Identification Of Nucleotide Polymorphisms Research Articles

Identification of nucleotide polymorphisms in the key promoter region of chicken annexins A2 gene associatied with egg laying traits

Annexin A2 (ANXA2) is a member of the A subfamily of a multifunctional calcium dependent membrane phospholipid binding protein family. The mRNA expression of ANXA2 is consistent with ovary function and egg laying in chickens. In this study, six nucleotide polymorphisms in the key promoter region of chicken ANXA2 gene (−2861 bp to −1394 bp), i.e.,: g.−2337 indel (GT), g.−2255 C > T, g. −2248 A > G, g.−2188 A > G, g.−2169 G > A, g.−2160 A > C, were identified. Their distributions in populations of Xinyang Brown, Recessive White Rock, Wenchang and Wenshang Barred chickens were analyzed. In the Recessive White Rock chicken population, CAA, CAG and TGG were three major haplotypes. Association analysis indicated that the individuals with diplotype TGG/TGG laid more eggs at 32 weeks, and the individual with diplotype CAG/TGG laid at the earlier age. Luciferase activity assay showed that mutation from C to T at −2255 increased trascriptional activity of chicken ANXA2, which is consistent with its effect on egg laying traits.

Identification of nucleotide polymorphism within the NeuroD1 candidate gene and its association with type 1 diabetes susceptibility in Iranian people by polymerase chain reaction-restriction fragment length polymorphism.

Objectives Diabetes is a serious disease, and the number of affected individuals with diabetes is considerably high. The aim of this study is the identification of NeuroD1 Ala45Thr polymorphism and its association with type 1 diabetes susceptibility in Iranian people. Methods Clinical and biochemical characteristics for 146 people (76 diabetics and 70 nondiabetics) were measured, such as fasting blood sugar, triacylglycerol, total cholesterol, age, and weight in each individual. Polymerase chain reaction-restriction fragment length polymorphism technique (MwoI restriction-enzyme) was used for genotyping of the NeuroD1 Ala45Thr polymorphism. Results In this study, the frequency of the A allele in diabetic patients in comparison with the healthy control group had a significantly higher percentage (p < 0.01), whereas diabetic patients had the AA genotype, approximately four times more than the healthy control group (p < 0.01). In addition, we observed that fasting blood sugar had a higher concentration in the AA genotype than in AG+GG genotypes (p < 0.01). Conclusions The A allele may be a risk factor for the expansion of type 1 diabetes in the Iranian population. However, the NeuroD1 Ala45Thr polymorphism and its rolein type 1 diabetes in different populations are controversial.

SNPector: SNP inspection tool for diagnosing gene pathogenicity and drug response in a naked sequence

Due to the ability to diagnose diseases early and evaluate the effectiveness of medicinal drugs, single nucleotide polymorphism (SNP) identification receives significant interest. Detection and diagnosis of genetic variation through skill-less computational tools would help researchers reducing the severity of such health complications and improving well-tailored therapies using discovered and previously known information. We introduce SNPector, which is a standalone SNP inspection software, which can be used to diagnose gene pathogenicity and drug reaction in naked genomic sequences. It identifies and extracts gene-related SNPs, and reports their genomic position, associated phenotype disorder, associated diseases, linkage disequilibrium, in addition to various drug reaction information. SNPector detects and verifies the existence of an SNP in a given DNA sequence based on different clinically relevant SNP databases, such as NCBI ClinVar, AWESOME, and PharmGKB, and generates highly informative visualizations of the recovered information.

수밀력 우수 꿀벌 계통 판별을 위한 계통 특이 분자마커 개발

수밀력 우수 꿀벌 계통 판별을 위한 계통 특이 분자마커 개발

Identification of sequence nucleotide polymorphisms in the D-loop region of mitochondrial DNA as a risk factor for epithelial ovarian cancer

Objective: Single nucleotide polymorphisms (SNPs) and mutations in the D-Loop region of mitochondrial DNA have been long proposed to drive the pathogenesis and progression of human malignancies. We investigated the links between SNPs of D-Loop and epithelial ovarian cancer risk. Method: Mitochondrial DNA (mtDNA) of peripheral blood from 93 epithelial ovarian cancer patients and controls were examined for single nucleotide polymorphisms (SNPs) and mutations in the D-Loop region. Results: The 73A/G, 207G/A and 523C/del (p < 0.05), which indicated that the patients who carry these alleles were susceptible to epithelial ovarian cancer. Additional SNPs 254T/G, 259A/G, 275G/A, 366G/A, 411C/G, 414T/G, 418C/G, 441C/A, 476C/A, 524C/del, 530C/T were significantly associated with the tendency toward the increased risk for epithelial ovarian cancer. In contrast, the alleles 249A/del and 263A/G were correlated with the reduced risk of epithelial ovarian cancer. Conclusion: In conclusion, SNPs in the mtDNA D-loop were found to be risk markers for epithelial ovarian cancer.

Identification of a Single Nucleotide Polymorphism Related to Late Toxicity in a Randomized Hypofractionation Trial for Prostate Cancer

Identification of a Single Nucleotide Polymorphism Related to Late Toxicity in a Randomized Hypofractionation Trial for Prostate Cancer

Development of an Online Tool to Scan Single Nucleotide Polymorphisms for Identification of Novel Minor Histocompatibility Antigens

Development of an Online Tool to Scan Single Nucleotide Polymorphisms for Identification of Novel Minor Histocompatibility Antigens

TreeSNPs: a laboratory information management system (LIMS) dedicated to SNP discovery in trees

TreeSNPs is a laboratory information management system with a user-friendly Web interface for the gathering and display of data generated through medium- to large-scale single nucleotide polymorphism (SNP) identification by resequencing, in the context of whole genome association, outlier detection, quantitative trait locus, and genetic mapping studies. Its multi-gene approach allows the tracking of all the steps from candidate gene classification and prioritization to SNP discovery. The system, source code, and documentation are available for download at http://treesnps-pub.arborea.ulaval.ca:3000/download. An online demo version can also be accessed from the above link.

Application of degenerate oligonucleotide primed PCR (DOP-PCR) for SNP discovery in soybean

As the majority of methods for single nucleotide polymorphism (SNP) identification are highly cost-prohibitive, it is necessary to develop new strategies that are more suitable for small and medium-scale laboratories. In this paper, we investigate the potential of degenerate oligonucleotide primed PCR (DOP-PCR) for SNP discovery in soybean. PCR fragments were amplified from two soybean cultivars, ‘Pureunkong’ and ‘Jinpumkong 2,’ shotgun cloned and sequenced. The sequences of both cultivars were then assembled and examined for occurrence of SNPs. The effectiveness of SNP discovery was much lower than expected. Over 1,300 analyzed sequences were grouped in 144 contigs, but only 51 putative SNP sites were found in 18 of these contigs. About 50% of the contigs contained identical sequences and in more than one-third (35.4%), putative paralogous fragments were assembled. Subsequent validation of SNPs allowed the confirmation of only eight SNP sites. The failure to validate the remaining SNPs was mostly due to amplification of duplicated or multiplicated genomic regions. A relatively high proportion of chloroplast and mitochondrial DNA sequences was another limitation of effective SNP detection. Although the DOP-PCR technique was not efficient enough for SNP discovery because of the degree of soybean genome complication, the relatively large number of paralogous sequences in our data collection can be used for further detailed analysis of the genome structure of this species.

Mutation Screening of the Urocortin Gene: Identification of New Single Nucleotide Polymorphisms and Association Studies with Obesity in French Caucasians

Mutation Screening of the Urocortin Gene: Identification of New Single Nucleotide Polymorphisms and Association Studies with Obesity in French Caucasians