Sentences with phrase «low frequency variants»

Overall, we suggest a preference for HiSeq2000 and Complete Genomics in cancer genome studies where sensitivity for detection of low frequency variants matters most, whereas the two Life Technologies platforms might be better suited when calling SNVs with high specificity.

Reykjavik, ICELAND, 9 October 2011 — Scientists at deCODE Genetics and academic collaborators from Iceland, Norway, Denmark, the Netherlands and the USA today report the discovery of low frequency variants in the human genome that associate with risk of gout, a common inflammatory arthritis, and serum uric acid levels.

Because low frequency variants have the potential to bias FST estimates and are more likely to represent technical artifacts such as sequencing and PCR errors [30], we excluded all SNPs with a MAF below 10 % (i.e. singletons and doubletons in our dataset).

Reykjavik, ICELAND, 9 October 2011 — Scientists at deCODE Genetics and academic collaborators from Iceland, Norway, Denmark, the Netherlands and the USA today report the discovery of low frequency variants in the human genome that associate with risk of gout, a common...

Thus, the overall baseline of differentiation is moderate even after excluding low frequency variants, which are more likely than high - frequency variants to represent sequencing and genotyping errors [30].

However, when we extracted gene expression levels from the brain transcriptome data following the methodology in Carneiro et al. [29], we found that levels of nucleotide diversity and the proportion of low frequency variants between lowly (bottom 5 %) and highly (top 5 %) expressed genes in our dataset (Table S7) were not significantly different in most comparisons (with the exception of π in O. c. cuniculus) nor did they consistently differ in the expected direction when assuming higher error rates in lowly expressed genes.

We developed BioBin, a flexible collapsing method inspired by biological knowledge that can be used to automate the binning of low frequency variants for association testing.

Through this effort we discovered several low frequency variants associated with a host of complex traits.

Not exact matches

An apparently new Variant of human serum albumin, albumin Naskapi, has been found in high frequency in the Naskapi Indians of Quebec and, in lower frequency, in other North American Indians.The family and population data of the albumin are consistent with its inheritance as a simple autosomal trait Controlled by a gene designated Al Naskapi.

«Rare variants alter gene function but occur at low frequency in a population.

The hunter - gatherers also had a high frequency of genetic variants linked to reduced skin pigmentation — a known adaptation to environments with low UV radiation, such as those at high latitude.

The frequency of the risk C variant in Spanish people over the age of one hundred was 47.0 %, lower than in healthy people that were taken as a control sample in the study (52.9 %) and individuals with cardiovascular disease (55.1 %).

«This mutation is one of a growing number of deCODE discoveries of relatively low frequency sequence variants with large effect,» said Kari Stefansson, deCODE's CEO and senior author of the study.

Only 23 low - frequency and rare variants achieved significance, which is nowhere close to the first two models (the ones that suggest a major role).

In the first two models, low - frequency variants explain a significant proportion of the heritability, and over a hundred of them should have been uncovered at the more forgiving significance threshold.

One possible explanation is that rare (low - frequency) variants — which are poorly represented on the arrays used for GWAS — underlie a substantial proportion of the variability.

They took the 10 T2D GWAS loci with the strongest support in their study, and looked for low - frequency missense variants within 2.5 million base pairs of the common index SNV.

Sure, you could do fewer samples, but then you lose the power for detecting association in the lowest - frequency variant classes.

We study common, low frequency and rare variants [1] in an ancestrally diverse population of > 40,000 individuals recruited from throughout New York City through the Mount Sinai's ongoing BioMe EMR - linked Biobank, [2] in the large - scale UK Biobank (n = 500,000), and [3] in a unique discordant - sib family study.

This idea is intuitive: in theory, large - effect variants would be kept at low frequency by natural selection, a pattern that's well established for mutations that cause rare single - gene disorders.

It's most similar to the common polygenic model of disease for T2D, suggesting that this study supports a minor role for rare and low - frequency variants.

They simulated three possible models which had seemed plausible prior to large - scale sequencing, and computed the number of associated low - frequency and rare variants that would be uncovered with their study design.

Identification of low - frequency variants associated with gout and serum uric acid levels.

Yet each one tells a different story: (a), how novel - to - dbSNP variants were rare; (b), how nonsynonymous variant frequencies are shifted to lower values relative to those of synonymous variants, (c), how this shift in allele frequencies is more pronounced for damaging nsSNPs, consistent with natural selection, and (d), how the sizes of observed indels are enriched for non-frameshift events divisible by 3.

Advances in sequencing technology enable focused explorations on the contribution of low - frequency and rare variants to human traits.

198/3: 00 Rare and low - frequency coding variants contribute independently to human stature variation.

Our findings add empirical support to the contribution of low - frequency variants in complex traits, demonstrate the advantage of including population - specific sequences in imputation panels and exemplify the power gains afforded by population isolates.

We demonstrate relaxation of purifying selection in the isolates, leading to enrichment of rare and low - frequency functional variants, using novel statistics, DVxy and SVxy.

We will provide a brief overview of results ranging from common, to low - and rare - frequency variant - trait association studies, studies leveraging the diversity across populations, and studies harnessing the power of genetic and genomic approaches to gain insights into the biological underpinnings of these traits.

A low - frequency variant, rs28929474, (beta = 0.04, P = 2 × 10 -LRB--10)-RRB- was associated with levels of alanine transaminase, an indicator of liver damage.

Here we report ∼ 9.5 million variants from whole - genome sequencing (WGS) of a Cretan - isolated population, and show enrichment of rare and low - frequency variants with predicted functional consequences.

Massive parallel sequencing (MPS) can accurately quantify mitochondrial DNA (mtDNA) single nucleotide variants (SNVs), but no MPS methods are currently validated to simultaneously and accurately establish the breakpoints and frequency of large deletions at low heteroplasmic loads.

In addition, the data reveal that this was a more genetically diverse population than the central and western European hunter - gatherers living during the same epoch and that they also show pattern of adaptation to high latitude environments, including high frequencies of low pigmentation variants as well as a gene region associated with physical performance, which shows strong continuity into modern - day northern Europeans.