CNV report
Description
If in the tested cell line (compared to the reference) new CNVs greater than 2 Mb and/or LOH greater than 5 Mb are detected the CNV QC test has “failed” regarding the internal QC criteria of CUSCO (Core Unit pluripotent Stem Cells and Organoids). The CNV analysis result suggests that the iPSC line contains neither CNVs > 2 Mb nor regions of LOH > 5 Mb.
Files
Steps to reproduce
Technology: Illumina BeadArray Product: Illumina Infinium Global Screening Array-24 BeadChip Manifest: GSAMD-24v3-0-EA_20034606_A1 Clusterfile: GSA-24v3-0_A1_ClusterFile Genotype Analysis GenomeStudio: GenomeStudio V2.0.5 Genotyping Module: V2.0.5 CNV Analysis Algorithm: CNV-Partition Version: 3.2.0 Parameters are set to detect copy number variations (CNVs) ≥ 45 kb and loss of heterozygosity (LOH) regions > 1 Mb with a confidence value > 35. Balanced translocations and inversions cannot be detected with this method. Aberrant copy number regions are identified by log R ratio and B allele frequency. Copy number changes (gains and losses) greater than 0.4 Mb and regions of LOH above 5 Mb are considered reportable and taken into account for interpretation. Genomic positions are based on genome build GRCh37/hg19.