Characterization Of Genetic Polymorphisms Research Articles

Characterization of genetic polymorphisms in oral cancer-related genes pertaining to oxidative stress, carcinogen detoxifying, and DNA repair: A case-control study.

The genetic polymorphism in the DNA repair and maintenance genes leads to mutations and deregulated growth hormones which have implications in cancer. Apart from identified carcinogens such as tobacco, specific genetic polymorphisms correspond to an individual's risk of oral cancer. The current study aims at identification of differences in genetic polymorphisms in subjects with and without oral cancer in Karad, India. The aim of the study was to characterize genetic polymorphisms in oral cancer-related genes pertaining to oxidative stress, carcinogen detoxifying, and DNA repair. A hospital-based case-control was conducted with 150 subjects sorted into cases (n = 75) and controls (n = 75). The polymerase chain reaction-based restriction fragment length polymorphism assay was used to genotype the polymorphisms of selected DNA repair, detoxifying, and oxidative stress-related genes. In the cases group, among the DNA repair set, Gene-1 (XRCC1), Gene-3 (XRCC3), Xeroderma Pigmentosum Group-D gene (XPD), and human 8-oxoguanine DNA glycosylase (hOGG1) showed significant genetic polymorphism. Similarly, the genetic polymorphism in the carcinogen detoxifying genes-n-acetyl transferase, GSTP1, and oxidative stress-related gene catalase were noted. The Cramer's V/odds ratio was applied to estimate the association of genetic risk factors with oral cancer. The polymorphisms of XRCC1, XRCC3, XPD, and hOGG1 genes were associated with a higher susceptibility to oral cancer as compared to controls. This information may be a useful novel marker in oral oncology for primary prevention and intervention.

Characterization of genetic polymorphisms in Nigerians residing in Guangzhou using massively parallel sequencing

African populations exhibit extensive linguistic and cultural diversity but are less studied from a population genetic standpoint. Although much genetic data on admixed African individuals, such as African Americans, have been published, genetic polymorphism data, especially that based on sequence-based typing, are still insufficient in indigenous Africans. In this study, we examined the genetic diversity of 85 Nigerians residing in Guangzhou, China. Forensically relevant genetic markers, including autosomal short tandem repeats (A-STRs), X-chromosomal STRs (X-STRs), Y-chromosomal STRs (Y-STRs), and identity-informative single nucleotide polymorphisms (iiSNPs) were genotyped to uncover the genetic polymorphisms of this population. Sequence-based allelic variations were observed in 22 A-STRs, ten Y-STRs, and four X-STRs. Using massively parallel sequencing (MPS), the allele number increased from 475 length-based alleles to 683 sequence-based alleles. Compared to other populations, the overall observed heterozygosity of the 27 A-STRs was the highest in Nigerians, which reflected the higher genetic diversity of this population. The combined match probability of the 27 A-STRs was low at 9.06 × 10-38. When both A-STRs and iiSNPs were considered, the cumulative discrimination power, and combined power of exclusion for duo and trio paternity testing was 1–2.97 × 10-57, 1–2.20 × 10-10 and 1–4.61 × 10-17, respectively, which demonstrated that the STRs and SNPs analyzed here can be applied to forensic investigations. In summary, this study uncovers the genetic features of the Nigerian population and provides valuable frequency data for forensic applications.

Osteoimmunology of Oral and Maxillofacial Diseases: Translational Applications Based on Biological Mechanisms.

The maxillofacial skeleton is highly dynamic and requires a constant equilibrium between the bone resorption and bone formation. The field of osteoimmunology explores the interactions between bone metabolism and the immune response, providing a context to study the complex cellular and molecular networks involved in oro-maxillofacial osteolytic diseases. In this review, we present a framework for understanding the potential mechanisms underlying the immuno-pathobiology in etiologically-diverse diseases that affect the oral and maxillofacial region and share bone destruction as their common clinical outcome. These otherwise different pathologies share similar inflammatory pathways mediated by central cellular players, such as macrophages, T and B cells, that promote the differentiation and activation of osteoclasts, ineffective or insufficient bone apposition by osteoblasts, and the continuous production of osteoclastogenic signals by immune and local stromal cells. We also present the potential translational applications of this knowledge based on the biological mechanisms involved in the inflammation-induced bone destruction. Such applications can be the development of immune-based therapies that promote bone healing/regeneration, the identification of host-derived inflammatory/collagenolytic biomarkers as diagnostics tools, the assessment of links between oral and systemic diseases; and the characterization of genetic polymorphisms in immune or bone-related genes that will help diagnosis of susceptible individuals.

Genotyping-by-Sequencing on the Ion Torrent Platform in Barley.

The characterization of genetic polymorphism is a crucial step in both genetic studies and breeding programs. Genotyping-by-sequencing (GBS) constitutes one of the most attractive approaches for this purpose, especially in a genome as large as that of barley. The genome sequencing project undertaken by the International Barley Sequencing Consortium (IBSC) has produced a structured reference genome for the cultivar Morex [1] that can serve as an excellent resource for the analysis of GBS data. The genome assembly for this species[2] is thought to adequately capture the gene-rich portion of the genome (~80% of the entire genome). In this chapter, we describe the entire GBS process, from library preparation to the analysis of read data to produce a high-quality catalog of single nucleotide polymorphism (SNP) markers using the barley reference genome.

Architecture of polymorphisms in the human genome reveals functionally important and positively selected variants in immune response and drug transporter genes

BackgroundGenetic polymorphisms can contribute to phenotypic differences amongst individuals, including disease risk and drug response. Characterization of genetic polymorphisms that modulate gene expression and/or protein function may facilitate the identification of the causal variants. Here, we present the architecture of genetic polymorphisms in the human genome focusing on those predicted to be potentially functional/under natural selection and the pathways that they reside.ResultsIn the human genome, polymorphisms that directly affect protein sequences and potentially affect function are the most constrained variants with the lowest single-nucleotide variant (SNV) density, least population differentiation and most significant enrichment of rare alleles. SNVs which potentially alter various regulatory sites, e.g. splicing regulatory elements, are also generally under negative selection.Interestingly, genes that regulate the expression of transcription/splicing factors and histones are conserved as a higher proportion of these genes is non-polymorphic, contain ultra-conserved elements (UCEs) and/or has no non-synonymous SNVs (nsSNVs)/coding INDELs. On the other hand, major histocompatibility complex (MHC) genes are the most polymorphic with SNVs potentially affecting the binding of transcription/splicing factors and microRNAs (miRNA) exhibiting recent positive selection (RPS). The drug transporter genes carry the most number of potentially deleterious nsSNVs and exhibit signatures of RPS and/or population differentiation. These observations suggest that genes that interact with the environment are highly polymorphic and targeted by RPS.ConclusionsIn conclusion, selective constraints are observed in coding regions, master regulator genes, and potentially functional SNVs. In contrast, genes that modulate response to the environment are highly polymorphic and under positive selection.

Genetic Susceptibility to Norovirus GII.4 Sydney Strain Infections in Taiwanese Children.

A comprehensive evaluation of associations between the susceptibility to norovirus infections and histo-blood group antigens is not available in the Taiwanese population, in which the nonsecretor phenotype is absent. A 1:1 matched case-control study was conducted in northern Taiwan from February 2013 to December 2014 when an epidemic of norovirus infection occurred. Cases were children <18 years old who were hospitalized because of diarrhea and were found to have laboratory-confirmed norovirus infections. Controls were healthy children matched to the cases by age and gender. The norovirus genotype was determined by polymerase chain reaction sequencing of the VP1 gene. The secretor status, Lewis antigen and ABO type were determined by characterization of genetic polymorphisms in the FUT2, FUT3 and ABO genes, respectively. A total of 147 case-control pairs were included. GII.4 Sydney strain was the major genotype and identified in 78.3% of the cases. The weak-secretor and Lewis-positive genotypes were less commonly identified in cases than in controls (5.4% vs. 23.1% and 79.6% vs. 89.8%, respectively). Multivariate analysis revealed that the secretor and Lewis-negative genotypes were both independent factors associated with increased risk of norovirus infections [matched odds ratio: 6.766, 95% confidence interval (CI): 2.649-17.285, P < 0.0001 and matched odds ratio: 3.071, 95% confidence interval [CI]: 1.322-7.084, P = 0.0085, respectively]. The ABO types were not significantly related to norovirus infections (P > 0.05). The weak-secretor genotype and the Lewis antigen-positive genotype were both protective factors against severe norovirus gastroenteritis during the GII.4 Sydney strain epidemic in Taiwan.

Genetic polymorphisms among and between blast disease resistant and susceptible finger millet,Eleusine coracana(L.) Gaertn.

AbstractFungal blast disease is one of the major constraints in finger millet production. Breeding for disease resistance in finger millet, needs characterization of genetic polymorphism among and between the resistant and susceptible genotypes. In total, 67 finger millet genotypes, which are resistant or susceptible to fungal blast disease, were analysed using sequence-related amplified polymorphism (SRAP) and simple sequence repeat (SSR) markers to assess genetic variations and select diverse parents. Twelve each of SRAP and SSR primers produced 95.1 and 93.1% polymorphic bands and grouped them into unweighted pair-group method with arithmetic average clusters. Two of the finger millet genotypes, IE 4709 (blast resistant) and INDAF 7 (susceptible) were distinguished as most diverse genotypes as parents. Several genotype-specific bands observed with SSR primers are potential in developing genotype-specific markers. A high genetic diversity within the resistant and susceptible genotypes, rather than between them, was revealed through Nei's gene diversity (h) index and analysis of molecular variance. The finding helps us to understand the extent of genetic polymorphism between blast disease resistant and susceptible finger millet genotypes to exploit in resistance breeding programs.

Pharmacogenetics of human ABC transporter ABCC11: new insights into apocrine gland growth and metabolite secretion.

Cell secretion is an important physiological process that ensures smooth metabolic activities and tissue repair as well as growth and immunological functions in the body. Apocrine secretion occurs when the secretory process is accomplished with a partial loss of cell cytoplasm. The secretory materials are contained within secretory vesicles and are released during secretion as cytoplasmic fragments into the glandular lumen or interstitial space. The recent finding that the non-synonymous single nucleotide polymorphisms (SNP) 538G > A (rs17822931; Gly180Arg) in the ABCC11 gene determines the type of earwax in humans has shed light on the novel function of this ABC (ATP-binding cassette) transporter in apocrine glands. The wild-type (Gly180) of ABCC11 is associated with wet-type earwax, axillary osmidrosis, and colostrum secretion from the mammary gland as well as the potential risk of mastopathy. Furthermore, the SNP (538G > A) in the ABCC11 gene is suggested to be a clinical biomarker for the prediction of chemotherapeutic efficacy. The aim of this review article is to provide an overview on the discovery and characterization of genetic polymorphisms in the human ABCC11 gene and to explain the impact of ABCC11 538G > A on the apocrine phenotype as well as the anthropological aspect of this SNP in the ABCC11 gene and patients’ response to nucleoside-based chemotherapy.

Functional characterization of genetic polymorphisms identified in the human cytochrome P450 4F12 (CYP4F12) promoter region

Functional characterization of genetic polymorphisms identified in the human cytochrome P450 4F12 (CYP4F12) promoter region

Applications of mechanistic data in risk assessment: the past, present, and future.

Mechanistic data, when available, have long been considered in risk assessment, such as in the development of the nitrate RfD based on effects in a sensitive group (infants). Recent advances in biology and risk assessment methods have led to a tremendous increase in the use of mechanistic data in risk assessment. Toxicokinetic data can improve extrapolation from animals to humans and characterization of human variability. This is done by the development of improved tissue dosimetry, by the use of uncertainty factors based on chemical-specific data, and in the development of physiologically based pharmacokinetic (PBPK) models. The development of the boron RfD illustrates the use of chemical-specific data in the improved choice of uncertainty factors. The draft cancer guidelines of the U.S. Environmental Protection Agency emphasize the use of mode of action data. The first choice under the guidelines is to use a chemical-specific, biologically based dose-response (BBDR) model. In the absence of a BBDR model, mode of action data are used to determine whether low-dose extrapolation is done using a linear or nonlinear (margin of exposure) approach. Considerations involved in evaluating a hypothesized mode of action are illustrated using 1,3-dichloropropene, and use of a BBDR model is illustrated using formaldehyde. Recent developments in molecular biology, including transgenic animals, microarrays, and the characterization of genetic polymorphisms, have significant potential for improving risk assessments, although further methods development is needed. Overall, use of mechanistic data has significant potential for reducing the uncertainty in assessments, while at the same time highlighting the areas of uncertainty.

Characterization of genetic polymorphism in the goat beta-lactoglobulin gene.

Two new variants have been detected and characterized for the goat beta-lactoglobulin gene at the cDNA level and confirmed at the genomic level. The two polymorphisms are located on exon 7 of the gene. One of the polymorphic sites is produced by a single nucleotide substitution in position +4601, allowing a polymerase chain reaction--restriction fragment length polymorphism (PCR-RFLP) genotyping procedure to be developed using SacII restriction enzyme. The other polymorphic position contains a 10 bp long insertion at position +4641 that can be detected by capillary electrophoresis of the PCR product amplified with a fluorescent primer. The association of these two polymorphisms was also investigated, resulting in the description of two new alleles. Both of these contained the point mutation at the SacII site, with or without the 10 bp insertion at position +4641. The distribution of these new polymorphisms was studied in a population of males of four different goat breeds. The gene frequencies for these variants were similar in Spanish and French breeds.