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. 2015 Dec 3;16(12):28765–28782. doi: 10.3390/ijms161226129

Figure 2.

Figure 2

The three analytical NGS (Next-Generation Sequencing) workflows are: (A) FFPE (Formalin-Fixed Paraffin-Embedded); (B) SF (Snap Frozen); and (C) Plasma. These workflows, currently designed for the Ion PGM platform, are divided into five steps: DNA extraction, gDNA Quality, gDNA Quantity, NGS Template preparation, and NGS sequencing and data analysis. The latter, in common among three workflows, includes: Ion PGM sequencing and variant identification using VC software and then GATK for SNVs call. The NGS cost (from DNA extraction to NGS data analysis), excluding personnel, is approximately 250€ for each FFPE, SF, and plasma sample (A–C). The NGS turnaround time for processing SF (B) and no-WGA cfDNA (C) samples is approximately five days, whereas for FFPE (A) and WGA cfDNA (C) samples one more day is required for the multiplex PCR DNA quality control (A) and WGA technique (C).