Single nucleotide polymorphism (SNP) allele frequency estimation in DNA pools using Pyrosequencing™

2006 ◽  
Vol 1 (6) ◽  
pp. 2573-2582 ◽  
Author(s):  
Catharina Lavebratt ◽  
Selim Sengul
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Allele Frequency ◽  
Frequency Estimation ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Allele Frequency Estimation ◽  
Dna Pools

Cheap, accurate and rapid allele frequency estimation of single nucleotide polymorphisms by primer extension and DHPLC in DNA pools

2000 ◽  
Vol 107 (5) ◽  
pp. 488-493 ◽  
Author(s):  
Bastiaan Hoogendoorn ◽  
Nadine Norton ◽  
George Kirov ◽  
Nigel Williams ◽  
Marian Hamshere ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Allele Frequency ◽  
Frequency Estimation ◽  
Primer Extension ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Allele Frequency Estimation ◽  
Dna Pools

Single-Nucleotide Polymorphism Genotyping in DNA Pools

2005 ◽  
pp. 147-164 ◽  
Author(s):  
Ian Craig ◽  
Emma Meaburn ◽  
Lee Butcher ◽  
Linzy Hill ◽  
Robert Plomin
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Single Nucleotide Polymorphism Genotyping ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Dna Pools

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.

Pyrosequencing?-based SNP allele frequency estimation in DNA pools

2003 ◽  
Vol 23 (1) ◽  
pp. 92-97 ◽  
Author(s):  
Catharina Lavebratt ◽  
Selim Sengul ◽  
Marten Jansson ◽  
Martin Schalling
Keyword(s):  
Allele Frequency ◽  
Frequency Estimation ◽  
Allele Frequency Estimation ◽  
Dna Pools

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.

Quantitative technologies for allele frequency estimation of SNPs in DNA pools

2002 ◽  
Vol 16 (6) ◽  
pp. 429-434 ◽  
Author(s):  
Sagiv Shifman ◽  
Anne Pisanté-Shalom ◽  
Benjamin Yakir ◽  
Ariel Darvasi
Keyword(s):  
Allele Frequency ◽  
Frequency Estimation ◽  
Allele Frequency Estimation ◽  
Dna Pools

scholarly journals SNP allele frequency estimation in DNA pools and variance components analysis

BioTechniques ◽  
2004 ◽  
Vol 36 (5) ◽  
pp. 840-845 ◽  
Author(s):  
Kate Downes ◽  
Bryan J. Barratt ◽  
Pelin Akan ◽  
Sue J. Bumpstead ◽  
Stacey D. Taylor ◽  
...  
Keyword(s):  
Allele Frequency ◽  
Variance Components ◽  
Frequency Estimation ◽  
Allele Frequency Estimation ◽  
Variance Components Analysis ◽  
Dna Pools ◽  
Components Analysis

scholarly journals Cancer Protection Elicited by a Single Nucleotide Polymorphism Close to the Adrenomedullin Gene

2013 ◽  
Vol 98 (4) ◽  
pp. E807-E810 ◽  
Author(s):  
Sonia Martínez-Herrero ◽  
Alfredo Martínez
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Allele Frequency ◽  
Minor Allele Frequency ◽  
Direct Sequencing ◽  
Minor Allele ◽  
Cardiac Insufficiency ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Healthy Donors ◽  
A Minor

Context: The risk of developing cancer is regulated by genetic variants, including polymorphisms. Characterizing such variants may help in developing protocols for personalized medicine. Objective: Adrenomedullin is a regulatory peptide involved in cancer promotion and progression. Carriers of a single nucleotide polymorphism (SNP) in the proximity of the adrenomedullin gene have lower levels of circulating peptide. The aim of the present work was to investigate whether carriers of this SNP (rs4910118) are protected against cancer. Design: This was a retrospective study. DNA samples were obtained from the Carlos III DNA National Bank (University of Salamanca, Salamanca, Spain). Setting: Samples represent a variety of donors and patients from Spain. Patients or Other Participants: DNA from patients with breast cancer (n = 238), patients with lung cancer (n = 348), patients with cardiac insufficiency (n = 474), and healthy donors of advanced age (n = 500) was used. Interventions: All samples were genotyped using double-mismatch PCR, and confirmation was achieved by direct sequencing. Main Outcome Measures: The minor allele frequency was calculated in all groups. The Pearson χ2 was used to compare SNP frequencies. Results: Of 1560 samples, 14 had the minor allele, with a minor allele frequency in healthy donors of 0.90%. Patients with cancer had a statistically significantly lower frequency than healthy donors (odds ratio = 0.216, 95% confidence interval = 0.048–0.967, P = .028). Conclusions: Carriers of the minor allele have a 4.6-fold lower risk of developing cancer than homozygotes for the major allele. Knowledge of the rs4910118 genotype may be useful for stratifying patients in clinical trials and for designing prevention strategies.

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