Sentences with phrase «s allele frequency»

For example, population processes associated with colonization, periods of geographic isolation, socially reinforced endogamy, and natural selection all have affected allele frequencies in certain populations (Jorde et al. 2000b; Bamshad and Wooding 2003).

The change in allele frequency may arise by any number of mechanisms including the addition of a novel allele via mutation.

Evolution the fact is defined as a change in allele frequency in a population over time.

Change in allele frequency in a population of time, common descent, punctuated equilibria, etc., etc. have no foundation in biogenesis.

Among individuals with two divergent mitochondrial haplotypes (mt - haplotypes), the genome - wide analyses revealed significant differences in nuclear allele frequencies.

The other examined how allele frequencies can change within a lifetime.

We tried to match up the allele frequency shifts in this experiment with the genome - level differentiation that we observed in our genome - resequencing populations.

The biobank included relatively few old people, but it did have information about participants» parents, so the team also looked for connections between parental death and allele frequencies in their children.

With the help of giant genomic data sets, scientists can now track these evolutionary shifts in allele frequencies over short timescales.

Genotype and allele frequency analyses did not result in significant associations when the combined endurance versus sprint athletes were compared (Supplemental Table 1).

Here, we report genome - wide allele frequencies in 347 extinct CC lines.

Stratification of endurance and sprint athletes based on sport classification resulted in significant genotypes and allele frequencies (Table 3).

Eigenstrat genotype file formats were generated per window using convertf from the EIGENSOFT package52 and custom scripts were used to convert the genotype files into matrix formats for visualization using matrix2png53 using a filtered subset of SNPs (minor allele frequencies between 0.05 and 0.49) for easing visualization of the matrices.

In the current study, the genotype and allele frequency of a SNP in exon 3 of the IL15RA gene were associated with elite human endurance athletes stratified by sport.

Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation.

SNP calling, genotype calling, and sample allele frequency estimation from new - generation sequencing data Nielsen, R. T. Korneliussen, A. Albrechtsen, Y. Li et al. 2012.

Adaptation in quantitative traits likely often occurs through subtle shifts in allele frequencies at many loci, a process called polygenic adaptation.

Estimation of 2Nes from temporal allele frequency data.

Estimation of 2Nes from temporal allele frequency data Bollback, J. P., T. L. York, and R. Nielsen.

It follows from the last point above that the vast majority of common human genetic variation, i.e. SNPs with derived allele frequencies of at least 5 %, is neutral or nearly neutral with respect to fitness.

Estimation of allele frequency and association mapping using next - generation sequencing data.

Results of this study has shown that there is a significant inter-population variability, as far as pharmacogenomic biomarker allele frequency is concerned, which has a direct impact on the rationalization of drug use at a population level.

Estimation of allele frequency and association mapping using next - generation sequencing data Kim, S. Y., K. E. Lohmueller, A. Albrechtsen, Y. Li et al. 2011.

Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation Vieira, F. G., M. Fumagalli, A. Albrechtsen, and R. Nielsen.

Seventy mtDNA SNPs met our minimum minor allele frequency threshold of 5 %, and were included in association tests with demographic and symptomatic variables associated with ME / CFS.

While 90 % of human SNPs have a minor allele frequency (MAF) below 5 % and therefore are hard to be identified as having an effect, the DO population is balanced by its design and rare variants are uncommon (only 2 % SNPs with MAF < 5 %).

As the Pf3k project evolves, there will be the option to include even more data, for example allele frequencies and neighbour - joining trees, as we've done in the Panoptes - based Ag1000G application.»

Genomic position is plotted on the x axis and observed mutant allele frequency on the y axis.

Of the genotyped Icelanders, 7.7 % are homozygotes or compound heterozygotes for loss - of - function mutations with a minor allele frequency (MAF) below 2 % in 1,171 genes (complete knockouts).

Look at the allele frequency plot for the same chromosome offers some clarification:

A clustering analysis of mutant allele frequencies suggested that there were four clones (tumor subpopulations) in the primary tumor defined by distinct sets of mutations.

Assuming that all mutations are heterozygous (which is likely), the observed allele frequencies suggest that shared mutations are present in virtually all tumor cells.

Using large - scale empirical and simulated data sets, we found that the sample sizes used in the HapMap project are sufficient to capture common variation, but that performance declines substantially for variants with minor allele frequencies of < 5 %.

Such high redundancy of coverage enabled us to accurately compute allele frequency, and thereby, the fraction of tumor cells harboring each mutation.

In these analyses, Ser482 allele frequencies were very similar (36.9 % in Spanish vs. 37.5 % in UK Caucasians, P = 0.83), suggesting that confounding by genetic stratification is unlikely to explain the association between Gly482Ser genotype and endurance capacity.

Allele frequency shifts under the amplifications: it looks like ERBB2 has 2 extra copies, and the other amplification has 3 or 4.

They applied a strategy for seraching genes with multiple rare (minor allele frequency < 0.001) variants in cases but not in controls with a potentially damaging effect.

Some of the associated variants were super rare (MAF < 1 %), suggesting that genotyping studies like this are well - powered to detect associations even at allele frequencies below one percent.

In fact, the most informative markers are likely to have high minor allele frequencies, which likely makes them neutral with respect to selection, and therefore not functional variants.

Not so long ago, there was a hope in the research community that common genetic variation, i.e. variants present at minor allele frequencies > 5 % in human populations, might explain most or all of the heritability of common complex disease.

As a central repository for variant allele frequency (VAF) data, dbSNP can be a powerful resource for human genetics studies.

To identify signatures of geographically restricted natural selection, the authors searched for DNase I peaks containing variants with significant allele frequency differences between individuals of African, European, and Asian ancestry.

Detection correlated with both the relative expression level of the gene and the allele frequency of the mutation in the genome.

They're not all rare variants, either: 86 million variants are classified as common (G5, G5A, or COMMON), with minor allele frequencies > 1 % in at least one population.

Allele frequency shifts for FMR1 and MSN from O. c. algirus to O. c. cuniculus are abrupt and few introgressed alleles are found in the other subspecies territory.

A) Histogram of FST values for all SNPs and SNPs showing a minor allele frequency (MAF) of 10 %.

It may sound surprising but even some basic concepts, like allele frequencies and genetic distance, are not straightforward when dealing with Plasmodium genomes.

Note that the loci represented are biased towards loci previously ascertained to show sharp allele frequency differences between both ends of the subspecies distributions, and even for some of these we are able to detect introgressed alleles.

The polyT repeat in intron 6 of TOMM40 (rs10524523) was genotyped using fluorescence - based fragment size analysis (Supplemental Figure 1; http://neuroscienceresearch.wustl.edu/pages/cruchaga2011.aspx).19 A detailed explanation of the fluorescence - based fragment size genotyping, quality control steps, allele frequency, and linkage disequilibrium between the studied polymorphisms can be found at http://neuroscienceresearch.wustl.edu/Pages/cruchaga2011.aspx.

A - Contrasting patterns of introgression between subspecies of the European rabbit summarized with pie charts of allele frequency data across the rabbit hybrid zone and shape of genealogies for four representative loci (DIAPH2, HPRT1, FMR1, and MSN; data from [21], [26]--[27].