Search results for "SNP"
showing 10 items of 366 documents
Identification of SNPs in the promoter of β-lactoglobulin gene in three Sicilian goat breeds
2009
The aim of this work was to sequence the full-length promoter region of the caprine β-lactoglobulin (β-lg) gene in three Sicilian goat breeds (Girgentana, Maltese, and Derivata di Siria), in order to identify polymorphisms, to search for transcription factors (TFs) sites, and to check if polymorphisms found lay within TFs binding sites. The promoter region of β-lg gene in Sicilian goat breeds showed high level of polymorphism due to the presence of 31 SNPs. Binding sites for several TFs were found within the goat β-lg promoter and within regions conserved between ovine and caprine species. Two SNPs were detected within TFs binding sites, such as MPBF and NF-I. Further st…
Analysis of extended genomic rearrangements in oncological research.
2007
Screening for genomic rearrangements is a fundamental task in the genetic diagnosis of many inherited disorders including cancer-predisposing syndromes. Several methods were developed for analysis of structural genomic abnormalities, some are targeted to the analysis of one or few specific loci, others are designed to scan the whole genome. Locus-specific methods are used when the candidate loci responsible for the specific pathological condition are known. Whole-genome methods are used to discover loci bearing structural abnormalities when the disease-associated locus is unknown. Three main approaches have been employed for the analysis of locus-specific structural changes. The first two a…
Minimum Free Energy Based Evaluation of mRNAs Secondary Structures Constructed by 18 Clinically Significant Exonic Single Nucleotide Polymorphisms (S…
2015
Clinically significant 18 Single Nucleotide Polymorphisms (SNPs) from exon regions of Retinoblastoma gene (RB1) were analyzed to find out the structural variations in mRNAs. Online bioinformatic tools i.e., Vienna RNA, RNAfold were used for secondary structure analysis of mRNAs. Predicted minimum Free Energy Change (MFE) was calculated for mRNAs structures. It has been observed that the average of predicted MFE value from 13 nonsense mutations was higher (0.76 kcal/mol) in comparison to 5 missense mutations. Presumably, 13 nonsense mutations are responsible for Nonsense Mediated mRNA Decay (NMD), therefore, excluded from haplotype analysis. From the statistical analysis all the thermodynami…
In Silico Analysis of the Novel Variant Q375R in the Phenylalanine Hydroxylase Gene
2019
Background: Phenylketonuria is an inborn metabolic disorder inherited in an autosomal recessive pattern. The detection of pathogenic variations improves the power of at-risk carrier and prenatal detection. We previously found Q375R a novel phenylalanine hydroxylase variation in phenylketonuria patients from the south-west of Iran. Objectives: Here, we aimed to evaluate the rate of the pathogenicity of this novel variant and three other intron variants (IVS9 + 32insA, IVS11 + 163delC, and IVS12 + 30C>T). Methods: The pathogenicity and some structural features of Q375R were analyzed using bioinformatics tools including SIFT, PolyPhen, Mutpred, MutationTaster, nSSNP Analyzer, SNP effect, 3DLig…
Forensic validation of the SNPforID 52-plex assay.
2007
The advantages of single nucleotide polymorphism (SNP) typing in forensic genetics are well known and include a wider choice of high-throughput typing platforms, lower mutation rates, and improved analysis of degraded samples. However, if SNPs are to become a realistic supplement to current short tandem repeat (STR) typing methods, they must be shown to successfully and reliably analyse the challenging samples commonly encountered in casework situations. The European SNPforID consortium, supported by the EU GROWTH programme, has developed a multiplex of 52 SNPs for forensic analysis, with the amplification of all 52 loci in a single reaction followed by two single base extension (SBE) react…
Forensic typing of autosomal SNPs with a 29 SNP-multiplex--results of a collaborative EDNAP exercise.
2008
We report the results of an inter-laboratory exercise on typing of autosomal single nucleotide polymorphisms (SNP) for forensic genetic investigations in crime cases. The European DNA Profiling Group (EDNAP), a working group under the International Society for Forensic Genetics (ISFG), organised the exercise. A total of 11 European and one US forensic genetic laboratories tested a subset of a 52 SNP-multiplex PCR kit developed by the SNPforID consortium. The 52 SNP-multiplex kit amplifies 52 DNA fragments with 52 autosomal SNP loci in one multiplex PCR. The 52 SNPs are detected in two separate single base extension (SBE) multiplex reactions with 29 and 23 SNPs, respectively, using SNaPshot …
A sensitive issue: Pyrosequencing as a valuable forensic SNP typing platform
2006
Analysing minute amounts of DNA is a routine challenge in forensics in part due to the poor sensitivity of an instrument and its inability to detect results from forensic samples. In this study, the sensitivity of the Pyrosequencing method is investigated using varying concentrations of DNA and five autosomal single nucleotide polymorphisms in singleplex on both available instrument models; the PSQ™ 96MA and PSQ™ HS 96A. A detailed comparison of the two models was completed while establishing a lower limit of detection on both instruments to give results supporting the use of Pyrosequencing as a valuable forensic SNP typing platform. © 2005 Elsevier B.V. All rights reserved.
Application of Nanogen microarray technology for forensic SNP analysis
2006
Abstract The NanoChip® Molecular Biology Workstation using electronic microarrays is an approach for rapid and high throughput analysis of SNPs. This instrument is fully automated and uses a microchip for electronic addressing of capture probes to specific array sites followed by electronic hybridisation of the single stranded PCR products, and passive hybridisation of fluorescently labelled reporter probes. Discrimination is achieved by applying thermal stringency to denature the mismatched reporters. 48 SNP assays have been designed using the ‘capture down’ assay which applies a thermal ‘touch down’ strategy to obtain the best reporter probe discrimination.
Interleukin-10 promoter polymorphism in sporadic Alzheimer's disease.
2003
Proinflammatory cytokines and acute-phase proteins play an important role in Alzheimer's disease (AD) neurodegeneration, and common polymorphisms of genes controlling their high production have been shown to be associated with AD. Thus, AD patients display a proinflammatory genotype and the control of inflammation might play a protective role in AD development. By sequence-specific probes, we have evaluated the role of anti-inflammatory cytokine interleukin(IL)-10 in AD, by analysing in 132 AD patients and 213 healthy controls the prevalence of three different haplotypes, involving three single-nucleotide polymorphisms (SNPs) at -1082 (G--A), -819 (C--T) and -592 (C--A) nucleotides of IL-10…
Analysis of interleukin 10 (IL-10) -1082G/A single nucleotide polymorphism (SNP) genotypes in breast cancer (BC) patients (pts) and in >95 years o…
2005
9656 Background:the anti-inflammatory IL-10 -1082 (G/A) SNP might be associated with different risk for breast tumor development. The -1082GG homozygous genotype is associated with an higher IL-10 ...