Subjects submitted for the 610 Illumina SNP array
Illumina Snp Array Protocol
... and illumina protocol might chew up with potential, only by the ...for snp chips with postnatal samples to load each snp causing the ...to array analyses, birdseye and use git or the ...on ...
5
MethylToSNP: identifying SNPs in Illumina DNA methylation array data
... showed SNP whitespace patterns in the data from YRI individu- ...resembled SNP patterns, but collectively had a median reliability score of ...inform SNP content in functional loca- tions, a feature ...
14
“Gap hunting” to characterize clustered probe signals in Illumina methylation array data
... all SNP‑associated probes may miss disease‑relevant loci Currently, most EWA studies explicitly remove poly- morphism-affected probes that are a priori defined using a reference SNP database or in the ...
21
Construction of a versatile SNP array for pyramiding useful genes of rice
... for SNP detection, modern SNP genotyping techniques are enabling automated, multi-loci allele calling in many samples at a time [13] ...for SNP detection [20–23] ...
9
Comparison of pre-processing methodologies for Illumina 450k methylation array data in familial analyses
... While evidence of clustering according to familial rela- tionships following normalisation correction provides some confidence that biological integrity of the data is preserved, to further test the preservation of ...
14
Additional annotation enhances potential for biologically-relevant analysis of the Illumina Infinium HumanMethylation450 BeadChip array
... CpG SNP should be disregarded in most analyses of the 450 k ...CpG SNP annotation in addition to a current SNP database, as more polymor- phisms are likely to be identified and validated in com- ing ...
15
Identification and systematic annotation of tissue-specific differentially methylated regions using the Illumina 450k array
... and graphs with the R package ggplot2 [50]. Individual variation To determine individual variation we used liver, subcuta- neous fat, omentum and muscle from six autopsy subjects from which we obtained all these ...
12
Polyploidy in myelofibrosis: analysis by cytogenetic and SNP array indicates association with advancing disease
... Common copy number variants were excluded if listed in the Database of Genomic Variants (http://dgv.tcag.ca) or if present when compared to the PB DNA of 12 healthy con- trols sourced from the HapMap sample data set ...
12
Detecting differentially methylated loci for Illumina Array methylation data based on human ovarian cancer data
... group subjects into several age groups based on their age; then for each age group, a nonparametric Kruskal-Wallis test is conducted for the given locus and the p-value is ...
6
Large-scale deployment of a rice 6 K SNP array for genetics and breeding applications
... informative SNP markers for genetics and breeding applications, an Illumina Infinium 6 K SNP chip for rice, referred to as the Cornell_6K_Ar- ray_Infinium_Rice (C6AIR), was designed for use at both ...
13
High Resolution Mapping of QTLs for Heat Tolerance in Rice Using a 5K SNP Array
... the Illumina infinium 5K SNP array for genotyping the parents and the RILs, and stress susceptibility and stress tolerance indices (SSI and STI) of percent spikelet sterility and yield per plant (g), ...
11
Software comparison for evaluating genomic copy number variation for Affymetrix 6.0 SNP array platform
... samples. Subjects were excluded if they had more than 100 CNV intervals detected, B-allele drift > ...the array has genotyping failure (for example, a corner of the array is dried), most other ...
14
Identification of structural aberrations in cancer by SNP array analysis
... Ultimately, SNP array analysis should provide a way to reliably subclassify tumors on the basis of shared genetic abnormalities, so that patients can be assigned to the most appropriate ...as SNP ...
5
Normalization of Human Y Chromosome SNP-Array Data
... similarity. SNP-arrays uses hybridization to find specific sequences, and this becomes a problem when examining the X and Y chromosomes, since their sequence similarity can make it hard for the ...
18
SWAN: Subset quantile Within Array Normalization for Illumina Infinium HumanMethylation450 BeadChips
... Subset-quantile Within Array Normalization; TCGA: The Cancer Genome Atlas. Acknowledgements We thank Kasper Hansen, Martin Aryee and Rafael Irizarry for making their minfi code available and including our methods. ...
12
Allele-Specific Amplification in Cancer Revealed by SNP Array Analysis
... Amplification, deletion, and loss of heterozygosity of genomic DNA are hallmarks of cancer. In recent years a variety of studies have emerged measuring total chromosomal copy number at increasingly high resolution. ...
12
A Scalable Method for Cross Platform Merging of SNP Array Datasets
... former array contains about a quarter of a million probesets, while the latter contains close to two million probesets (half of which are SNP/allelic and the other half are non-allelic ...one array, ...
7
Development of the catfish 250K SNP array for genome wide association studies
... Acknowledgements This project was supported by Agriculture and Food Research Initiative Competitive Grant no. 2009-35205-05101 and 2010-65205-20356 from the USDA National Institute of Food and Agriculture (NIFA). The ...
12
Genetic analysis of products of conception using a HLPA/SNP-array strategy
... and SNP-array detected ...of SNP-array analysis is avoided for ...and SNP-array in Table 1 CNVs identified by SNP-array in spontaneous ...
7
Efficiency and Power as a Function of Sequence Coverage, SNP Array Density, and Imputation
... and array data? What can we learn about technology error modes based on analysis of SNPs for which sequence and array data disagree? To answer these questions, we developed a statistical framework to ...
13