Infinium lcg assay

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.

To estimate our method's ability to identify both true regions of copy-number changes and copy-neutral regions, we analyzed a subset of 16 samples from the validation set using the 2.3 million–feature Illumina Human Omni2.5–8 BeadChip array at the Princess Margaret Genomics Centre, Toronto, Canada (http://www.pmgenomics.ca). Each sample was processed following the Illumina Infinium LCG assay protocol, hybridized to two BeadChips, stained as per Illumina protocol, and scanned on an Illumina iScan. The data files were quantified and normalized in the GenomeStudio version 2010.2 genotyping module using HumanOmni25-8v1-1_C.bpm manifest.
To call CNVs, data were exported from Genome Studio and uploaded into Biodiscovery Nexus v7.5 program. The significance threshold for segmentation was set at 1 × 10⁻⁸ and also required a minimum of three probes per segment and a maximum probe spacing of 1,000 between adjacent probes before breaking a segment. The log ratio thresholds for single-copy gain and single-copy loss were set at 0.13 and −0.23, respectively. Systematic GC wave correction was applied using Linear Correction with the HumanOmni2-5-8v1-1-C_hg19_illum_correction.txt file.

Genomic DNA was purified from the whole blood using Puregene chemistry on the Qiagen Autopure LS according to standard automated Qiagen protocols (Valencia, CA, USA). As part of a larger study, the samples were genotyped using Illumina’s Infinium^® Expanded Multi-Ethnic Genotyping Array (MEGA^EX) (Illumina, Inc., San, Diego, CA, USA), which interrogates approximately 2 million markers. The samples were processed according to Illumina Procedures for processing of the Infinium LCG ^® Assay (Illumina, Inc., San Diego, CA, USA). Data were extracted by the Illumina ^® Genome Studio software (GenomeStudio, v2.0.5) from data files created by the Illumina iscan. Samples with call rates below 98% were excluded from the analysis and a GenCall cutoff score of 0.15 was used for all of the Infinium II ^® products. We then extracted the genotype calls for rs1800693, our biallelic SNP of interest. Participants were characterized as homozygous for the major allele T, and heterozygous or homozygous for the minor allele C.