Concordance of Genotyping Array Data

Human genotyping array data is from Illumina HumanOmni2.5-8 platform. This array has about 2.37 million tag SNPs from 1000 genomes pilot project with MAF ≥2.5%. Illumina Inc. supplied genotypes for all the samples from HumanOmni2.5-8 by performing Illumina Infinium LCG assay and thereupon calling the genotypes using their propriety software called GenomeStudio. They provide genotype for each of these probes with GenCall scores. Illumina recommends a GenCall score cut-off of 0.15 for their infinium assay based products
[20 (link)]. This recommended GenCall score cut-off of 0.15 was used to test the concordance with the GATK and CASAVA pipelines.

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Kumar P., Al-Shafai M., Al Muftah W.A., Chalhoub N., Elsaid M.F., Aleem A.A, & Suhre K. (2014). Evaluation of SNP calling using single and multiple-sample calling algorithms by validation against array base genotyping and Mendelian inheritance. BMC Research Notes, 7, 747.

Publication 2014

HumanOmni2.5-8 platform Infinium LCG assay

Assay Genomes Genotype Human Snps

Corresponding Organization : Helmholtz Zentrum München

Other organizations : Weill Cornell Medical College in Qatar, Hamad Medical Corporation

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Variable analysis

independent variables

GenCall score cut-off of 0.15

dependent variables

Concordance with the GATK and CASAVA pipelines

control variables

Illumina HumanOmni2.5-8 platform
Approximately 2.37 million tag SNPs from 1000 genomes pilot project with MAF ≥2.5%
Illumina Infinium LCG assay performed by Illumina Inc. to call genotypes using their propriety software called GenomeStudio

Annotations

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