A comparison of genomic copy number calls by Partek Genomics Suite, Genotyping Console and Birdsuite algorithms to quantitative PCR

Using data from 29 Affymetrix SNP 6.0 arrays, we determined copy numbers using three programs: Partek Genomics Suite, Affymetrix Genotyping Console 2.0 and Birdsuite. We compared array calls at 25 chromosomal regions to those determined by qPCR and found nearly identical calls in regions of copy number 2. Conversely, agreement differed in regions called variant by at least one method. The highest overall agreement in calls, 91%, was between Birdsuite and quantitative PCR. Partek Genomics Suite calls agreed with quantitative PCR 76% of the time while the agreement of Affymetrix Genotyping Console 2.0 with quantitative PCR was 79%.In 38 independent samples, 96% of Birdsuite calls agreed with quantitative PCR. Analysis of three copy number calling programs and quantitative PCR showed Birdsuite to have the greatest agreement with quantitative PCR.Copy Number Variants (CNVs) are defined as amplifications or deletions of >1 kilobase segments of the genome [1,2]. Gene duplications were first identified in the pathogenesis of Charcot-Marie Tooth disease in the 1980s; a copy number (CN) amplification of the PMP22 gene was shown to be sufficient to cause disease [3]. These regions of variance were thought to be rare and when the human genome was published, variance amongst humans was primarily attributed to base-pair level single nucleotide polymorphisms (SNPs) [4,5]. However, CNVs were discovered to be present and widespread in the genome shortly thereafter [1,2]. These variants are generated during normal recombination events, leading to inherited CNVs, as well as somatically throughout life in rapidly dividing cells [6-8]. CNVs can directly influence gene expression through dosage effects where more copies of the gene produce greater expression, and also by altering transcriptional regulation in the genome, both in the region of variance itself and also in regions up to 1 megabase away [9-11].CNVs can be detected by fluorescence in situ hybridization, bacterial artificial