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Whole Exome Sequencing Analysis of Archival Formalin Fixed Paraffin Embedded Tissue (FFPE): Comparison of Different Library Preparation Methods.

Formalin Fixed Paraffin Embedded Tissue (FFPE) procurement is the standard for tumor banking and remains part of clinical standard of care. These samples are an invaluable resource which provides an excellent opportunity to progress cancer research with well characterized histological and pathological annotation combined with extensive clinical data. Exploitation of FFPE samples utilizing Next Generation Sequencing approaches has been challenging. Great strides using targeted DNA sequencing strategies to screen known actionable mutations in FFPE samples have been accomplished however the use of DNA extracted from FFPE for whole exome sequencing (WES) is presently limited. The ability to use archival FFPE samples to screen entire exomes for both known and novel mutations will have strong impact on clinical and basic research initiatives. The pre-capture PCR step within the WES protocol is the most critical when working with degraded samples, which can therefore significantly affect the quality of sequencing data and downstream analysis. To increase efficacy of template production we have tested several different methods to add adaptors (pre-capture PCR) within the WES protocol.