Beckman Research Institute of the City of Hope, Duarte, California, United States of America
| | | | - Steven Gallinger
- Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Polly A. Newcomb
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - John L. Hopper
- Departments of Public Health and Medicine, University of Melbourne, Victoria, Australia
| | - Mark A. Jenkins
- Departments of Public Health and Medicine, University of Melbourne, Victoria, Australia
| | - Graham Casey
- Department of Preventive Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Fredrick Schumacher
- Department of Preventive Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Zhu Chen
- Department of Preventive Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Melissa S. DeRycke
- Departments of Health Sciences Research, Laboratory Medicine and Pathology, and Medical Genetics, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Allyson S. Templeton
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Ingrid Winship
- Departments of Public Health and Medicine, University of Melbourne, Victoria, Australia
| | - Roger C. Green
- Faculty of Medicine, Memorial University of Newfoundland, St. Johns, Newfoundland, Canada
| | - Jane S. Green
- Faculty of Medicine, Memorial University of Newfoundland, St. Johns, Newfoundland, Canada
| | - Finlay A. Macrae
- Colorectal Medicine and Genetics and Department of Medicine, University of Melbourne, The Royal Melbourne Hospital, Victoria, Australia
| | - Susan Parry
- New Zealand Familial GI Cancer Registry, Auckland City Hospital, Auckland, New Zealand
- Department of Gastroenterology, Middlemore Hospital, Auckland, New Zealand
| | - Graeme P. Young
- Flinders Centre for Cancer Prevention and Control, Flinders University, Adelaide, Australia
| | - Joanne P. Young
- Familial Cancer Laboratory, Queensland Institute of Medical Research, Queensland, Australia
| | - Daniel Buchanan
- Familial Cancer Laboratory, Queensland Institute of Medical Research, Queensland, Australia
| | - Duncan C. Thomas
- Department of Preventive Medicine, University of Southern California, Los Angeles, California, United States of America
| | - D. Timothy Bishop
- University of Leeds, Leeds Institute of Molecular Medicine, Leeds, United Kingdom
| | - Noralane M. Lindor
- Departments of Health Sciences Research, Laboratory Medicine and Pathology, and Medical Genetics, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Stephen N. Thibodeau
- Departments of Health Sciences Research, Laboratory Medicine and Pathology, and Medical Genetics, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - John D. Potter
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Centre for Public Health Research, Massey University, Wellington, New Zealand
| | - Ellen L. Goode
- Departments of Health Sciences Research, Laboratory Medicine and Pathology, and Medical Genetics, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
- * E-mail:
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Clarke E, Green RC, Green JS, Mahoney K, Parfrey PS, Younghusband HB, Woods MO. Inherited deleterious variants in GALNT12 are associated with CRC susceptibility. Hum Mutat 2012; 33:1056-8. [PMID: 22461326 DOI: 10.1002/humu.22088] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Accepted: 03/09/2012] [Indexed: 01/23/2023]
Abstract
A recent report detailed the occurrence of both somatic and constitutional variants in the GALNT12 gene, located at 9q22.33, in some colorectal cancer (CRC) patients. In this study, we investigate the occurrence of inherited deleterious variants in GALNT12 in 118 families referred to a cancer genetics clinic. We discovered two deleterious variants (c.907G>A (p.Asp303Asn); c.1187A>G (p.Tyr396Cys)) in 4/118 probands. The variants, which were not found in 149 control individuals (P = 0.0376), cosegregate with CRC and/or adenomatous polyps in other family members. The probability by chance that cosegregation of c.907G>A with CRC and/or adenomatous polyps occurred, in the two pedigrees combined, was 1.56%. Although this study does not provide irrefutable evidence that GALNT12 variants are highly penetrant alleles that predispose to CRC in the majority of unexplained hereditary CRC families, it does provide additional evidence to support an important role of these variants in a proportion of this considerable high-risk group.
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Affiliation(s)
- Erica Clarke
- Discipline of Genetics, Memorial University, St. John's, Newfoundland, Canada
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Zhao J, Zhu Y, Wang PP, West R, Buehler S, Sun Z, Squires J, Roebothan B, McLaughlin JR, Campbell PT, Parfrey PS. Interaction between alcohol drinking and obesity in relation to colorectal cancer risk: a case-control study in Newfoundland and Labrador, Canada. BMC Public Health 2012; 12:94. [PMID: 22296784 PMCID: PMC3280927 DOI: 10.1186/1471-2458-12-94] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2011] [Accepted: 02/01/2012] [Indexed: 12/02/2022] Open
Abstract
Background While substantive epidemiological literature suggests that alcohol drinking and obesity are potential risk factors of colorectal cancer (CRC), the possible interaction between the two has not been adequately explored. We used a case-control study to examine if alcohol drinking is associated with an increased risk of CRC and if such risk differs in people with and without obesity. Methods Newly diagnosed CRC cases were identified between 1999 and 2003 in Newfoundland and Labrador (NL). Cases were frequency-matched by age and sex with controls selected using random digit dialing. Cases (702) and controls (717) completed self-administered questionnaires assessing health and lifestyle variables. Estimates of alcohol intake included types of beverage, years of drinking, and average number of alcohol drinks per day. Odds ratios were estimated to investigate the associations of alcohol independently and when stratified by obesity status on the risk of CRC. Results Among obese participants (BMI ≥ 30), alcohol was associated with higher risk of CRC (OR: 2.2; 95% CI: 1.2-4.0) relative to the non-alcohol category. Among obese individuals, 3 or more different types of drinks were associated with a 3.4-fold higher risk of CRC relative to non-drinkers. The risk of CRC also increased with drinking years and drinks daily among obese participants. However, no increased risk was observed in people without obesity. Conclusion The effect of alcohol of drinking on CRC seems to be modified by obesity.
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Affiliation(s)
- Jinhui Zhao
- Division of Community Health and Humanities, Faculty of Medicine, Memorial University of Newfoundland, 300 Prince Philip Drive, St, John's, NL, A1B 3V6, Canada
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Rawson JB, Mrkonjic M, Daftary D, Dicks E, Buchanan DD, Younghusband HB, Parfrey PS, Young JP, Pollett A, Green RC, Gallinger S, McLaughlin JR, Knight JA, Bapat B. Promoter methylation of Wnt5a is associated with microsatellite instability and BRAF V600E mutation in two large populations of colorectal cancer patients. Br J Cancer 2011; 104:1906-12. [PMID: 21587258 PMCID: PMC3111198 DOI: 10.1038/bjc.2011.165] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Background: In colorectal cancer (CRC), tumour microsatellite instability (MSI) status and CpG island methylator phenotype (CIMP) status are indicators of patient outcome, but the molecular events that give rise to these outcomes remain largely unknown. Wnt5a is a critical regulator of non-canonical Wnt activity and promoter hypermethylation of this gene has emerging prognostic roles in CRC; however the frequency and prognostic significance of this epigenetic event have not been explored in the context of colorectal tumour subtype. Consequently, we investigated the frequency and prognostic significance of Wnt5a methylation in a large cohort of MSI-stratified CRCs. Methods: Methylation was quantified in a large cohort of 1232 colorectal carcinomas from two clinically distinct populations from Canada. Associations were examined between methylation status and clinicopathlogical features, including tumour MSI status, BRAF V600E mutation, and patient survival. Results: In Ontario, Wnt5a methylation was strongly associated with MSI tumours after adjustment for age, sex, and tumour location (odds ratio (OR)=4.2, 95% confidence interval (CI)=2.4–7.4, P<10−6) and with BRAF V600E mutation, a marker of CIMP (OR=12.3, 95% CI=6.9–21.7, P<10−17), but was not associated with patient survival. Concordant results were obtained in Newfoundland. Conclusion: Methylation of Wnt5a is associated with distinct tumour subtypes, strengthening the evidence of an epigenetic-mediated Wnt bias in CRC.
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Affiliation(s)
- J B Rawson
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada M5S 1A1
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