APR 06, 2016 01:30 PM PDT

Validation and Implementation of Whole-Exome Sequencing to Guide Precision Cancer Care

  • Assistant Professor of Pathology and Laboratory Medicine, Weill Medical College of Cornell University
      Hanna Rennert, Ph.D., F.A.C.M.G. is Assistant Professor of Pathology and Laboratory Medicine at Weill Medical College of Cornell University, and Director of the Molecular Pathology Laboratory at the New York Presbyterian Hospital – Weill Cornell Medical Center. She received her Ph.D. in Biochemistry from the Technion-Israel Institute of Technology Medical School. Following postdoctoral training at the University of Pennsylvania, Dr. Rennert served in oversight roles within the Molecular Pathology Laboratory in the Department of Pathology and Laboratory Medicine. From 2000 until 2002, she directed a Microarray Research and Development Laboratory at Tel-Aviv Sourasky Medical Center. Dr. Rennert rejoined the University of Pennsylvania School of Medicine in 2002 as a Senior Molecular Genetics Scientist and adjunct faculty in Molecular Pathology. She is certified by the American Board of Medical Genetics in Clinical Molecular Genetics, and is obtaining a certificate in Clinical Epidemiology from the Center for Clinical Epidemiology and Biostatistics at the University of Pennsylvania. Dr. Rennert directed the Molecular Diagnosis and Genotyping Facility within the Pathology Department until July 2005 when she came to Weill Cornell Medical College. Dr. Rennert's primary research interest is the genetic epidemiology of prostate cancer. In collaboration with researchers from Sanjay Gandhi Post Graduate Institute of Medical Sciences in India and the University of Pennsylvania, we established in 2004 a study for examining the role of genetic factors in the disparity in prostate cancer incidence and disease characteristics between high risk (African Americans) and low risk (Asian Indians) populations. Currently, wide-genome scan association studies have identified numerous single nucleotide polymorphisms (SNPs) and susceptibility loci associated with prostate cancer risk, including a region on chromosome 8q which is commonly amplified in prostate cancer. The role of candidate inherited susceptibility gene variations and their association with prostate cancer risk in these two populations are being studied. A second research interest is the development of clinical molecular tests and applications. Her current efforts as the Director of the Molecular Pathology Laboratory at NYPH-WCMC are focused on expanding the Molecular Pathology test menu, particularly in virology, genetics, and oncology. Specific tests under development include quantification assays for the herpes viruses using real-time PCR, pharmacogenetic testing and EGFR/RAS mutation analysis. In addition, in collaboration with clinicians and researchers at the Rogosin Institute, Dr. Rennert's group has developed and implemented a new strategy to screen for mutations in the polycystic kidney disease 1 and 2 genes (PKD1 and PKD2), using a mismatch-specific DNA endonuclease and DHPLC. This work also included the development of an in-silco algorithm for evaluating the pathogenic potential of gene variations of unknown significance (VUS), and she is currently working with her collaborators on automated mutation calling and evaluation of VUS.


    Cancer remains the second leading cause of death in the United States.  Most tumors arise from a myriad of genetic changes that dysregulate cell growth and prompt survival.  Identification of genetic alterations by next generation sequencing (NGS), using either targeted sequencing or whole exome sequencing (WES) has become the standard of care in genomic medicine.  WES applies NGS technology to identify genetic variants in the coding regions (exons) of genes, harboring the majority of disease causing-mutations.  Using WES, it is currently feasible to not only detect a rapidly growing set of known clinically relevant mutations, but also identify novel or unexpected important variations, including constitutional mutations in cancer predisposing genes.  Thus far, the use of WES in cancer has largely taken place in the setting of large research studies.  Integration of WES into precision cancer care has lagged behind primarily due to technical challenges such as small and poor quality (FFPE) tissues and low-tumor purity samples that have not been rigorously validated in the clinical setting.  Another challenge is the analytical and computational approaches used to detect the wide-spectrum of mutations and genes queried by WES, which requires a comprehensive validation procedure to demonstrate the ability of the test to identify actionable mutations with high accuracy and at an acceptable analytical sensitivity.  The third challenge is a clinical challenge to attain meaningful interpretations of the genomic data which then can be used for patient care.  While these challenges are well recognized and despite a wide range of assays and platforms available, WES application in cancer has not yet been validated for the clinical laboratory and has not been fully characterized in the literature with regard to the analytic and clinical validity of the testing and the various types of relevant mutations.  The few existing guidelines given by professional societies give only high-level directions for implementing NGS testing geared primarily towards the use of targeted panels rather than WES.  By all accounts, New York State-Department of Health (NYS-DOH) requirements are among the most rigorous guidelines yet published and are likely to serve as a paradigm for suggested future type of guidelines that might be required by the Food and Drug Administration (FDA).  These efforts are also in line with the new precision medicine initiative announced by U.S. President Obama with the intent to bring us closer to curing cancer and give all of us access to a more personalized and genomic-driven medicine.
       This presentation describes the development and analytical characteristics of NYS-DOH approved clinical exome cancer test suitable for simultaneous detection of somatic dingle nucleotide variants (SNVs), indels and copy number alterations (CNAs) using the Agilent HaloPlex capture platform and the Illumina HiSeq2500 system for sequencing.  Initial validation has focused on actionable mutations in five principal, clinically relevant genes and according to NYS-DOH guidelines.  The automated computational framework for data analysis, variant interpretation and reporting is also discussed. 

    The objectives of this presentation are:

    • To describe the development and analytical characteristics of a New York State-Department of Health (NYS-DOH) approved clinical Exome Cancer Test suitable for simultaneous detection of somatic single nucleotide variations (SNVs), indels and copy number alterations (CNAs). 
    • To discuss the automated computational framework for data analysis, variant interpretation and reporting of whole exome sequencing (WES) data, using examples of clinical cases and reporting of WES results. 

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