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Guo F, Weigl K, Carr PR, Heisser T, Jansen L, Knebel P, Chang-Claude J, Hoffmeister M, Brenner H. Use of Polygenic Risk Scores to Select Screening Intervals After Negative Findings From Colonoscopy. Clin Gastroenterol Hepatol 2020; 18:2742-2751.e7. [PMID: 32376506 DOI: 10.1016/j.cgh.2020.04.077] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/22/2020] [Accepted: 04/24/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Polygenic risk scores (PRSs) could help to define starting ages for colorectal cancer (CRC) screening. However, the role of PRS in determining the length of screening interval after negative findings from colonoscopies is unclear. We aimed to evaluate CRC risk according to PRS and time since last negative colonoscopy. METHODS We collected data from 3827 cases and 2641 CRC-free controls in a population-based case-control study in Germany. We constructed a polygenic risk scoring system, based on 90 single-nucleotide polymorphisms, associated with risk of CRC in people of European descent. Participants were classified as having low, medium, or high genetic risk according to tertiles of PRSs among controls. Multiple logistic regression models were used to assess CRC risk according to PRS and time since last negative colonoscopy. RESULTS Compared to individuals without colonoscopy in the low PRS category, a 42%-85% lower risk of CRC was observed for individuals who had a negative finding from colonoscopy within 10 years. Beyond 10 years after a negative finding from colonoscopy, significantly lower risk only persisted for the low and medium PRS groups, but not for the high PRS group. Adjusted odds ratios were 0.44 (95% CI, 0.29-0.68), 0.51 (95% CI, 0.34-0.77), and 0.85 (95% CI, 0.58-1.23) in the low, medium, and high PRS group, respectively. Within any time interval, risks were lower for distal than for proximal CRCs. CONCLUSIONS Based on findings from a population-based case-control study, the recommended 10-year screening interval for colonoscopy may not need to be shortened among people with high PRSs, but could potentially be prolonged for people with low and medium PRSs. Studies are needed to address personalized time intervals for repeat colonoscopies in average-risk screening cohorts.
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Affiliation(s)
- Feng Guo
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg; Medical Faculty Heidelberg, University of Heidelberg, Heidelberg
| | - Korbinian Weigl
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg; German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg
| | - Prudence Rose Carr
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg
| | - Thomas Heisser
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg; Medical Faculty Heidelberg, University of Heidelberg, Heidelberg
| | - Lina Jansen
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg
| | - Philip Knebel
- Department for General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center, Heidelberg; Genetic Tumour Epidemiology Group, University Medical Center Hamburg-Eppendorf, University Cancer Center Hamburg, Hamburg
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg; German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg; Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany.
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Evaluating the predictive value of genetic risk score in colorectal cancer among Chinese Han population. J Hum Genet 2019; 65:271-279. [PMID: 31857674 DOI: 10.1038/s10038-019-0703-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/11/2019] [Accepted: 11/25/2019] [Indexed: 01/02/2023]
Abstract
Increasing single nucleotide polymorphisms (SNPs) have been identified to be associated with colorectal cancer (CRC). We aimed to investigate whether genetic risk scores (GRS) that aggregate information from multiple genetic variants can predict the risk of CRC in a Chinese population. Fifty candidate SNPs were selected to explore the associations with CRC in a discovery sample with 1002 CRC cases and 999 healthy controls. We modeled the significant SNPs identified by the case-control study as a multilocus weighted GRS and estimated the association of GRS with CRC. Furthermore, 300 pairs of cases and controls were included as a validation sample to confirm the finding. Area under the receiver operating characteristic curve (AUROC) was used to evaluate the predictive power of GRS in CRC. A total of seven SNPs were found to increase the risk of CRC, and two SNPs were found to be negatively associated with CRC in the discovery sample. Relative to participants with the lowest quartile of GRS, those with the highest quartile had a 2.64-fold (95% CI: 1.99-3.51) higher risk for CRC. For every 0.1 point of GRS increase, the risk of CRC increase by 11% (95% CI: 8-14%). AUROC for GRS alone were 0.59 (95% CI: 0.57-0.62) and 0.52 (95% CI: 0.46-0.58) in the discovery and validation sample, respectively. AUROC increased to 0.62 (95% CI: 0.59-0.64) and 0.71 (95% CI: 0.65-0.76) by combining environmental risk factors. Our findings support an association between GRS and risk of CRC, which provides evidence of improved prediction model for CRC in China.
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Weigl K, Thomsen H, Balavarca Y, Hellwege JN, Shrubsole MJ, Brenner H. Genetic Risk Score Is Associated With Prevalence of Advanced Neoplasms in a Colorectal Cancer Screening Population. Gastroenterology 2018; 155:88-98.e10. [PMID: 29574091 PMCID: PMC6035076 DOI: 10.1053/j.gastro.2018.03.030] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 03/06/2018] [Accepted: 03/14/2018] [Indexed: 02/08/2023]
Abstract
BACKGROUND & AIMS The presence of specific single nucleotide polymorphisms (SNPs) can be used to calculate an individual's risk for colorectal cancer (CRC), called a genetic risk score (GRS). We investigated whether GRS can identify individuals with clinically relevant neoplasms in a screening colonoscopy population. METHODS We derived a GRS based on 48 SNPs associated with CRC, identified in a comprehensive literature search. We obtained genetic data from 1043 participants (50-79 years old) in a screening colonoscopy study in Germany, recruited from 2005 through 2013 (294 with advanced neoplasms, 249 with non-advanced adenoma (NAAs), and 500 without neoplasms). Each participant was assigned a GRS by aggregating their risk alleles (0, 1, or 2). Risk of advanced neoplasms and NAA according to GRS was calculated by multiple logistic regression. Risk advancement periods were calculated. We replicated our findings using data from a subset of the Tennessee Colorectal Polyp Study. RESULTS An increased GRS was associated with higher prevalence of advanced neoplasms, but not NAAs. Participants in the middle and upper tertiles of GRS had a 2.2-fold and 2.7-fold increase in risk, respectively, of advanced neoplasms compared to those in the lower tertile. Adjusted odds ratios (ORs) were 1.09 (95% confidence interval [CI], 0.76-1.57) for NAA in the middle tertile and 1.05 (95% CI, 0.70-1.55) for NAA in the upper tertile. The ORs were largest for proximal advanced neoplasms for participants in the middle tertile (OR, 3.55; 95% CI 1.85-6.82) and the upper tertile (OR, 3.61; 95% CI 1.84-7.10). The risk advancement period for medium vs low GRS was 13.4 years (95% CI 4.8-22.0) and for high vs low GRS was 17.5 years (95% CI, 7.8-27.3). CONCLUSIONS In a genetic analysis of participants in a CRC screening study in Germany, an increased GRS (based on CRC-associated SNPs) was associated with increased prevalence of advanced neoplasms. These findings might be used in defining risk-adapted screening ages.
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Affiliation(s)
- Korbinian Weigl
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany; German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany; Medical Faculty Heidelberg, University of Heidelberg, Heidelberg, Germany
| | - Hauke Thomsen
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Yesilda Balavarca
- Division of Preventive Oncology, German Cancer Research Center and National Center of Tumor Diseases, Heidelberg, Germany
| | - Jacklyn N Hellwege
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, Tennessee; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Martha J Shrubsole
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany; German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany; Division of Preventive Oncology, German Cancer Research Center and National Center of Tumor Diseases, Heidelberg, Germany.
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4
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Li D, Zhang R, Jin T, He N, Ren L, Zhang Z, Zhang Q, Xu R, Tao H, Zeng G, Gao J. ADH1B and CDH1 polymorphisms predict prognosis in male patients with non-metastatic laryngeal cancer. Oncotarget 2018; 7:73216-73228. [PMID: 27689323 PMCID: PMC5341974 DOI: 10.18632/oncotarget.12301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 09/20/2016] [Indexed: 01/10/2023] Open
Abstract
In this study, we assessed the association between single nucleotide polymorphisms (SNPs) in candidate genes and the prognosis of laryngeal cancer (LC) patients. Thirty-seven SNPs in 26 genes were genotyped in 170 male Han Chinese patients with LC. The effects of the candidate genes on the prognosis of LC patients were evaluated using Kaplan-Meier curves and Cox proportional hazards regression models. The GA genotype of rs1229984 (hazard ratio [HR], 0.537; 95% confidence interval [CI], 0.340-0.848; p = 0.008) in alcohol dehydrogenase 1B (ADH1B), and the AA genotype of rs9929218 (HR, 6.074; 95% CI, 1.426-25.870; p = 0.015) in CDH1 were associated with overall survival. Our data suggest that polymorphisms in ADH1B and CDH1 may be prognostic indicators in LC.
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Affiliation(s)
- Daxu Li
- Department of Stomatology, First Affiliated Hospital, Xi'an Jiaotong University School of Medicine, Xi'an, Shaanxi 710061, China
| | - Ruizhi Zhang
- Department of Stomatology, Ankang Central Hospital, Ankang 725000, Shaanxi
| | - Tianbo Jin
- School of Medicine, Xizang Minzu University, Xianyang, Shaanxi 712082, China
| | - Na He
- School of Medicine, Xizang Minzu University, Xianyang, Shaanxi 712082, China
| | - Le Ren
- Department of Stomatology, First Affiliated Hospital, Xi'an Jiaotong University School of Medicine, Xi'an, Shaanxi 710061, China
| | - Zhe Zhang
- Department of Stomatology, First Affiliated Hospital, Xi'an Jiaotong University School of Medicine, Xi'an, Shaanxi 710061, China
| | - Qingna Zhang
- Department of Stomatology, First Affiliated Hospital, Xi'an Jiaotong University School of Medicine, Xi'an, Shaanxi 710061, China
| | - Ran Xu
- Department of Stomatology, First Affiliated Hospital, Xi'an Jiaotong University School of Medicine, Xi'an, Shaanxi 710061, China
| | - Hong Tao
- Department of Stomatology, First Affiliated Hospital, Xi'an Jiaotong University School of Medicine, Xi'an, Shaanxi 710061, China
| | - Guang Zeng
- Department of Plastic and Burn Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, Shaanxi 710038, China
| | - Jing Gao
- State Key Laboratory of Military Stomatology & National Clinical Research Center for Oral Diseases & Shaanxi Key Laboratory of Stomatology, Department of Prosthodontics, School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi 710032, China
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Song N, Shin A, Jung HS, Oh JH, Kim J. Effects of interactions between common genetic variants and smoking on colorectal cancer. BMC Cancer 2017; 17:869. [PMID: 29258461 PMCID: PMC5737484 DOI: 10.1186/s12885-017-3886-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 12/08/2017] [Indexed: 12/17/2022] Open
Abstract
Background Although genome-wide association studies (GWAS) have identified variants in approximately 40 susceptibility loci for colorectal cancer (CRC), there are few studies on the interactions between identified single-nucleotide polymorphisms (SNPs) and lifestyle risk factors. We evaluated whether smoking could modify associations between these genetic variants and CRC risk. Methods A total of 703 CRC patients and 1406 healthy controls were included in this case-control study from the National Cancer Center in Korea. Thirty CRC susceptibility SNPs identified in previous GWAS were genotyped. A logistic regression model was used to examine associations between the SNPs and smoking behaviors by sex. The interaction was estimated by including an additional interaction term in the model. Results In men, an increased CRC risk was observed for longer durations (OR>28 vs. ≤28years = 1.49 (95% CI = 1.11–1.98)), greater quantities (OR≥20 vs. <20cigarettes/day = 2.12 (1.61–2.79)), and longer pack-years of smoking (OR≥21 vs. <21pack-years = 1.78 (1.35–2.35)). In women, longer pack-years of smoking significantly increased CRC risk (OR≥5 vs. <5pack-years = 6.11 (1.10–34.00)). Moreover, there were significant interactions between smoking status and the polymorphisms rs1957636 at 14q22.3 (Pinteraction = 5.5 × 10−4) and rs4813802 at 20p12.3 (Pinteraction = 0.04) in men. Interactions between smoking status and the rs6687758 at 1q41 (Pinteraction = 0.03), duration and the rs174537 at 11q12.2 (Pinteraction = 0.05), and pack-years and the rs4813802 (Pinteraction = 0.04) were also found in women. Conclusions Associations between susceptibility SNPs and CRC risk may be modified by smoking behaviors, supporting the existence of gene-smoking interactions. Electronic supplementary material The online version of this article (10.1186/s12885-017-3886-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nan Song
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Aesun Shin
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea. .,Department of Preventive Medicine, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 03080, South Korea. .,Molecular Epidemiology Branch, National Cancer Center, Goyang, South Korea.
| | - Hye Soo Jung
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Jae Hwan Oh
- Center for Colorectal Cancer, National Cancer Center, Goyang, South Korea
| | - Jeongseon Kim
- Molecular Epidemiology Branch, National Cancer Center, Goyang, South Korea. .,Molecular Epidemiology Branch, Division of Cancer Epidemiology and Prevention, Research Institute, National Cancer Center, 323 Ilsan-ro, Insandong-gu, Goyang-si, Gyeonggi-do, 10408, South Korea.
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Trifa AP, Bănescu C, Tevet M, Bojan A, Dima D, Urian L, Török-Vistai T, Popov VM, Zdrenghea M, Petrov L, Vasilache A, Murat M, Georgescu D, Popescu M, Pătrinoiu O, Balea M, Costache R, Coleș E, Șaguna C, Berbec N, Vlădăreanu AM, Mihăilă RG, Bumbea H, Cucuianu A, Popp RA. TERT rs2736100 A>C SNP and JAK2 46/1 haplotype significantly contribute to the occurrence of JAK2 V617F and CALR mutated myeloproliferative neoplasms - a multicentric study on 529 patients. Br J Haematol 2016; 174:218-26. [PMID: 27061303 DOI: 10.1111/bjh.14041] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Accepted: 01/22/2016] [Indexed: 12/14/2022]
Abstract
Polycythaemia vera (PV), essential thrombocythaemia (ET) and primary myelofibrosis (PMF) represent typical myeloproliferative neoplasms (MPN), usually characterized by specific somatic driver mutations (JAK2 V617F, CALR and MPL). JAK2 46/1 haplotype and telomerase reverse transcriptase gene (TERT) rs2736100 A>C single nucleotide polymorphism (SNP) could represent a large fraction of the genetic predisposition seen in MPN. The rs10974944 C>G SNP, tagging the JAK2 46/1 haplotype, and the TERT rs2736100 A>C SNP were genotyped in 529 MPN patients with known JAK2 V617F, CALR and MPL status, and 433 controls. JAK2 46/1 haplotype strongly correlated to JAK2 V617F-positive MPN and, to a lesser extent, CALR-positive MPN. The TERT rs2736100 A>C SNP strongly correlated to all MPN, regardless of the phenotype (PV, ET or PMF) and major molecular subtype (JAK2 V617F- or CALR-positive). While both variants have a significant contribution, they have nuanced consequences, with JAK2 46/1 predisposing essentially to JAK2 V617F-positive MPN, and TERT rs2736100 A>C having a more general, non-specific effect on all MPN, regardless of phenotype or major molecular subtype.
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Affiliation(s)
- Adrian P Trifa
- Department of Medical Genetics, 'Iuliu Hațieganu' University of Medicine and Pharmacy, Cluj-Napoca, Romania.,Department of Genetics, 'Ion Chiricuță' Cancer Institute, Cluj-Napoca, Romania
| | - Claudia Bănescu
- Department of Genetics, University of Medicine and Pharmacy, Tîrgu-Mureș, Romania
| | - Mihaela Tevet
- Department of Haematology, Colentina Hospital, Bucharest, Romania
| | - Anca Bojan
- Department of Haematology, 'Ion Chiricuță' Cancer Institute, Cluj-Napoca, Romania.,Department of Haematology, 'Iuliu Hațieganu' University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Delia Dima
- Department of Haematology, 'Ion Chiricuță' Cancer Institute, Cluj-Napoca, Romania
| | - Laura Urian
- Department of Haematology, 'Ion Chiricuță' Cancer Institute, Cluj-Napoca, Romania.,Department of Haematology, 'Iuliu Hațieganu' University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Tünde Török-Vistai
- Department of Haematology, 'Ion Chiricuță' Cancer Institute, Cluj-Napoca, Romania.,Department of Haematology, 'Iuliu Hațieganu' University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Viola M Popov
- Department of Haematology, Colentina Hospital, Bucharest, Romania
| | - Mihnea Zdrenghea
- Department of Haematology, 'Ion Chiricuță' Cancer Institute, Cluj-Napoca, Romania.,Department of Haematology, 'Iuliu Hațieganu' University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Ljubomir Petrov
- Department of Haematology, 'Ion Chiricuță' Cancer Institute, Cluj-Napoca, Romania.,Department of Haematology, 'Iuliu Hațieganu' University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Anca Vasilache
- Department of Haematology, 'Ion Chiricuță' Cancer Institute, Cluj-Napoca, Romania
| | - Meilin Murat
- Department of Haematology, Colentina Hospital, Bucharest, Romania
| | | | - Mihaela Popescu
- Department of Haematology, Colentina Hospital, Bucharest, Romania
| | - Oana Pătrinoiu
- Department of Haematology, Colentina Hospital, Bucharest, Romania
| | - Marius Balea
- Department of Haematology, Colentina Hospital, Bucharest, Romania
| | - Roxana Costache
- Department of Medical Genetics, 'Iuliu Hațieganu' University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Elena Coleș
- Department of Haematology, Colțea Hospital, 'Carol Davila' University of Medicine and Pharmacy, Bucharest, Romania
| | - Carmen Șaguna
- Department of Haematology, Colțea Hospital, 'Carol Davila' University of Medicine and Pharmacy, Bucharest, Romania
| | - Nicoleta Berbec
- Department of Haematology, Colțea Hospital, 'Carol Davila' University of Medicine and Pharmacy, Bucharest, Romania
| | - Ana-Maria Vlădăreanu
- Department of Haematology, University Emergency Hospital, 'Carol Davila' University of Medicine and Pharmacy, Bucharest, Romania
| | - Romeo G Mihăilă
- Department of Haematology, Sibiu County Emergency Hospital, 'Lucian Blaga' University, Sibiu, Romania
| | - Horia Bumbea
- Department of Haematology, University Emergency Hospital, 'Carol Davila' University of Medicine and Pharmacy, Bucharest, Romania
| | - Andrei Cucuianu
- Department of Haematology, 'Ion Chiricuță' Cancer Institute, Cluj-Napoca, Romania.,Department of Haematology, 'Iuliu Hațieganu' University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Radu A Popp
- Department of Medical Genetics, 'Iuliu Hațieganu' University of Medicine and Pharmacy, Cluj-Napoca, Romania
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Jenkins MA, Makalic E, Dowty JG, Schmidt DF, Dite GS, MacInnis RJ, Ait Ouakrim D, Clendenning M, Flander LB, Stanesby OK, Hopper JL, Win AK, Buchanan DD. Quantifying the utility of single nucleotide polymorphisms to guide colorectal cancer screening. Future Oncol 2016; 12:503-13. [PMID: 26846999 DOI: 10.2217/fon.15.303] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
AIM To determine whether single nucleotide polymorphisms (SNPs) can be used to identify people who should be screened for colorectal cancer. METHODS We simulated one million people with and without colorectal cancer based on published SNP allele frequencies and strengths of colorectal cancer association. We estimated 5-year risks of colorectal cancer by number of risk alleles. RESULTS We identified 45 SNPs with an average 1.14-fold increase colorectal cancer risk per allele (range: 1.05-1.53). The colorectal cancer risk for people in the highest quintile of risk alleles was 1.81-times that for the average person. CONCLUSION We have quantified the extent to which known susceptibility SNPs can stratify the population into clinically useful colorectal cancer risk categories.
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Affiliation(s)
- Mark A Jenkins
- Centre for Epidemiology & Biostatistics, Melbourne School of Population & Global Health, The University of Melbourne, Parkville Victoria, VIC 3010, Australia
| | - Enes Makalic
- Centre for Epidemiology & Biostatistics, Melbourne School of Population & Global Health, The University of Melbourne, Parkville Victoria, VIC 3010, Australia
| | - James G Dowty
- Centre for Epidemiology & Biostatistics, Melbourne School of Population & Global Health, The University of Melbourne, Parkville Victoria, VIC 3010, Australia
| | - Daniel F Schmidt
- Centre for Epidemiology & Biostatistics, Melbourne School of Population & Global Health, The University of Melbourne, Parkville Victoria, VIC 3010, Australia
| | - Gillian S Dite
- Centre for Epidemiology & Biostatistics, Melbourne School of Population & Global Health, The University of Melbourne, Parkville Victoria, VIC 3010, Australia
| | - Robert J MacInnis
- Centre for Epidemiology & Biostatistics, Melbourne School of Population & Global Health, The University of Melbourne, Parkville Victoria, VIC 3010, Australia.,Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, VIC 3004, Australia
| | - Driss Ait Ouakrim
- Centre for Epidemiology & Biostatistics, Melbourne School of Population & Global Health, The University of Melbourne, Parkville Victoria, VIC 3010, Australia
| | - Mark Clendenning
- Colorectal Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, School of Medicine, The University of Melbourne, Parkville Victoria, VIC 3010, Australia
| | - Louisa B Flander
- Centre for Epidemiology & Biostatistics, Melbourne School of Population & Global Health, The University of Melbourne, Parkville Victoria, VIC 3010, Australia
| | - Oliver K Stanesby
- Centre for Epidemiology & Biostatistics, Melbourne School of Population & Global Health, The University of Melbourne, Parkville Victoria, VIC 3010, Australia
| | - John L Hopper
- Centre for Epidemiology & Biostatistics, Melbourne School of Population & Global Health, The University of Melbourne, Parkville Victoria, VIC 3010, Australia
| | - Aung K Win
- Centre for Epidemiology & Biostatistics, Melbourne School of Population & Global Health, The University of Melbourne, Parkville Victoria, VIC 3010, Australia
| | - Daniel D Buchanan
- Centre for Epidemiology & Biostatistics, Melbourne School of Population & Global Health, The University of Melbourne, Parkville Victoria, VIC 3010, Australia.,Colorectal Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, School of Medicine, The University of Melbourne, Parkville Victoria, VIC 3010, Australia
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8
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Krahling T, Balassa K, Kiss KP, Bors A, Batai A, Halm G, Egyed M, Fekete S, Remenyi P, Masszi T, Tordai A, Andrikovics H. Co-occurrence of Myeloproliferative Neoplasms and Solid Tumors Is Attributed to a Synergism Between Cytoreductive Therapy and the Common TERT Polymorphism rs2736100. Cancer Epidemiol Biomarkers Prev 2015; 25:98-104. [DOI: 10.1158/1055-9965.epi-15-0805] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Accepted: 10/16/2015] [Indexed: 11/16/2022] Open
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Usher-Smith JA, Walter FM, Emery JD, Win AK, Griffin SJ. Risk Prediction Models for Colorectal Cancer: A Systematic Review. Cancer Prev Res (Phila) 2015; 9:13-26. [PMID: 26464100 DOI: 10.1158/1940-6207.capr-15-0274] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 09/15/2015] [Indexed: 12/12/2022]
Abstract
Colorectal cancer is the second leading cause of cancer-related death in Europe and the United States. Survival is strongly related to stage at diagnosis and population-based screening reduces colorectal cancer incidence and mortality. Stratifying the population by risk offers the potential to improve the efficiency of screening. In this systematic review we searched Medline, EMBASE, and the Cochrane Library for primary research studies reporting or validating models to predict future risk of primary colorectal cancer for asymptomatic individuals. A total of 12,808 papers were identified from the literature search and nine through citation searching. Fifty-two risk models were included. Where reported (n = 37), half the models had acceptable-to-good discrimination (the area under the receiver operating characteristic curve, AUROC >0.7) in the derivation sample. Calibration was less commonly assessed (n = 21), but overall acceptable. In external validation studies, 10 models showed acceptable discrimination (AUROC 0.71-0.78). These include two with only three variables (age, gender, and BMI; age, gender, and family history of colorectal cancer). A small number of prediction models developed from case-control studies of genetic biomarkers also show some promise but require further external validation using population-based samples. Further research should focus on the feasibility and impact of incorporating such models into stratified screening programmes.
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Affiliation(s)
- Juliet A Usher-Smith
- The Primary Care Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom.
| | - Fiona M Walter
- The Primary Care Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom. Department of General Practice, Melbourne Medical School Faculty of Medicine, Dentistry & Health Sciences The University of Melbourne, Carlton, Victoria, Australia
| | - Jon D Emery
- The Primary Care Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom. Department of General Practice, Melbourne Medical School Faculty of Medicine, Dentistry & Health Sciences The University of Melbourne, Carlton, Victoria, Australia
| | - Aung K Win
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, Level 4, The University of Melbourne, Victoria, Australia
| | - Simon J Griffin
- The Primary Care Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
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Sood S, Gallagher IJ, Lunnon K, Rullman E, Keohane A, Crossland H, Phillips BE, Cederholm T, Jensen T, van Loon LJC, Lannfelt L, Kraus WE, Atherton PJ, Howard R, Gustafsson T, Hodges A, Timmons JA. A novel multi-tissue RNA diagnostic of healthy ageing relates to cognitive health status. Genome Biol 2015; 16:185. [PMID: 26343147 PMCID: PMC4561473 DOI: 10.1186/s13059-015-0750-x] [Citation(s) in RCA: 146] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 08/12/2015] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Diagnostics of the human ageing process may help predict future healthcare needs or guide preventative measures for tackling diseases of older age. We take a transcriptomics approach to build the first reproducible multi-tissue RNA expression signature by gene-chip profiling tissue from sedentary normal subjects who reached 65 years of age in good health. RESULTS One hundred and fifty probe-sets form an accurate classifier of young versus older muscle tissue and this healthy ageing RNA classifier performed consistently in independent cohorts of human muscle, skin and brain tissue (n = 594, AUC = 0.83-0.96) and thus represents a biomarker for biological age. Using the Uppsala Longitudinal Study of Adult Men birth-cohort (n = 108) we demonstrate that the RNA classifier is insensitive to confounding lifestyle biomarkers, while greater gene score at age 70 years is independently associated with better renal function at age 82 years and longevity. The gene score is 'up-regulated' in healthy human hippocampus with age, and when applied to blood RNA profiles from two large independent age-matched dementia case-control data sets (n = 717) the healthy controls have significantly greater gene scores than those with cognitive impairment. Alone, or when combined with our previously described prototype Alzheimer disease (AD) RNA 'disease signature', the healthy ageing RNA classifier is diagnostic for AD. CONCLUSIONS We identify a novel and statistically robust multi-tissue RNA signature of human healthy ageing that can act as a diagnostic of future health, using only a peripheral blood sample. This RNA signature has great potential to assist research aimed at finding treatments for and/or management of AD and other ageing-related conditions.
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Affiliation(s)
- Sanjana Sood
- XRGenomics Ltd, London, UK
- Division of Genetics & Molecular Medicine, King's College London, 8th Floor, Tower Wing, Guy's Hospital, London, SE1 9RT, UK
| | - Iain J Gallagher
- XRGenomics Ltd, London, UK
- School of Health, Stirling University, Stirling, Scotland, UK
| | - Katie Lunnon
- Department of Old Age Psychiatry, King's College London, London, UK
- Present address: University of Exeter Medical School, Exeter, UK
| | - Eric Rullman
- Division of Clinical Physiology, Karolinska University Hospital, Stockholm, Sweden
| | - Aoife Keohane
- Department of Old Age Psychiatry, King's College London, London, UK
| | - Hannah Crossland
- Division of Genetics & Molecular Medicine, King's College London, 8th Floor, Tower Wing, Guy's Hospital, London, SE1 9RT, UK
- School of Medicine, Derby Royal Hospital, Derbyshire, UK
| | | | - Tommy Cederholm
- Department of Public Health, Caring Sciences, Clinical Nutrition and Metabolism, Uppsala University, Uppsala, Sweden
| | | | | | - Lars Lannfelt
- Department of Public Health and Caring Sciences/Molecular Geriatrics, Uppsala University, Uppsala, Sweden
| | - William E Kraus
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
| | | | - Robert Howard
- Department of Old Age Psychiatry, King's College London, London, UK
| | - Thomas Gustafsson
- Division of Clinical Physiology, Karolinska University Hospital, Stockholm, Sweden
| | - Angela Hodges
- Department of Old Age Psychiatry, King's College London, London, UK
| | - James A Timmons
- XRGenomics Ltd, London, UK.
- Division of Genetics & Molecular Medicine, King's College London, 8th Floor, Tower Wing, Guy's Hospital, London, SE1 9RT, UK.
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11
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Nucleotide variants of the cancer predisposing gene CDH1 and the risk of non-syndromic cleft lip with or without cleft palate. Fam Cancer 2015; 13:415-21. [PMID: 24838934 PMCID: PMC4164844 DOI: 10.1007/s10689-014-9727-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The CDH1 gene plays an important role during carcinogenesis and craniofacial morphogenesis. Germline mutations in this gene have been described in families presenting syndromic diffuse gastric cancer and orofacial clefts. The aim of this study was to evaluate the association between nucleotide variants of CDH1 and the risk of non-syndromic cleft lip with or without cleft palate (NSCL/P). Six single nucleotide polymorphisms (SNPs) of the CDH1 gene (rs16260, rs9929218, rs7186053, rs4783573, rs16958383, and rs1801552) were genotyped using the TaqMan SNP genotyping assays in 250 patients with NSCL/P and 540 controls from the Polish population. Comparison between patient and control groups showed that the CDH1 rs1801552 variant, under the assumption of recessive model, was associated with a two-fold decrease in the risk of NSCL/P (ORTT vs CT + CC = 0.481, 95 % CI 0.281–0.824, p = 0.007). This association remained statistically significant even after the multiple testing correction. No significant associations with NSCL/P risk were found for the other five tested SNPs. We found a strong association between the cancer predisposing gene CDH1 and the risk of NSCL/P in the Polish population. This result, together with previous observations of co-occurrence of orofacial clefts and a variety of cancer types, suggests the need for replication studies testing rs1801552 in NSCL/P cohorts with a known cancer history.
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12
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Systematic search for rare variants in Finnish early-onset colorectal cancer patients. Cancer Genet 2014; 208:35-40. [PMID: 25749350 DOI: 10.1016/j.cancergen.2014.12.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 12/12/2014] [Accepted: 12/17/2014] [Indexed: 12/31/2022]
Abstract
The heritability of colorectal cancer (CRC) is incompletely understood, and the contribution of undiscovered rare variants may be important. In search of rare disease-causing variants, we exome sequenced 22 CRC patients who were diagnosed before the age of 40 years. Exome sequencing data from 95 familial CRC patients were available as a validation set. Cases with known CRC syndromes were excluded. All patients were from Finland, a country known for its genetically homogenous population. We searched for rare nonsynonymous variants with allele frequencies below 0.1% in 3,374 Finnish and 58,112 non-Finnish controls. In addition, homozygous and compound heterozygous variants were studied. No genes with rare loss-of-function variants were present in more than one early-onset CRC patient. Three genes (ADAMTS4, CYTL1, and SYNE1) harbored rare loss-of-function variants in both early-onset and familial CRC cases. Five genes with homozygous variants in early-onset CRC cases were found (MCTP2, ARHGAP12, ATM, DONSON, and ROS1), including one gene (MCTP2) with a homozygous splice site variant. All discovered homozygous variants were exclusive to one early-onset CRC case. Independent replication is required to associate the discovered variants with CRC. These findings, together with a lack of family history in 19 of 22 (86%) early-onset patients, suggest genetic heterogeneity in unexplained early-onset CRC patients, thus emphasizing the requirement for large sample sizes and careful study designs to elucidate the role of rare variants in CRC susceptibility.
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Jäger R, Harutyunyan AS, Rumi E, Pietra D, Berg T, Olcaydu D, Houlston RS, Cazzola M, Kralovics R. Common germline variation at the TERT locus contributes to familial clustering of myeloproliferative neoplasms. Am J Hematol 2014; 89:1107-10. [PMID: 25196853 PMCID: PMC4657470 DOI: 10.1002/ajh.23842] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 09/02/2014] [Indexed: 01/30/2023]
Abstract
The C allele of the rs2736100 single nucleotide polymorphism located in the second intron of the TERT gene has recently been identified as a susceptibility factor for myeloproliferative neoplasms (MPN) in the Icelandic population. Here, we evaluate the role of TERT rs2736100_C in sporadic and familial MPN in the context of the previously identified JAK2 GGCC predisposition haplotype. We have confirmed the TERT rs2736100_C association in a large cohort of Italian sporadic MPN patients. The risk conferred by TERT rs2736100_C is present in all molecular and diagnostic MPN subtypes. TERT rs2736100_C and JAK2 GGCC are independently predisposing to MPN and have an additive effect on disease risk, together explaining a large fraction of the population attributable fraction (PAF = 73.06%). We found TERT rs2736100_C significantly enriched (P = 0.0090) in familial MPN compared to sporadic MPN, suggesting that low-penetrance variants may be responsible for a substantial part of familial clustering in MPN.
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Affiliation(s)
- Roland Jäger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of SciencesVienna, Austria
| | - Ashot S Harutyunyan
- CeMM Research Center for Molecular Medicine of the Austrian Academy of SciencesVienna, Austria
| | - Elisa Rumi
- Department of Hematology Oncology, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Policlinico San MatteoPavia, Italy
- Department of Molecular Medicine, University of PaviaPavia, Italy
| | - Daniela Pietra
- Department of Hematology Oncology, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Policlinico San MatteoPavia, Italy
| | - Tiina Berg
- CeMM Research Center for Molecular Medicine of the Austrian Academy of SciencesVienna, Austria
| | - Damla Olcaydu
- CeMM Research Center for Molecular Medicine of the Austrian Academy of SciencesVienna, Austria
| | - Richard S Houlston
- Division of Genetics and Epidemiology, Institute of Cancer ResearchSutton, Surrey, United Kingdom
| | - Mario Cazzola
- Department of Hematology Oncology, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Policlinico San MatteoPavia, Italy
- Department of Molecular Medicine, University of PaviaPavia, Italy
| | - Robert Kralovics
- CeMM Research Center for Molecular Medicine of the Austrian Academy of SciencesVienna, Austria
- Department of Internal Medicine I, Division of Hematology and Blood Coagulation, Medical University of ViennaVienna, Austria
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14
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Quantitative assessment of the influence of common variation rs16892766 at 8q23.3 with colorectal adenoma and cancer susceptibility. Mol Genet Genomics 2014; 290:461-9. [DOI: 10.1007/s00438-014-0928-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 09/19/2014] [Indexed: 01/04/2023]
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15
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Kantor ED, Hutter CM, Minnier J, Berndt SI, Brenner H, Caan BJ, Campbell PT, Carlson CS, Casey G, Chan AT, Chang-Claude J, Chanock SJ, Cotterchio M, Du M, Duggan D, Fuchs CS, Giovannucci EL, Gong J, Harrison TA, Hayes RB, Henderson BE, Hoffmeister M, Hopper JL, Jenkins MA, Jiao S, Kolonel LN, Le Marchand L, Lemire M, Ma J, Newcomb PA, Ochs-Balcom HM, Pflugeisen BM, Potter JD, Rudolph A, Schoen RE, Seminara D, Slattery ML, Stelling DL, Thomas F, Thornquist M, Ulrich CM, Warnick GS, Zanke BW, Peters U, Hsu L, White E. Gene-environment interaction involving recently identified colorectal cancer susceptibility Loci. Cancer Epidemiol Biomarkers Prev 2014; 23:1824-33. [PMID: 24994789 PMCID: PMC4209726 DOI: 10.1158/1055-9965.epi-14-0062] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Genome-wide association studies have identified several single nucleotide polymorphisms (SNPs) that are associated with risk of colorectal cancer. Prior research has evaluated the presence of gene-environment interaction involving the first 10 identified susceptibility loci, but little work has been conducted on interaction involving SNPs at recently identified susceptibility loci, including: rs10911251, rs6691170, rs6687758, rs11903757, rs10936599, rs647161, rs1321311, rs719725, rs1665650, rs3824999, rs7136702, rs11169552, rs59336, rs3217810, rs4925386, and rs2423279. METHODS Data on 9,160 cases and 9,280 controls from the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO) and Colon Cancer Family Registry (CCFR) were used to evaluate the presence of interaction involving the above-listed SNPs and sex, body mass index (BMI), alcohol consumption, smoking, aspirin use, postmenopausal hormone (PMH) use, as well as intake of dietary calcium, dietary fiber, dietary folate, red meat, processed meat, fruit, and vegetables. Interaction was evaluated using a fixed effects meta-analysis of an efficient Empirical Bayes estimator, and permutation was used to account for multiple comparisons. RESULTS None of the permutation-adjusted P values reached statistical significance. CONCLUSIONS The associations between recently identified genetic susceptibility loci and colorectal cancer are not strongly modified by sex, BMI, alcohol, smoking, aspirin, PMH use, and various dietary factors. IMPACT Results suggest no evidence of strong gene-environment interactions involving the recently identified 16 susceptibility loci for colorectal cancer taken one at a time.
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Affiliation(s)
- Elizabeth D Kantor
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts. Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington. Department of Epidemiology, University of Washington School of Public Health, Seattle, Washington.
| | - Carolyn M Hutter
- Division of Cancer Control and Population Sciences, National Cancer Institute, NIH, Bethesda, Maryland
| | - Jessica Minnier
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington. Department of Public Health and Preventive Medicine, Oregon Health and Science University, Portland, Oregon
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany. German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Bette J Caan
- Division of Research, Kaiser Permanente Medical Care Program, Oakland, California
| | - Peter T Campbell
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia
| | - Christopher S Carlson
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington. Department of Epidemiology, University of Washington School of Public Health, Seattle, Washington
| | - Graham Casey
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Andrew T Chan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts. Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland
| | - Michelle Cotterchio
- Prevention and Cancer Control, Cancer Care Ontario, Toronto, Ontario, Canada
| | - Mengmeng Du
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington. Department of Epidemiology, University of Washington School of Public Health, Seattle, Washington. Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - David Duggan
- Translational Genomics Research Institute, Phoenix, Arizona
| | - Charles S Fuchs
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts. Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts
| | - Edward L Giovannucci
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts. Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts. Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts
| | - Jian Gong
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Tabitha A Harrison
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Richard B Hayes
- Division of Epidemiology, Department of Population Health, New York University School of Medicine, New York, New York
| | - Brian E Henderson
- Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - John L Hopper
- Melbourne School of Population Health, The University of Melbourne, VIC, Australia
| | - Mark A Jenkins
- Melbourne School of Population Health, The University of Melbourne, VIC, Australia
| | - Shuo Jiao
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Laurence N Kolonel
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii
| | - Mathieu Lemire
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Jing Ma
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Polly A Newcomb
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington. Department of Epidemiology, University of Washington School of Public Health, Seattle, Washington
| | - Heather M Ochs-Balcom
- Department of Social and Preventive Medicine, University at Buffalo, Buffalo, New York
| | - Bethann M Pflugeisen
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - John D Potter
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington. Department of Epidemiology, University of Washington School of Public Health, Seattle, Washington. Centre for Public Health Research, Massey University, Wellington, New Zealand
| | - Anja Rudolph
- Division of Cancer Epidemiology, Unit of Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Robert E Schoen
- Department of Medicine and Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Daniela Seminara
- Division of Cancer Control and Population Sciences, National Cancer Institute, NIH, Bethesda, Maryland
| | - Martha L Slattery
- Department of Internal Medicine, University of Utah Health Sciences Center, Salt Lake City, Utah
| | - Deanna L Stelling
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Fridtjof Thomas
- Department of Preventive Medicine, University of Tennessee Health Science Center, University of Tennessee, Memphis, Tennessee
| | - Mark Thornquist
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Cornelia M Ulrich
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington. Department of Epidemiology, University of Washington School of Public Health, Seattle, Washington. Division of Preventive Oncology, National Center for Tumor Diseases and German Cancer Research Center, Heidelberg, Germany
| | - Greg S Warnick
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Brent W Zanke
- Clinical Epidemiology Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington. Department of Epidemiology, University of Washington School of Public Health, Seattle, Washington
| | - Li Hsu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington. Department of Biostatistics, University of Washington School of Public Health, Seattle, Washington
| | - Emily White
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington. Department of Epidemiology, University of Washington School of Public Health, Seattle, Washington
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16
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Liu L, Su Q, Li L, Lin X, Gan Y, Chen S. The common variant rs4444235 near BMP4 confers genetic susceptibility of colorectal cancer: an updated meta-analysis based on a comprehensive statistical strategy. PLoS One 2014; 9:e100133. [PMID: 24932582 PMCID: PMC4059743 DOI: 10.1371/journal.pone.0100133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Accepted: 05/21/2014] [Indexed: 12/28/2022] Open
Abstract
OBJECTIVE We performed an updated meta-analysis, using a comprehensive strategy of a logistic regression and a model-free approach, to evaluate more precisely the role of the rs4444235 variant near the Bone morphogenetic protein-4 (BMP4) gene in susceptibility to colorectal cancer (CRC). METHODS A total of 19 studies with 28770 cases and 28234 controls were included. Metagen system with logistic regression was applied to choose the most plausible genetic model for rs4444235. Generalized odds ratio (ORG) metric was used to provide a global test of relationship between rs4444235 and CRC risk. RESULTS Metagen analysis suggested the rs4444235 fitted best to an additive model. In assessment of the additive model, heterogeneity was observed (P = 0.059, I2 = 36.1), and pooled per-allele OR was 1.08 (95% CI = 1.05-1.11). Based on the model-free approach, pooled ORG was 1.09 (95% CI = 1.05-1.14) under a random-effect model. Stratified analyses suggested heterogeneity could be in part explained by population ethnicity, study design, sources of controls, and sample size. Sensitivity analysis further supported the robust stability of the current results, by showing similar pooled estimates before and after sequential removal of each study. CONCLUSIONS This meta-analysis provides a robust estimate of the positive association between the rs4444235 and CRC risk and further emphasizes the importance of the rs4444235 in CRC risk prediction.
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Affiliation(s)
- Li Liu
- Guangdong Key Laboratory of Molecular Epidemiology and Department of Epidemiology and Biostatistics, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
- * E-mail:
| | - Qinji Su
- Mental Health Center, the First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, China
| | - Lixia Li
- Guangdong Key Laboratory of Molecular Epidemiology and Department of Epidemiology and Biostatistics, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
| | - Xiaohui Lin
- Guangdong Key Laboratory of Molecular Epidemiology and Department of Epidemiology and Biostatistics, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
| | - Yu Gan
- Guangdong Key Laboratory of Molecular Epidemiology and Department of Epidemiology and Biostatistics, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
| | - Sidong Chen
- Guangdong Key Laboratory of Molecular Epidemiology and Department of Epidemiology and Biostatistics, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, Guangdong, China
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17
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Kundu S, Mihaescu R, Meijer CMC, Bakker R, Janssens ACJW. Estimating the predictive ability of genetic risk models in simulated data based on published results from genome-wide association studies. Front Genet 2014; 5:179. [PMID: 24982668 PMCID: PMC4056181 DOI: 10.3389/fgene.2014.00179] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 05/27/2014] [Indexed: 01/18/2023] Open
Abstract
Background: There is increasing interest in investigating genetic risk models in empirical studies, but such studies are premature when the expected predictive ability of the risk model is low. We assessed how accurately the predictive ability of genetic risk models can be estimated in simulated data that are created based on the odds ratios (ORs) and frequencies of single-nucleotide polymorphisms (SNPs) obtained from genome-wide association studies (GWASs). Methods: We aimed to replicate published prediction studies that reported the area under the receiver operating characteristic curve (AUC) as a measure of predictive ability. We searched GWAS articles for all SNPs included in these models and extracted ORs and risk allele frequencies to construct genotypes and disease status for a hypothetical population. Using these hypothetical data, we reconstructed the published genetic risk models and compared their AUC values to those reported in the original articles. Results: The accuracy of the AUC values varied with the method used for the construction of the risk models. When logistic regression analysis was used to construct the genetic risk model, AUC values estimated by the simulation method were similar to the published values with a median absolute difference of 0.02 [range: 0.00, 0.04]. This difference was 0.03 [range: 0.01, 0.06] and 0.05 [range: 0.01, 0.08] for unweighted and weighted risk scores. Conclusions: The predictive ability of genetic risk models can be estimated using simulated data based on results from GWASs. Simulation methods can be useful to estimate the predictive ability in the absence of empirical data and to decide whether empirical investigation of genetic risk models is warranted.
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Affiliation(s)
- Suman Kundu
- Department of Epidemiology, Erasmus University Medical Center Rotterdam, Netherlands
| | - Raluca Mihaescu
- Department of Epidemiology, Erasmus University Medical Center Rotterdam, Netherlands
| | - Catherina M C Meijer
- Department of Epidemiology, Erasmus University Medical Center Rotterdam, Netherlands
| | - Rachel Bakker
- Department of Epidemiology, Erasmus University Medical Center Rotterdam, Netherlands
| | - A Cecile J W Janssens
- Department of Epidemiology, Erasmus University Medical Center Rotterdam, Netherlands ; Department of Epidemiology, Rollins School of Public Health, Emory University Atlanta, GA, USA
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18
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Whiffin N, Houlston RS. Architecture of inherited susceptibility to colorectal cancer: a voyage of discovery. Genes (Basel) 2014; 5:270-84. [PMID: 24705330 PMCID: PMC4094933 DOI: 10.3390/genes5020270] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2013] [Revised: 03/07/2014] [Accepted: 03/10/2014] [Indexed: 01/29/2023] Open
Abstract
This review looks back at five decades of research into genetic susceptibility to colorectal cancer (CRC) and the insights these studies have provided. Initial evidence of a genetic basis of CRC stems from epidemiological studies in the 1950s and is further provided by the existence of multiple dominant predisposition syndromes. Genetic linkage and positional cloning studies identified the first high-penetrance genes for CRC in the 1980s and 1990s. More recent genome-wide association studies have identified common low-penetrance susceptibility loci and provide support for a polygenic model of disease susceptibility. These observations suggest a high proportion of CRC may arise in a group of susceptible individuals as a consequence of the combined effects of common low-penetrance risk alleles and rare variants conferring moderate CRC risks. Despite these advances, however, currently identified loci explain only a small fraction of the estimated heritability to CRC. It is hoped that a new generation of sequencing projects will help explain this missing heritability.
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Affiliation(s)
- Nicola Whiffin
- Molecular and Population Genetics Team, Genetics and Epidemiology, The Institute of Cancer Research, Sutton, SM2 5NG, UK.
| | - Richard S Houlston
- Molecular and Population Genetics Team, Genetics and Epidemiology, The Institute of Cancer Research, Sutton, SM2 5NG, UK.
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19
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Eleven candidate susceptibility genes for common familial colorectal cancer. PLoS Genet 2013; 9:e1003876. [PMID: 24146633 PMCID: PMC3798264 DOI: 10.1371/journal.pgen.1003876] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 08/29/2013] [Indexed: 01/18/2023] Open
Abstract
Hereditary factors are presumed to play a role in one third of colorectal cancer (CRC) cases. However, in the majority of familial CRC cases the genetic basis of predisposition remains unexplained. This is particularly true for families with few affected individuals. To identify susceptibility genes for this common phenotype, we examined familial cases derived from a consecutive series of 1514 Finnish CRC patients. Ninety-six familial CRC patients with no previous diagnosis of a hereditary CRC syndrome were included in the analysis. Eighty-six patients had one affected first-degree relative, and ten patients had two or more. Exome sequencing was utilized to search for genes harboring putative loss-of-function variants, because such alterations are likely candidates for disease-causing mutations. Eleven genes with rare truncating variants in two or three familial CRC cases were identified: UACA, SFXN4, TWSG1, PSPH, NUDT7, ZNF490, PRSS37, CCDC18, PRADC1, MRPL3, and AKR1C4. Loss of heterozygosity was examined in all respective cancer samples, and was detected in seven occasions involving four of the candidate genes. In all seven occasions the wild-type allele was lost (P = 0.0078) providing additional evidence that these eleven genes are likely to include true culprits. The study provides a set of candidate predisposition genes which may explain a subset of common familial CRC. Additional genetic validation in other populations is required to provide firm evidence for causality, as well as to characterize the natural history of the respective phenotypes.
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20
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Pu X, Ye Y, Wu X. Development and validation of risk models and molecular diagnostics to permit personalized management of cancer. Cancer 2013; 120:11-9. [PMID: 24114238 DOI: 10.1002/cncr.28393] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 08/25/2013] [Accepted: 08/29/2013] [Indexed: 01/29/2023]
Abstract
Despite the advances made in cancer management over the past few decades, improvements in cancer diagnosis and prognosis are still poor, highlighting the need for individualized strategies. Toward this goal, risk prediction models and molecular diagnostic tools have been developed, tailoring each step of risk assessment from diagnosis to treatment and clinical outcomes based on the individual's clinical, epidemiological, and molecular profiles. These approaches hold increasing promise for delivering a new paradigm to maximize the efficiency of cancer surveillance and efficacy of treatment. However, they require stringent study design, methodology development, comprehensive assessment of biomarkers and risk factors, and extensive validation to ensure their overall usefulness for clinical translation. In the current study, the authors conducted a systematic review using breast cancer as an example and provide general guidelines for risk prediction models and molecular diagnostic tools, including development, assessment, and validation.
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Affiliation(s)
- Xia Pu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
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Jiao S, Hsu L, Bézieau S, Brenner H, Chan AT, Chang-Claude J, Le Marchand L, Lemire M, Newcomb PA, Slattery ML, Peters U. SBERIA: set-based gene-environment interaction test for rare and common variants in complex diseases. Genet Epidemiol 2013; 37:452-64. [PMID: 23720162 PMCID: PMC3713231 DOI: 10.1002/gepi.21735] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 04/04/2013] [Accepted: 04/30/2013] [Indexed: 01/28/2023]
Abstract
Identification of gene-environment interaction (G × E) is important in understanding the etiology of complex diseases. However, partially due to the lack of power, there have been very few replicated G × E findings compared to the success in marginal association studies. The existing G × E testing methods mainly focus on improving the power for individual markers. In this paper, we took a different strategy and proposed a set-based gene-environment interaction test (SBERIA), which can improve the power by reducing the multiple testing burdens and aggregating signals within a set. The major challenge of the signal aggregation within a set is how to tell signals from noise and how to determine the direction of the signals. SBERIA takes advantage of the established correlation screening for G × E to guide the aggregation of genotypes within a marker set. The correlation screening has been shown to be an efficient way of selecting potential G × E candidate SNPs in case-control studies for complex diseases. Importantly, the correlation screening in case-control combined samples is independent of the interaction test. With this desirable feature, SBERIA maintains the correct type I error level and can be easily implemented in a regular logistic regression setting. We showed that SBERIA had higher power than benchmark methods in various simulation scenarios, both for common and rare variants. We also applied SBERIA to real genome-wide association studies (GWAS) data of 10,729 colorectal cancer cases and 13,328 controls and found evidence of interaction between the set of known colorectal cancer susceptibility loci and smoking.
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Affiliation(s)
- Shuo Jiao
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.
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Nishihara R, Morikawa T, Kuchiba A, Lochhead P, Yamauchi M, Liao X, Imamura Y, Nosho K, Shima K, Kawachi I, Qian ZR, Fuchs CS, Chan AT, Giovannucci E, Ogino S. A prospective study of duration of smoking cessation and colorectal cancer risk by epigenetics-related tumor classification. Am J Epidemiol 2013; 178:84-100. [PMID: 23788674 PMCID: PMC3698990 DOI: 10.1093/aje/kws431] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Accepted: 10/24/2012] [Indexed: 02/07/2023] Open
Abstract
The effect of duration of cigarette smoking cessation on colorectal cancer risk by molecular subtypes remains unclear. Using duplication-method Cox proportional-hazards regression analyses, we examined associations between duration of smoking cessation and colorectal cancer risk according to status of CpG island methylator phenotype (CIMP), microsatellite instability, v-raf murine sarcoma viral oncogene homolog B1 (BRAF) mutation, or DNA methyltransferase-3B (DNMT3B) expression. Follow-up of 134,204 individuals in 2 US nationwide prospective cohorts (Nurses' Health Study (1980-2008) and Health Professionals Follow-up Study (1986-2008)) resulted in 1,260 incident rectal and colon cancers with available molecular data. Compared with current smoking, 10-19, 20-39, and ≥40 years of smoking cessation were associated with a lower risk of CIMP-high colorectal cancer, with multivariate hazard ratios (95% confidence intervals) of 0.53 (0.29, 0.95), 0.52 (0.32, 0.85), and 0.50 (0.27, 0.94), respectively (Ptrend = 0.001), but not with the risk of CIMP-low/CIMP-negative cancer (Ptrend = 0.25) (Pheterogeneity = 0.02, between CIMP-high and CIMP-low/CIMP-negative cancer risks). Differential associations between smoking cessation and cancer risks by microsatellite instability (Pheterogeneity = 0.02), DNMT3B expression (Pheterogeneity = 0.03), and BRAF (Pheterogeneity = 0.10) status appeared to be driven by the associations of CIMP-high cancer with microsatellite instability-high, DNMT3B-positive, and BRAF-mutated cancers. These molecular pathological epidemiology data suggest a protective effect of smoking cessation on a DNA methylation-related carcinogenesis pathway leading to CIMP-high colorectal cancer.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Shuji Ogino
- Correspondence to Dr. Shuji Ogino, Department of Medical Oncology, Dana-Farber Cancer Institute, Department of Epidemiology, Harvard School of Public Health, 450 Brookline Avenue, Room JF-215C, Boston, MA 02215 (e-mail: )
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Qin Q, Liu L, Zhong R, Zou L, Yin J, Zhu B, Cao B, Chen W, Chen J, Li X, Li T, Lu X, Lou J, Ke J, Wei S, Miao X, Nie S. The genetic variant on chromosome 10p14 is associated with risk of colorectal cancer: results from a case-control study and a meta-analysis. PLoS One 2013; 8:e64310. [PMID: 23717594 PMCID: PMC3661459 DOI: 10.1371/journal.pone.0064310] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 04/10/2013] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND A common single nucleotide polymorphism (SNP), rs10795668, located at 10p14, was first identified to be significantly associated with risk of colorectal cancer (CRC) by a genome-wide association study (GWAS) in 2008; however, another GWAS and following replication studies yielded conflicting results. METHODS We conducted a case-control study of 470 cases and 475 controls in a Chinese population and then performed a meta-analysis, integrating the current study and 9 publications to evaluate the association between rs10795668 and CRC risk. Heterogeneity among studies and publication bias were assessed by the χ²-based Q statistic test and Egger's test, respectively. RESULTS In the case-control study, significant association between the SNP and CRC risk was observed, with per-A-allele OR of 0.71 (95%CI: 0.54-0.94, P = 0.017). The following meta-analysis further confirmed the significant association, with per-A-allele OR of 0.91 (95%CI: 0.89-0.93, P(heterogeneity) >0.05) in European population and 0.86 (95%CI: 0.78-0.96, P(heterogeneity) <0.05) in Asian population. Besides, sensitivity analyses and publication bias assessment indicated the robust stability and reliability of the results. CONCLUSIONS Results from our case-control study and the followed meta-analysis confirmed the significant association of rs10795668 with CRC risk.
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Affiliation(s)
- Qin Qin
- Department of Epidemiology and Biostatistics, and the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Li Liu
- Department of Epidemiology and Biostatistics, and the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Rong Zhong
- Department of Epidemiology and Biostatistics, and the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Li Zou
- Department of Epidemiology and Biostatistics, and the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jieyun Yin
- Department of Epidemiology and Biostatistics, and the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - BeiBei Zhu
- Department of Epidemiology and Biostatistics, and the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - BeiBei Cao
- Department of Epidemiology and Biostatistics, and the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Wei Chen
- Department of Epidemiology and Biostatistics, and the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jigui Chen
- Department of Surgery, The Eighth Hospital of Wuhan, Wuhan, Hubei, China
| | - Xiaorong Li
- Department of Epidemiology and Biostatistics, and the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Tingting Li
- Department of Epidemiology and Biostatistics, and the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xuzai Lu
- Department of Epidemiology and Biostatistics, and the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jiao Lou
- Department of Epidemiology and Biostatistics, and the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Juntao Ke
- Department of Epidemiology and Biostatistics, and the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Sheng Wei
- Department of Epidemiology and Biostatistics, and the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xiaoping Miao
- Department of Epidemiology and Biostatistics, and the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- * E-mail: (XM); (SN)
| | - Shaofa Nie
- Department of Epidemiology and Biostatistics, and the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- * E-mail: (XM); (SN)
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Kilpivaara O, Aaltonen LA. Diagnostic cancer genome sequencing and the contribution of germline variants. Science 2013; 339:1559-62. [PMID: 23539595 DOI: 10.1126/science.1233899] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Whole-genome sequencing (WGS) is revolutionizing medical research and has the potential to serve as a powerful and cost-effective diagnostic tool in the management of cancer. We review the progress to date in the use of WGS to reveal how germline variants and mutations may be associated with cancer. We use colorectal cancer as an example of how the current level of knowledge can be translated into predictions of predisposition. We also address challenges in the clinical implementation of the variants in germline DNA identified through cancer genome sequencing. We call for the international development of standards to facilitate the clinical use of germline information arising from diagnostic cancer genome sequencing.
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Affiliation(s)
- O Kilpivaara
- Department of Medical Genetics, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland
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Zou L, Zhong R, Lou J, Lu X, Wang Q, Yang Y, Xia J, Ke J, Zhang T, Sun Y, Liu L, Cui Y, Xiao H, Chang L, Xia D, Xu H. Replication study in Chinese population and meta-analysis supports association of the 11q23 locus with colorectal cancer. PLoS One 2012; 7:e45461. [PMID: 23029024 PMCID: PMC3445543 DOI: 10.1371/journal.pone.0045461] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 08/22/2012] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND A common single nucleotide polymorphism (SNP), rs3802842, located at 11q23, was identified by genome-wide association studies (GWAS) to be significantly associated with the risk of colorectal cancer (CRC); however, the results of following replication studies were not always concordant. Thus, a case-control study and a meta-analysis were performed to clearly discern the effect of this variant in CRC. METHOD AND FINDINGS We determined the genotypes of rs3802842 in 641 unrelated Chinese patients with CRC and 1037 cancer-free controls. Additionally, a meta-analysis comprising current and previously published studies was conducted. In our case-control study, significant associations between the polymorphism and CRC risk were observed in all genetic models, with an additive OR being 1.45 (95% CI = 1.26-1.67). The meta-analysis of 38534 cases and 39446 controls further confirmed the significant associations in all genetic models but with obvious between-study heterogeneity. Nevertheless, ethnicity, study type and whether subjects affected by Lynch syndrome could synthetically accounted for the heterogeneity. Besides, the cumulative and sensitivity analyses indicated the robust stability of the results. CONCLUSION The results from our case-control study and meta-analysis provided convincing evidence that rs3802842 significantly contributed to CRC risk.
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Affiliation(s)
- Li Zou
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Epidemiology and Biostatistics and MOE Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Rong Zhong
- Department of Epidemiology and Biostatistics and MOE Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiao Lou
- Department of Epidemiology and Biostatistics and MOE Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xuzai Lu
- Department of Epidemiology and Biostatistics and MOE Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qi Wang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yang Yang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiahong Xia
- Department of Cardiovascular Surgery, Union Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Juntao Ke
- Department of Epidemiology and Biostatistics and MOE Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ti Zhang
- Department of Epidemiology and Biostatistics and MOE Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yu Sun
- Department of Epidemiology and Biostatistics and MOE Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Li Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Yongping Cui
- Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi, China
| | - Haibing Xiao
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lei Chang
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ding Xia
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hua Xu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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