scholarly journals Statistical modeling of STR capillary electrophoresis signal

2019 ◽  
Vol 20 (S16) ◽  
Author(s):  
Slim Karkar ◽  
Lauren E. Alfonse ◽  
Catherine M. Grgicak ◽  
Desmond S. Lun
Keyword(s):  
Capillary Electrophoresis ◽  
Tandem Repeats ◽  
A Priori ◽  
Single Copy ◽  
Genetic Profile ◽  
Signal Model ◽  
Amplicon Size ◽  
Dna Amounts ◽  
Short Tandem

Abstract Background In order to isolate an individual’s genotype from a sample of biological material, most laboratories use PCR and Capillary Electrophoresis (CE) to construct a genetic profile based on polymorphic loci known as Short Tandem Repeats (STRs). The resulting profile consists of CE signal which contains information about the length and number of STR units amplified. For samples collected from the environment, interpretation of the signal can be challenging given that information regarding the quality and quantity of the DNA is often limited. The signal can be further compounded by the presence of noise and PCR artifacts such as stutter which can mask or mimic biological alleles. Because manual interpretation methods cannot comprehensively account for such nuances, it would be valuable to develop a signal model that can effectively characterize the various components of STR signal independent of a priori knowledge of the quantity or quality of DNA. Results First, we seek to mathematically characterize the quality of the profile by measuring changes in the signal with respect to amplicon size. Next, we examine the noise, allele, and stutter components of the signal and develop distinct models for each. Using cross-validation and model selection, we identify a model that can be effectively utilized for downstream interpretation. Finally, we show an implementation of the model in NOCIt, a software system that calculates the a posteriori probability distribution on the number of contributors. Conclusion The model was selected using a large, diverse set of DNA samples obtained from 144 different laboratory conditions; with DNA amounts ranging from a single copy of DNA to hundreds of copies, and the quality of the profiles ranging from pristine to highly degraded. Implemented in NOCIt, the model enables a probabilisitc approach to estimating the number of contributors to complex, environmental samples.

Monozygotic twins: Identical or distinguishable for science and law?

2021 ◽  
Vol 61 (1_suppl) ◽  
pp. 62-66
Author(s):  
Stefania Turrina ◽  
Elena Bortoletto ◽  
Giacomo Giannini ◽  
Domenico De Leo
Keyword(s):  
Capillary Electrophoresis ◽  
Next Generation Sequencing ◽  
Tandem Repeats ◽  
Massively Parallel Sequencing ◽  
Forensic Genetics ◽  
Monozygotic Twins ◽  
Copy Number Variations ◽  
Next Generation ◽  
Generation Sequencing ◽  
Short Tandem

Monozygotic twins, also known as monovular twins, share an identical genetic heritage because they are two individuals who derive from the same zygote. For this reason, they have been considered indistinguishable. They represent a limit for the application of markers and analytical methods that are routinely used in forensic science because analyses of DNA fragments (short tandem repeats analysed by capillary electrophoresis) are unable to distinguish monozygotic twins. The recent introduction of ultra-deep next generation sequencing in forensic genetics, also known as massively parallel sequencing, has made it possible to identify a number of genetic variations through genome sequencing (such as copy number variations, single nucleotide polymorphisms and DNA methylation) that make it possible to distinguish monozygotic twins. Here, we present a case of ascertaining biological paternity, in which the alleged father had a monozygotic twin brother. This case led to the examination of international law in similar cases in which the only available biological evidence derives from classical forensic genetic analysis, performed with short tandem repeat (autosomal and/or gonosomal) capillary electrophoresis and the probative value, if recognised, of the next generation sequencing technology in the courtroom.

Allele typing of short tandem repeats by capillary electrophoresis

1999 ◽  
Vol 113 (1) ◽  
pp. 26-32 ◽  
Author(s):  
A. Tagliabracci ◽  
Loredana Buscemi ◽  
Corrado Sassaroli ◽  
Massimo Paoli ◽  
Daniele Rodriguez
Keyword(s):  
Capillary Electrophoresis ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Short Tandem

scholarly journals Relative telomere length of the residents of Lviv oblast

1970 ◽  
Vol 21 ◽  
pp. 316-320
Author(s):  
N. L. Huleiuk ◽  
M. Tyrka
Keyword(s):  
Telomere Length ◽  
Whole Blood ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Single Copy ◽  
Rt Pcr ◽  
Relative Telomere Length ◽  
Low Correlation ◽  
Whole Blood Cells ◽  
Short Tandem

Aim. Telomeres are short, tandem repeats of DNA that cap linear chromosome ends by binding members of the shelterin protein complex to form protective telomere loops. An insufficient number of telomere repeats leads to chromosome uncapping, cell senescence, and death. Aim of this thesis is the analysis of relative telomere length (RTL) in whole blood among residents of Lviv region. Methods. The RTL in the whole blood cells was measured in 86 residents of various age (47 men and 39 women aged 18–72) using quantitative real-time PCR (Cawthon’s method). It is based on the simultaneous amplification of telomeric repeats (T) and a single copy gene (S). Results. There is a tendency to decrease RTL with age. The low correlation between RTL and age can be linked to various factors, including the heterogeneity of telomere length at birth, chronic socioeconomic stress, genetic determinism, sensitivity to exogenous pressures. Women and men did not differ significantly in the rate of RTL shortening. Conclusions. The results indicate the absence of reliable differences relative telomere length in individuals of different sexes. The low correlation between RTL and age can be linked to various factors, including insufficient sample size of people aged over 50 years. So in the future we plan to continue these studies in older people. Keywords: relative telomere length, RT-PCR, age, gender.

scholarly journals Characterizing Y-STRs in the Evaluation of Population Differentiation Using the Mean of Allele Frequency Difference between Populations

Genes ◽  
2020 ◽  
Vol 11 (5) ◽  
pp. 566
Author(s):  
Yuxiang Zhou ◽  
Yining Yao ◽  
Baonian Liu ◽  
Qinrui Yang ◽  
Zhihan Zhou ◽  
...  
Keyword(s):  
Allele Frequency ◽  
Population Differentiation ◽  
Tandem Repeats ◽  
Single Copy ◽  
Genetic Distances ◽  
Frequency Difference ◽  
Population Substructure ◽  
Allele Frequency Difference ◽  
The Mean ◽  
Short Tandem

Y-chromosomal short tandem repeats (Y-STRs) are widely used in human research for the evaluation of population substructure or population differentiation. Previous studies show that several haplotype sets can be used for the evaluation of population differentiation. However, little is known about whether each Y-STR in these sets performs well during this procedure. In this study, a total of 20,927 haplotypes of a Yfiler Plus set were collected from 41 global populations. Different configurations were observed in multidimensional scaling (MDS) plots based on pairwise genetic distances evaluated using a Yfiler set and a Yfiler Plus set, respectively. Subsequently, 23 single-copy Y-STRs were characterized in the evaluation of population differentiation using the mean of allele frequency difference (mAFD) between populations. Our results indicated that DYS392 had the largest mAFD value (0.3802) and YGATAH4 had the smallest value (0.1845). On the whole, larger pairwise genetic distances could be obtained using the set with the top fifteen markers from these 23 single-copy Y-STRs, and clear clustering or separation of populations could be observed in the MDS plot in comparison with those using the set with the minimum fifteen markers. In conclusion, the mAFD value is reliable to characterize Y-STRs for efficiency in the evaluation of population differentiation.

Von Willebrand gene tracking by single-tube automated fluorescent analysis of four short tandem repeat polymorphisms

2005 ◽  
Vol 93 (05) ◽  
pp. 976-981 ◽  
Author(s):  
Francisco Vidal ◽  
Antoni Julià ◽  
Carme Altisent ◽  
Lluís Puig ◽  
Dominique Gallardo
Keyword(s):  
Capillary Electrophoresis ◽  
Linkage Analysis ◽  
Tandem Repeats ◽  
Association Studies ◽  
Von Willebrand Disease ◽  
Automated Method ◽  
Fluorescent Pcr ◽  
Electrophoresis Method ◽  
Von Willebrand ◽  
Short Tandem

SummaryMolecular diagnosis of von Willebrand disease (VWD) has been hampered by the large size and complex genomic characteristics of the gene involved. For this reason, indirect methods using in-tragenic polymorphic markers described along the von Wille-brand factor (VWF) gene are valuable tools for gene monitoring and linkage analysis. Several studies have demonstrated the four commonly utilized short tandem repeats (STRs), three located in intron 40 and one in the promoter region of the VWF gene, to be highly informative for this task. Our objective was to develop a rapid, automated method to simultaneously analyze these four STRs for VWF gene tracking. Amplification of the four loci is achieved in a single multiplex fluorescent PCR which is then analyzed in the same run by capillary electrophoresis. Data processing with Gene Scan and Genotyper software has simplified management and tabulation of the resulting haplotypes. Analysis of the VWF gene in DNA from 102 individuals (204 chromosomes) revealed that the three STRs within intron 40 showed significant linkage disequilibrium against each other but not against the VWP locus. Moreover, the combination of the four markers offers a high heterozygosity rate (>99%) that improves tracing VWF gene inheritance. In conclusion, the automated fluorescent capillary electrophoresis method presented here is an extremely rapid, simple and highly informative technique for association studies between VWD and the VWF gene in addition to genetic counseling and prenatal diagnosis by precise linkage analysis in VWD-affected families.

The Impact of Competitive Quasi-Market on Service Delivery in Benue State University, Makurdi Nigeria

GIS Business ◽  
2019 ◽  
Vol 14 (4) ◽  
pp. 85-98
Author(s):  
Idoko Peter
Keyword(s):  
Service Delivery ◽  
A Priori ◽  
Least Square ◽  
Secondary Source ◽  
State University ◽  
Ordinary Least Square ◽  
Negative Effect ◽  
The Impact ◽  
The Relationship

This research the impact of competitive quasi market on service delivery in Benue State University, Makurdi Nigeria. Both primary and secondary source of data and information were used for the study and questionnaire was used to extract information from the purposively selected respondents. The population for this study is one hundred and seventy three (173) administrative staff of Benue State University selected at random. The statistical tools employed was the classical ordinary least square (OLS) and the probability value of the estimates was used to tests hypotheses of the study. The result of the study indicates that a positive relationship exist between Competitive quasi marketing in Benue State University, Makurdi Nigeria (CQM) and Transparency in the service delivery (TRSP) and the relationship is statistically significant (p<0.05). Competitive quasi marketing (CQM) has a negative effect on Observe Competence in Benue State University, Makurdi Nigeria (OBCP) and the relationship is not statistically significant (p>0.05). Competitive quasi marketing (CQM) has a positive effect on Innovation in Benue State University, Makurdi Nigeria (INVO) and the relationship is statistically significant (p<0.05) and in line with a priori expectation. This means that a unit increases in Competitive quasi marketing (CQM) will result to a corresponding increase in innovation in Benue State University, Makurdi Nigeria (INVO) by a margin of 22.5%. It was concluded that government monopoly in the provision of certain types of services has greatly affected the quality of service experience in the institution. It was recommended among others that the stakeholders in the market has to be transparent so that the system will be productive to serve the society effectively

scholarly journals Physiological parameters of mental health predict the emergence of post-traumatic stress symptoms in physicians treating COVID-19 patients

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
T. Dolev ◽  
S. Zubedat ◽  
Z. Brand ◽  
B. Bloch ◽  
E. Mader ◽  
...  
Keyword(s):  
Mental Health ◽  
Sleep Quality ◽  
Traumatic Stress ◽  
A Priori ◽  
Treatment Strategies ◽  
Physiological Measures ◽  
Post Traumatic Stress ◽  
Stress Symptoms ◽  
Post Traumatic

AbstractLack of established knowledge and treatment strategies, and change in work environment, may altogether critically affect the mental health and functioning of physicians treating COVID-19 patients. Thus, we examined whether treating COVID-19 patients affect the physicians’ mental health differently compared with physicians treating non-COVID-19 patients. In this cohort study, an association was blindly computed between physiologically measured anxiety and attention vigilance (collected from 1 May 2014 to 31 May 31 2016) and self-reports of anxiety, mental health aspects, and sleep quality (collected from 20 April to 30 June 2020, and analyzed from 1 July to 1 September 2020), of 91 physicians treating COVID-19 or non-COVID-19 patients. As a priori hypothesized, physicians treating COVID-19 patients showed a relative elevation in both physiological measures of anxiety (95% CI: 2317.69–2453.44 versus 1982.32–2068.46; P < 0.001) and attention vigilance (95% CI: 29.85–34.97 versus 22.84–26.61; P < 0.001), compared with their colleagues treating non-COVID-19 patients. At least 3 months into the pandemic, physicians treating COVID-19 patients reported high anxiety and low quality of sleep. Machine learning showed clustering to the COVID-19 and non-COVID-19 subgroups with a high correlation mainly between physiological and self-reported anxiety, and between physiologically measured anxiety and sleep duration. To conclude, the pattern of attention vigilance, heightened anxiety, and reduced sleep quality findings point the need for mental intervention aimed at those physicians susceptible to develop post-traumatic stress symptoms, owing to the consequences of fighting at the forefront of the COVID-19 pandemic.

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