Under the direction of Carlo B. Bifulco, M.D., the Molecular Pathology Core is a fundamental component of translational research at Providence Cancer Institute.
It provides translational immunologists with molecular correlates to their research questions, leveraging shared clinical infrastructures dedicated to the deployment of an institute-wide personalized medicine program enabling high-throughput “omics” projects with clinically-validated bioinformatics pipelines supported by a dedicated in-house software development team.
Services include performance of NanoString, mRNASeq, whole exome sequencing, T-cell receptor sequencing and the analysis and quantification of circulating tumor DNA. The core maintains a significant and diverse sequencing infrastructure including the high-capacity Illumina HiSeq 4000, Illumina cBot 2 clustering system, Thermo Fisher IonTorrent S5 sequencer, Beckman BioMek FXP liquid handler robotics for automated library preparation sequencing, as well as instruments for performing Sanger sequencing and quantitative polymerase chain reaction.
Software tools developed in-house include applications for variants annotation and visualization, as well as scalable, state-of-the-art cloud-based pipelines for comprehensive analysis of exome data for both research and clinical CLIA-certified reporting. All applications include data security, access logs, data storage, and backup, and are built to operate in the clinical setting.
As a part of Providence Health & Services laboratories, the facility is licensed by the Oregon State Health Division and accredited by various agencies such as the College of American Pathologists, Joint Commission, American Association of Blood Banks and the FDA.