scholarly journals Gene Environment Interactions and Predictors of Colorectal Cancer in Family-Based, Multi-Ethnic Groups

2018 ◽  
Vol 8 (1) ◽  
pp. 10 ◽  
Author(s):  
S. Shiao ◽  
James Grayson ◽  
Chong Yu ◽  
Brandi Wasek ◽  
Teodoro Bottiglieri
Keyword(s):  
Colorectal Cancer ◽  
Ethnic Groups ◽  
Gene Environment ◽  
Family Based

scholarly journals Gene-environment interactions and predictors of breast cancer in family-based multi-ethnic groups

Oncotarget ◽  
2018 ◽  
Vol 9 (49) ◽  
pp. 29019-29035 ◽  
Author(s):  
Mildred C. Gonzales ◽  
James Grayson ◽  
Amanda Lie ◽  
Chong Ho Yu ◽  
Shyang-Yun Pamela K. Shiao
Keyword(s):  
Breast Cancer ◽  
Ethnic Groups ◽  
Gene Environment ◽  
Family Based

scholarly journals Family-based gene-environment interaction using sequence kernel association test (FGE-SKAT) for complex quantitative traits

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Chao-Yu Guo ◽  
Reng-Hong Wang ◽  
Hsin-Chou Yang
Keyword(s):  
Complex Traits ◽  
Association Studies ◽  
Association Test ◽  
Whole Genome Sequence ◽  
Environment Interaction ◽  
Genome Wide Association Studies ◽  
Whole Genome ◽  
Sequence Kernel Association Test ◽  
Gene Environment ◽  
Family Based

AbstractAfter the genome-wide association studies (GWAS) era, whole-genome sequencing is highly engaged in identifying the association of complex traits with rare variations. A score-based variance-component test has been proposed to identify common and rare genetic variants associated with complex traits while quickly adjusting for covariates. Such kernel score statistic allows for familial dependencies and adjusts for random confounding effects. However, the etiology of complex traits may involve the effects of genetic and environmental factors and the complex interactions between genes and the environment. Therefore, in this research, a novel method is proposed to detect gene and gene-environment interactions in a complex family-based association study with various correlated structures. We also developed an R function for the Fast Gene-Environment Sequence Kernel Association Test (FGE-SKAT), which is freely available as supplementary material for easy GWAS implementation to unveil such family-based joint effects. Simulation studies confirmed the validity of the new strategy and the superior statistical power. The FGE-SKAT was applied to the whole genome sequence data provided by Genetic Analysis Workshop 18 (GAW18) and discovered concordant and discordant regions compared to the methods without considering gene by environment interactions.

scholarly journals Left-Sided Colorectal Cancer Distinct in Indigenous African Patients Compared to Other Ethnic Groups in South Africa.

2021 ◽  
Author(s):  
M. McCabe ◽  
C. Penny ◽  
P. Magangane ◽  
S. Mirza ◽  
Y. Perner
Keyword(s):  
Colorectal Cancer ◽  
South Africa ◽  
Ethnic Groups ◽  
Mirna Expression ◽  
Expression Profiling ◽  
Expression Patterns ◽  
Molecular Characteristics ◽  
Anatomical Site ◽  
Molecular Features ◽  
Mirna Expression Profiling

Abstract Introduction: A large proportion of indigenous African (IA) colorectal cancer (CRC) patients in South Africa are young (<50years), with no unique histopathological or molecular characteristics. Anatomical site as well as microsatellite instability (MSI) status have shown to be associated with different clinicopathological and molecular features. This study aimed to ascertain key histopathological and miRNA expression patterns in microsatellite stable (MSS) and low-frequency MSI (MSI-L) patients, to provide insight into the mechanism of the disease. Methods: A retrospective cohort (2011-2015) of MSS/MSI-L CRC patient samples diagnosed at Charlotte Maxeke Johannesburg Academic Hospital was analyzed. Samples were categorized by site [Right colon cancer (RCC) versus left (LCC)], ethnicity [IA versus other ethnic groups (OEG)] and MSI status (MSI-L vs MSS). T-test, Fischer’s exact and Chi-square tests were conducted. Additional miRNA expression profiling was performed on IA patient samples. Results: IA patients with LCC demonstrated an increased prevalence in males, sigmoid colon, signet-ring-cell morphology, MSI-L with BAT25/26 marker instability and advanced disease association. MiRNA expression profiling revealed unique clustering, with dysregulation of let-7 and miRNA-125. Conclusion: This study revealed distinct histopathological features for LCC, and suggests BAT25/26, miRNAs let-7a-5p and miRNA-125a/b-5p as negative prognostic markers in African CRC patients. Larger confirmatory studies are recommended.

scholarly journals Evaluation of gene-environment interactions for colorectal cancer susceptibility loci using case-only and case-control designs

BMC Cancer ◽  
2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Nan Song ◽  
Jeeyoo Lee ◽  
Sooyoung Cho ◽  
Jeongseon Kim ◽  
Jae Hwan Oh ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Cancer Risk ◽  
Protective Factors ◽  
Risk Allele ◽  
Cancer Susceptibility ◽  
Case Control ◽  
Regular Exercise ◽  
Susceptibility Loci ◽  
Gene Environment ◽  
Regular Aspirin

Abstract Background Genome-wide association studies (GWAS) have identified more than 40 colorectal cancer susceptibility loci, but only a small fraction of heritability was explained. To account for missing heritability, we investigated gene-environment interactions (G × Es) between GWAS-identified single-nucleotide polymorphisms (SNPs) and established risk or protective factors for colorectal cancer using both case-only and case-control study designs. Methods Data on 703 colorectal cancer cases and 1406 healthy controls from the National Cancer Center in Korea were used. We tested interactions between 31 GWAS-identified SNPs and 13 established risk or protective factors for colorectal cancer (family history, body mass index, history of colorectal polyps, inflammatory bowel disease, and diabetes mellitus, alcohol drinking, smoking, regular exercise, regular aspirin use, postmenopausal hormone replace therapy, red meat and processed meat intake, and dairy consumption). Logistic regression models were used to assess G × Es for colorectal cancer risk. Results The SNP rs4444235 at 14q22.2 interacted with regular exercise in colorectal cancer (pcase-only = 2.4 × 10− 3, pcase-control = 1.5 × 10− 3). The risk allele (C) of rs4444235 increased the risk of colorectal cancer in regularly exercising individuals (OR = 1.47, 95% CI = 1.02–2.10) but decreased the risk in non-exercising individuals (OR = 0.76, 95% CI = 0.62–0.94). Furthermore, the G × E between the SNP rs2423279 at 20p12.3 and regular aspirin use was statistically significant (pcase-only = 7.7 × 10− 3, pcase-control = 1.6 × 10− 3). The additive effect of the risk allele (T) of rs2423279 on colorectal cancer risk was increased among regular aspirin users (OR = 4.62, 95% CI = 1.97–10.80). Conclusion Our results suggest that SNP rs4444235 at 14q22.2 and SNP rs2423279 at 20p12.3 may interact with regular exercise and aspirin use in colorectal carcinogenesis.

scholarly journals Gene–Environment Interaction Involving Recently Identified Colorectal Cancer Susceptibility Loci

2014 ◽  
Vol 23 (9) ◽  
pp. 1824-1833 ◽  
Author(s):  
Elizabeth D. Kantor ◽  
Carolyn M. Hutter ◽  
Jessica Minnier ◽  
Sonja I. Berndt ◽  
Hermann Brenner ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Cancer Susceptibility ◽  
Environment Interaction ◽  
Susceptibility Loci ◽  
Gene Environment Interaction ◽  
Gene Environment

Detection of gene-environment interactions in a family-based population using SCAD

2017 ◽  
Vol 36 (22) ◽  
pp. 3547-3559 ◽  
Author(s):  
Gwangsu Kim ◽  
Chao-Qiang Lai ◽  
Donna K. Arnett ◽  
Laurence D. Parnell ◽  
Jose M. Ordovas ◽  
...  
Keyword(s):  
Gene Environment ◽  
Family Based

Genome-wide investigation of gene–environment interactions in colorectal cancer

2012 ◽  
Vol 132 (2) ◽  
pp. 219-231 ◽  
Author(s):  
Sabine Siegert ◽  
Jochen Hampe ◽  
Clemens Schafmayer ◽  
Witigo von Schönfels ◽  
Jan-Hendrik Egberts ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Gene Environment ◽  
Genome Wide

scholarly journals Characterization of Gene–Environment Interactions for Colorectal Cancer Susceptibility Loci

2012 ◽  
Vol 72 (8) ◽  
pp. 2036-2044 ◽  
Author(s):  
Carolyn M. Hutter ◽  
Jenny Chang-Claude ◽  
Martha L. Slattery ◽  
Bethann M. Pflugeisen ◽  
Yi Lin ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Cancer Susceptibility ◽  
Susceptibility Loci ◽  
Gene Environment
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