Figure 1.
Estimation of copy number from exome sequencing data in the X chromosome of males and females.
For each individual exon we calculated the coverage ratio as the ratio of RPKMs for that exon divided by the average RPKMs for that particular exon in females. (A) Distribution of ratios for more than 566,000 individual exons from either males (blue) or females (red). Effect of the number of consecutive exons considered for copy number estimation in sensitivity and false discovery rate. (B) For each different number of exons (numbers close to dots), the sensitivity is expressed as the fraction of male regions detected as copy number one when compared to the female average for the same regions. False discovery rate was calculated as the fraction of female regions detected as copy number one when compared to the female average for the same regions.
Figure 2.
Scheme depicting the strategy used by exome2cnv for detecting CNAs using exome coverage data for a tumor sample and a normal sample from the same patient.
Normalized coverage (RPKMs) is determined for each individual capturing exon, and the ratio tumor/normal is calculated for each probe. Genome-wide analysis of ratios allows the identification of regions having somatic copy number alterations in the tumor (red lines).
Figure 3.
Comparison of CNAs obtained by exome2cnv and aCGH in 86 CLL cases.
CNAs were classified in four different classes represented by different colors in the figure. CNAs detected by both exome2cnv and aCGH approaches are labeled in yellow; those detected specifically by exome2cnv are shown in green; CNAs only detected by aCGH are shown in red; and CNAs detected by exome2cnv and considered as subclones by aCGH or corresponding to immunoglobulin regions are shown in purple. Regions recurrently altered in CLL are indicated on top.
Figure 4.
Comparison between CNAs detected by exome2cnv and aCGH.
Grey dots represent log2 ratios of tumor/normal probe intensities from aCGH, while black dots show log2 ratios of tumor/normal from exome sequencing data. The local averages determined for exome data (red lines) and aCGH data (green lines) are shown. (a) Homozygous deletion of a small region of chromosome 13 detected by both approaches. (b) Detailed view of the same chromosomal region shown in (a).