Explore chapters and articles related to this topic
Bioinformatics and Applications in Biotechnology
Published in Ram Chandra, R.C. Sobti, Microbes for Sustainable Development and Bioremediation, 2019
SNP is a single nucleotide DNA variation on the genomes of different members of a species and occurring ay specific positions. They occur due to substitutions, deletions, and insertions and give a fundamental insight into allelic variations and individual, ethnic predispositions. A major effort is being made to correlate the SNP variations and their contributions to disease and health in different individuals. The international HapMap project aims to develop a halotype map of human genome to find genetic variations responsible for disease, response to drugs, environmental factor, etc. In phase III of the project, 11 global ancestry groups have been assembled: ASW (African ancestry in Southwest USA); CEU (Utah residents with Northern and Western European ancestry from the CEPH collection); CHB (Han Chinese in Beijing, China); CHD (Chinese in Metropolitan Denver, Colorado); GIH (Gujarati Indians in Houston, Texas); JPT (Japanese in Tokyo, Japan); LWK (Luhya in Webuye, Kenya); MEX (Mexican ancestry in Los Angeles, California); MKK (Maasai in Kinyawa, Kenya); TSI (Tuscans in Italy); YRI (Yoruba in Ibadan, Nigeria) (Altshuler et al., 2010). We have also undertaken a study on genetic variations in Arg5Pro and Leu6Pro, which modulate the structure and activity of GPX1 and increase genetic risk for vitiligo (Mansuri et al., 2016). Bioinformatics tools of sequence alignment, modeling, etc. were extensively used in this study.
Graphical Models in Genetics, Genomics, and Metagenomics
Published in Marloes Maathuis, Mathias Drton, Steffen Lauritzen, Martin Wainwright, Handbook of Graphical Models, 2018
Genome-wide association studies (GWAS) attempt to identify commonly occurring genetic variants that contribute to disease risk, and so far have identified thousands of SNPs that are associated with many human traits [5]. In its simplest form, GWAS analysis is formulated as a sequence of logistic regressions where the disease status from all individuals serve as the response and each genotyped SNP is the covariate. The resulting p-value for each SNP is then corrected for multiple comparisons using e.g. the Bonferroni adjustment. Although this standard approach has the power of identifying common SNPs with strong effects on phenotypes, it ignores the possible synergistic effects of genetic variants on disease phenotypes. Therefore network-assisted methods have been proposed to prioritize the GWASresults and to identify subnetwork of genes that are associated with phenotypes. The rationale of such network-based methods is that topologically related genetic variants are more likely to produce similar phenotypic effects.
The relationship polymorphism of gene RFC1 A80G and NSCLP in Sumatera Utara, Indonesia
Published in Cut Adeya Adella, Stem Cell Oncology, 2018
B.Y. Febrianto, U.A. Tarigan, F.B. Buchari, Hidayat
Nowadays, researchers have investigated the association of Single Nucleotide Polymorphism (SnPs) with the occurrence of a disease or drug side effects due to amino acid substitution caused and affecting the activity of the protein produced (Mostowska et al., 2010; Hasni et al., 2016). This study analyses the relationship of polymorphism of the RFC1 gene on the long arm of chromosome 21 (21q22.2-q22.3) exon 2, which causes the amino acid substitution of histidine to arginine (H27R; rs1051266) due to the substitution of nucleotide 80 adenine to guanine (A80G) (Wang et al., 2009; Yee et al., 2010). These RFC1 proteins play a role in regulating folate transport to red blood cells; in a previous study it was found that subjects with RFC1 alleles G experienced a decrease in plasma folic acid and increased levels of homocysteine due to negative regulation caused by the RFC1 protein in allele G patients (Cai et al., 2016).
The polymorphisms in cGAS-STING pathway are associated with mitochondrial DNA copy number in coke oven workers
Published in International Journal of Environmental Health Research, 2022
Xiaohua Liu, Xinling Li, Wan Wei, Yahui Fan, Zhifeng Guo, Xiaoran Duan, Xiaoshan Zhou, Yongli Yang, Wei Wang
Since mitochondrial DNA (mtDNA) has a high copy number and lacks repairing mechanisms, the mtDNAcn is a sensitive genotoxic stress sentinel upon PAHs exposure. It has been shown that PAHs exposure could lead to mitochondria dysfunction (Wang et al. 2018; Lindberg and Di Giulio 2019) decrease the mitochondrial membrane potential (Ling et al. 2017), and affect mitophagy (Das et al. 2017). When the mitochondrial permeability transition pore changes or apoptosis occur, mtDNA can be released or extruded into the cytoplasm from mitochondria (Garcia and Chavez 2007; McArthur et al. 2018; Riley et al. 2018). The cyclic GMP-AMP synthase (cGAS) is able to recognize and bind to the released mtDNA, then activates the cGAS-stimulator of interferon genes (STING) pathway resulting in interferon stimulated gene (ISG) expression, ultimately promoting innate immunity and influencing nuclear DNA repair (Wu et al. 2019). The mechanisms of mitochondrial DNA replication are complex which regulated by nuclear genes and mitochondrial DNA (Al-Kafaji et al. 2018). Hence, STING and cGAS genes are likely involved in the maintenance of mtDNAcn through DNA damage repair or cell cycle change. Single nucleotide polymorphism (SNP) is the single base variation in genes, which could change the gene expression or the protein function. Our previous studies have shown that polymorphisms in cGAS-STING genes influence telomere shortening in coke oven workers (Duan et al. 2020). However, whether the polymorphisms in cGAS-STING genes are associated with mtDNAcn in coke oven workers remains unknown.
The association between polymorphisms in miRNA and the cholinesterase activity of workers in an omethoate-exposed environment
Published in International Journal of Environmental Health Research, 2022
Kaili Zou, Xiaoshan Zhou, Wei Wang, Liuhua Shi, Xiaoli Fu
Single nucleotide polymorphisms (SNPs) are the most common type of human genetic variation and contribute to differences in human phenotypes. SNPs are DNA sequence polymorphism caused by the transition, transversion, insertion, or deletion of a single base at the level of the genome. Evidence has shown that SNPs in miRNAs may potentially alter multiple biological processes through affecting the process and/or selection of miRNA’s target (Duan et al. 2007). A growing body of studies has also shown that SNPs in miRNA genes could potentially affect the risk of human diseases through regulating expression of miRNA or its target genes (Di Leva et al. 2014; Mullany et al. 2015). The results of our previous studies suggest that the TERT rs2736098 and P21 rs1801270 polymorphism loci are related to a decrease of ChE activity in omethoate-exposed workers (Ding et al. 2018; Duan et al. 2018). In an omethoate-exposed environment, the role of miRNAs polymorphisms in cholinesterase activity of the exposed workers is still unknown.
Association of semenogelin (SEMG) gene variants in idiopathic male infertility in Chinese-Han population
Published in Journal of Toxicology and Environmental Health, Part A, 2019
Jing Wu, Xingxuan Dong, Kaifan Liu, Yankai Xia, Xinru Wang, Ouxi Shen, Xinliang Ding, Jie Zhang
Genomic DNA was isolated from coagulated blood by proteinase K digestion and phenol–chloroform extraction (Shen et al. 2004). SNP analysis was carried out using TaqMan Universal PCR Master Mix and TaqMan SNPs Genotyping Assays (Applied Biosystems, USA), employing pre-designed and validated primers and probes presented in Table 1. The probes were conjugated with HEX-MGB or FAM-MGB dyes, one for each allele. Subsequently, the probe SNP mixture was subjected to PCR for denaturation 30 sec at 95°C, 34 cycles with 10 sec annealing at 95°C and extension at 72°C for 10 min using an MJ PTC-200 PCR Detection Analyzer (Applied Biosystems). 7900HT Sequencing Detection System (Applied Biosystems) distributed data points were obtained according to signals generated depending upon the allele composition in each sample. For quality control, 5% of samples were randomly selected and confirmed by sequencing. These results were 100% concordant.