Peter L Nagy
Columbia University, USA
Title: Optimizing sensitivity and specificity of clinical next generation sequencing in constitutional and cancer applications
Biography
Biography: Peter L Nagy
Abstract
Our Laboratory of Personalized Genomic Medicine (LPGM) at Columbia University Medical Center started to offer clinical whole exome sequencing (WES) in January 2013 and clinical cancer whole exome/transcriptome(CWES) sequencing since January 2014. We processed and issued reports on over 500constitutional and about 100 cancer cases. The majority of these samples are from the pediatric population (>80%) both for constitutional and cancer testing. Of the cases analyzed to date we have identified pathogenic or probable pathogenic mutations responsible for the patients’ condition in about 30 percent of the cases and changed clinical management of pediatric malignancies in about 20 percent of our patients. The fact that a large percentage of cases remain without molecular diagnosis or useful clinical treatment recommendation indicates that we need to improve our assignment of pathogenic effect to mutations in genes not previously linked to disease. We have developed a database we refer to as “SNP-catcher” that integrates patient information with a molecularsystems approach to evaluate the significance of mutations. Such systems driven analysis of clinical exome and transcriptome sequencing data is an important step in the accelerateddiscovery of novel disease causing genes and disease mechanisms and obtaining useful treatment recommendations. Through my presentation the audience will obtain an understanding of the current state of the art of clinical genomic testing; will become familiar with the major factors that determine the precision and sensitivity of pathogenic mutation detection; have a thorough understanding of the importance of proper implementation of structural and functional basic science data sources into the clinical analysis pipeline. I will outline the contribution of clinical data collection to discoveries in basic science and review the obstacles to and opportunities for more efficient collaboration between clinical medical centers and the pharmaceutical industry.