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1.

Figure 2. From: Exome Enrichment and SOLiD Sequencing of Formalin Fixed Paraffin Embedded (FFPE) Prostate Cancer Tissue.

Copy number variation analysis of exome sequenced fresh frozen tumor and FFPE tumor after normalization with FFPE normal prostatic tissue. Copy number variation analysis of fresh frozen tumor and FFPE tumor versus FFPE normal prostatic on three chromosomes. For each window the ratio between normal and tumor tissue has been calculated. Furthermore, the log2 has been applied to these ratios. The genomic position is represented on the x-axis. The log2 ratios of the fragments are represented on the y-axis. The average is depicted by the red line.

Roopika Menon, et al. Int J Mol Sci. 2012;13(7):8933-8942.
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Figure 1

Figure 1. From: Exome Enrichment and SOLiD Sequencing of Formalin Fixed Paraffin Embedded (FFPE) Prostate Cancer Tissue.

Venn diagrams representing single nucleotide variation (SNV) profiles. The SNV analysis showed a total of 6853 SNVs for FFPE normal prostatic, 5445 SNVs for FFPE tumor and 7707 SNVs for fresh frozen tumor. (a) FFPE tumor vs. fresh frozen tumor tissue: The total number of common SNVs between FFPE tumor and fresh frozen tumor were 4618. 84.9% of the FFPE SNVs were common to the fresh frozen sample. (b) FFPE tumor vs. FFPE normal prostatic tissue: Upon normalization with FFPE normal prostatic, the tumor specific SNVs for FFPE tumor were 864. There was a 84.1% overlap between the fresh frozen tumor and FFPE non prostatic tissue. (c) Fresh-frozen tumor vs. FFPE normal prostatic tissue: Upon normalization with FFPE normal prostatic, the tumor specific SNVs for fresh frozen tumor were 2151. There was a 72.1% overlap between FFPE tumor and FFPE normal prostatic tissue.

Roopika Menon, et al. Int J Mol Sci. 2012;13(7):8933-8942.

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