IFFPE DNA poses many challenges for preparing NGS libraries, including low input amounts and highly variable damage from fixation, storage, and extraction. It is difficult to obtain libraries with sufficient coverage and sequencing artifacts arising from damaged DNA bases confound somatic variant detection.
We have developed a novel NGS library prep method compatible with both high quality and very low quality FFPE DNA samples, employing a novel enzymatic DNA repair mix, enzymatic fragmentation mix, and PCR master mix. This workflow was validated on real patient samples, using DNA extracted from matched tumor and normal tissue of various tissue types preserved by both fresh frozen and FFPE (DIN 1.5 – 6.8).
This new workflow reduced the false positive rate in somatic variant detection by repairing damagederived mutations in FFPE DNA samples but also improved the library yield, library quality metrics (including mapping, chimeras, and properly-paired reads), complexity, coverage depth, and hybrid  capture library quality metrics. Comparing the variant calls from matched FFPE and frozen tissues  revealed an improved sensitivity and accuracy of variant calling compared to mechanical shearing and other enzymatic fragmentation library prep approaches. This new suite of enzyme mixes improves the overall library prep success rate from challenging FFPE 
samples, allowing even highly damaged FFPE samples to achieve high quality libraries with a greater sensitivity for somatic variant identification and coverage for CNV analysis. The workflow is robust and flexible, compatible with both FFPE DNA and matched high quality DNA samples as well as automation-friendly for convenience in sample processing