Sentences with phrase «snp arrays»

July 16, 2009: Clemson University is on schedule to order the SNP arrays this month.

January 2010: Dr. Leigh Anne Clark has had the EPI Genetic SNP arrays ready to go to NIH for over a month, however, it has been difficult to secure a scheduled time to process this with NIH.

That would have been convenient, because such variants can be genotyped with precise, inexpensive, high - density SNP arrays in tens of thousands of samples.

SNP arrays will always miss this class of variants, because their positions and alleles aren't known before the experiment.

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

This month in Nature, researchers from BC Cancer Agency have characterized the landscape of genomic aberrations in 104 TNBC cases with a combination of whole - genome sequencing, exome sequencing, RNA - seq, and high - density SNP arrays.

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

Undoubtedly there is sequence variation that influences gene expression but isn't well - captured by SNP arrays.

Bioinformatics services include data QC, outlier detection and general data management, and data analysis from platforms including Illumina or Affymetrix microarrays, RNA - Seq, SNP arrays, Exome - sequencing, ChIP - chips and CHIP - seq.

The genetic markers on high - density SNP arrays are carefully chosen to capture (or «tag») most common haplotypes in human populations.

Many such pharmacogenomics projects are under way, though most are employing SNP arrays or targeted sequencing.

We had high hopes for SNP arrays and GWAS, but as I discussed in my previous post, sequencing at large scale is required to uncover the full scope of genetic variation underlying complex phenotypes.

We therefore performed unsupervised clustering analyses with ADMIXTURE (SNP array data; Supplementary Fig. 15) and NGSadmix (whole - genome data; Fig. 4 and Supplementary Fig. 16)(Supplementary Note 9) and found that, unlike contemporary European village dogs, all three ancient genomes possess a significant ancestry component that is present in modern Southeast Asian dogs.

We used the golden jackal and Andean fox as outgroups for the SNP array and the whole - genome data sets, respectively.

No mention of dbSNP or Affy SNP array concordance for SNVmix calls was offered, so one can not evaluate the algorithm.

After initially applying the genomic SNP chromosomal microarray only in fetuses with ultrasound abnormalities, since July 2012, we routinely performed the SNP array also in cases without fetal ultrasound anomalies where invasive prenatal diagnosis was indicated.

The patterns of somatic copy number changes, as assessed by high - density SNP array, suggest widespread segmental CNA instability:

Most of these compare gene expression data (microarray or RNA - seq) to high - density SNP array genotypes.

PCA was carried out using SNPs overlapping with the genomic coordinates covered by the equine SNP array for nine Przewalski's horses, as well as 14 (8) and 32 (40) domestic breeds, representing a total of 348 and 729 individuals, respectively.

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:

Often, we know this in advance, either because the parents know they're related, or a SNP array revealed less than the expected amount of heterozygosity (variability between chromosomes).

To this end, we are presently collecting samples from additional dogs that will be used to probe the SNP array as part of a larger study.»

To reduce the background (e.g., reduce false positives), it is necessary to collect SNP array data for additional EPI - affected and normal GSDs.

The next step is that the researchers need to prepare the DNA for use on the SNP array.

In 2008, preliminary data were collected for 18 EPI - affected and 25 unaffected GSDs using the canine SNP array.

Genome wide genotyping using the Illumina version 1 SNP array has been performed on 366 dogs of several breeds (Zhou et al., 2010).

Not exact matches

In particular, one of the platforms used in their work, the Illumina 610 - Quad array, has been shown in unpublished studies by other investigators to produce artifactual genotype data at a subset of SNPs.

MyOPGP data has facilitated the development of important genomic platforms, such as single nucleotide polymorphism (SNP), oligo and methylation arrays.

A series of SNP genotyping arrays for the house mouse (Mus musculus) on the Illumina Infinium platform.

(B) Analysis is based on array data for ∼ 54,000 SNPs.

Other efforts include array - based sequencing - by - hybridization with Callida Genomics, and simultaneous typing of SNPs on chromosomal regions undergoing LOH using customized Affymetrix tag - arrays.

We have in - house computational pipelines built for metagenomic viral discovery, RNASeq quantification, exome sequencing and whole genome sequencing for variants detection using GATK, Affymetrix & Illumina expression array and SNP chips, GWAS, digital PCR analysis, mass spectrometry and biomarker discovery.

First, we noticed that a tiny fraction of 0.025 % of all SNPs (229/907, 551 SNPs) were not correctly identified by any of the four technologies suggesting that those SNPs may not be correctly identified on the arrays.

As gold standard for SNV calling, we used genotypes determined by Affymetrix SNP 6.0 Array Technology (total of 907,551 SNPs after quality filtering).

The SNP calls by the SNP6 array were compared based on the genotype level.

Percentage of genome covered by different types of genomic elements, in comparison to the distribution of SNP6 array SNPs on these genomic elements.

Distribution of Affymetrix SNP6 array SNPs in genomic elements analyzed.

As the gold standard for all four samples we used SNPs found by Affymetrix SNP6 arrays as an independent and well - established SNP calling technology (see Figure S10 and Figure S11 for an overview on the distribution of array SNPs in different regions of the genome).

For validation of SNP calls with an independent technology, Affymetrix SNP 6 arrays were hybridized and analyzed as previously described [18].

The level of inbreeding based on the proportion of SNPs that were homozygous in canine 170 K arrays was virtually identical in the two breeds; 0.65 ± 0.03 in English bulldogs and 0.63 ± 0.03 in Standard Poodles.

The second independent dataset was also run on the Affymetrix Version 2 Canine array with 49,663 SNPs (50K).

Experienced in developing pipelines and subsequent analysis / interpretation of high - throughput array data (microarrays, SNPs and CNVs), NGS data (RNA - Seq, miRNA - Seq and ChIP -...