scholarly journals Using imputed genotype data in the joint score tests for genetic association and gene-environment interactions in case-control studies

2017 ◽  
Vol 42 (2) ◽  
pp. 146-155 ◽  
Author(s):  
Minsun Song ◽  
William Wheeler ◽  
Neil E. Caporaso ◽  
Maria Teresa Landi ◽  
Nilanjan Chatterjee
Keyword(s):  
Genetic Association ◽  
Case Control ◽  
Genotype Data ◽  
Case Control Studies ◽  
Score Tests ◽  
Gene Environment

scholarly journals Using imputed genotype data in the joint score tests for genetic association and gene-environment interactions in case-control studies

2016 ◽  
Author(s):  
Minsun Song ◽  
William Wheeler ◽  
Neil E. Caporaso ◽  
Maria Teresa Landi ◽  
Nilanjan Chatterjee
Keyword(s):  
Genetic Association ◽  
Association Studies ◽  
Case Control ◽  
Maximum Likelihood Estimates ◽  
Genome Wide Association ◽  
Alternative Methods ◽  
Case Control Studies ◽  
Score Tests ◽  
Gene Environment ◽  
Genome Wide

AbstractBackgroundGenome-wide association studies (GWAS) are now routinely imputed for untyped SNPs based on various powerful statistical algorithms for imputation trained on reference datasets. The use of predicted allele count for imputed SNPs as the dosage variable is known to produce valid score test for genetic association.MethodsIn this paper, we investigate how to best handle imputed SNPs in various modern complex tests for genetic association incorporating gene-environment interactions. We focus on case-control association studies where inference in an underlying logistic regression model can be performed using alternative methods that rely on varying degree on an assumption of gene-environment independence in the underlying population. As increasingly large scale GWAS are being performed through consortia effort where it is preferable to share only summary-level information across studies, we also describe simple mechanisms for implementing score-tests based on standard meta-analysis of “one-step” maximum-likelihood estimates across studies.ResultsApplications of the methods in simulation studies and a dataset from genome-wide association study of lung cancer illustrate ability of the proposed methods to maintain type-I error rates for underlying testing procedures. For analysis of imputed SNPs, similar to typed SNPs, retrospective methods can lead to considerable efficiency gain for modeling of gene-environment interactions under the assumption of gene-environment independence.ConclusionsProposed methods allow valid analysis of imputed SNPs in case-control studies of gene-environment interaction using alternative strategies that had been earlier available only for genotyped SNPs.

scholarly journals Case-Control Studies of Gene-Environment Interaction: Bayesian Design and Analysis

Biometrics ◽  
2009 ◽  
Vol 66 (3) ◽  
pp. 934-948 ◽  
Author(s):  
Bhramar Mukherjee ◽  
Jaeil Ahn ◽  
Stephen B. Gruber ◽  
Malay Ghosh ◽  
Nilanjan Chatterjee
Keyword(s):  
Case Control ◽  
Environment Interaction ◽  
Case Control Studies ◽  
Bayesian Design ◽  
Gene Environment Interaction ◽  
Gene Environment

Assessment of the relationship between methylenetetrahydrofolate reductase polymorphism and acute lymphoblastic leukemia: Evidence from an updated meta-analysis

2020 ◽  
Vol 26 (7) ◽  
pp. 1598-1610
Author(s):  
Rim Frikha
Keyword(s):  
Acute Lymphoblastic Leukemia ◽  
Methylenetetrahydrofolate Reductase ◽  
Lymphoblastic Leukemia ◽  
Meta Analysis ◽  
Case Control ◽  
C677t Polymorphism ◽  
Case Control Studies ◽  
Gene Environment ◽  
Reductase Gene ◽  
The Relationship

Objective The methylenetetrahydrofolate reductase gene C677T polymorphism is closely related to the acute lymphoblastic leukemia. Several case–control studies have investigated this association; however, no conclusions could be drawn. A comprehensive updated meta-analysis is established to explain these contradictions and clarify the overall impact of this variant on the susceptibility to acute lymphoblastic leukemia. Methods Electronic searches were conducted to select published studies prior to June 2018. Pooled odds ratios and stratification analysis were performed under different genetic comparison models, age, and ethnicity. Results Totally, 66 case–control studies including 9619 acute lymphoblastic leukemia cases and 17,396 controls were selected. Our analyses showed that methylenetetrahydrofolate reductase C677T polymorphism was protective mainly in Asian and European countries, under all genetic models and regardless of age, but leukemogenic in mixed population. Conclusion Thus, C677T polymorphism may be a promising acute lymphoblastic leukemia biomarker, but they should be interpreted with caution considering other factors such as folic acid intake, gene–gene and gene–environment interactions.

Retrospective versus prospective score tests for genetic association with case‐control data

Biometrics ◽  
2020 ◽  
Author(s):  
Yukun Liu ◽  
Pengfei Li ◽  
Lei Song ◽  
Kai Yu ◽  
Jing Qin
Keyword(s):  
Genetic Association ◽  
Case Control ◽  
Control Data ◽  
Score Tests

scholarly journals Association of the MTHFR 677C>T and 1298A>C polymorphisms and male infertility risk: a meta-analysis

2020 ◽  
Vol 18 (1) ◽  
Author(s):  
Fereshteh Aliakbari ◽  
Farkhondeh Pouresmaeili ◽  
Nahal Eshghifar ◽  
Zahra Zolghadr ◽  
Faezeh Azizi
Keyword(s):  
Male Infertility ◽  
Methylenetetrahydrofolate Reductase ◽  
Meta Analysis ◽  
Case Control ◽  
Inclusion Criteria ◽  
Case Control Studies ◽  
Crude Odds Ratio ◽  
Mthfr Polymorphism ◽  
Gene Environment ◽  
The Relationship

Abstract Background and objectives One of the possible male sterility risk factors are polymorphisms of Methylenetetrahydrofolate reductase (MTHFR). However, the epidemiologic investigations described inconsistent results regarding MTHFR polymorphism and the risk of male infertility. For that reason, we carried out a meta-analysis of published case-control studies to re-examine the controversy. Methods Electronic searches of Cochrane, EMBASE, Google Scholar, and PubMed were conducted to select eligible studies for this meta-analysis (updated to May 2019). According to our exclusion and inclusion criteria, only high-quality studies that remarked the association between MTHFR polymorphisms and male infertility risk were included. The Crude odds ratio (OR) with a confidence interval of 95% (CI) was used to assess the relationship between MTHFR polymorphism and male infertility risk. Results Thirty-four case-control studies with 9662 cases and 9154 controls concerning 677C/T polymorphism and 22 case-control studies with 5893 cases and 6303 controls concerning 1298A/C polymorphism were recruited. Both MTHFR polymorphisms had significant associations with male infertility risk (CT + TT vs. CC: OR = 1.37, 95% CI: 1.21–1.55, P = 0.00, I2 = 41.9%); (CC vs. CA + AA: OR = 0.82, 95% CI: 0.52–1.30, P = 0.04, I2 = 50.1%). Further, when stratified by ethnicity, the significant association results were observed in Asians and Caucasians for 677C/T and just Asians for 1298A/C. Conclusions Some of MTHFR polymorphisms like MTHFR 677C > T are associated with an elevated male infertility risk. To confirm our conclusion and to provide more accurate and complete gene-environment communication with male infertility risk, more analytical studies are needed.

scholarly journals High-temperature requirement factor A1 rs11200638 polymorphism and age-related macular degenerative from a comprehensive analysis about 15316 subjects

2020 ◽  
Author(s):  
Ying Liu ◽  
Huipeng Jin ◽  
Dong Wei ◽  
Wenxiu Li
Keyword(s):  
High Temperature ◽  
Meta Analysis ◽  
Case Control ◽  
Dominant Model ◽  
Case Control Studies ◽  
Temperature Requirement ◽  
Age Related ◽  
Gene Environment ◽  
Increased Risk ◽  
Taqman Pcr

Abstract Background The high-temperature requirement factor A1 (HTRA1) gene at the 10q26 locus has been associated with age-related macular degenerative (AMD) risk, with the significantly associated polymorphism being (rs11200638, -625G/A), however, above association is not consistent. We investigated an updated meta-analysis to evaluate the association between rs11200638 polymorphism and AMD risk thoroughly addressing this issue. Methods An identification was covered with the Pubmed and Chinese Wanfang databases through 27th Jan, 2020. Odds ratios (OR) and 95% confidence intervals (CI) were used to assess the strength of associations. After a thorough and meticulous search, 35 different articles (33 case-control studies with HWE, 22 case-control studies about wet/dry AMD) were retrieved. Results Individuals carrying A-allele or AA genotype may have an increased risk to be AMD disease. For example, there has a significantly increased relationship between rs11200638 polymorphism and AMD both for Asians (OR: 2.50, 95%CI: 2.22-2.80 for A-allele vs. G-allele) and Caucasians (OR: 2.11, 95%CI: 1.43-3.13 for A-allele vs. G-allele). Moreover, a similar trend in the source of control subgroup was detected. To classify the type of AMD, increased association was also observed in both wet (OR: 3.40, 95%CI: 2.90-3.99 for dominant model) and dry (OR: 2.08, 95%CI: 1.24-3.48 for dominant model) AMD. Finally, based on the different genotyping methods, increased relationships were identified by sequencing, TaqMan, PCR-RFLP. Conclusions Our present meta-analysis suggests that the HTRA1 rs11200638 polymorphism are potentially associated with the risk of AMD development, especially about individuals carrying A-allele or AA genotype, who may be as identified targets to detect and intervene in advance. Further studies using larger sample sizes and including information about gene-environment interactions should be conducted to elucidate.

scholarly journals High-temperature requirement factor A1 rs11200638 polymorphism and age-related macular degenerative from a comprehensive analysis about 15316 subjects

2020 ◽  
Author(s):  
Ying Liu ◽  
Huipeng Jin ◽  
Dong Wei ◽  
Wenxiu Li
Keyword(s):  
High Temperature ◽  
Meta Analysis ◽  
Case Control ◽  
Dominant Model ◽  
Case Control Studies ◽  
Temperature Requirement ◽  
Age Related ◽  
Gene Environment ◽  
Increased Risk ◽  
Taqman Pcr

Abstract Background: The high-temperature requirement factor A1 (HTRA1) gene at the 10q26 locus has been associated with age-related macular degenerative (AMD) risk, with the significantly associated polymorphism being (rs11200638, -625G/A), however, above association is not consistent. We investigated an updated meta-analysis to evaluate the association between rs11200638 polymorphism and AMD risk thoroughly addressing this issue. Methods: An identification was covered with the Pubmed and Chinese Wanfang databases through 27th Jan, 2020. Odds ratios (OR) and 95% confidence intervals (CI) were used to assess the strength of associations. After a thorough and meticulous search, 35 different articles (33 case-control studies with HWE, 22 case-control studies about wet/dry AMD) were retrieved. Results: Individuals carrying A-allele or AA genotype may have an increased risk to be AMD disease. For example, there has a significantly increased relationship between rs11200638 polymorphism and AMD both for Asians (OR: 2.51, 95%CI: 2.22-2.83 for A-allele vs. G-allele) and Caucasians (OR: 2.63, 95%CI: 2.29-3.02 for A-allele vs. G-allele). Moreover, a similar trend in the source of control subgroup was detected. To classify the type of AMD, increased association was also observed in both wet (OR: 3.40, 95%CI: 2.90-3.99 for dominant model) and dry (OR: 2.08, 95%CI: 1.24-3.48 for dominant model) AMD. Finally, based on the different genotyping methods, increased relationships were identified by sequencing, TaqMan, PCR-RFLP and RT-PCR. Conclusions: Our present meta-analysis suggests that the HTRA1 rs11200638 polymorphism are potentially associated with the risk of AMD development, especially about individuals carrying A-allele or AA genotype, who may be as identified targets to detect and intervene in advance. Further studies using larger sample sizes and including information about gene-environment interactions should be conducted to elucidate.

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