| Analysis | Normalised microarray signal intensity data for both cohorts was analysed with PennCNV (2009Aug27 v.) and QuantiSNP (v.2) programs to call putative CNVs in each individual. Settings and parameters suggested by authors were used for both algorithms together with the 'genomic wave' adjustment for the signal intensity data. Additionally, with PennCNV we used separate B allele-frequency files (PFB-file) - for the EGCUT dataset we used general Estonian population-based dataset as the reference (n=1000). As a quality control measure, we checked that all samples met the following quality criteria calculated by the PennCNV program: LRR_SD <= 0.25, BAF_SD <= 0.05, BAF_DRIFT <= 0.002 and GCWF <= |0.04|. Raw CNV calls from PennCNV and QuantiSNP were then merged (as intersection, for each individual separately) with custom PERL script and only CNVs that were similarly called (same type of overlapping copy number change - gain or loss) were considered. From the resulting list of CNVs we filtered out CNVs i) called on X/Y chromosomes; ii) shorter than 1000 bp in length; iii) with QuantiSNP log Bayes Factor (LBF) less than 5. In order to achieve high-quality CNV dataset, we confirmed our HapMap YRI CNV calls with an independent set of validated CNV calls for the same HapMap YRI individuals. CNV calls generated and confirmed with custom Affymetrix (Emeryville, CA, USA) high-resolution microarrays (with 32 million unique oligonucleotide probes for CNV discovery and 800,000 unique probes for CNV confirmation) by Matsuzaki et al. [Matsuzaki H, Wang PH, Hu J, Rava R, Fu GK (2009) High resolution discovery and confirmation of copy number variants in 90 Yoruba Nigerians. Genome Biol 10: R125.] were downloaded from http://genomebiology.com/2009/10/11/R125/additional/. CNVs called by us and CNVs called and confirmed by Matsuzaki et al. were compared for each individual separately (custom PERL script) and only CNVs that were called in both datasets were considered. Throughout this study we used the NCBI Build 36/hg18 assembly coordinates of the human reference sequence. |
