FFPE is the most common method used to store precious clinical samples at room temperature for extended periods (sometimes>15 years). FFPE samples are therefore one of the most commonly available samples that can be used for discovery and diagnosis. Whole Exome Sequencing (WES) is one of the most used NGS assays that is used for profiling somatic and tumor mutations. With future clinical trials moving towards less invasive collection methodology, core needle biopsy samples are becoming a method of choice. The FFPE fixation process leads to the degradation of nucleic acids due to cross-linkage and the availability of sufficient nucleic acid from CNB fixed samples for downstream NGS assays is becoming limited. Here we report a comparison of two Whole Exome capture kits the xGen Exome Hyb Panel v2 (IDT) Kit and the Twist Exome 2.0 (TWIST) Kit. Libraries were prepared in triplicate using the Ultra™ II DNA Library Prep (NEB) kit. The performance of each capture kit was evaluated on the number of libraries eligible for capture, percent duplication rate, median insert size, and mean target coverage. Taken together, our testing shows that TWIST and IDT kits generated comparable sequencing metrics. However, the TWIST Kit outperforms the IDT Kit in percent eligible libraries qualifying for hybridization capture. TWIST Kit is a great qualifier for highly degraded FFPE samples, especially those with limited input DNA material.
