scholarly journals Quality control method for RNA ‐seq using single nucleotide polymorphism allele frequency

2014 ◽  
Vol 19 (11) ◽  
pp. 821-829 ◽  
Author(s):  
Takaho A. Endo
Keyword(s):  
Quality Control ◽  
Single Nucleotide Polymorphism ◽  
Allele Frequency ◽  
Control Method ◽  
Single Nucleotide Polymorphism Allele ◽  
Rna Seq ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Quality Control Method

scholarly journals The AGT M235T (RS699, 4072T>C) polymorphism is not associated with elite weightlifting performance

2018 ◽  
Vol 23 ◽  
pp. 34
Author(s):  
Sigal Ben-Zaken ◽  
Yoav Meckel ◽  
Dan Nemet ◽  
Michal Pantanowitz ◽  
Alon Eliakim
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Allele Frequency ◽  
Genetic Background ◽  
Elite Athletes ◽  
National Level ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Common Features ◽  
Genotype Frequencies ◽  
The Common

It is now well established that genetic background influences an athlete’s ability to excel in different sport disciplines. Previous studies have demonstrated that among power athletes, single nucleotide polymorphism (SNP) in the AGT genotype (Thr-Thr), was significantly more prevalent among weightlifters compared to sprinters and jumpers indicating that despite the common features of these sport subtypes (short and very intense), they vary in their strength and speed abilities, as well as in their genetic make-up. The aim of the present study was to assess whether the AGT SNP can be used also to distinguish elite from national levels weightlifters. The AGT M235T genotype frequencies were assessed in 47 weightlifters (30 elite, 17 national level) and 86 non-athletes control. The Thr-Thr genotype was significantly higher among weightlifters (29.8%) compared to controls (12.8%) (p=0.048). Thr allele frequency was significantly higher among weightlifters (55.3%) compared to controls (37.8%) (p=0.021). However, there was no difference in the prevalence of the polymorphism between national level and elite athletes. In conclusion, the results suggest that the AGT polymorphism cannot predict elite competitive weightlifting performance.

scholarly journals Single nucleotide polymorphism discovery in bovine liver using RNA-seq technology

PLoS ONE ◽  
2017 ◽  
Vol 12 (2) ◽  
pp. e0172687 ◽  
Author(s):  
Chandra Shekhar Pareek ◽  
Paweł Błaszczyk ◽  
Piotr Dziuba ◽  
Urszula Czarnik ◽  
Leyland Fraser ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Bovine Liver ◽  
Single Nucleotide Polymorphism Discovery ◽  
Rna Seq ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Polymorphism Discovery

scholarly journals Sequence Imputation from Low Density Single Nucleotide Polymorphism Panel in a Black Poplar Breeding population

2018 ◽  
Author(s):  
Marie Pégard ◽  
Odile Rogier ◽  
Aurélie Bérard ◽  
Patricia Faivre-Rampant ◽  
Marie-Christine Le Paslier ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Allele Frequency ◽  
Minor Allele Frequency ◽  
Breeding Population ◽  
Minor Allele ◽  
Low Density ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Black Poplar

AbstractBackgroundGenomic selection accuracy increases with the use of high SNP (single nucleotide polymorphism) coverage. However, such gains in coverage come at high costs, preventing their operational implementation by breeders. Low density panels imputed to higher densities offer a cheaper alternative. Our study is one of the first to explore the imputation in a tree species: black poplar. About 1000 pure-breed Populus nigra trees corresponding to a subsample of the French breeding population were selected and genotyped with a 12K custom Infinium Bead-Chip. Forty-three of those individuals corresponding mostly to nodal trees in the pedigree were fully sequenced (reference), while the remaining majority (target) was imputed from 8K to 1.4 million SNPs using FImpute. Each SNP and individual was evaluated for imputation errors by leave-one-out cross validation in the training sample of 43 sequenced trees. Some summary statistics such as Hardy Weinberg Equilibrium exact test p-value, quality of sequencing, depth of sequencing per site and per individual, minor allele frequency, marker density ratio or SNP information redundancy were calculated. Principal component and Boruta analyses were used on all these parameters to rank the factors affecting the quality of imputation. Additionally, we characterize the impact of the relatedness between reference population and target population.ResultsDuring the imputation process, we used 7,540 SNPs from the chip to impute 1,438,827 SNPs from sequences along the 19 Chromosomes. At the individual level, imputation accuracy was very high with a proportion of SNPs correctly imputed between 0.84 and 0.99. The variation in accuracies was mostly due to differences in relatedness between individuals. At a SNP level, the imputation quality strongly depended on genotyped SNP density and to a lesser extent on the original minor allele frequency. The imputation did not appear to result in an increase of linkage disequilibrium. The genotype densification not only brought a better distribution of markers all along the genome, but also we did not detect any substantial bias in annotation categories.ConclusionsThis study shows that it is possible to impute low-density marker panels to whole genome sequence with good accuracy under certain conditions that could be common to many breeding populations.

scholarly journals Single Nucleotide Polymorphism Discovery in Bovine Pituitary Gland Using RNA-Seq Technology

PLoS ONE ◽  
2016 ◽  
Vol 11 (9) ◽  
pp. e0161370 ◽  
Author(s):  
Chandra Shekhar Pareek ◽  
Rafał Smoczyński ◽  
Haja N. Kadarmideen ◽  
Piotr Dziuba ◽  
Paweł Błaszczyk ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Pituitary Gland ◽  
Single Nucleotide Polymorphism Discovery ◽  
Rna Seq ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Polymorphism Discovery
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