scholarly journals The Role of SNP Interactions when Determining Independence of Novel Signals in Genetic Association Studies—An Application to ARG1 and Bronchodilator Response

2021 ◽  
Vol 11 (2) ◽  
pp. 145
Author(s):  
Ryan Walsh ◽  
Kirsten Voorhies ◽  
Merry-Lynn McDonald ◽  
Michael McGeachie ◽  
Joanne E. Sordillo ◽  
...  
Keyword(s):  
Genetic Association ◽  
Association Studies ◽  
Critical Role ◽  
Genetic Association Studies ◽  
Genome Wide Association Studies ◽  
The Novel ◽  
Simulation Studies ◽  
Nucleotide Polymorphisms ◽  
Bronchodilator Response

Genome-wide association studies (GWAS) play a critical role in identifying many loci for common diseases and traits. There has been a rapid increase in the number of GWAS over the past decade. As additional GWAS are being conducted, it is unclear whether a novel signal associated with the trait of interest is independent of single nucleotide polymorphisms (SNPs) in the same region that has been previously associated with the trait of interest. The general approach to determining whether the novel association is independent of previous signals is to examine the association of the novel SNP with the trait of interest conditional on the previously identified SNP and/or calculate linkage disequilibrium (LD) between the two SNPs. However, the role of epistasis and SNP by SNP interactions are rarely considered. Through simulation studies, we examined the role of SNP by SNP interactions when determining the independence of two genetic association signals. We have created an R package on Github called gxgRC to generate these simulation studies based on user input. In genetic association studies of asthma, we considered the role of SNP by SNP interactions when determining independence of signals for SNPs in the ARG1 gene and bronchodilator response.

scholarly journals Fine scale human genetic structure in three regions of Cameroon reveals episodic diversifying selection

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kevin K. Esoh ◽  
Tobias O. Apinjoh ◽  
Steven G. Nyanjom ◽  
Ambroise Wonkam ◽  
Emile R. Chimusa ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Ethnic Groups ◽  
Genetic Association ◽  
Association Studies ◽  
Genetic Association Studies ◽  
Genomic Region ◽  
Sub Saharan Africa ◽  
Genome Wide Association Studies ◽  
Fine Scale ◽  
Sub Saharan

AbstractInferences from genetic association studies rely largely on the definition and description of the underlying populations that highlight their genetic similarities and differences. The clustering of human populations into subgroups (population structure) can significantly confound disease associations. This study investigated the fine-scale genetic structure within Cameroon that may underlie disparities observed with Cameroonian ethnicities in malaria genome-wide association studies in sub-Saharan Africa. Genotype data of 1073 individuals from three regions and three ethnic groups in Cameroon were analyzed using measures of genetic proximity to ascertain fine-scale genetic structure. Model-based clustering revealed distinct ancestral proportions among the Bantu, Semi-Bantu and Foulbe ethnic groups, while haplotype-based coancestry estimation revealed possible longstanding and ongoing sympatric differentiation among individuals of the Foulbe ethnic group, and their Bantu and Semi-Bantu counterparts. A genome scan found strong selection signatures in the HLA gene region, confirming longstanding knowledge of natural selection on this genomic region in African populations following immense disease pressure. Signatures of selection were also observed in the HBB gene cluster, a genomic region known to be under strong balancing selection in sub-Saharan Africa due to its co-evolution with malaria. This study further supports the role of evolution in shaping genomes of Cameroonian populations and reveals fine-scale hierarchical structure among and within Cameroonian ethnicities that may impact genetic association studies in the country.

scholarly journals Smad7 and Colorectal Carcinogenesis: A Double-Edged Sword

Cancers ◽  
2019 ◽  
Vol 11 (5) ◽  
pp. 612 ◽  
Author(s):  
Edoardo Troncone ◽  
Giovanni Monteleone
Keyword(s):  
Immune Cells ◽  
Transforming Growth Factor ◽  
Intestinal Inflammation ◽  
Association Studies ◽  
Cell Subset ◽  
Colorectal Carcinogenesis ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Chronic Intestinal Inflammation

Colorectal carcinogenesis is a complex process in which many immune and non-immune cells and a huge number of mediators are involved. Among these latter factors, Smad7, an inhibitor of the transforming growth factor (TGF)-β1 signaling that has been involved in the amplification of the inflammatory process sustaining chronic intestinal inflammation, is supposed to make a valid contribution to the growth and survival of colorectal cancer (CRC) cells. Smad7 is over-expressed by tumoral cells in both sporadic CRC and colitis-associated CRC, where it sustains neoplastic processes through activation of either TGFβ-dependent or non-dependent pathways. Consistently, genome-wide association studies have identified single nucleotide polymorphisms of the Smad7 gene associated with CRC and shown that either amplification or deletion of the Smad7 gene associates with a poor prognosis or better outcome, respectively. On the other hand, there is evidence that over-expression of Smad7 in immune cells infiltrating the inflamed gut of patients with inflammatory bowel disease can elicit anti-tumor responses, with the down-stream effect of attenuating CRC cell growth. Taken together, these observations suggest a double role of Smad7 in colorectal carcinogenesis, which probably depends on the cell subset and the biological context analyzed. In this review, we summarize the available evidences about the role of Smad7 in both sporadic and colitis-associated CRC.

scholarly journals A systematic review and meta-analysis of genetic association studies for the role of inflammation and the immune system in diabetic nephropathy

2017 ◽  
Vol 10 (3) ◽  
pp. 293-300 ◽  
Author(s):  
Maria Tziastoudi ◽  
Ioannis Stefanidis ◽  
Georgios M. Hadjigeorgiou ◽  
Konstantinos Stravodimos ◽  
Elias Zintzaras
Keyword(s):  
Systematic Review ◽  
Diabetic Nephropathy ◽  
Immune System ◽  
Genetic Association ◽  
Association Studies ◽  
Meta Analysis ◽  
Genetic Association Studies

Efficient estimation of disease odds ratios for follow-up genetic association studies

2017 ◽  
Vol 28 (7) ◽  
pp. 1927-1941
Author(s):  
Jiyuan Hu ◽  
Wei Zhang ◽  
Xinmin Li ◽  
Dongdong Pan ◽  
Qizhai Li
Keyword(s):  
Genetic Association ◽  
Association Studies ◽  
Genetic Association Studies ◽  
Efficient Estimation ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Odds Ratios ◽  
Genome Wide ◽  
Follow Up Studies

In the past decade, genome-wide association studies have identified thousands of susceptible variants associated with complex human diseases and traits. Conducting follow-up genetic association studies has become a standard approach to validate the findings of genome-wide association studies. One problem of high interest in genetic association studies is to accurately estimate the strength of the association, which is often quantified by odds ratios in case-control studies. However, estimating the association directly by follow-up studies is inefficient since this approach ignores information from the genome-wide association studies. In this article, an estimator called GFcom, which integrates information from genome-wide association studies and follow-up studies, is proposed. The estimator includes both the point estimate and corresponding confidence interval. GFcom is more efficient than competing estimators regarding MSE and the length of confidence intervals. The superiority of GFcom is particularly evident when the genome-wide association study suffers from severe selection bias. Comprehensive simulation studies and applications to three real follow-up studies demonstrate the performance of the proposed estimator. An R package, “GFcom”, implementing our method is publicly available at https://github.com/JiyuanHu/GFcom .

scholarly journals Lack of Association betweenPRNPM129V Polymorphism and Multiple Sclerosis, Mild Cognitive Impairment, Alcoholism and Schizophrenia in a Korean Population

2010 ◽  
Vol 28 (5) ◽  
pp. 315-321 ◽  
Author(s):  
Ihn-Geun Choi ◽  
Sung-Il Woo ◽  
Ho Jin Kim ◽  
Dai-Jin Kim ◽  
Byung Lae Park ◽  
...  
Keyword(s):  
Multiple Sclerosis ◽  
Cognitive Impairment ◽  
Mild Cognitive Impairment ◽  
Genetic Association ◽  
Prion Diseases ◽  
Association Studies ◽  
Genetic Association Studies ◽  
Korean Population ◽  
Weak Influence

The genetic variant at codon 129 (M129V) of the prion protein gene (PRNP) is considered to be a major genetic risk factor for prion diseases. In this study, we examined the possible genetic association ofPRNP*129Valwith multiple sclerosis (MS,n= 681), mild cognitive impairment (MCI,n= 801), alcoholism (n= 761) and schizophrenia (n= 715) in a Korean population, and compared the data with previous genetic association studies of the variant. The minor allele frequency ofPRNP*129Val(MAF = 0.025) was significantly lower in Korean population (n= 2,479) compared to Caucasian populations (P< 0.0001), suggestive of a weak influence of the variant in the previous population. Statistical analysis revealed no significant association betweenPRNP*129Valand MS (P = 0.76), MCI (P = 0.46), alcoholism (P = 0.84) and schizophrenia (P = 0.69). These findings were discussed in the context of prior inconsistent reports on the role ofPRNP*129Valpolymorphism in several diseases. Results from this study may provide further evidence thatPRNP M129Vis not a genetic susceptibility factor for MS, MCI, alcoholism and schizophrenia in a Korean population.

scholarly journals Carotid Artery Atherosclerosis: A Review on Heritability and Genetics

2018 ◽  
Vol 21 (5) ◽  
pp. 333-346 ◽  
Author(s):  
Bianka Forgo ◽  
Emanuela Medda ◽  
Anita Hernyes ◽  
Laszlo Szalontai ◽  
David Laszlo Tarnoki ◽  
...  
Keyword(s):  
Association Studies ◽  
Genetic Association Studies ◽  
Intima Media Thickness ◽  
Carotid Intima Media Thickness ◽  
Phenotypic Variance ◽  
Genome Wide Association Studies ◽  
Genetic Associations ◽  
Carotid Artery Atherosclerosis ◽  
Meta Analyses

Carotid atherosclerosis (CAS) is associated with increased cardiovascular risk, and therefore, assessing the genetic versus environmental background of CAS traits is of key importance. Carotid intima-media-thickness and plaque characteristics seem to be moderately heritable, with remarkable differences in both heritability and presence or severity of these traits among ethnicities. Although the considerable role of additive genetic effects is obvious, based on the results so far, there is an important emphasis on non-shared environmental factors as well. We aimed to collect and summarize the papers that investigate twin and family studies assessing the phenotypic variance attributable to genetic associations with CAS. Genes in relation to CAS markers were overviewed with a focus on genetic association studies and genome-wide association studies. Although the role of certain genes is confirmed by studies conducted on large populations and meta-analyses, many of them show conflicting results. A great focus should be on future studies elucidating the exact pathomechanism of these genes in CAS in order to imply them as novel therapeutic targets.

scholarly journals Role of Interleukin- (IL-) 17 in the Pathogenesis and Targeted Therapies in Spondyloarthropathies

2018 ◽  
Vol 2018 ◽  
pp. 1-8 ◽  
Author(s):  
I-Tsu Chyuan ◽  
Ji-Yih Chen
Keyword(s):  
Animal Studies ◽  
Association Studies ◽  
Critical Role ◽  
Genetic Association Studies ◽  
Joint Inflammation ◽  
New Bone Formation ◽  
Unique Type ◽  
Targeting Therapy ◽  
Bone Damage

Spondyloarthropathy (SpA) is a unique type of joint inflammation characterized by coexisting erosive bone damage and pathological new bone formation. Previous genetic association studies have demonstrated that several cytokine pathways play a critical role in the pathogenesis of ankylosing spondylitis (AS), psoriatic arthritis (PsA), and other types of SpA. In addition to several well-known proinflammatory cytokines, recent studies suggest that IL-17 plays a pivotal role in the pathogenesis of SpA. Further evidence from human and animal studies have defined that IL-17 and IL-17-producing cells contribute to tissue inflammation, autoimmunity, and host defense, leading to the following pathologic events associated with SpA. Recently, several clinical trials targeting IL-17 pathways demonstrated the positive response of IL-17 blockade in treating AS, indicating a great potential of IL-17-targeting therapy in SpA. In this review article, we have discussed the contributing role of IL-17 and different IL-17-producing cells in the pathogenesis of SpA and provided an outline of therapeutic application of the IL-17 blockade in the treatment of SpA. Other targeted cytokines associated with IL-17 axis in SpA will also be included.

scholarly journals Systemic Sclerosis is a Complex Disease Associated Mainly with Immune Regulatory and Inflammatory Genes

2014 ◽  
Vol 8 (1) ◽  
pp. 29-42 ◽  
Author(s):  
Jingxiao Jin ◽  
Chou Chou ◽  
Maria Lima ◽  
Danielle Zhou ◽  
Xiaodong Zhou
Keyword(s):  
Systemic Sclerosis ◽  
Genetic Association ◽  
Dna Cleavage ◽  
Complex Disease ◽  
Association Studies ◽  
Genetic Association Studies ◽  
Genome Wide Association Studies ◽  
Functional Changes ◽  
Circulating Autoantibodies ◽  
Genetic Contributions

Systemic sclerosis (SSc) is a fibrotic and autoimmune disease characterized clinically by skin and internal organ fibrosis and vascular damage, and serologically by the presence of circulating autoantibodies. Although etiopathogenesis is not yet well understood, the results of numerous genetic association studies support genetic contributions as an important factor to SSc. In this paper, the major genes of SSc are reviewed. The most recent genome-wide association studies (GWAS) are taken into account along with robust candidate gene studies. The literature search was performed on genetic association studies of SSc in PubMed between January 2000 and March 2014 while eligible studies generally had over 600 total participants with replication. A few genetic association studies with related functional changes in SSc patients were also included. A total of forty seven genes or specific genetic regions were reported to be associated with SSc, although some are controversial. These genes include HLA genes, STAT4, CD247, TBX21, PTPN22, TNFSF4, IL23R, IL2RA, IL-21, SCHIP1/IL12A, CD226, BANK1, C8orf13-BLK, PLD4, TLR-2, NLRP1, ATG5, IRF5, IRF8, TNFAIP3, IRAK1, NFKB1, TNIP1, FAS, MIF, HGF, OPN, IL-6, CXCL8, CCR6, CTGF, ITGAM, CAV1, MECP2, SOX5, JAZF1, DNASEIL3, XRCC1, XRCC4, PXK, CSK, GRB10, NOTCH4, RHOB, KIAA0319, PSD3 and PSOR1C1. These genes encode proteins mainly involved in immune regulation and inflammation, and some of them function in transcription, kinase activity, DNA cleavage and repair. The discovery of various SSc-associated genes is important in understanding the genetics of SSc and potential pathogenesis that contribute to the development of this disease.

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