Comparison of FFPE and snap frozen tissue material for whole exome re-sequencing approaches. (A) Exonwise coverage comparison of snap frozen and FFPE DNA preparations for a benign tissue sample. Coefficients of variation are calculated exonwise and plotted by the smallest coverage of each exon-exon comparison. As reference, coefficients of variation were calculated for two sequencing replicates of the snap frozen preparation (B) Mean coverage by GC content for snap frozen and FFPE DNA preparations. All exons were split into 800 bins by GC content and the average exon coverage was averaged within each bin. (C) Comparison of SNVs and InDels detected in snap frozen and FFPE DNA preparations for a benign tissue sample. False negative SNVs/InDels are detected in the snap frozen preparation but not in the FFPE preparation. False positive SNVs/InDels are detected in the FFPE preparation but not in the snap frozen preparation. (D) Comparison of SNVs detected in snap frozen and FFPE DNA preparations with Affymetrix SNP array 6.0 plotted by minimal coverage.