Sentences with phrase «snp variants»

Based on the proportions of SNP variants in the human population as estimated from a population - level mitochondrial database (mtDB)[50], the probability of sharing all 6 SNPs in common between VP42 and LNCaP by random chance alone is estimated at less than 0.00146 %.

Interestingly, the three most common SNP variants detected in the LNCaP and 22Rv1 - associated XMRV genomes, the aforementioned A → G polymorphism at position 790, an A → G polymorphism at position 4264 and a C → G polymorphism at position 8112, can also be found in the VP35, VP42, and VP62 XMRV genomes, with the exception that the C → G polymorphism is not observed in VP35 due to lack of sequence coverage.

It is therefore striking that the three most common SNP variants identified in LNCaP - and 22Rv1 - associated XMRV by deep sequencing, A790G, A4264G, and C8122G, are also present in the 3 prostate cancer - associated XMRV genomes.

(A and B) SNP variants within the XMRV genome for 22Rv1 and LNCaP (x-axis) are shown in order of decreasing frequency (y - axis).

However as we look at many genomes with this method, we discover that the rate of non-SNP alleles we call is high, and in some cases they occur at loci with simple SNP variants on the other allele.

Yet the particular SNP variants documented in these reports would place both women's male fetuses, and their alleged fathers, onto three branches of the tree simultaneously (see one example).

Reports from the lab obtained by New Scientist listed SNP variants on the X chromosome and chromosome 1 when the fetus was female, and on the Y chromosome when the fetus was male.

But when we showed the results for two cases from 2008 involving male fetuses to specialists on the Y chromosome's evolutionary history, it became clear that something was awry: the combinations of SNP variants reported were inconsistent with the Y chromosome's known ancestry (see «Implausible chromosomes»).

When the report came back, it included a profile for a non-existent fetus, which listed 11 SNP variants across the X chromosome and chromosome 1.

For each prostate cancer - associated mitochondrial genome (z - axis), the minority SNP frequency (y - axis) is plotted against the cell line - associated SNP variant (x-axis), using a frequency cutoff of 3 %.

The proportion of each LNCaP − / 22Rv1 - associated SNP variant in the general human population, with the exception of SNPs 2617T, 10562G, 13227T, 2617T, 5985A, and 9247A for which information was not available, was estimated by searching mtDB, a population - level database of sequenced human mitochondrial genomes [50].

Not exact matches

The strong association of rs117026326 with SLE and the functional implications of nearby NCF1 took the team to their next hypothesis: that the rs117026326 SNP might tag causal variants of NCF1 that were not present in the 1000 Genomes Project database.

Reviewing thousands of genome wide associate studies (GWAS) to identify genetic variants in single nucleotide polymorphisms (SNPs), investigators at Dartmouth's Norris Cotton Cancer Center found that some alleles (one of a pair of genes located on a specific chromosome) are more frequently risk - associated with disease than protective.

The lab has also shifted from testing genetic markers known as short tandem repeats (STRs), which are standard in paternity testing, to recording single letter variants in the genetic code known as single nucleotide polymorphisms, or SNPs, which are rarely used for this purpose.

Adds Visscher: «This is entirely in line with theory and previous inference from SNP [variant] data, yet for some reason many researchers in human genetics and epidemiology continue to believe that there is a lot of non-additive genetic variation for common diseases and quantitative traits.»

All of these studies were genome - wide association studies (GWAS) based on millions of genetic variants called Single Nucleotide Polymorphisms (SNPs).

Having one copy of the risky variant boosts a person's chances of developing ET by 55 percent; having two copies confers a 140 percent greater risk — and the SNP contributes to the condition in only a fifth of cases.

The most common variants are SNPs (single nucleotide polymorphisms).

Their analysis identified new «extreme longevity - promoting variants» on chromosomes 4 and 7, while also confirming variants (SNPs, or single nucleotide polymorphisms) previously associated with longevity.

Each of the genetic variants studied by the researchers is a single - nucleotide polymorphism, or SNP — a site at which the DNA code is altered by a single «letter» or nucleotide in some individuals, and where one «letter» is more commonly found in individuals with higher fracture risk.

These variants, called single - nucleotide polymorphisms (SNPs, pronounced «snips»), are the route through which variations in traits such as hair and eye color, as well as many diseases, are often passed to future generations.

The researchers were looking for variants called single - nucleotide polymorphisms (SNPs, pronounced «snips») that might account for traits unique to pygmies.

It will build on the recently completed HapMap, which describes how blocks of DNA tagged by common variants, called single - nucleotide polymorphisms (SNPs), vary in different populations (ScienceNOW, 26 October 2005).

It will potentially eliminate the need to sequence around a newly discovered disease SNP to find the variant that actually alters the gene product, says NHGRI Director Francis Collins.

Eichler predicted, «In five years there might be a long - read sequence technology that will allow clinical laboratories to sequence a patient's chromosomes from tip to tip and say, «Yes, you have about three to four million SNPs and insertions deletions but you also have approximately 30,000 - 40,000 structural variants.

For these 3 SNPs, we report the ORs for use of aspirin, NSAIDs, or both across genotypes corresponding to 0, 1, or 2 copies of the variant allele (eTable 5 in the Supplement) and the ORs for each SNP by strata of use of aspirin, NSAIDs, or both with 1 common reference group (eTable 6 in the Supplement), to fully describe the interaction.

In general, the results supported the GWAS findings: the variants yielding the lowest p - value were either the lead GWAS SNP or were in perfect LD with the lead GWAS SNP.

Through a combination of SNP genotyping and computational techniques utilizing the extensive Icelandic genealogy, they were able to propagate those 16 million variants into over 40,000 Icelanders for use in this study.

In this study, the authors assessed the impact of SNPs, inherited copy number variants (CNVs), and acquired copy number alterations (CNAs) on the gene expression landscape.

Red SNPs indicate discordant homozygous calls between MAGIC and BRLMM, which are indicative of the presence of «null alleles» (individuals lacking specific binding to either probe, usually because of a variant at the probe binding site).

This variant was in complete LD with the lead SNP from the prior GWAS.

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 %).

The alliance will employ Illumina's platform for high - multiplex single - nucleotide polymorphism (SNP) genotyping to develop tests for gene variants deCODE has previously shown to have impact on the risk of a growing number of common diseases with major public health impact.

Such genetic variants are known as SNPs.

The analysis revealed three SNPs that were more common in the non-healing group than in the normal - healing group — hinting that their respective gene variants may somehow impair or fail to support fracture healing.

Reykjavik, ICELAND, December 16, 2009 — Scientists at deCODE genetics, Inc. (Nasdaq: DCGN) publish in the journal Nature the discovery of a version of a common single - letter variant in the sequence of the human genome (SNP) with a major impact on susceptibility to type 2 diabetes (T2D).

(D) Diagrammatic image of four transcript isoforms that were detected as alternative splice variants resulting from a SNP in the 2nd intron of bsl1 - 2.

Approximately 20 % of people of European descent carry two copies of the first variant, a version of a SNP on chromosome 8q24, putting them at a 50 % higher risk of developing bladder cancer than those without the variant.

Reykjavik, ICELAND, September 14, 2008 — Scientists at deCODE genetics (Nasdaq: DCGN) and colleagues at Radboud University Medical Center in the Netherlands today report the discovery of two common single - letter variants in the human genome (SNPs) that confer increased risk of urinary bladder cancer.

Reykjavik, ICELAND, 6 March 2011 — Scientists at deCODE genetics and academic colleagues from Iceland, The Netherlands, Denmark, USA and Illumina, Inc., today report the discovery of single - letter variants (SNPs) in the sequence of the human genome associated with high risk of sick sinus syndrome (SSS).

NextGENe software contains analysis modules for SNP / INDEL resequencing and amplicon analysis and Structural Variant Detection; Whole Genome Alignment; Prediction and Rare Disease Discovery; Copy Number Variation (CNV); RNA - Seq and Alternative Splicing; small RNA and ChIP - Seq Expression Analysis; Metagenomics; de novo assembly.

Thus far, nearly all association studies have used data from SNP arrays that measure only a subset of all the common variants.

As an accompaniying editorial in the NEJM points out, although BMD has long been known to have a signficant inherited component, these are the first validated and replicated genetic variants ever linked to BMD through a genome - wide scan of SNPs.

As expected, when one considers not just the associated SNP but the nearby variants it represents, a much larger proportion (58 %) overlaps some kind of ENCODE - annotated regulatory region.

While far less prevalent than SNPs, structural variants (SVs) can affect more bases in an individual's genome simply because of their size.

They took 5,694 curated genotype - phenotype associations from the NHGRI GWAS catalog (comprising 4,724 unique SNPs associated with 470 different phenotypes), and performed a functional annotation of those variants using data from ENCODE and other sources.

Notably, that GWAS was conducted using a custom high - throughput SNP array with classic GWAS variants (tag SNPs), a catalog of known protein - altering variants (exome chip) and several custom sets based on prior studies of AMD:

No matter how comprehensive a SNP chip might be, the design still relies on known variant positions.

One possible explanation was that rare variants, which are largely untested by high - density SNP arrays, might account for some of that missing heritability.

Studying a specific type of genetic variation in the DNA sequences of wolves and domestic dogs - called Single Nucleotide Polymorphisms (SNPs)- the scientists identified the transfer of dog gene variants into wolf genomes.