FFPE NGS Analysis
FFPE samples are the archive of clinical research — decades of banked tumor tissue with matched outcomes data, waiting to be sequenced. The problem isn't access. It's that formalin fixation fragments DNA, crosslinks RNA to protein, and introduces C-to-T deamination artifacts that contaminate variant calls if not accounted for in the prep workflow.
This page covers FireGene products designed for the FFPE-to-NGS pipeline, from tissue processing through library submission.
FFPE DNA Extraction The FFPE gDNA Extraction Kit includes a dedicated deparaffinization step followed by proteinase K digestion and heat-based decrosslinking to reverse formaldehyde-induced crosslinks before column purification. The result is inhibitor-free gDNA usable for targeted NGS panels, whole-exome sequencing, and somatic variant calling — the applications where FFPE input quality directly determines call accuracy.
FFPE RNA Extraction The FFPE RNA Extraction Kit uses the same deparaffinization and decrosslinking workflow adapted for RNA. Formalin crosslinking degrades RNA over time and reduces recoverable fragment sizes to the range that targeted RT-PCR and RNA-seq panels require. The kit recovers usable RNA down to the short fragment sizes consistent with aged archival blocks.
NGS Library Preparation Two library prep options for FFPE-derived DNA. The DNA Rapid Sequencing Kit for Illumina covers standard-quality FFPE inputs. For higher-quality inputs where duplication bias would distort allele frequency measurements — copy number analysis, somatic variant panels at low VAF — the Non-Amplification DNA Library Kit eliminates PCR amplification entirely, preserving the library complexity of the original extract.
Compatible with Illumina sequencing platforms. For custom panel workflows, contact us directly.
