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Vaughan-Shaw PG, Timofeeva M, Ooi LY, Svinti V, Grimes G, Smillie C, Blackmur JP, Donnelly K, Theodoratou E, Campbell H, Zgaga L, Din FVN, Farrington SM, Dunlop MG. Differential genetic influences over colorectal cancer risk and gene expression in large bowel mucosa. Int J Cancer 2021; 149:1100-1108. [PMID: 33937989 DOI: 10.1002/ijc.33616] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 03/05/2021] [Accepted: 03/31/2021] [Indexed: 12/30/2022]
Abstract
Site-specific variation in colorectal cancer (CRC) incidence, biology and prognosis are poorly understood. We sought to determine whether common genetic variants influencing CRC risk might exhibit topographical differences on CRC risk through regional differences in effects on gene expression in the large bowel mucosa. We conducted a site-specific genetic association study (10 630 cases, 31 331 controls) to identify whether established risk variants exert differential effects on risk of proximal, compared to distal CRC. We collected normal colorectal mucosa and blood from 481 subjects and assessed mucosal gene expression using Illumina HumanHT-12v4 arrays in relation to germline genotype. Expression quantitative trait loci (eQTLs) were explored by anatomical location of sampling. The rs3087967 genotype (chr11q23.1 risk variant) exhibited significant site-specific effects-risk of distal CRC (odds ratio [OR] = 1.20, P = 8.20 × 10-20 ) with negligible effects on proximal CRC risk (OR = 1.05, P = .10). Expression of 1261 genes differed between proximal and distal colonic mucosa (top hit PRAC gene, fold-difference = 10, P = 3.48 × 10-57 ). In eQTL studies, rs3087967 genotype was associated with expression of 8 cis- and 21 trans-genes. Four of these (AKAP14, ADH5P4, ASGR2, RP11-342M1.7) showed differential effects by site, with strongest trans-eQTL signals in proximal colonic mucosa (eg, AKAP14, beta = 0.61, P = 5.02 × 10-5 ) and opposite signals in distal mucosa (AKAP14, beta = -0.17, P = .04). In summary, genetic variation at the chr11q23.1 risk locus imparts greater risk of distal rather than proximal CRC and exhibits site-specific differences in eQTL effects in normal mucosa. Topographical differences in genomic control over gene expression relevant to CRC risk may underlie site-specific variation in CRC. Results may inform individualised CRC screening programmes.
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Affiliation(s)
- Peter G Vaughan-Shaw
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Maria Timofeeva
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Department of Public Health, D-IAS, Danish Institute for Advanced Study, University of Southern Denmark, Odense, Denmark
| | - Li-Yin Ooi
- Department of Pathology, National University Hospital, Singapore
| | - Victoria Svinti
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Graeme Grimes
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Claire Smillie
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - James P Blackmur
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Kevin Donnelly
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Evi Theodoratou
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Harry Campbell
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Lina Zgaga
- Department of Public Health and Primary Care, Trinity College Dublin, Dublin, Ireland
| | - Farhat V N Din
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Susan M Farrington
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Malcolm G Dunlop
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
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Gargallo CJ, Lanas Á, Carrera‐Lasfuentes P, Ferrandez Á, Quintero E, Carrillo M, Alonso‐Abreu I, García‐Gonzalez MA. Genetic susceptibility in the development of colorectal adenomas according to family history of colorectal cancer. Int J Cancer 2018; 144:489-502. [PMID: 30194776 PMCID: PMC6587859 DOI: 10.1002/ijc.31858] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 07/30/2018] [Accepted: 08/29/2018] [Indexed: 12/25/2022]
Abstract
Our study aimed to evaluate the relevance of genetic susceptibility in the development of colorectal adenomas (CRA) and its relationship with the presence of family history of colorectal cancer (CRC). Genomic DNA from 750 cases (first degree relatives of patients with CRC) and 750 controls (subjects with no family history of CRC) was genotyped for 99 single nucleotide polymorphisms (SNPs) previously associated with CRC/CRA risk by GWAS and candidate gene studies by using the MassArray™ (Sequenom) platform. Cases and controls were matched by gender, age and histological lesion. Eight hundred and fifty‐eight patients showed no neoplastic lesions, whereas 288 patients showed low‐risk adenomas, and 354 patients presented high‐risk adenomas. Two SNPs (rs10505477, rs6983267) in the CASC8 gene were associated with a reduced risk of CRA in controls (log‐additive models, OR: 0.67, 95%CI:0.54–0.83, and OR:0.66, 95%CI:0.54–0.84, respectively). Stratified analysis by histological lesion revealed the association of rs10505477 and rs6983267 variants with reduced risk of low‐ and high‐risk adenomas in controls, being this effect stronger in low‐risk adenomas (log‐additive models, OR:0.63, 95%CI:0.47–0.84 and OR:0.64, 95%CI:0.47–0.86, respectively). Moreover, 2 SNPs (rs10795668, rs11255841) in the noncoding LINC00709 gene were significantly associated with a reduced risk of low‐risk adenomas in cases (recessive models, OR:0.22, 95%CI:0.06–0.72, and OR:0.08, 95%CI:0.03–0.61) and controls (dominant models, OR:0.50, 95%CI:0.34–0.75, and OR:0.52, 95%CI:0.35–0.78, respectively). In conclusion, some variants associated with CRC risk (rs10505477, rs6983267, rs10795668 and rs11255841) are also involved in the susceptibility to CRA and specific subtypes. These associations are influenced by the presence of family history of CRC. What's new? While numerous candidate gene variants have been associated with colorectal cancer, little is known about the relevance of genetic susceptibility or influence of family history in the development of precancerous colorectal adenomas. In the present study, certain genetic variants previously associated with colorectal cancer risk, including two variants in the CASC8 gene and two in the lnc‐RNA LINC00709 gene, were found to be also involved in susceptibility to colorectal adenomas. The associations were modified by family history of colorectal cancer. The results could have implications for colorectal cancer screening and the identification of individuals at increased risk of colorectal adenoma.
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Affiliation(s)
- Carla J. Gargallo
- Department of GastroenterologyHospital Clínico Universitario Lozano BlesaZaragozaSpain
- Aragon Health Research Institute (IIS Aragon)ZaragozaSpain
| | - Ángel Lanas
- Department of GastroenterologyHospital Clínico Universitario Lozano BlesaZaragozaSpain
- Aragon Health Research Institute (IIS Aragon)ZaragozaSpain
- University of Zaragoza School of MedicineZaragozaSpain
- CIBERehdZaragozaSpain
| | | | - Ángel Ferrandez
- Department of GastroenterologyHospital Clínico Universitario Lozano BlesaZaragozaSpain
- Aragon Health Research Institute (IIS Aragon)ZaragozaSpain
| | - Enrique Quintero
- University of La Laguna, School of MedicineCanary IslandsSpain
- Hospital Universitario de CanariasCanary IslandsSpain
| | | | | | - María Asunción García‐Gonzalez
- Aragon Health Research Institute (IIS Aragon)ZaragozaSpain
- CIBERehdZaragozaSpain
- Aragon Institute of Health Sciences (IACS)ZaragozaSpain
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Ghorbanoghli Z, Nieuwenhuis MH, Houwing-Duistermaat JJ, Jagmohan-Changur S, Hes FJ, Tops CM, Wagner A, Aalfs CM, Verhoef S, Gómez García EB, Sijmons RH, Menko FH, Letteboer TG, Hoogerbrugge N, van Wezel T, Vasen HFA, Wijnen JT. Colorectal cancer risk variants at 8q23.3 and 11q23.1 are associated with disease phenotype in APC mutation carriers. Fam Cancer 2017; 15:563-70. [PMID: 26880076 PMCID: PMC5010832 DOI: 10.1007/s10689-016-9877-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Familial adenomatous polyposis (FAP) is a dominantly inherited syndrome caused by germline mutations in the APC gene and characterized by the development of multiple colorectal adenomas and a high risk of developing colorectal cancer (CRC). The severity of polyposis is correlated with the site of the APC mutation. However, there is also phenotypic variability within families with the same underlying APC mutation, suggesting that additional factors influence the severity of polyposis. Genome-wide association studies identified several single nucleotide polymorphisms (SNPs) that are associated with CRC. We assessed whether these SNPs are associated with polyp multiplicity in proven APC mutation carriers. Sixteen CRC-associated SNPs were analysed in a cohort of 419 APC germline mutation carriers from 182 families. Clinical data were retrieved from the Dutch Polyposis Registry. Allele frequencies of the SNPs were compared for patients with <100 colorectal adenomas versus patients with ≥100 adenomas, using generalized estimating equations with the APC genotype as a covariate. We found a trend of association of two of the tested SNPs with the ≥100 adenoma phenotype: the C alleles of rs16892766 at 8q23.3 (OR 1.71, 95 % CI 1.05-2.76, p = 0.03, dominant model) and rs3802842 at 11q23.1 (OR 1.51, 95 % CI 1.03-2.22, p = 0.04, dominant model). We identified two risk variants that are associated with a more severe phenotype in APC mutation carriers. These risk variants may partly explain the phenotypic variability in families with the same APC gene defect. Further studies with a larger sample size are recommended to evaluate and confirm the phenotypic effect of these SNPs in FAP.
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Affiliation(s)
- Z Ghorbanoghli
- Netherlands Foundation for the Detetion of Hereditary Tumors, Leiden, The Netherlands.
- Department of Gastroenterology and Hepatology, Leiden University Medical Centre, Rijnsburgerweg 10, 2333 AA, Leiden, The Netherlands.
| | - M H Nieuwenhuis
- Netherlands Foundation for the Detetion of Hereditary Tumors, Leiden, The Netherlands
| | - J J Houwing-Duistermaat
- Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, The Netherlands
| | - S Jagmohan-Changur
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - F J Hes
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - C M Tops
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - A Wagner
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - C M Aalfs
- Department of Clinical Genetics, Amsterdam Medical Centre, Amsterdam, The Netherlands
| | - S Verhoef
- Family Cancer Clinic, the Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - E B Gómez García
- Department of Clinical Genetics, University of Maastricht, Maastricht, The Netherlands
| | - R H Sijmons
- Department of Genetics, University Medical Centre Groningen, University of Groningen, Groningen, The Netherlands
| | - F H Menko
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - T G Letteboer
- Department of Medical Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - N Hoogerbrugge
- Department of Human Genetics, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - T van Wezel
- Departments of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - H F A Vasen
- Netherlands Foundation for the Detetion of Hereditary Tumors, Leiden, The Netherlands
- Department of Gastroenterology and Hepatology, Leiden University Medical Centre, Rijnsburgerweg 10, 2333 AA, Leiden, The Netherlands
| | - J T Wijnen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
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Aziz MA, Yousef Z, Saleh AM, Mohammad S, Al Knawy B. Towards personalized medicine of colorectal cancer. Crit Rev Oncol Hematol 2017; 118:70-78. [PMID: 28917272 DOI: 10.1016/j.critrevonc.2017.08.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Revised: 04/18/2017] [Accepted: 08/21/2017] [Indexed: 02/07/2023] Open
Abstract
Efforts in colorectal cancer (CRC) research aim to improve early detection and treatment for metastatic stages which could translate into better prognosis of this disease. One of the major challenges that hinder these efforts is the heterogeneous nature of CRC and involvement of diverse molecular pathways. New large-scale 'omics' technologies are making it possible to generate, analyze and interpret biological data from molecular determinants of CRC. The developments of sophisticated computational analyses would allow information from different omics platforms to be integrated, thus providing new insights into the biology of CRC. Together, these technological advances and an improved mechanistic understanding might allow CRC to be clinically managed at the level of the individual patient. This review provides an account of the current challenges in CRC management and an insight into how new technologies could allow the development of personalized medicine for CRC.
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Affiliation(s)
- Mohammad Azhar Aziz
- King Abdullah International Medical Research Center [KAIMRC], King Saud Bin Abdulaziz University for Health Sciences, Colorectal Cancer Research Program, National Guard Health Affairs, P.O. Box 22490, Riyadh 11426, Saudi Arabia.
| | - Zeyad Yousef
- King Abdullah International Medical Research Center [KAIMRC], King Saud Bin Abdulaziz University for Health Sciences, Department of Surgery, National Guard Health Affairs, P.O. Box 22490, Riyadh 11426, Saudi Arabia.
| | - Ayman M Saleh
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, National Guard Health Affairs, Mail Code 6610, P. O. Box 9515 Jeddah 21423, Saudi Arabia; King Abdullah International Medical Research Center [KAIMRC], King Abdulaziz Medical City, National Guard Health Affairs, P. O. Box 9515, Jeddah 21423, Saudi Arabia.
| | - Sameer Mohammad
- King Abdullah International Medical Research Center [KAIMRC], King Saud Bin Abdulaziz University for Health Sciences, Department of Experimental Medicine, National Guard Health Affairs, P.O. Box 22490, Riyadh 11426, Saudi Arabia.
| | - Bandar Al Knawy
- King Abdullah International Medical Research Center [KAIMRC], King Saud Bin Abdulaziz University for Health Sciences, Office of the Chief Executive Officer, National Guard Health Affairs, P.O. Box 22490, Riyadh 11426, Saudi Arabia.
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Zhai K, Chang J, Hu J, Wu C, Lin D. Germline variation in the 3'-untranslated region of the POU2AF1 gene is associated with susceptibility to lymphoma. Mol Carcinog 2017; 56:1945-1952. [PMID: 28345816 DOI: 10.1002/mc.22652] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Revised: 03/05/2017] [Accepted: 03/23/2017] [Indexed: 01/06/2023]
Abstract
Genetic variations in certain genes may alter the susceptibility to lymphoma. We searched electronic databases and selected candidate single-nucleotide polymorphisms (SNPs) located within 3'-untranslated regions (3'-UTRs) that might affect miRNA-binding ability in the 50 most dysregulated genes in lymphoma for further study. We found that rs1042752-located in the 3'-UTR of POU2AF1, which plays a vital role in lymphomagenesis-was significantly associated with lymphoma risk in a case-control study with 793 patients and 939 controls. Compared with individuals with the rs1042752TT genotype, those with the rs1042752CC genotype had a higher risk of lymphoma (OR = 2.14, 95% CI: 1.55-2.95, P < 0.001), even in stratified analysis for non-Hodgkin lymphoma (OR = 4.58, 95% CI: 2.38-8.81, P < 0.001), B-cell lymphoma (OR = 4.89, 95% CI: 2.46-9.73, P < 0.001), T-cell lymphoma (OR = 4.20, 95% CI: 1.76-10.05, P = 0.001), and Hodgkin lymphoma (OR = 3.62, 95% CI: 1.25-10.46, P = 0.018). Similar results were also observed in a recessive genetic model. Database findings suggested that rs1042752 might affect the interaction of POU2AF1 mRNA with hsa-miR-633. Functional assays confirmed that rs1042752C altered the binding site of hsa-miR-633 and increased POU2AF1 expression in Ramos, HuT 102, and Jurkat E6-1 cell lines. These findings demonstrate for the first time that functional polymorphism in the 3'-UTR of POU2AF1 is associated with susceptibility, and that SNP interaction with hsa-miR-633 affects gene expression and increases the risk of lymphoma.
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Affiliation(s)
- Kan Zhai
- Medical Research Center, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Jiang Chang
- State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment and Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan) and School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jinlong Hu
- Department of Oncology, People's Hospital of Zhengzhou University and Henan Provincial People's Hospital, Zhengzhou, China
| | - Chen Wu
- Department of Etiology and Carcinogenesis, Chinese Academy of Medical Science and Peking Union Medical College, Cancer Institute and Hospital, Beijing, China
| | - Dongxin Lin
- Department of Etiology and Carcinogenesis, Chinese Academy of Medical Science and Peking Union Medical College, Cancer Institute and Hospital, Beijing, China
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Du M, Jiao S, Bien SA, Gala M, Abecasis G, Bezieau S, Brenner H, Butterbach K, Caan BJ, Carlson CS, Casey G, Chang-Claude J, Conti DV, Curtis KR, Duggan D, Gallinger S, Haile RW, Harrison TA, Hayes RB, Hoffmeister M, Hopper JL, Hudson TJ, Jenkins MA, Küry S, Le Marchand L, Leal SM, Newcomb PA, Nickerson DA, Potter JD, Schoen RE, Schumacher FR, Seminara D, Slattery ML, Hsu L, Chan AT, White E, Berndt SI, Peters U. Fine-Mapping of Common Genetic Variants Associated with Colorectal Tumor Risk Identified Potential Functional Variants. PLoS One 2016; 11:e0157521. [PMID: 27379672 PMCID: PMC4933364 DOI: 10.1371/journal.pone.0157521] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 06/01/2016] [Indexed: 01/27/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified many common single nucleotide polymorphisms (SNPs) associated with colorectal cancer risk. These SNPs may tag correlated variants with biological importance. Fine-mapping around GWAS loci can facilitate detection of functional candidates and additional independent risk variants. We analyzed 11,900 cases and 14,311 controls in the Genetics and Epidemiology of Colorectal Cancer Consortium and the Colon Cancer Family Registry. To fine-map genomic regions containing all known common risk variants, we imputed high-density genetic data from the 1000 Genomes Project. We tested single-variant associations with colorectal tumor risk for all variants spanning genomic regions 250-kb upstream or downstream of 31 GWAS-identified SNPs (index SNPs). We queried the University of California, Santa Cruz Genome Browser to examine evidence for biological function. Index SNPs did not show the strongest association signals with colorectal tumor risk in their respective genomic regions. Bioinformatics analysis of SNPs showing smaller P-values in each region revealed 21 functional candidates in 12 loci (5q31.1, 8q24, 11q13.4, 11q23, 12p13.32, 12q24.21, 14q22.2, 15q13, 18q21, 19q13.1, 20p12.3, and 20q13.33). We did not observe evidence of additional independent association signals in GWAS-identified regions. Our results support the utility of integrating data from comprehensive fine-mapping with expanding publicly available genomic databases to help clarify GWAS associations and identify functional candidates that warrant more onerous laboratory follow-up. Such efforts may aid the eventual discovery of disease-causing variant(s).
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Affiliation(s)
- Mengmeng Du
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
- * E-mail: (MD); (UP)
| | - Shuo Jiao
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Stephanie A. Bien
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
- School of Public Health, University of Washington, Seattle, WA, United States of America
| | - Manish Gala
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
| | - Goncalo Abecasis
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, United States of America
| | | | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Katja Butterbach
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bette J. Caan
- Division of Research, Kaiser Permanente Medical Care Program of Northern California, Oakland, CA, United States of America
| | - Christopher S. Carlson
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Graham Casey
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David V. Conti
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America
| | - Keith R. Curtis
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - David Duggan
- Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Steven Gallinger
- Department of Surgery, Mount Sinai Hospital, Toronto, ON, Canada
| | - Robert W. Haile
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America
| | - Tabitha A. Harrison
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Richard B. Hayes
- Division of Epidemiology, Department of Population Health, New York University School of Medicine, New York, NY, United States of America
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - John L. Hopper
- Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Thomas J. Hudson
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Departments of Medical Biophysics and Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Mark A. Jenkins
- Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Sébastien Küry
- Service de Génétique Médicale, CHU Nantes, Nantes, France
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, United States of America
| | - Suzanne M. Leal
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States of America
| | - Polly A. Newcomb
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
- School of Public Health, University of Washington, Seattle, WA, United States of America
| | - Deborah A. Nickerson
- Genome Sciences, University of Washington, Seattle, WA, United States of America
| | - John D. Potter
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
- School of Public Health, University of Washington, Seattle, WA, United States of America
- Centre for Public Health Research, Massey University, Wellington, New Zealand
| | - Robert E. Schoen
- Department of Medicine and Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, PA, United States of America
| | - Fredrick R. Schumacher
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America
| | - Daniela Seminara
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, MD, United States of America
| | - Martha L. Slattery
- Department of Internal Medicine, University of Utah Health Sciences Center, Salt Lake City, UT, United States of America
| | - Li Hsu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Andrew T. Chan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States of America
| | - Emily White
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
- School of Public Health, University of Washington, Seattle, WA, United States of America
| | - Sonja I. Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, United States of America
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
- School of Public Health, University of Washington, Seattle, WA, United States of America
- * E-mail: (MD); (UP)
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Rudkjøbing LA, Eiberg H, Mikkelsen HB, Binderup ML, Bisgaard ML. The analysis of a large Danish family supports the presence of a susceptibility locus for adenoma and colorectal cancer on chromosome 11q24. Fam Cancer 2015; 14:393-400. [PMID: 25724759 DOI: 10.1007/s10689-015-9791-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Hereditary colorectal cancer accounts for approximately 30% of all colorectal cancers, but currently only 5% of these families can be explained by highly penetrant, inherited mutations. In the remaining 25% it is not possible to perform a gene test to identify the family members who would benefit from prophylactic screening. Consequently, all family members are asked to follow a screening program. The purpose of this study was to localize a new gene which causes colorectal cancer. We performed a linkage analysis using data from a SNP6.0 chip in one large family with 12 affected family members. We extended the linkage analysis with microsatellites (STS) and single nucleotide polymorphisms (SNP's) and looked for the loss of heterozygosity in tumour tissue. Furthermore, we performed the exome sequencing of one family member and we sequenced candidate genes by use of direct sequencing. Major rearrangements were excluded after karyotyping. The linkage analysis with SNP6 data revealed three candidate areas, on chromosome 2, 6 and 11 respectively, with a LOD score close to two and no negative LOD scores. After extended linkage analysis, the area on chromosome 6 was excluded, leaving areas on chromosome 2 and chromosome 11 with the highest possible LOD scores of 2.6. Two other studies have identified 11q24 as a candidate area for colorectal cancer susceptibility and this area is supported by our results.
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Salomon MP, Li WLS, Edlund CK, Morrison J, Fortini BK, Win AK, Conti DV, Thomas DC, Duggan D, Buchanan DD, Jenkins MA, Hopper JL, Gallinger S, Le Marchand L, Newcomb PA, Casey G, Marjoram P. GWASeq: targeted re-sequencing follow up to GWAS. BMC Genomics 2016; 17:176. [PMID: 26940994 PMCID: PMC4776370 DOI: 10.1186/s12864-016-2459-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 02/09/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND For the last decade the conceptual framework of the Genome-Wide Association Study (GWAS) has dominated the investigation of human disease and other complex traits. While GWAS have been successful in identifying a large number of variants associated with various phenotypes, the overall amount of heritability explained by these variants remains small. This raises the question of how best to follow up on a GWAS, localize causal variants accounting for GWAS hits, and as a consequence explain more of the so-called "missing" heritability. Advances in high throughput sequencing technologies now allow for the efficient and cost-effective collection of vast amounts of fine-scale genomic data to complement GWAS. RESULTS We investigate these issues using a colon cancer dataset. After QC, our data consisted of 1993 cases, 899 controls. Using marginal tests of associations, we identify 10 variants distributed among six targeted regions that are significantly associated with colorectal cancer, with eight of the variants being novel to this study. Additionally, we perform so-called 'SNP-set' tests of association and identify two sets of variants that implicate both common and rare variants in the etiology of colorectal cancer. CONCLUSIONS Here we present a large-scale targeted re-sequencing resource focusing on genomic regions implicated in colorectal cancer susceptibility previously identified in several GWAS, which aims to 1) provide fine-scale targeted sequencing data for fine-mapping and 2) provide data resources to address methodological questions regarding the design of sequencing-based follow-up studies to GWAS. Additionally, we show that this strategy successfully identifies novel variants associated with colorectal cancer susceptibility and can implicate both common and rare variants.
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Affiliation(s)
- Matthew P Salomon
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA. .,Department of Molecular Oncology, John Wayne Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, USA.
| | - Wai Lok Sibon Li
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA.
| | - Christopher K Edlund
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA.
| | - John Morrison
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA.
| | - Barbara K Fortini
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA.
| | - Aung Ko Win
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Melbourne, VIC, Australia.
| | - David V Conti
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA.
| | - Duncan C Thomas
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA.
| | - David Duggan
- Translational Genomics Research Institute, Phoenix, AZ, USA.
| | - Daniel D Buchanan
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Melbourne, VIC, Australia. .,Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Parkville, Melbourne, VIC, Australia.
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Melbourne, VIC, Australia.
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Melbourne, VIC, Australia.
| | - Steven Gallinger
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, ON, Canada.
| | | | - Polly A Newcomb
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
| | - Graham Casey
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA.
| | - Paul Marjoram
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA.
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9
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Hong SN, Park C, Kim JI, Kim DH, Kim HC, Chang DK, Rhee PL, Kim JJ, Rhee JC, Son HJ, Kim YH. Colorectal cancer-susceptibility single-nucleotide polymorphisms in Korean population. J Gastroenterol Hepatol 2015; 30:849-57. [PMID: 23875689 DOI: 10.1111/jgh.12331] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/25/2013] [Indexed: 01/08/2023]
Abstract
BACKGROUND AND AIM Considering the significant racial and ethnic diversity in genetic variation, it is unclear whether the genome-wide association studies-identified colorectal cancer (CRC)-susceptibility single-nucleotide polymorphisms (SNPs) discovered in European populations are also relevant to the Korean population. However, studies on CRC-susceptibility SNPs in Koreans are limited. METHODS To investigate the racial and ethnic diversity of CRC-susceptibility genetic variants, we genotyped for the established European CRC-susceptibility SNPs in 198 CRC cases and 329 controls in Korea. To identify novel genetic variants using genome-wide screening in Korea, Illumina HumanHap 370K/610K BeadChips were performed on 105 CRC patients, and candidate CRC-susceptibility SNPs were selected. Subsequently, genotyping for replication was done in 189 CRC cases and 190 controls. RESULTS Among the European CRC-susceptibility SNPs, rs4939827 in SMAD7 was associated with a significant decreased risk of Korean CRC (age-/gender-adjusted odds ratio [95% confidence interval]: additive model, 0.67 [95% CI, 0.47-0.95]; dominant model, 0.59 [95% CI, 0.39-0.91]). rs4779584 and rs10795668 were associated with CRC risk in females and males, respectively. Among candidate CRC-susceptibility SNPs selected from genome-wide screening, novel SNP, rs17051076, was found to be associated with a significantly increased risk of microsatellite instability-high CRC (age-/gender-adjusted odds ratio [95% confidence interval]: additive model, 4.25 [95% CI, 1.51-11.98]; dominant model, 3.52 [95% CI, 1.13-10.94]) in the replication study. CONCLUSIONS rs4939827, rs4779584, and rs10795668 may contribute to the risk of CRC in the Korean population as well as in European populations. Novel rs17051076 could be associated with microsatellite instability-high CRC in Koreans. These associations support the ethnic diversity of CRC-susceptibility SNPs and should be taken into account in large-scale studies.
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Affiliation(s)
- Sung Noh Hong
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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10
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Schmit SL, Schumacher FR, Edlund CK, Conti DV, Raskin L, Lejbkowicz F, Pinchev M, Rennert HS, Jenkins MA, Hopper JL, Buchanan DD, Lindor NM, Le Marchand L, Gallinger S, Haile RW, Newcomb PA, Huang SC, Rennert G, Casey G, Gruber SB. A novel colorectal cancer risk locus at 4q32.2 identified from an international genome-wide association study. Carcinogenesis 2014; 35:2512-9. [PMID: 25023989 PMCID: PMC4271131 DOI: 10.1093/carcin/bgu148] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 05/21/2014] [Accepted: 06/14/2014] [Indexed: 12/17/2022] Open
Abstract
Only a fraction of colorectal cancer heritability is explained by known risk-conferring genetic variation. This study was designed to identify novel risk alleles in Europeans. We conducted a genome-wide association study (GWAS) meta-analysis of colorectal cancer in participants from a population-based case-control study in Israel (n = 1616 cases, 1329 controls) and a consortium study from the Colon Cancer Family Registry (n = 1977 cases, 999 controls). We used a two-stage (discovery-replication) GWAS design, followed by a joint meta-analysis. A combined analysis identified a novel susceptibility locus that reached genome-wide significance on chromosome 4q32.2 [rs35509282, risk allele = A (minor allele frequency = 0.09); odds ratio (OR) per risk allele = 1.53; P value = 8.2 × 10(-9); nearest gene = FSTL5]. The direction of the association was consistent across studies. In addition, we confirmed that 14 of 29 previously identified susceptibility variants were significantly associated with risk of colorectal cancer in this study. Genetic variation on chromosome 4q32.2 is significantly associated with risk of colorectal cancer in Ashkenazi Jews and Europeans in this study.
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Affiliation(s)
- Stephanie L Schmit
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA, Vanderbilt Epidemiology Center, Vanderbilt University, Nashville, TN 37232, USA, Department of Community Medicine and Epidemiology, Carmel Medical Center, Haifa, Israel, Clalit Health Services, National Cancer Control Center, Haifa, Israel, Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia, Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Victoria, Australia, Department of Health Science Research, Mayo Clinic Arizona, Scottsdale, 8525 AZ, USA, Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada, Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA, Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Fredrick R Schumacher
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA, Vanderbilt Epidemiology Center, Vanderbilt University, Nashville, TN 37232, USA, Department of Community Medicine and Epidemiology, Carmel Medical Center, Haifa, Israel, Clalit Health Services, National Cancer Control Center, Haifa, Israel, Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia, Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Victoria, Australia, Department of Health Science Research, Mayo Clinic Arizona, Scottsdale, 8525 AZ, USA, Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada, Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA, Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Christopher K Edlund
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA, Vanderbilt Epidemiology Center, Vanderbilt University, Nashville, TN 37232, USA, Department of Community Medicine and Epidemiology, Carmel Medical Center, Haifa, Israel, Clalit Health Services, National Cancer Control Center, Haifa, Israel, Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia, Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Victoria, Australia, Department of Health Science Research, Mayo Clinic Arizona, Scottsdale, 8525 AZ, USA, Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada, Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA, Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - David V Conti
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA, Vanderbilt Epidemiology Center, Vanderbilt University, Nashville, TN 37232, USA, Department of Community Medicine and Epidemiology, Carmel Medical Center, Haifa, Israel, Clalit Health Services, National Cancer Control Center, Haifa, Israel, Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia, Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Victoria, Australia, Department of Health Science Research, Mayo Clinic Arizona, Scottsdale, 8525 AZ, USA, Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada, Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA, Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Leon Raskin
- Vanderbilt Epidemiology Center, Vanderbilt University, Nashville, TN 37232, USA
| | - Flavio Lejbkowicz
- Department of Community Medicine and Epidemiology, Carmel Medical Center, Haifa, Israel, Clalit Health Services, National Cancer Control Center, Haifa, Israel
| | - Mila Pinchev
- Department of Community Medicine and Epidemiology, Carmel Medical Center, Haifa, Israel, Clalit Health Services, National Cancer Control Center, Haifa, Israel
| | - Hedy S Rennert
- Department of Community Medicine and Epidemiology, Carmel Medical Center, Haifa, Israel, Clalit Health Services, National Cancer Control Center, Haifa, Israel
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Daniel D Buchanan
- Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Victoria, Australia
| | - Noralane M Lindor
- Department of Health Science Research, Mayo Clinic Arizona, Scottsdale, 8525 AZ, USA
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA
| | - Steven Gallinger
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Robert W Haile
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA
| | - Polly A Newcomb
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA and
| | - Shu-Chen Huang
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA, Vanderbilt Epidemiology Center, Vanderbilt University, Nashville, TN 37232, USA, Department of Community Medicine and Epidemiology, Carmel Medical Center, Haifa, Israel, Clalit Health Services, National Cancer Control Center, Haifa, Israel, Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia, Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Victoria, Australia, Department of Health Science Research, Mayo Clinic Arizona, Scottsdale, 8525 AZ, USA, Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada, Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA, Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Gad Rennert
- Department of Community Medicine and Epidemiology, Carmel Medical Center, Haifa, Israel, Clalit Health Services, National Cancer Control Center, Haifa, Israel, Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Graham Casey
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA, Vanderbilt Epidemiology Center, Vanderbilt University, Nashville, TN 37232, USA, Department of Community Medicine and Epidemiology, Carmel Medical Center, Haifa, Israel, Clalit Health Services, National Cancer Control Center, Haifa, Israel, Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia, Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Victoria, Australia, Department of Health Science Research, Mayo Clinic Arizona, Scottsdale, 8525 AZ, USA, Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada, Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA, Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Stephen B Gruber
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089, USA, Vanderbilt Epidemiology Center, Vanderbilt University, Nashville, TN 37232, USA, Department of Community Medicine and Epidemiology, Carmel Medical Center, Haifa, Israel, Clalit Health Services, National Cancer Control Center, Haifa, Israel, Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia, Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Victoria, Australia, Department of Health Science Research, Mayo Clinic Arizona, Scottsdale, 8525 AZ, USA, Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada, Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA, Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
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11
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Kurlapska A, Serrano-Fernández P, Baszuk P, Gupta S, Starzyńska T, Małecka-Panas E, Dabrowski A, Dębniak T, Kurzawski G, Suchy J, Rogoza-Mateja W, Scott RJ, Lubiński J. Cumulative effects of genetic markers and the detection of advanced colorectal neoplasias by population screening. Clin Genet 2014; 88:234-40. [PMID: 25117299 DOI: 10.1111/cge.12481] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 07/25/2014] [Accepted: 08/05/2014] [Indexed: 01/12/2023]
Abstract
Genetic markers associated with colorectal cancer may be used in population screening for the early identification of patients at elevated risk of disease. We genotyped 3059 individuals with no cancer family history for eight markers previously associated with colorectal cancer. After colonoscopy, the genetic profile of cases with advanced colorectal neoplasia (213) was compared with the rest (2846). rs2066847 and rs6983267 were significantly associated with the risk of advanced colorectal neoplasia but with limited effect on their own [odds ratio (OR) 1.59; 95% confidence interval (CI) 1.02-2.41; p = 0.033 and OR 1.45; 95% CI 1.02-2.12; p = 0.044, respectively]. Cumulative effects, in contrast, were associated with high risk: the combination of rs2066847, rs6983267, rs4779584, rs3802842 and rs4939827 minimized the number of markers considered, while maximizing the relative size of the carrier group and the risk associated to it, for example, for at least two cumulated risk markers, OR is 2.57 (95% CI 1.50-4.71; corrected p-value 0.0079) and for three or more, OR is 3.57 (95% CI 1.91-6.96; corrected p-value 0.00074). The identification of cumulative models of - otherwise - low-risk markers could be valuable in defining risk groups, within an otherwise low-risk population (no cancer family history).
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Affiliation(s)
- A Kurlapska
- Department of Genetics, Pomeranian Medical University, Szczecin, Poland
| | | | - P Baszuk
- Department of Genetics, Pomeranian Medical University, Szczecin, Poland
| | - S Gupta
- Department of Genetics, Pomeranian Medical University, Szczecin, Poland
| | - T Starzyńska
- Department of Gastroenterology, Pomeranian Medical University, Szczecin, Poland
| | - E Małecka-Panas
- Department of Digestive Tract Diseases, Faculty of Medicine, Medical University of Łódź, Łódź, Poland
| | - A Dabrowski
- Department of Gastroenterology and Internal Medicine, Medical University of Białystok, Białystok, Poland
| | - T Dębniak
- Department of Genetics, Pomeranian Medical University, Szczecin, Poland
| | - G Kurzawski
- Department of Genetics, Pomeranian Medical University, Szczecin, Poland
| | - J Suchy
- Department of Genetics, Pomeranian Medical University, Szczecin, Poland
| | - W Rogoza-Mateja
- Department of Gastroenterology, Pomeranian Medical University, Szczecin, Poland
| | - R J Scott
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, Australia
| | - J Lubiński
- Department of Genetics, Pomeranian Medical University, Szczecin, Poland
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12
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Lan YT, Yang SH, Lin JK, Lin CC, Wang HS, Chen WS, Lin TC, Jiang JK, Chang SC. Genetic variations are associated with lymph node metastasis in colorectal cancer patients. J Surg Oncol 2014; 110:307-12. [DOI: 10.1002/jso.23613] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 03/12/2014] [Indexed: 01/01/2023]
Affiliation(s)
- Yuan-Tzu Lan
- Division of Colon and Rectal Surgery, Department of Surgery; Taipei Veterans General Hospital; Taipei Taiwan
- Department of Surgery; National Yang-Ming University; Taipei Taiwan
| | - Shung-Haur Yang
- Division of Colon and Rectal Surgery, Department of Surgery; Taipei Veterans General Hospital; Taipei Taiwan
- Department of Surgery; National Yang-Ming University; Taipei Taiwan
| | - Jen-Kou Lin
- Division of Colon and Rectal Surgery, Department of Surgery; Taipei Veterans General Hospital; Taipei Taiwan
- Department of Surgery; National Yang-Ming University; Taipei Taiwan
| | - Chun-Chi Lin
- Division of Colon and Rectal Surgery, Department of Surgery; Taipei Veterans General Hospital; Taipei Taiwan
- Department of Surgery; National Yang-Ming University; Taipei Taiwan
| | - Huann-Sheng Wang
- Division of Colon and Rectal Surgery, Department of Surgery; Taipei Veterans General Hospital; Taipei Taiwan
- Department of Surgery; National Yang-Ming University; Taipei Taiwan
| | - Wei-Shone Chen
- Division of Colon and Rectal Surgery, Department of Surgery; Taipei Veterans General Hospital; Taipei Taiwan
- Department of Surgery; National Yang-Ming University; Taipei Taiwan
| | - Tzu-Chen Lin
- Division of Colon and Rectal Surgery, Department of Surgery; Taipei Veterans General Hospital; Taipei Taiwan
- Department of Surgery; National Yang-Ming University; Taipei Taiwan
| | - Jeng-Kai Jiang
- Division of Colon and Rectal Surgery, Department of Surgery; Taipei Veterans General Hospital; Taipei Taiwan
- Department of Surgery; National Yang-Ming University; Taipei Taiwan
| | - Shih-Ching Chang
- Division of Colon and Rectal Surgery, Department of Surgery; Taipei Veterans General Hospital; Taipei Taiwan
- Department of Surgery; National Yang-Ming University; Taipei Taiwan
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13
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Yang CY, Lu RH, Lin CH, Jen CH, Tung CY, Yang SH, Lin JK, Jiang JK, Lin CH. Single nucleotide polymorphisms associated with colorectal cancer susceptibility and loss of heterozygosity in a Taiwanese population. PLoS One 2014; 9:e100060. [PMID: 24968322 DOI: 10.1371/journal.pone.0100060] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 05/22/2014] [Indexed: 01/01/2023] Open
Abstract
Given the significant racial and ethnic diversity in genetic variation, we are intrigued to find out whether the single nucleotide polymorphisms (SNPs) identified in genome-wide association studies of colorectal cancer (CRC) susceptibility in East Asian populations are also relevant to the population of Taiwan. Moreover, loss of heterozygosity (LOH) may provide insight into how variants alter CRC risk and how regulatory elements control gene expression. To investigate the racial and ethnic diversity of CRC-susceptibility genetic variants and their relevance to the Taiwanese population, we genotyped 705 CRC cases and 1,802 healthy controls (Taiwan Biobank) for fifteen previously reported East Asian CRC-susceptibility SNPs and four novel genetic variants identified by whole-exome sequencing. We found that rs10795668 in FLJ3802842 and rs4631962 in CCND2 were significantly associated with CRC risk in the Taiwanese population. The previously unreported rs1338565 was associated with a significant increased risk of CRC. In addition, we also genotyped tumor tissue and paired adjacent normal tissues of these 705 CRC cases to search for LOH, as well as risk-associated and protective alleles. LOH analysis revealed preferential retention of three SNPs, rs12657484, rs3802842, and rs4444235, in tumor tissues. rs4444235 has been recently reported to be a cis-acting regulator of BMP4 gene; in this study, the C allele was preferentially retained in tumor tissues (p = 0.0023). rs4631962 and rs10795668 contribute to CRC risk in the Taiwanese and East Asian populations, and the newly identified rs1338565 was specifically associated with CRC, supporting the ethnic diversity of CRC-susceptibility SNPs. LOH analysis suggested that the three CRC risk variants, rs12657484, rs3802842, and rs4444235, exhibited somatic allele-specific imbalance and might be critical during neoplastic progression.
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Closa A, Cordero D, Sanz-Pamplona R, Solé X, Crous-Bou M, Paré-Brunet L, Berenguer A, Guino E, Lopez-Doriga A, Guardiola J, Biondo S, Salazar R, Moreno V. Identification of candidate susceptibility genes for colorectal cancer through eQTL analysis. Carcinogenesis 2014; 35:2039-46. [PMID: 24760461 DOI: 10.1093/carcin/bgu092] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
In this study, we aim to identify the genes responsible for colorectal cancer risk behind the loci identified in genome-wide association studies (GWAS). These genes may be candidate targets for developing new strategies for prevention or therapy. We analyzed the association of genotypes for 26 GWAS single nucleotide polymorphisms (SNPs) with the expression of genes within a 2 Mb region (cis-eQTLs). Affymetrix Human Genome U219 expression arrays were used to assess gene expression in two series of samples, one of healthy colonic mucosa (n = 47) and other of normal mucosa adjacent to colon cancer (n = 97, total 144). Paired tumor tissues (n = 97) were also analyzed but did not provide additional findings. Partial Pearson correlation (r), adjusted for sample type, was used for the analysis. We have found Bonferroni-significant cis-eQTLs in three loci: rs3802842 in 11q23.1 associated to C11orf53, COLCA1 (C11orf92) and COLCA2 (C11orf93; r = 0.60); rs7136702 in 12q13.12 associated to DIP2B (r = 0.63) and rs5934683 in Xp22.3 associated to SHROOM2 and GPR143 (r = 0.47). For loci in chromosomes 11 and 12, we have found other SNPs in linkage disequilibrium that are more strongly associated with the expression of the identified genes and are better functional candidates: rs7130173 for 11q23.1 (r = 0.66) and rs61927768 for 12q13.12 (r = 0.86). These SNPs are located in DNA regions that may harbor enhancers or transcription factor binding sites. The analysis of trans-eQTLs has identified additional genes in these loci that may have common regulatory mechanisms as shown by the analysis of protein-protein interaction networks.
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Affiliation(s)
- Adria Closa
- Cancer Prevention and Control Program, Catalan Institute of Oncology, and Consortium for Biomedical Research on Epidemiology and Public Health (CIBERESP), Barcelona E08907, Spain, Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona E08907, Spain
| | - David Cordero
- Cancer Prevention and Control Program, Catalan Institute of Oncology, and Consortium for Biomedical Research on Epidemiology and Public Health (CIBERESP), Barcelona E08907, Spain, Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona E08907, Spain
| | - Rebeca Sanz-Pamplona
- Cancer Prevention and Control Program, Catalan Institute of Oncology, and Consortium for Biomedical Research on Epidemiology and Public Health (CIBERESP), Barcelona E08907, Spain, Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona E08907, Spain
| | - Xavier Solé
- Cancer Prevention and Control Program, Catalan Institute of Oncology, and Consortium for Biomedical Research on Epidemiology and Public Health (CIBERESP), Barcelona E08907, Spain, Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona E08907, Spain
| | - Marta Crous-Bou
- Cancer Prevention and Control Program, Catalan Institute of Oncology, and Consortium for Biomedical Research on Epidemiology and Public Health (CIBERESP), Barcelona E08907, Spain, Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona E08907, Spain
| | - Laia Paré-Brunet
- Cancer Prevention and Control Program, Catalan Institute of Oncology, and Consortium for Biomedical Research on Epidemiology and Public Health (CIBERESP), Barcelona E08907, Spain, Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona E08907, Spain
| | - Antoni Berenguer
- Cancer Prevention and Control Program, Catalan Institute of Oncology, and Consortium for Biomedical Research on Epidemiology and Public Health (CIBERESP), Barcelona E08907, Spain, Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona E08907, Spain
| | - Elisabet Guino
- Cancer Prevention and Control Program, Catalan Institute of Oncology, and Consortium for Biomedical Research on Epidemiology and Public Health (CIBERESP), Barcelona E08907, Spain, Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona E08907, Spain
| | - Adriana Lopez-Doriga
- Cancer Prevention and Control Program, Catalan Institute of Oncology, and Consortium for Biomedical Research on Epidemiology and Public Health (CIBERESP), Barcelona E08907, Spain, Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona E08907, Spain
| | - Jordi Guardiola
- Gastroenterology Service, Bellvitge University Hospital, Barcelona E08907, Spain and
| | - Sebastiano Biondo
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona E08907, Spain, General and Digestive Surgery Service, Bellvitge University Hospital, Barcelona E08907, Spain
| | - Ramon Salazar
- Medical Oncology Service, Catalan Institute of Oncology, Barcelona E08907, Spain
| | - Victor Moreno
- Cancer Prevention and Control Program, Catalan Institute of Oncology, and Consortium for Biomedical Research on Epidemiology and Public Health (CIBERESP), Barcelona E08907, Spain, Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona E08907, Spain, Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona E08907, Spain,
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15
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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16
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Hes FJ, Ruano D, Nieuwenhuis M, Tops CM, Schrumpf M, Nielsen M, Huijts PEA, Wijnen JT, Wagner A, Gómez García EB, Sijmons RH, Menko FH, Letteboer TGW, Hoogerbrugge N, Harryvan J, Kampman E, Morreau H, Vasen HFA, van Wezel T. Colorectal cancer risk variants on 11q23 and 15q13 are associated with unexplained adenomatous polyposis. J Med Genet 2013; 51:55-60. [PMID: 24253443 DOI: 10.1136/jmedgenet-2013-102000] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
BACKGROUND Colorectal adenomatous polyposis is associated with a high risk of colorectal cancer (CRC) and is frequently caused by germline mutations in APC or MUTYH. However, in about 20-30% of patients no underlying gene defect can be identified. In this study, we tested if recently identified CRC risk variants play a role in patients with >10 adenomas. METHODS We analysed a total of 16 SNPs with a reported association with CRC in a cohort of 252 genetically unexplained index patients with >10 colorectal adenomas and 745 controls. In addition, we collected detailed clinical information from index patients and their first-degree relatives (FDRs). RESULTS We found a statistically significant association with two of the variants tested: rs3802842 (at chromosome 11q23, OR=1.60, 95% CI 1.3 to 2.0) and rs4779584 (at chromosome 15q13, OR=1.50, 95% CI 1.2 to 1.9). The majority of index patients (84%) had between 10 and 100 adenomas and 15% had >100 adenomas. Only two index patients (1%), both with >100 adenomas, had FDRs with polyposis. Forty-one per cent of the index patients had one or more FDRs with CRC. CONCLUSIONS These SNPs are the first common, low-penetrant variants reported to be associated with adenomatous polyposis not caused by a defect in the APC, MUTYH, POLD1 and POLE genes. Even though familial occurrence of polyposis was very rare, CRC was over-represented in FDRs of polyposis patients and, if confirmed, these relatives will therefore benefit from surveillance.
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Affiliation(s)
- Frederik J Hes
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
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17
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Peltekova VD, Lemire M, Qazi AM, Zaidi SHE, Trinh QM, Bielecki R, Rogers M, Hodgson L, Wang M, D'Souza DJA, Zandi S, Chong T, Kwan JYY, Kozak K, De Borja R, Timms L, Rangrej J, Volar M, Chan-Seng-Yue M, Beck T, Ash C, Lee S, Wang J, Boutros PC, Stein LD, Dick JE, Gryfe R, McPherson JD, Zanke BW, Pollett A, Gallinger S, Hudson TJ. Identification of genes expressed by immune cells of the colon that are regulated by colorectal cancer-associated variants. Int J Cancer 2013; 134:2330-41. [PMID: 24154973 PMCID: PMC3949167 DOI: 10.1002/ijc.28557] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 09/27/2013] [Indexed: 12/19/2022]
Abstract
A locus on human chromosome 11q23 tagged by marker rs3802842 was associated with colorectal cancer (CRC) in a genome-wide association study; this finding has been replicated in case–control studies worldwide. In order to identify biologic factors at this locus that are related to the etiopathology of CRC, we used microarray-based target selection methods, coupled to next-generation sequencing, to study 103 kb at the 11q23 locus. We genotyped 369 putative variants from 1,030 patients with CRC (cases) and 1,061 individuals without CRC (controls) from the Ontario Familial Colorectal Cancer Registry. Two previously uncharacterized genes, COLCA1 and COLCA2, were found to be co-regulated genes that are transcribed from opposite strands. Expression levels of COLCA1 and COLCA2 transcripts correlate with rs3802842 genotypes. In colon tissues, COLCA1 co-localizes with crystalloid granules of eosinophils and granular organelles of mast cells, neutrophils, macrophages, dendritic cells and differentiated myeloid-derived cell lines. COLCA2 is present in the cytoplasm of normal epithelial, immune and other cell lineages, as well as tumor cells. Tissue microarray analysis demonstrates the association of rs3802842 with lymphocyte density in the lamina propria (p = 0.014) and levels of COLCA1 in the lamina propria (p = 0.00016) and COLCA2 (tumor cells, p = 0.0041 and lamina propria, p = 6 × 10–5). In conclusion, genetic, expression and immunohistochemical data implicate COLCA1 and COLCA2 in the pathogenesis of colon cancer. Histologic analyses indicate the involvement of immune pathways.
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18
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Graves KD, Leventhal KG, Nusbaum R, Salehizadeh Y, Hooker GW, Peshkin BN, Butrick M, Tuong W, Mathew J, Goerlitz D, Fishman MB, Shields PG, Schwartz MD. Behavioral and psychosocial responses to genomic testing for colorectal cancer risk. Genomics 2013; 102:123-30. [PMID: 23583311 DOI: 10.1016/j.ygeno.2013.04.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 03/28/2013] [Accepted: 04/03/2013] [Indexed: 11/28/2022]
Abstract
We conducted a translational genomic pilot study to evaluate the impact of genomic information related to colorectal cancer (CRC) risk on psychosocial, behavioral and communication outcomes. In 47 primary care participants, 96% opted for testing of three single nucleotide polymorphisms (SNPs) related to CRC risk. Participants averaged 2.5 of 6 possible SNP risk alleles (10% lifetime risk). At 3-months, participants did not report significant increases in cancer worry/distress; over half reported physical activity and dietary changes. SNP risk scores were unrelated to behavior change at 3-months. Many participants (64%) shared their SNP results, including 28% who shared results with a physician. In this pilot, genomic risk education, including discussion of other risk factors, appeared to impact patients' health behaviors, regardless of the level of SNP risk. Future work can compare risk education with and without SNP results to evaluate if SNP information adds value to existing approaches.
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Affiliation(s)
- Kristi D Graves
- Cancer Prevention and Control Program and the Fisher Center for Familial Cancer Research, Lombardi Comprehensive Cancer Center, Georgetown University, 3300 Whitehaven Street, NW, Suite 4100, Washington, DC 20007, USA.
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19
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Fernandez-Rozadilla C, Palles C, Carvajal-Carmona L, Peterlongo P, Nici C, Veneroni S, Pinheiro M, Teixeira MR, Moreno V, Lamas MJ, Baiget M, Lopez-Fernandez LA, Gonzalez D, Brea-Fernandez A, Clofent J, Bujanda L, Bessa X, Andreu M, Xicola R, Llor X, Jover R, Castells A, Castellvi-Bel S, Carracedo A, Tomlinson I, Ruiz-Ponte C. BMP2/BMP4 colorectal cancer susceptibility loci in northern and southern European populations. Carcinogenesis 2013; 34:314-8. [PMID: 23161572 DOI: 10.1093/carcin/bgs357] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Genome-wide association studies have successfully identified 20 colorectal cancer susceptibility loci. Amongst these, four of the signals are defined by tagging single nucleotide polymorphisms (SNPs) on regions 14q22.2 (rs4444235 and rs1957636) and 20p12.3 (rs961253 and rs4813802). These markers are located close to two of the genes involved in bone morphogenetic protein (BMP) signaling (BMP4 and BMP2, respectively). By investigating these four SNPs in an initial cohort of Spanish origin, we found substantial evidence that minor allele frequencies (MAFs) may be different in northern and southern European populations. Therefore, we genotyped three additional southern European cohorts comprising a total of 2028 cases and 4273 controls. The meta-analysis results show that only one of the association signals (rs961253) is effectively replicated in the southern European populations, despite adequate power to detect all four. The other three SNPs (rs4444235, rs1957636 and rs4813802) presented discordant results in MAFs and linkage disequilibrium patterns between northern and southern European cohorts. We hypothesize that this lack of replication could be the result of differential tagging of the functional variant in both sets of populations. Were this true, it would have complex consequences in both our ability to understand the nature of the real causative variants, as well as for further study designs.
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Affiliation(s)
- Ceres Fernandez-Rozadilla
- Fundación Pública Galega de Medicina Xenómica-Grupo de Medicina Xenómica-Centro de Investigación Biomédica en Red de Enfermedades Raras-IDIS, Santiago de Compostela 15706, Spain
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20
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Li FX, Yang XX, Hu NY, Du HY, Ma Q, Li M. Single-nucleotide polymorphism associations for colorectal cancer in southern chinese population. Chin J Cancer Res 2013; 24:29-35. [PMID: 23359760 DOI: 10.1007/s11670-012-0029-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2011] [Accepted: 10/17/2011] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVE Genome-wide association studies (GWAS) have identified 11 loci that influence the risk of developing colorectal cancer (CRC). Given that these studies were conducted in European Caucasian populations, it is not clear whether the results are relevant for populations with different ethnicities. The aim of this study was to examine these associations in a southern Chinese population. METHODS Eleven single-nucleotide polymorphisms (SNPs), rs12701937, rs16892766, rs7014346, rs6983267, rs719725, rs10795668, rs3802842, rs4444235, rs9929218, rs10411210, and rs961253, were genotyped in 229 CRC patients and 267 controls using the MassArray SNP genotyping system. RESULTS Evidence of an association with CRC was found for four of the 11 loci. The strongest associations were with rs4444235 and rs961253, with significant odds ratios close to those reported in previous GWAS. Among these four loci, rs719725 and rs4444235 were significantly associated with female gender, rs3802842, rs961253, and rs4444235 with early disease onset, and rs3802842 with later disease onset. However, no associations with CRC risk were detected for six other loci (rs9929218, rs10411210, rs12701937, rs7014346, rs6983267, and rs10795668), and one SNP, rs16892766, was not polymorphic in any of the study participants. CONCLUSION The rs4444235 and rs961253 loci are strongly associated with the risk of CRC in southern Chinese.
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Affiliation(s)
- Fen-Xia Li
- School of Biotechnology, Southern Medical University, Guangzhou 510515, China
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21
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Fernandez-Rozadilla C, Cazier JB, Tomlinson IP, Carvajal-Carmona LG, Palles C, Lamas MJ, Baiget M, López-Fernández LA, Brea-Fernández A, Abulí A, Bujanda L, Clofent J, Gonzalez D, Xicola R, Andreu M, Bessa X, Jover R, Llor X. A colorectal cancer genome-wide association study in a Spanish cohort identifies two variants associated with colorectal cancer risk at 1p33 and 8p12. BMC Genomics 2013; 14:55. [PMID: 23350875 PMCID: PMC3616862 DOI: 10.1186/1471-2164-14-55] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 01/23/2013] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is a disease of complex aetiology, with much of the expected inherited risk being due to several common low risk variants. Genome-Wide Association Studies (GWAS) have identified 20 CRC risk variants. Nevertheless, these have only been able to explain part of the missing heritability. Moreover, these signals have only been inspected in populations of Northern European origin. RESULTS Thus, we followed the same approach in a Spanish cohort of 881 cases and 667 controls. Sixty-four variants at 24 loci were found to be associated with CRC at p-values <10-5. We therefore evaluated the 24 loci in another Spanish replication cohort (1481 cases and 1850 controls). Two of these SNPs, rs12080929 at 1p33 (Preplication=0.042; Ppooled=5.523x10-03; OR (CI95%)=0.866(0.782-0.959)) and rs11987193 at 8p12 (Preplication=0.039; Ppooled=6.985x10-5; OR (CI95%)=0.786(0.705-0.878)) were replicated in the second Phase, although they did not reach genome-wide statistical significance. CONCLUSIONS We have performed the first CRC GWAS in a Southern European population and by these means we were able to identify two new susceptibility variants at 1p33 and 8p12 loci. These two SNPs are located near the SLC5A9 and DUSP4 loci, respectively, which could be good functional candidates for the association signals. We therefore believe that these two markers constitute good candidates for CRC susceptibility loci and should be further evaluated in other larger datasets. Moreover, we highlight that were these two SNPs true susceptibility variants, they would constitute a decrease in the CRC missing heritability fraction.
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Affiliation(s)
- Ceres Fernandez-Rozadilla
- Galician Public Fundation of Genomic Medicine (FPGMX)-Grupo de Medicina Xenómica-Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERer)-IDIS, Santiago de Compostela, 15706, Spain
| | - Jean-Baptiste Cazier
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Ian P Tomlinson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- NIHR Comprehensive Biomedical Research Centre, University of Oxford, Oxford, OX3 7BN, UK
| | - Luis G Carvajal-Carmona
- Department of Biochemistry and Molecular Medicine School of Medicine University of California, Davis, California, USA
| | - Claire Palles
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - María J Lamas
- Oncology Pharmacy Unit, Complejo Hospitalario Universitario of Santiago (CHUS), Santiago de Compostela, 15706, Spain
| | - Montserrat Baiget
- Genetics Department, Hospital de Santa Creu I Sant Pau, Barcelona, 08025, Spain
| | - Luis A López-Fernández
- Pharmacogenetics & Pharmacogenomics Laboratory, Servicio de Farmacia, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón,, Madrid, 28007, Spain
| | - Alejandro Brea-Fernández
- Galician Public Fundation of Genomic Medicine (FPGMX)-Grupo de Medicina Xenómica-Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERer)-IDIS, Santiago de Compostela, 15706, Spain
| | - Anna Abulí
- Gastroenterology Department, Hospital del Mar, Barcelona, 08003, Spain
- Department of Gastroenterology, Hospital Clínic, CIBERehd, IDIBAPS, University of Barcelona, Barcelona, 08036, Spain
| | - Luis Bujanda
- Gastroenterology Department, Donostia Hospital, CIBERehd, University of the Basque Country, San Sebastián, 20014, Spain
| | - Juan Clofent
- Gastroenterology Department, Hospital do Meixoeiro, Vigo, 36214, Spain
- Section of Digestive Diseases, Internal Medicine Department, Hospital Sagunto, Valencia, 46520, Spain
| | - Dolors Gonzalez
- Servicio de Patologia Digestiva, Hospital Sant PAu, Barcelona, 08003, Spain
| | - Rosa Xicola
- Section of Digestive Diseases and Nutrition, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Montserrat Andreu
- Gastroenterology Department, Hospital del Mar, Barcelona, 08003, Spain
| | - Xavier Bessa
- Gastroenterology Department, Hospital del Mar, Barcelona, 08003, Spain
| | - Rodrigo Jover
- Gastroenterology Department, Hospital General Universitario de Alicante, Alicante, 03010, Spain
| | - Xavier Llor
- Section of Digestive Diseases and Nutrition, University of Illinois at Chicago, Chicago, IL, 60607, USA
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Ladero JM, Agúndez JAG, Martínez C, Amo G, Ayuso P, García-Martín E. Analysis of the Functional Polymorphism in the Cytochrome P450 CYP2C8 Gene rs11572080 with Regard to Colorectal Cancer Risk. Front Genet 2012; 3:278. [PMID: 23420707 PMCID: PMC3572883 DOI: 10.3389/fgene.2012.00278] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 11/15/2012] [Indexed: 11/26/2022] Open
Abstract
In addition to the known effects on drug metabolism and response, functional polymorphisms of genes coding for xenobiotic-metabolizing enzymes (XME) play a role in cancer. Genes coding for XME act as low-penetrance genes and confer modest but consistent and significant risks for a variety of cancers related to the interaction of environmental and genetic factors. Consistent evidence supports a role for polymorphisms of the cytochrome P450 CYP2C9 gene as a protecting factor for colorectal cancer susceptibility. It has been shown that CYP2C8 and CYP2C9 overlap in substrate specificity. Because CYP2C8 has the common functional polymorphisms rs11572080 and rs10509681 (CYP2C8*3), it could be speculated that part of the findings attributed to CYP2C9 polymorphisms may actually be related to the presence of polymorphisms in the CYP2C8 gene. Nevertheless, little attention has been paid to the role of the CYP2C8 polymorphism in colorectal cancer. We analyzed the influence of the CYP2C8*3 allele in the risk of developing colorectal cancer in genomic DNA from 153 individuals suffering colorectal cancer and from 298 age- and gender-matched control subjects. Our findings do not support any effect of the CYP2C8*3 allele (OR for carriers of functional CYP2C8 alleles = 0.50 (95% CI = 0.16–1.59; p = 0.233). The absence of a relative risk related to CYP2C8*3 did not vary depending on the tumor site. We conclude that the risk of developing colorectal cancer does not seem to be related to the commonest functional genetic variation in the CYP2C8 gene.
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Affiliation(s)
- José M Ladero
- Service of Gastroenterology, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos Madrid, Spain ; Department of Medicine, Medical School, Universidad Complutense Madrid, Spain
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Chen J, Pande M, Huang YJ, Wei C, Amos CI, Talseth-Palmer BA, Meldrum CJ, Chen WV, Gorlov IP, Lynch PM, Scott RJ, Frazier ML. Cell cycle-related genes as modifiers of age of onset of colorectal cancer in Lynch syndrome: a large-scale study in non-Hispanic white patients. Carcinogenesis 2012; 34:299-306. [PMID: 23125224 DOI: 10.1093/carcin/bgs344] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Heterogeneity in age of onset of colorectal cancer in individuals with mutations in DNA mismatch repair genes (Lynch syndrome) suggests the influence of other lifestyle and genetic modifiers. We hypothesized that genes regulating the cell cycle influence the observed heterogeneity as cell cycle-related genes respond to DNA damage by arresting the cell cycle to provide time for repair and induce transcription of genes that facilitate repair. We examined the association of 1456 single nucleotide polymorphisms (SNPs) in 128 cell cycle-related genes and 31 DNA repair-related genes in 485 non-Hispanic white participants with Lynch syndrome to determine whether there are SNPs associated with age of onset of colorectal cancer. Genotyping was performed on an Illumina GoldenGate platform, and data were analyzed using Kaplan-Meier survival analysis, Cox regression analysis and classification and regression tree (CART) methods. Ten SNPs were independently significant in a multivariable Cox proportional hazards regression model after correcting for multiple comparisons (P < 5 × 10(-4)). Furthermore, risk modeling using CART analysis defined combinations of genotypes for these SNPs with which subjects could be classified into low-risk, moderate-risk and high-risk groups that had median ages of colorectal cancer onset of 63, 50 and 42 years, respectively. The age-associated risk of colorectal cancer in the high-risk group was more than four times the risk in the low-risk group (hazard ratio = 4.67, 95% CI = 3.16-6.92). The additional genetic markers identified may help in refining risk groups for more tailored screening and follow-up of non-Hispanic white patients with Lynch syndrome.
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Affiliation(s)
- Jinyun Chen
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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24
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Talseth-Palmer BA, Wijnen JT, Brenne IS, Jagmohan-Changur S, Barker D, Ashton KA, Tops CM, Evans TJ, McPhillips M, Groombridge C, Suchy J, Kurzawski G, Spigelman A, Møller P, Morreau HM, Van Wezel T, Lubinski J, Vasen HFA, Scott RJ. Combined analysis of three Lynch syndrome cohorts confirms the modifying effects of 8q23.3 and 11q23.1 in MLH1 mutation carriers. Int J Cancer 2012; 132:1556-64. [PMID: 22987364 DOI: 10.1002/ijc.27843] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Accepted: 08/16/2012] [Indexed: 01/14/2023]
Abstract
Two colorectal cancer (CRC) susceptibility loci have been found to be significantly associated with an increased risk of CRC in Dutch Lynch syndrome (LS) patients. Recently, in a combined study of Australian and Polish LS patients, only MLH1 mutation carriers were found to be at increased risk of disease. A combined analysis of the three data-sets was performed to better define this association. This cohort-study includes three sample populations combined totaling 1,352 individuals from 424 families with a molecular diagnosis of LS. Seven SNPs, from six different CRC susceptibility loci, were genotyped by both research groups and the data analyzed collectively. We identified associations at two of the six CRC susceptibility loci in MLH1 mutation carriers from the combined LS cohort: 11q23.1 (rs3802842, HR = 2.68, p ≤ 0.0001) increasing risk of CRC, and rs3802842 in a pair-wise combination with 8q23.3 (rs16892766) affecting age of diagnosis of CRC (log-rank test; p ≤ 0.0001). A significant difference in the age of diagnosis of CRC of 28 years was observed in individuals carrying three risk alleles compared to those with 0 risk alleles for the pair-wise SNP combination. A trend (due to significance threshold of p ≤ 0.0010) was observed in MLH1 mutation carriers towards an increased risk of CRC for the pair-wise combination (p = 0.002). This study confirms the role of modifier loci in LS. We consider that LS patients with MLH1 mutations would greatly benefit from additional genotyping of SNPs rs3802842 and rs16892766 for personalized risk assessment and a tailored surveillance program.
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Affiliation(s)
- Bente A Talseth-Palmer
- Medical Genetics, School of Biomedical Sciences and Pharmacy, University of Newcastle, Australia.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Baca-López K, Mayorga M, Hidalgo-Miranda A, Gutiérrez-Nájera N, Hernández-Lemus E. The role of master regulators in the metabolic/transcriptional coupling in breast carcinomas. PLoS One 2012; 7:e42678. [PMID: 22952604 PMCID: PMC3428335 DOI: 10.1371/journal.pone.0042678] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 07/10/2012] [Indexed: 12/24/2022] Open
Abstract
Metabolic transformations have been reported as involved in neoplasms survival. This suggests a role of metabolic pathways as potential cancer pharmacological targets. Modulating tumor's energy production pathways may become a substantial research area for cancer treatment. The significant role of metabolic deregulation as inducing transcriptional instabilities and consequently whole-system failure, is thus of foremost importance. By using a data integration approach that combines experimental evidence for high-throughput genome wide gene expression, a non-equilibrium thermodynamics analysis, nonlinear correlation networks as well as database mining, we were able to outline the role that transcription factors MEF2C and MNDA may have as main master regulators in primary breast cancer phenomenology, as well as the possible interrelationship between malignancy and metabolic dysfunction. The present findings are supported by the analysis of 1191 whole genome gene expression experiments, as well as probabilistic inference of gene regulatory networks, and non-equilibrium thermodynamics of such data. Other evidence sources include pathway enrichment and gene set enrichment analyses, as well as motif comparison with a comprehensive gene regulatory network (of homologue genes) in Arabidopsis thaliana. Our key finding is that the non-equilibrium free energies provide a realistic description of transcription factor activation that when supplemented with gene regulatory networks made us able to find deregulated pathways. These analyses also suggest a novel potential role of transcription factor energetics at the onset of primary tumor development. Results are important in the molecular systems biology of cancer field, since deregulation and coupling mechanisms between metabolic activity and transcriptional regulation can be better understood by taking into account the way that master regulators respond to physicochemical constraints imposed by different phenotypic conditions.
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Affiliation(s)
- Karol Baca-López
- Computational Genomics Department, National Institute of Genomic Medicine, México City, México
- School of Sciences, Autonomous University of the State of México, Toluca, México
| | - Miguel Mayorga
- School of Sciences, Autonomous University of the State of México, Toluca, México
| | | | - Nora Gutiérrez-Nájera
- Proteomics Core Facility, National Institute of Genomic Medicine, México City, México
| | - Enrique Hernández-Lemus
- Computational Genomics Department, National Institute of Genomic Medicine, México City, México
- Center for Complexity Sciences, National Autonomous University of México, México City, México
- * E-mail:
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DASGUPTA SANTANU, PAL PRODIPTO, MUKHOPADHYAY NITAID, FU YUMEI, RATOVITSKI EDWARDA, MOON CHULSO, HOQUE MOHAMMADOBAIDUL, FISHER PAULB, TRINK BARRY. A single nucleotide polymorphism in the human PIGK gene associates with low PIGK expression in colorectal cancer patients. Int J Oncol 2012; 41:1405-10. [DOI: 10.3892/ijo.2012.1567] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 05/21/2012] [Indexed: 11/05/2022] Open
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Nusbaum R, Leventhal KG, Hooker GW, Peshkin BN, Butrick M, Salehizadeh Y, Tuong W, Eggly S, Mathew J, Goerlitz D, Shields PG, Schwartz MD, Graves KD. Translational Genomic Research: Protocol Development and Initial Outcomes following SNP Testing for Colon Cancer Risk. Transl Behav Med 2013; 3:17-29. [PMID: 23565131 DOI: 10.1007/s13142-012-0149-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
Although single nucleotide polymorphism (SNP) testing for disease susceptibility is commercially available, translational studies are necessary to understand how to communicate genomic information and potential implications for public health. We explored attitudes about and initial responses to genomic testing for colon cancer risk. Following development of the educational materials, we offered testing for three colon cancer SNPs in a pilot study with primary care patients. Participants completed pre- and post-test sessions and interviews. We analyzed interview transcripts with qualitative software using thematic analysis. All 20 participants opted for SNP testing. Qualitative analysis identified several themes: Motivations for SNP Testing, Before/After: Meaning of Results, Emotional Responses to SNP Results and Genomic Literacy/ Information Delivery. Results demonstrate that individuals will pursue SNP testing in the context of pre and post-test education. SNP results may influence health behaviors like healthy eating and exercise yet did not appear to impact colon cancer screening intentions.
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Gerber MM, Hampel H, Schulz NP, Fernandez S, Wei L, Zhou XP, de la Chapelle A, Toland AE. Evaluation of allele-specific somatic changes of genome-wide association study susceptibility alleles in human colorectal cancers. PLoS One 2012; 7:e37672. [PMID: 22629442 PMCID: PMC3357346 DOI: 10.1371/journal.pone.0037672] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 04/26/2012] [Indexed: 12/11/2022] Open
Abstract
Background Tumors frequently exhibit loss of tumor suppressor genes or allelic gains of activated oncogenes. A significant proportion of cancer susceptibility loci in the mouse show somatic losses or gains consistent with the presence of a tumor susceptibility or resistance allele. Thus, allele-specific somatic gains or losses at loci may demarcate the presence of resistance or susceptibility alleles. The goal of this study was to determine if previously mapped susceptibility loci for colorectal cancer show evidence of allele-specific somatic events in colon tumors. Methods We performed quantitative genotyping of 16 single nucleotide polymorphisms (SNPs) showing statistically significant association with colorectal cancer in published genome-wide association studies (GWAS). We genotyped 194 paired normal and colorectal tumor DNA samples and 296 paired validation samples to investigate these SNPs for allele-specific somatic gains and losses. We combined analysis of our data with published data for seven of these SNPs. Results No statistically significant evidence for allele-specific somatic selection was observed for the tested polymorphisms in the discovery set. The rs6983267 variant, which has shown preferential loss of the non-risk T allele and relative gain of the risk G allele in previous studies, favored relative gain of the G allele in the combined discovery and validation samples (corrected p-value = 0.03). When we combined our data with published allele-specific imbalance data for this SNP, the G allele of rs6983267 showed statistically significant evidence of relative retention (p-value = 2.06×10−4). Conclusions Our results suggest that the majority of variants identified as colon cancer susceptibility alleles through GWAS do not exhibit somatic allele-specific imbalance in colon tumors. Our data confirm previously published results showing allele-specific imbalance for rs6983267. These results indicate that allele-specific imbalance of cancer susceptibility alleles may not be a common phenomenon in colon cancer.
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Affiliation(s)
- Madelyn M. Gerber
- Integrated Biomedical Sciences Graduate Program, The Ohio State University, Columbus, Ohio, United States of America
| | - Heather Hampel
- The Ohio State University College of Medicine, Columbus, Ohio, United States of America
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University, Columbus, Ohio, United States of America
- Human Cancer Genetics Program, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States of America
| | - Nathan P. Schulz
- The Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Soledad Fernandez
- The Center for Biostatistics, The Ohio State University, Columbus, Ohio, United States of America
| | - Lai Wei
- The Center for Biostatistics, The Ohio State University, Columbus, Ohio, United States of America
| | - Xiao-Ping Zhou
- Department of Pathology, The Ohio State University, Columbus, Ohio, United States of America
| | - Albert de la Chapelle
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University, Columbus, Ohio, United States of America
- Human Cancer Genetics Program, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States of America
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, Ohio, United States of America
| | - Amanda Ewart Toland
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University, Columbus, Ohio, United States of America
- Human Cancer Genetics Program, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States of America
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail:
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Castellví-Bel S, Ruiz-Ponte C, Fernández-Rozadilla C, Abulí A, Muñoz J, Bessa X, Brea-Fernández A, Ferro M, Giráldez MD, Xicola RM, Llor X, Jover R, Piqué JM, Andreu M, Castells A, Carracedo A. Seeking genetic susceptibility variants for colorectal cancer: the EPICOLON consortium experience. Mutagenesis 2012; 27:153-9. [PMID: 22294762 DOI: 10.1093/mutage/ger047] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The EPICOLON consortium was initiated in 1999 by the Gastrointestinal Oncology Group of the Spanish Gastroenterology Association. It recruited consecutive, unselected, population-based colorectal cancer (CRC) cases and control subjects matched by age and gender without personal or familial history of cancer all over Spain with the main goal of gaining knowledge in Lynch syndrome and familial CRC. This epidemiological, prospective and multicentre study collected extensive clinical data and biological samples from ∼2000 CRC cases and 2000 controls in Phases 1 and 2 involving 25 and 14 participating hospitals, respectively. Genetic susceptibility projects in EPICOLON have included candidate-gene approaches evaluating single-nucleotide polymorphisms/genes from the historical category (linked to CRC risk by previous studies), from human syntenic CRC susceptibility regions identified in mouse, from the CRC carcinogenesis-related pathways Wnt and BMP, from regions 9q22 and 3q22 with positive linkage in CRC families, and from the mucin gene family. This consortium has also participated actively in the identification 5 of the 16 common, low-penetrance CRC genetic variants identified so far by genome-wide association studies. Finishing their own pangenomic study and performing whole-exome sequencing in selected CRC samples are among EPICOLON future research prospects.
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Affiliation(s)
- Sergi Castellví-Bel
- Department of Gastroenterology, Hospital Clínic, CIBERehd, IDIBAPS, University of Barcelona, Villarroel 170, 08036 Barcelona, Catalonia, Spain.
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Pardini B, Naccarati A, Vodicka P, Kumar R. Gene expression variations: potentialities of master regulator polymorphisms in colorectal cancer risk. Mutagenesis 2012; 27:161-7. [PMID: 22294763 DOI: 10.1093/mutage/ger057] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most common cancers worldwide with a peak of incidence in industrialised countries. It is a complex disease related to environmental and genetic risk factors. Low-penetrance genetic variations contribute significantly to sporadic and familial form of CRC. Genome-wide association studies (GWAS) have uncovered numerous robust associations between common variants and CRC risk; only a few of those were protein altering non-synonymous polymorphisms. One of the hypotheses is that non-coding and intergenic variants may change the expression levels of one or several target genes and, thus, account for a fraction of phenotypic differences, including susceptibility to CRC. Such genetic variations have been detected as expression quantitative loci (eQTLs) that show linkage/association to a large number of genes and have been defined as "master regulators of transcription". In the present work, we overview the potentialities to use results from GWAS and eQTL studies in the identification as well as investigation of master regulators in CRC susceptibility.
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Affiliation(s)
- Barbara Pardini
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, Videnska 1083, 14220 Prague 4, Czech Republic.
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Abstract
Many colorectal cancers (CRCs) develop in genetically susceptible individuals most of whom are not carriers of germ line mismatch repair or APC gene mutations and much of the heritable risk of CRC appears to be attributable to the co-inheritance of multiple low-risk variants. The accumulated experience to date in identifying this class of susceptibility allele has highlighted the need to conduct statistically and methodologically rigorous studies and the need for the multi-centre collaboration. This has been the motivation for establishing the COGENT (COlorectal cancer GENeTics) consortium which now includes over 20 research groups in Europe, Australia, the Americas, China and Japan actively working on CRC genetics. Here, we review the rationale for identifying low-penetrance variants for CRC and the current and future challenges for COGENT.
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Affiliation(s)
- Richard S Houlston
- Division of Genetics and Epidemiology, Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK.
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Lubbe SJ, Di Bernardo MC, Broderick P, Chandler I, Houlston RS. Comprehensive evaluation of the impact of 14 genetic variants on colorectal cancer phenotype and risk. Am J Epidemiol 2012; 175:1-10. [PMID: 22156018 DOI: 10.1093/aje/kwr285] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
To comprehensively evaluate the impact of recently identified colorectal cancer (CRC) variants at 1q41, 3q26.2, 8q23.3, 8q24.21, 10p14, 11q23.1, 12q13.13, 14q22.2, 15q13.3, 16q22.1, 18q21.1, 19q13.11, 20p12.3, and 20q13.33 on risk and CRC phenotype, the authors analyzed 8,878 cases and 6,051 controls from the United Kingdom ascertained in 1999-2007. The impact of variants on the familial CRC risk was enumerated from age-, sex-, and calendar-specific CRC rates in the 50,924 first-degree relatives of cases. Each of the 14 susceptibility loci independently influences CRC with the risk increasing with increasing number of risk alleles carried (per allele odds ratio = 1.13; P = 2.99 × 10(-58)) and, for those within the upper quintile, there is a 2.3-fold increased risk. In first-degree relatives of cases with ≤17, 18-21, and ≥22 risk alleles, standardized incidence ratios were 1.76, 2.08, and 2.25, respectively. Although the discriminatory attributes of the 14 CRC susceptibility loci for individual risk prediction are poor (area under the curve = 0.58), they may allow subgroups of the population at different CRC risks to be distinguished.
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Affiliation(s)
- Steven J Lubbe
- Section of Cancer Genetics, Institute of Cancer Research, Sutton, Surrey, United Kingdom
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Abstract
Colorectal cancer is a major health burden, and a leading cause of cancer-related deaths in industrialized countries. The steady improvements in surgery and chemotherapy have improved survival, but the ability to identify high- and low-risk patients is still somewhat poor. Molecular biology has, over the years, given insight into basic principles of colorectal cancer initiation and development. These findings include aberrations increasing risk of tumor development, genetic changes associated with the stepwise progression of the disease, and errors predicting response to a specific treatment. Potential biomarkers in colorectal cancer are extensively studied, and how the molecular aberrations relate to clinical features. Yet, little of this knowledge has been possible to transfer into clinical practice. In this review, an overview of colorectal cancer genetics will be given, as well as how aberrations found in this tumor type are proposed as biomarkers for risk prediction, as diagnostic tools, for prognosis or prediction of treatment outcome.
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Affiliation(s)
- Marianne Berg
- Department of Surgery, Stavanger University Hospital, P O Box 8100, N-4068 Stavanger, Norway
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +47-51-51-80-00; Fax: +47-51-88-08-95
| | - Kjetil Søreide
- Department of Surgery, Stavanger University Hospital, P O Box 8100, N-4068 Stavanger, Norway
- Department of Surgical Sciences, University of Bergen, 5021 Bergen, Norway; E-Mail:
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Mimori K, Tanaka F, Shibata K, Mori M. Review: Single nucleotide polymorphisms associated with the oncogenesis of colorectal cancer. Surg Today 2011; 42:215-9. [PMID: 22127532 DOI: 10.1007/s00595-011-0038-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2011] [Accepted: 03/24/2011] [Indexed: 01/12/2023]
Abstract
Colorectal cancer (CRC) is provoked by interactions between genetic and environmental factors. We herein review the incidence and the mechanisms of action of the reported single nucleotide polymorphisms (SNPs) in the oncogenesis of CRC. More than 15 reports have studied the SNPs at 8q24, which are associated with the incidence of CRC as well as prostate cancer. We have also reported a SNP at the 10p14 locus, and the risks of other loci for CRC oncogenesis. With regard to the underlying mechanism for CRC, 8q24 is a locus of the long-enhancer site for MYC, which could determine the efficacy of MYC transcription. We suggest that 8q24 SNPs might be associated with the progression of CRC cases mediated by MYC expression. In this report, we summarize the published studies of the genetic background SNPs in the oncogenesis of CRC. The level of risk (most studies indicated less than a twofold increase) for CRC was lower than anticipated. Therefore, it is necessary to identify bona fide SNPs that precisely predict the risk for CRC. Alternatively, it is important to consider other factors, such as environmental or lifestyle-related factors, for the future prevention of CRC.
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Affiliation(s)
- Koshi Mimori
- Department of Surgery, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu, Japan
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Carvajal-Carmona LG, Cazier JB, Jones AM, Howarth K, Broderick P, Pittman A, Dobbins S, Tenesa A, Farrington S, Prendergast J, Theodoratou E, Barnetson R, Conti D, Newcomb P, Hopper JL, Jenkins MA, Gallinger S, Duggan DJ, Campbell H, Kerr D, Casey G, Houlston R, Dunlop M, Tomlinson I. Fine-mapping of colorectal cancer susceptibility loci at 8q23.3, 16q22.1 and 19q13.11: refinement of association signals and use of in silico analysis to suggest functional variation and unexpected candidate target genes. Hum Mol Genet 2011; 20:2879-88. [PMID: 21531788 DOI: 10.1093/hmg/ddr190] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
We have previously identified several colorectal cancer (CRC)-associated polymorphisms using genome-wide association (GWA) analysis. We sought to fine-map the location of the functional variants for three of these regions at 8q23.3 (EIF3H), 16q22.1 (CDH1/CDH3) and 19q13.11 (RHPN2). We genotyped two case-control sets at high density in the selected regions and used existing data from four other case-control sets, comprising a total of 9328 CRC cases and 10 480 controls. To improve marker density, we imputed genotypes from the 1000 Genomes Project and Hapmap3 data sets. All three regions contained smaller areas in which a cluster of single nucleotide polymorphisms (SNPs) showed clearly stronger association signals than surrounding SNPs, allowing us to assign those areas as the most likely location of the disease-associated functional variant. Further fine-mapping within those areas was generally unhelpful in identifying the functional variation based on strengths of association. However, functional annotation suggested a relatively small number of functional SNPs, including some with potential regulatory function at 8q23.3 and 16q22.1 and a non-synonymous SNP in RPHN2. Interestingly, the expression quantitative trait locus browser showed a number of highly associated SNP alleles correlated with mRNA expression levels not of EIF3H and CDH1 or CDH3, but of UTP23 and ZFP90, respectively. In contrast, none of the top SNPs within these regions was associated with transcript levels at EIF3H, CDH1 or CDH3. Our post-GWA study highlights benefits of fine-mapping of common disease variants in combination with publicly available data sets. In addition, caution should be exercised when assigning functionality to candidate genes in regions discovered through GWA analysis.
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Affiliation(s)
- Luis G Carvajal-Carmona
- Wellcome Trust Centre for Human Genetics and Department of Clinical Pharmacology, University of Oxford, Oxford, UK.
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Poretti G, Kwee I, Bernasconi B, Rancoita PMV, Rinaldi A, Capella C, Zucca E, Neri A, Tibiletti MG, Bertoni F. Chromosome 11q23.1 is an unstable region in B-cell tumor cell lines. Leuk Res 2011; 35:808-13. [PMID: 21420167 DOI: 10.1016/j.leukres.2010.10.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 10/18/2010] [Accepted: 10/31/2010] [Indexed: 01/08/2023]
Abstract
Chromosome 11q23 region is a frequent target of chromosome aberrations in B-cell lymphoid tumors. Here, we present the cytogenetic and molecular characterization of an amplification affecting 11q23.1 in four cell lines derived from B-cell lymphoid tumors. A minimal common region of amplification of 330 kb was identified in three cell lines using Affymetrix Human Mapping 250K arrays. When analyzed with three BAC clones, the amplifications appeared different at cytogenetic level in each cell line. Possibly affected transcripts were evaluated using tiling arrays, and validated by real time PCR. Since no effect of the amplification at the local transcription level was observed, it is possible that 11q23 amplification might mainly represent the effect of unstable chromosomal region.
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Affiliation(s)
- Giulia Poretti
- Laboratory of Experimental Oncology and Lymphoma Unit, Oncology Institute of Southern Switzerland (IOSI), Bellinzona, Switzerland
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Niittymäki I, Tuupanen S, Li Y, Järvinen H, Mecklin JP, Tomlinson IPM, Houlston RS, Karhu A, Aaltonen LA. Systematic search for enhancer elements and somatic allelic imbalance at seven low-penetrance colorectal cancer predisposition loci. BMC Med Genet 2011; 12:23. [PMID: 21314996 PMCID: PMC3045878 DOI: 10.1186/1471-2350-12-23] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/26/2010] [Accepted: 02/14/2011] [Indexed: 01/20/2023]
Abstract
BACKGROUND Common single-nucleotide polymorphisms (SNPs) in ten chromosomal loci have been shown to predispose to colorectal cancer (CRC) in genome-wide association studies. A plausible biological mechanism of CRC susceptibility associated with genetic variation has so far only been proposed for three loci, each pointing to variants that affect gene expression through distant regulatory elements. In this study, we aimed to gain insight into the molecular basis of seven low-penetrance CRC loci tagged by rs4779584 at 15q13, rs10795668 at 10p14, rs3802842 at 11q23, rs4444235 at 14q22, rs9929218 at 16q22, rs10411210 at 19q13, and rs961253 at 20p12. METHODS Possible somatic gain of the risk allele or loss of the protective allele was studied by analyzing allelic imbalance in tumour and corresponding normal tissue samples of heterozygous patients. Functional variants were searched from in silico predicted enhancer elements locating inside the CRC-associating linkage-disequilibrium regions. RESULTS No allelic imbalance targeting the SNPs was observed at any of the seven loci. Altogether, 12 SNPs that were predicted to disrupt potential transcription factor binding sequences were genotyped in the same population-based case-control series as the seven tagging SNPs originally. None showed association with CRC. CONCLUSIONS The results of the allelic imbalance analysis suggest that the seven CRC risk variants are not somatically selected for in the neoplastic progression. The bioinformatic approach was unable to pinpoint cancer-causing variants at any of the seven loci. While it is possible that many of the predisposition loci for CRC are involved in control of gene expression by targeting transcription factor binding sites, also other possibilities, such as regulatory RNAs, should be considered.
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Affiliation(s)
- Iina Niittymäki
- Department of Medical Genetics, Genome-Scale Biology Research Program, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland
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Gervasini G, de Murillo SG, Ladero JM, Agúndez JAG. CYP2W1 variant alleles in Caucasians and association of the CYP2W1 G541A (Ala181Thr) polymorphism with increased colorectal cancer risk. Pharmacogenomics 2011; 11:919-25. [PMID: 20602611 DOI: 10.2217/pgs.10.66] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIMS To detect differences in the frequency of the known nonsynonymous CYP2W1 polymorphisms between colorectal cancer patients and healthy subjects. MATERIALS & METHODS The study group consisted of 150 colorectal patients and 263 controls. The presence of five nonsynonymous CYP2W1 polymorphisms was analyzed by novel amplification-restriction methods. RESULTS Two nonsynonymous SNPs causing the amino acid substitutions Val432Ile and Gln482His were monomorphic in the population study. Two nonsynonymous SNPs previously unknown in Caucasians, 1463T (rs3808348) and 173C (no rs number assigned), were detected in the population study, although these were not associated with colorectal cancer risk. Regarding the 541G/A polymorphism (rs3735684), the 541G allele (odds ratio: 2.2; 95% CI: 1.2-4.1) and the 541GG genotype (odds ratio: 2.06; 95% CI: 1.1-3.9) were associated with increased colorectal cancer risk in the population studied. Conversely, the 173C-541A-1463C haplotype (odds ratio: 0.46; 95% CI: 0.2-0.9) showed a protective odds ratio value. CONCLUSION CYP2W1 variant alleles are common among Caucasian individuals and, of these, the CYP2W1 G541A (Ala181Thr) polymorphism is associated with increased colorectal cancer risk.
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Affiliation(s)
- Guillermo Gervasini
- Department of Pharmacology, School of Medicine, University of Extremadura, 06071 Badajoz, Spain.
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He J, Wilkens LR, Stram DO, Kolonel LN, Henderson BE, Wu AH, Le Marchand L, Haiman CA. Generalizability and epidemiologic characterization of eleven colorectal cancer GWAS hits in multiple populations. Cancer Epidemiol Biomarkers Prev 2010; 20:70-81. [PMID: 21071539 DOI: 10.1158/1055-9965.epi-10-0892] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) in populations of European ancestry have identified several loci that confer an increased risk of colorectal cancer (CRC). METHODS We studied the generalizability of the associations with 11 risk variants for CRC on 8q23 (rs16892766), 8q24 (rs6983267), 9p24 (rs719725), 10p14 (rs10795668), 11q23 (rs3802842), 14q22 (rs4444235), 15q13 (rs4779584), 16q22 (rs9929218), 18q21 (rs4939827), 19q13 (rs10411210), and 20p12 (rs961253) in a multiethnic sample of 2,472 CRC cases, 839 adenoma cases and 4,466 controls comprised of European American, African American, Native Hawaiian, Japanese American, and Latino men and women. Because findings for CRC and adenoma were similar, we combined both groups in the analyses. RESULTS We confirmed the associations with an increased risk of CRC/adenoma for the 8q24, 11q23 and 15q13 loci in European Americans, and observed significant associations between the 8q24 and 20p12 loci with CRC/adenoma risk in African Americans. Moreover, we found statistically significant cumulative effects of risk alleles on CRC/adenoma risk in all populations (odds ratio [OR] per allele = 1.07-1.09, P ≤ 0.039) except in Japanese Americans (OR = 1.01, P = 0.52). We found heterogeneity in the associations by tumor subsite, age of CRC/adenoma onset, sex, body mass index (BMI), and smoking status for some of the variants. CONCLUSIONS These results provide evidence that the known variants are in aggregate significantly associated with CRC/adenoma risk in multiple populations except Japanese Americans, and the influences may differ across groups defined by clinicopathological characteristics for some variants. IMPACT These results underline the importance of studying the epidemiologic architecture of these genetic effects in large and diverse populations.
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Affiliation(s)
- Jing He
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, USC/Norris Comprehensive Cancer Center, Harlyne Norris Research Tower, 1450 Biggy Street, Los Angeles, CA 90033, USA
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Kupfer SS, Anderson JR, Hooker S, Skol A, Kittles RA, Keku TO, Sandler RS, Ellis NA. Genetic heterogeneity in colorectal cancer associations between African and European americans. Gastroenterology 2010; 139:1677-85, 1685.e1-8. [PMID: 20659471 PMCID: PMC3721963 DOI: 10.1053/j.gastro.2010.07.038] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Revised: 06/14/2010] [Accepted: 07/16/2010] [Indexed: 01/29/2023]
Abstract
BACKGROUND & AIMS Genome-wide association studies of colorectal cancer (CRC) have identified risk variants in 10 genomic regions. None of these studies included African Americans, who have the highest incidence and mortality from CRC in the United States. For the 10 genomic regions, we performed an association study of Americans of African and European descent. METHODS We genotyped 22 single nucleotide polymorphisms (SNPs) in DNA samples from 1194 patients with CRC (795 African Americans and 399 European Americans) and 1352 controls (985 African Americans and 367 European Americans). At chromosome 8q24.21 region 3, we analyzed 6 SNPs from 1000 African American cases and 1393 controls. Association testing was done using multivariate logistic regression controlling for ancestry, age, and sex. RESULTS Among African Americans, the SNP rs6983267 at 8q24.21 was not associated with CRC (odds ratio, 1.18; P = .12); instead, the 8q24.21 SNP rs7014346 (odds ratio, 1.15; P = .03) was associated with CRC in this population. At 15q13.3, rs10318 was associated with CRC in both populations. At 11q23.1, rs3802842 was significantly associated with rectal cancer risk only among African Americans (odds ratio, 1.34; P = .01); this observation was made in previous studies. Among European Americans, SNPs at 8q24.21, 11q23.1, and 16q22.1 were significantly associated with CRC, and the odds ratios were of the same magnitude and direction for all SNPs tested, consistent with previously published studies. In contrast, in African Americans, the opposite allele of rs10795668 at 10p14 was associated with colorectal cancer (odds ratio, 1.35; P = .04), and altogether the odds ratios were in the opposite direction for 9 of the 22 SNPs tested. CONCLUSIONS There is genetic heterogeneity in CRC associations in Americans of African versus European descent.
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Affiliation(s)
- Sonia S. Kupfer
- Department of Medicine, Section of Gastroenterology University of Chicago Medical Center, Chicago, IL
| | - Jeffrey R. Anderson
- Department of Medicine, Section of Gastroenterology University of Chicago Medical Center, Chicago, IL
| | - Stanley Hooker
- Department of Medicine, Section of Genetic Medicine University of Chicago Medical Center, Chicago, IL
| | - Andrew Skol
- Department of Medicine, Section of Genetic Medicine University of Chicago Medical Center, Chicago, IL
| | - Rick A. Kittles
- Department of Medicine, Section of Genetic Medicine University of Chicago Medical Center, Chicago, IL
| | - Temitope O. Keku
- Department of Medicine, Division of Gastroenterology and Hepatology, University of North Carolina, Chapel Hill, NC
| | - Robert S. Sandler
- Department of Medicine, Division of Gastroenterology and Hepatology, University of North Carolina, Chapel Hill, NC
| | - Nathan A. Ellis
- Department of Medicine, Section of Gastroenterology University of Chicago Medical Center, Chicago, IL
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Adán L, Álvarez-Castro A, Castells A. Aproximación al cáncer colorrectal familiar. Gastroenterología y Hepatología 2010; 33:652-9. [DOI: 10.1016/j.gastrohep.2009.11.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Accepted: 11/27/2009] [Indexed: 12/26/2022]
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Van Der Kraak L, Meunier C, Turbide C, Jothy S, Gaboury L, Marcus V, Chang SY, Beauchemin N, Gros P. A two-locus system controls susceptibility to colitis-associated colon cancer in mice. Oncotarget 2010; 1:436-446. [PMID: 21311099 PMCID: PMC3248117 DOI: 10.18632/oncotarget.177] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Accepted: 10/10/2010] [Indexed: 11/25/2022] Open
Abstract
We have previously shown that the differential susceptibility of A/J (susceptible) and C57BL/6J (B6, resistant) mouse strains to azoxymethane (AOM)-induced colorectal cancer (CRC) is controlled by the chromosome 3 locus, Ccs3. We report that A/J and B6 mice also show differential susceptibility to colitis-associated colorectal cancer (CA-CRC) induced by combined administration of AOM and dextran sulfate. This differential susceptibility is not controlled by Ccs3, but is under distinct genetic control. Linkage analyses in (A/J x B6)F2 mice detected a major CA-CRC susceptibility locus on chromosome 9 (Ccs4) which controls tumor multiplicity and tumor surface area. Susceptibility alleles at Ccs4 are inherited in a recessive fashion, with A/J alleles being associated with susceptibility. We also detected a second locus on chromosome 14 that acts in an additive fashion with Ccs4. Strikingly, F2 mice homozygous for A/J alleles at both loci (Ccs4 and chromosome 14) are as susceptible to CA-CRC as the A/J controls while mice homozygous for B6 alleles are as resistant as the B6 controls, thus supporting the role of two interacting loci in this CA-CRC model. This indicates that susceptibility to chemically-induced CRC and susceptibility to CA-CRC are under distinct genetic control in mice, and probably involve distinct cellular pathways.
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Affiliation(s)
- Lauren Van Der Kraak
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Charles Meunier
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Claire Turbide
- Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Serge Jothy
- Department of Laboratory Medicine and Pathobiology, St. Michael's Hospital and University of Toronto, Toronto, Ontario, Canada
| | - Louis Gaboury
- Institut de Recherche en Immunologie et en Cancérologie, Université de Montréal, Montreal, Quebec, Canada
| | - Victoria Marcus
- Department of Pathology, McGill University Health Centre, Montreal, Quebec, Canada
| | - Sing Yun Chang
- Department of Pathology, McGill University Health Centre, Montreal, Quebec, Canada
| | - Nicole Beauchemin
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
- Departments of Medicine and Oncology, McGill University, Montreal, Quebec, Canada
| | - Philippe Gros
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
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von Holst S, Picelli S, Edler D, Lenander C, Dalén J, Hjern F, Lundqvist N, Lindforss U, Påhlman L, Smedh K, Törnqvist A, Holm J, Janson M, Andersson M, Ekelund S, Olsson L, Ghazi S, Papadogiannakis N, Tenesa A, Farrington SM, Campbell H, Dunlop MG, Lindblom A. Association studies on 11 published colorectal cancer risk loci. Br J Cancer 2010; 103:575-80. [PMID: 20648012 DOI: 10.1038/sj.bjc.6605774] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Background: Recently, several genome-wide association studies (GWAS) have independently found numerous loci at which common single-nucleotide polymorphisms (SNPs) modestly influence the risk of developing colorectal cancer. The aim of this study was to test 11 loci, reported to be associated with an increased or decreased risk of colorectal cancer: 8q23.3 (rs16892766), 8q24.21 (rs6983267), 9p24 (rs719725), 10p14 (rs10795668), 11q23.1 (rs3802842), 14q22.2 (rs4444235), 15q13.3 (rs4779584), 16q22.1 (rs9929218), 18q21.1 (rs4939827), 19q13.1 (rs10411210) and 20p12.3 (rs961253), in a Swedish-based cohort. Methods: The cohort was composed of 1786 cases and 1749 controls that were genotyped and analysed statistically. Genotype–phenotype analysis, for all 11 SNPs and sex, age of onset, family history of CRC and tumour location, was performed. Results: Of eleven loci, 5 showed statistically significant odds ratios similar to previously published findings: 8q23.3, 8q24.21, 10p14, 15q13.3 and 18q21.1. The remaining loci 11q23.1, 16q22.1, 19q13.1 and 20p12.3 showed weak trends but somehow similar to what was previously published. The loci 9p24 and 14q22.2 could not be confirmed. We show a higher number of risk alleles in affected individuals compared to controls. Four statistically significant genotype–phenotype associations were found; the G allele of rs6983267 was associated to older age, the G allele of rs1075668 was associated with a younger age and sporadic cases, and the T allele of rs10411210 was associated with younger age. Conclusions: Our study, using a Swedish population, supports most genetic variants published in GWAS. More studies are needed to validate the genotype–phenotype correlations.
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Lascorz J, Försti A, Chen B, Buch S, Steinke V, Rahner N, Holinski-Feder E, Morak M, Schackert HK, Görgens H, Schulmann K, Goecke T, Kloor M, Engel C, Büttner R, Kunkel N, Weires M, Hoffmeister M, Pardini B, Naccarati A, Vodickova L, Novotny J, Schreiber S, Krawczak M, Bröring CD, Völzke H, Schafmayer C, Vodicka P, Chang-Claude J, Brenner H, Burwinkel B, Propping P, Hampe J, Hemminki K. Genome-wide association study for colorectal cancer identifies risk polymorphisms in German familial cases and implicates MAPK signalling pathways in disease susceptibility. Carcinogenesis 2010; 31:1612-9. [PMID: 20610541 DOI: 10.1093/carcin/bgq146] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Genetic susceptibility accounts for approximately 35% of all colorectal cancer (CRC). Ten common low-risk variants contributing to CRC risk have been identified through genome-wide association studies (GWASs). In our GWAS, 610 664 genotyped single-nucleotide polymorphisms (SNPs) passed the quality control filtering in 371 German familial CRC patients and 1263 controls, and replication studies were conducted in four additional case-control sets (4915 cases and 5607 controls). Known risk loci at 8q24.21 and 11q23 were confirmed, and a previously unreported association, rs12701937, located between the genes GLI3 (GLI family zinc finger 3) and INHBA (inhibin, beta A) [P = 1.1 x 10(-3), odds ratio (OR) 1.14, 95% confidence interval (CI) 1.05-1.23, dominant model in the combined cohort], was identified. The association was stronger in familial cases compared with unselected cases (P = 2.0 x 10(-4), OR 1.36, 95% CI 1.16-1.60, dominant model). Two other unreported SNPs, rs6038071, 40 kb upstream of CSNK2A1 (casein kinase 2, alpha 1 polypeptide) and an intronic marker in MYO3A (myosin IIIA), rs11014993, associated with CRC only in the familial CRC cases (P = 2.5 x 10(-3), recessive model, and P = 2.7 x 10(-4), dominant model). Three software tools successfully pointed to the overrepresentation of genes related to the mitogen-activated protein kinase (MAPK) signalling pathways among the 1340 most strongly associated markers from the GWAS (allelic P value < 10(-3)). The risk of CRC increased significantly with an increasing number of risk alleles in seven genes involved in MAPK signalling events (P(trend) = 2.2 x 10(-16), OR(per allele) = 1.34, 95% CI 1.11-1.61).
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Affiliation(s)
- Jesús Lascorz
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany.
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Nisa H, Kono S, Yin G, Toyomura K, Nagano J, Mibu R, Tanaka M, Kakeji Y, Maehara Y, Okamura T, Ikejiri K, Futami K, Maekawa T, Yasunami Y, Takenaka K, Ichimiya H, Terasaka R. Cigarette smoking, genetic polymorphisms and colorectal cancer risk: the Fukuoka Colorectal Cancer Study. BMC Cancer 2010; 10:274. [PMID: 20534171 PMCID: PMC2906477 DOI: 10.1186/1471-2407-10-274] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2009] [Accepted: 06/10/2010] [Indexed: 12/11/2022] Open
Abstract
Background It is uncertain whether smoking is related to colorectal cancer risk. Cytochrome P-450 CYP1A1, glutathione-S-transferase (GST) and NAD(P)H:quinone oxidoreductase 1 (NQO1) are important enzymes in the metabolism of tobacco carcinogens, and functional genetic polymorphisms are known for these enzymes. We investigated the relation of cigarette smoking and related genetic polymorphisms to colorectal cancer risk, with special reference to the interaction between smoking and genetic polymorphism. Methods We used data from the Fukuoka Colorectal Cancer Study, a population-based case-control study, including 685 cases and 778 controls who gave informed consent to genetic analysis. Interview was conducted to assess lifestyle factors, and DNA was extracted from buffy coat. Results In comparison with lifelong nonsmokers, the odds ratios (OR) of colorectal cancer for <400, 400-799 and ≥800 cigarette-years were 0.65 (95% confidence interval [CI], 0.45-0.89), 1.16 (0.83-1.62) and 1.14 (0.73-1.77), respectively. A decreased risk associated with light smoking was observed only for colon cancer, and rectal cancer showed an increased risk among those with ≥400 cigarette-years (OR 1.60, 95% CI 1.04-2.45). None of the polymorphisms under study was singly associated with colorectal cancer risk. Of the gene-gene interactions studied, the composite genotype of CYP1A1*2A or CYP1A1*2C and GSTT1 polymorphisms was associated with a decreased risk of colorectal cancer, showing a nearly statistically significant (Pinteraction = 0.06) or significant interaction (Pinteraction = 0.02). The composite genotypes of these two polymorphisms, however, showed no measurable interaction with cigarette smoking in relation to colorectal cancer risk. Conclusions Cigarette smoking may be associated with increased risk of rectal cancer, but not of colon cancer. The observed interactions between CYP1A1 and GSTT1 polymorphisms warrant further confirmation.
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Affiliation(s)
- Hoirun Nisa
- Department of Preventive Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
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Xiong F, Wu C, Bi X, Yu D, Huang L, Xu J, Zhang T, Zhai K, Chang J, Tan W, Cai J, Lin D. Risk of genome-wide association study-identified genetic variants for colorectal cancer in a Chinese population. Cancer Epidemiol Biomarkers Prev 2010; 19:1855-61. [PMID: 20530476 DOI: 10.1158/1055-9965.epi-10-0210] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Recent genome-wide association studies have identified 10 single nucleotide polymorphisms (SNP) associated with colorectal cancer (CRC) in Caucasians. This study evaluated the effects of these newly identified SNPs in a Chinese population. METHODS We assessed the associations of these 10 SNPs with CRC in a case-control study that consisted of 2,124 cases and 2,124 controls. Odds ratios (OR) and 95% confidence intervals were computed by logistic regression, and cumulative effect of risk genotypes were also calculated. RESULTS We found that only five SNPs (rs6983267, rs4939827, rs10795668, rs3802842, and rs961253) were significantly associated with risk of CRC in our study population in the same direction as reported by previous genome-wide association studies, with the ORs ranging from 1.11 to 2.96. A cumulative effect was observed with the ORs being gradually elevated with increasing number of risk genotypes (P(trend) = 1.32 x 10(-21)), and patients carrying > or = 4 risk genotypes had 3.25-fold increased CRC risk (95% confidence interval, 2.24-4.72) compared with patients carrying no risk genotype. Furthermore, we found that rs10795668 was associated with increased risk only in rectal cancer but not colon cancer, and rs3802842 was also significantly associated with advanced stages of CRC. CONCLUSIONS These results suggest that rs6983267, rs4939827, rs10795668, rs3802842, and rs961253 SNPs are associated with the risk of CRC in the Chinese population individually and jointly. IMPACT Our results provide new insights into colorectal tumorigenesis and have potential implications in early detection and target treatment of CRC in non-Western populations.
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Affiliation(s)
- Fang Xiong
- Department of Etiology & Carcinogenesis, Cancer Institute and Hospital, Chinese Academy of Medical Sciences, Beijing 100021, China
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Varghese JS, Easton DF. Genome-wide association studies in common cancers—what have we learnt? Curr Opin Genet Dev 2010; 20:201-9. [DOI: 10.1016/j.gde.2010.03.012] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2010] [Revised: 03/18/2010] [Accepted: 03/19/2010] [Indexed: 01/31/2023]
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Niittymäki I, Kaasinen E, Tuupanen S, Karhu A, Järvinen H, Mecklin JP, Tomlinson IPM, Di Bernardo MC, Houlston RS, Aaltonen LA. Low-penetrance susceptibility variants in familial colorectal cancer. Cancer Epidemiol Biomarkers Prev 2010; 19:1478-83. [PMID: 20501757 DOI: 10.1158/1055-9965.epi-09-1320] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Genomewide association studies have identified 10 low-penetrance loci that confer modestly increased risk for colorectal cancer (CRC). Although they underlie a significant proportion of CRC in the general population, their impact on the familial risk for CRC has yet to be formally enumerated. The aim of this study was to examine the combined contribution of the 10 variants, rs6983267, rs4779584, rs4939827, rs16892766, rs10795668, rs3802842, rs4444235, rs9929218, rs10411210, and rs961253, on familial CRC. METHODS The population-based series of CRC samples included in this study consisted of 97 familial cases and 691 sporadic cases. Genotypes in the 10 loci and clinical data, including family history of cancer verified from the Finnish Cancer Registry, were available. The overall number of risk alleles (0-20) was determined, and its association with familial CRC was analyzed. Excess familial risk was estimated using cancer incidence data from the first-degree relatives of the cases. RESULTS A linear association between the number of risk alleles and familial CRC was observed (P = 0.006). With each risk-allele addition, the odds of having an affected first-degree relative increased by 1.16 (95% confidence interval, 1.04-1.30). The 10 low-penetrance loci collectively explain approximately 9% of the variance in familial risk for CRC. CONCLUSIONS This study provides evidence to support the previous indirect estimations that these low-penetrance variants account for a relatively small proportion of the familial aggregation of CRC. IMPACT Our results emphasize the need to characterize the remaining molecular basis of familial CRC, which should eventually yield in individualized targeting of preventive interventions.
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Affiliation(s)
- Iina Niittymäki
- Department of Medical Genetics, Genome-Scale Biology Research Program, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland
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