Figure 10

Comparison of CNV callings by AluScanCNV and FREEC. (A) Chromosomal distribution of CNV gains obtained by FREEC based on hg18 [7] (green bands above cytobands) or by the CBS-based extended CNV calling in AluScanCNV (orange bands below cytobands). Correlation between the two sets of results yielded Pearson’s R =0.776. (B) Chromosomal distribution of CNV losses obtained by FREEC (green bands above cytobands) and by AluScanCNV (orange bands below cytobands). Correlation between the two sets of results yielded Pearson’s R =0.935. The same dataset on cancer cell line HCC1143 from ref.27 was employed in all the CNV estimations. Correlation R values were estimated using the human genome graph function in UCSC (http://genome.ucsc.edu/cgi-bin/hgGenome).