Abstract

From Sequencing to Interpretation: Bioinformatics Challenges in Next Generation Sequencing Cancer Diagnostics

Jeremy Segal, Director, University of Chicago

Next generation sequencing (NGS) technologies are rapidly transforming clinical oncology diagnostics, allowing for dramatically expanded surveillance of nucleic acid signatures to support personalized prognostics and therapeutic interventions. New assay types and clinical targets continue to emerge, as does the associated data volume and complexity, creating unique and exciting challenges for those tasked with managing, analyzing and interpreting the resulting data. These challenges can be of a technical nature, as cancer specimens can be vanishingly small, with degraded nucleic acids, tumor cell heterogeneity and tumor/normal admixture, all of which are likely to produce signal-to-noise problems at the data level. They may also be of a holistic nature. High quality clinical NGS bioinformatics requires teamwork and interconnectedness, not only being responsive to laboratory and clinician needs but also helping to guide and inform laboratory practices, clinical interpretations as well as the overall mission. This lecture will use our experiences at The University of Chicago Medicine to highlight some of the common analytical, technical, and regulatory challenges that bioinformatics groups face when helping to set up oncology genomics clinical diagnostics practices.