scholarly journals Evaluation and SNP typing of DNA from ultraviolet-irradiated human bloodstains using TaqMan assay

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jian Tie ◽  
Seisaku Uchigasaki ◽  
Eiji Isobe
Keyword(s):  
Taqman Assay ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Str Profile ◽  
The Common ◽  
Dna Template ◽  
Dna Profiles ◽  
Short Tandem ◽  
Made In ◽  
Damaged Dna

AbstractWhen detecting DNA profiles from forensic materials, it is pivotal to know the extent of degradation and which DNA marker can be genotyped. Ultraviolet (UV) is one of the common external factors that causes DNA damage, through which, an attempt to reveal cardinal genetic information can be made. In this study, after irradiation with three different UV wavelengths, UV-damaged DNA in the bloodstains was analyzed with long and short TaqMan assays using real-time PCR. In addition, both short tandem repeat (STR) profiles and single nucleotide polymorphisms (SNPs) from the damaged DNA at different stages of UV exposure were also assessed. With increasing in UV irradiation cycles, there was a delay of the amplification curves accompanied with a decrease in the DNA amounts collected. Despite the amplification of STR genotype was not altered after 75 cycles of UVC irradiation, all 12 SNP loci could still be detected. Furthermore, a short-assay line was detected in the absence of an amplification of the evaluation curve. The results indicate that, although the DNA template might not be useful and suitable for analysis of STR profile, this approach is of some values in detecting SNPs.

scholarly journals A NOTE ON PHASING LONG GENOMIC REGIONS USING LOCAL HAPLOTYPE PREDICTIONS

2006 ◽  
Vol 04 (03) ◽  
pp. 639-647 ◽  
Author(s):  
ELEAZAR ESKIN ◽  
RODED SHARAN ◽  
ERAN HALPERIN
Keyword(s):  
Large Scale ◽  
Computational Cost ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Novel Approach ◽  
Maximum Likelihood Criterion ◽  
The Common ◽  
Genomic Regions ◽  
High Computational Cost ◽  
Combining Information

The common approaches for haplotype inference from genotype data are targeted toward phasing short genomic regions. Longer regions are often tackled in a heuristic manner, due to the high computational cost. Here, we describe a novel approach for phasing genotypes over long regions, which is based on combining information from local predictions on short, overlapping regions. The phasing is done in a way, which maximizes a natural maximum likelihood criterion. Among other things, this criterion takes into account the physical length between neighboring single nucleotide polymorphisms. The approach is very efficient and is applied to several large scale datasets and is shown to be successful in two recent benchmarking studies (Zaitlen et al., in press; Marchini et al., in preparation). Our method is publicly available via a webserver at .

Abstract 15318: Association of Single-Nucleotide Polymorphisms with Left Atrial Scar in Patients with Atrial Fibrillation

Circulation ◽  
2014 ◽  
Vol 130 (suppl_2) ◽  
Author(s):  
Sanghamitra Mohanty ◽  
Amelia W Hall ◽  
Prasant Mohanty ◽  
Chintan Trivedi ◽  
Luigi Di Biase ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Left Atrial ◽  
Transforming Growth Factor ◽  
Univariate Analysis ◽  
Scar Formation ◽  
Taqman Assay ◽  
Inverse Association ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Caveolin 1

Introduction: Earlier studies have demonstrated that some AF patients develop spontaneous atrial scarring that leads to genesis and perpetuation of the arrhythmia. However, it is still unclear why it happens in some and not in others. Therefore, we hypothesized that the atrial scar phenotype is associated with certain specific genetic variants and examined the relationship between AF-related single-nucleotide polymorphisms (SNP) and left atrial scar. Methods: Four hundred AF patients (67% male, 62±12 year, left atrial size 45.3±7 mm, 64% non-paroxysmal) undergoing catheter ablation were prospectively enrolled at our center. DNA extraction and genotyping for 16 AF-associated SNPS identified by GWAS study were performed from the collected blood samples using Qiagen QiaAMP 96 well blood kit and TaqMan assay respectively. Three hundred seventy-two DNA samples were available for genotyping. The Hardy-Weinberg equilibrium was assessed using Chi-square analyses. Multivariable logistic model was utilized to identify predictors of LA scar after adjusting for age, gender, LA size, hypertension and diabetes mellitus and odds ratio (OR) and 95% confidence intervals were computed. Results: Of all 16 SNPs, rs3807989 showed a strong inverse association with LA scar at univariate analysis (0.54 [0.348-0.89] p= 0.014) in the overall population. After adjustment for covariates, the association became highly significant indicating a 50% reduction in scar risk (OR 0.50 (0.30-0.83) p=0.007). When stratified by type of AF, rs3807989 genotype predicted a substantially stronger 69% risk-reduction in the non-PAF population (OR 0.31 (0.15-0.62) p=0.0009). Conclusion: The SNP, rs3807989 on chromosome 7p31, was demonstrated to be associated with reduced risk of left atrial scar formation in AF patients. This genetic variant is located in close proximity to the caveolin-1 gene which is known to have an anti-fibrotic role by inhibiting transforming growth factor-β1, a key mediator in the fibrosis process. Therefore, it can be postulated that by some unknown mechanism the candidate chromosomal variant potentially upregulates caveolin-1 function resulting in attenuation of fibrosis and scar formation.

scholarly journals The efficacy of short tandem repeat polymorphisms versus single-nucleotide polymorphisms for resolving population structure

BMC Genetics ◽  
2005 ◽  
Vol 6 (Suppl 1) ◽  
pp. S84 ◽  
Author(s):  
John SK Kauwe ◽  
Sarah Bertelsen ◽  
Laura Bierut ◽  
Gerald Dunn ◽  
Anthony L Hinrichs ◽  
...  
Keyword(s):  
Population Structure ◽  
Single Nucleotide Polymorphisms ◽  
Tandem Repeat ◽  
Short Tandem Repeat ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Short Tandem

scholarly journals Detection of Single Nucleotide Polymorphisms (SNPs) for Genes Cause Drug-Resistant in Iraqi Mycobacterium Tuberculosis isolates by new Pyrophosphate Technique.

2020 ◽  
Vol 10 (01) ◽  
pp. 145-149
Author(s):  
Hassan Kadhim Nemir ◽  
Ismail Aziz ◽  
Alaa Kareem Mohammed
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Single Nucleotide Polymorphisms ◽  
Firefly Luciferase ◽  
Negative Control ◽  
Drug Resistant ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Taq Polymerase ◽  
Base Extension ◽  
Dna Template

In this search, a new pyrophosphate technique was proved. The technique was employed to single- nucleotide polymorphisms (SNPs), which diagnosis using a one-base extension reaction. Three Mycobacterium tuberculosis genes were chosen (Rpob, InhA, KatG) genes. Fifty-four specimens were used in this study fifty-three proved as drug-resistant specimens by The Iraqi Institute of Chest and Respiratory Diseases in Baghdad.; also one specimen was used as a negative control. The steps of this technique were by used a specific primer within each aliquot that has a short 3-OH end of the base of the target gene that was hybridized to the single-stranded DNA template. Then, the Taq polymerase enzyme and one of either α-thio-dATP, dTTP, dGTP, or dCTP were supplemented and incubated for 1 min. ATP is synthesis by convert Pyrophosphate freed by DNA polymerase using pyruvate phosphate dikinase (PPDK), and the amount of ATP estimates by the firefly luciferase reaction. This technique, which does not demand expensive equipment, can be applied to rapidly monitor a one-point mutation in the gene that causes drug-resistant in mycobacterium tuberculosis. The results showed a high variation in values of ATP formation through matching and mismatch bases added. So, this assay (which required only five minutes), enable to find the gene SNP causes resistant for the specific drug.

scholarly journals The Genetic Changes of Hepatoblastoma

2021 ◽  
Vol 11 ◽  
Author(s):  
Huitong Chen ◽  
Qian Guan ◽  
Huiqin Guo ◽  
Lei Miao ◽  
Zhenjian Zhuo
Keyword(s):  
Nucleotide Polymorphisms ◽  
Genetic Syndromes ◽  
Disease Treatment ◽  
Single Nucleotide ◽  
Genetic Changes ◽  
Future Studies ◽  
The Past ◽  
Malignant Liver ◽  
Genetic Events ◽  
Made In

Hepatoblastoma is the most common malignant liver cancer in childhood. The etiology of hepatoblastoma remains obscure. Hepatoblastoma is closely related to genetic syndromes, hinting that hepatoblastoma is a genetic predisposition disease. However, no precise exposures or genetic events are reported to hepatoblastoma occurrence. During the past decade, significant advances have been made in the understanding of etiology leading to hepatoblastoma, and several important genetic events that appear to be important for the development and progression of this tumor have been identified. Advances in our understanding of the genetic changes that underlie hepatoblastoma may translate into better patient outcomes. Single nucleotide polymorphisms (SNPs) have been generally applied in the research of etiology’s exploration, disease treatment, and prognosis assessment. Here, we reviewed and discussed the molecular epidemiology, especially SNPs progresses in hepatoblastoma, to provide references for future studies and promote the study of hepatoblastoma’s etiology.

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