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CHI's Next-Generation Sequencing as a Diagnostics Platform - Short Course

Short Course One*
Next-Generation Sequencing as a Diagnostics Platform

Monday, June 4 • 9:00 am-12:00 pm


Next generation sequencing (NGS) has revolutionized genomics and is now on the verge of being widely adopted for medical sequencing. Until recently, comprehensive genetic testing for genetically heterogeneous diseases was limited by the high cost of traditional (Sanger) sequencing technology. NGS technologies have now completely eliminated this limit such that virtually any gene with a published association to the disease of interest can be tested. Whole exome or whole genome sequencing (WES/WGS) is the ultimate genetic test and early success stories provide a taste of its power; however, while the cost of generating high-quality whole genome sequence data is rapidly dropping, analysis of the enormous number of variants detected is still too complex to implement WGS/WES as a first line genetic test. Targeted NGS based gene panels are typically an order of magnitude smaller than WES/WGS based testing but follow the same principles. Screening large sets of genes is particularly useful when the clinical diagnosis is uncertain as it eliminates the need for costly and lengthy cascade testing that has dominated genetic testing in the past. Drawbacks are significantly increased numbers of detected variants, which poses novel challenges for post-analytic data analyses. The focus of this short course will be on understanding the use of NGS in clinical diagnosis, practical implementation of NGS in clinical laboratories and analysis of large data sets by using bioinformatics tools to parse and interpret data in relation to the clinical phenotype.


Madhuri Hegde, Ph.D., FACMG, Associate Professor, Senior Director, Emory Genetics Laboratory, Department of Human Genetics, Emory University School of Medicine

Birgit Funke, PhD, FACMG, Assistant Professor of Pathology, MGH/Harvard Medical School, Director Clinical Research and Development, Laboratory for Molecular Medicine, Partners HealthCare Center for Personalized Genetic Medicine


Tim Hague, CTO, Omixon


Session 1: Overview of Next Generation Sequencing (NGS) Technology and Clinical Laboratory Implementation

From Sanger Sequencing to NGS: Overview of techniques and clinical applications

Madhuri Hegde

Implementation and clinical validation of NGS in a diagnostic laboratory

Birgit Funke


Precise and Validated Analysis of Mutations in Targeted NGS Data
Tim Hague

Coffee Break 

Session 2: Data analysis and clinical interpretation

Data analysis and variant interpretation pipeline – Example inherited cardiomyopathy

Birgit Funke

Clinical Interpretation of NGS data – Cancer and Whole Exome Sequencing

Madhuri Hegde

Reimbursement for Molecular Dx Tests – Review of current and future landscape

Madhuri Hegde

*A separate registration is required.

Short Course Two 
In Vivo Microscopy and Intraoperative Imaging

Tuesday, June 5 • 2:45 - 5:30 pm

Endoscopic Microscopy: Bridging the Radiology-Pathology Divide 

Guillermo Tearney, M.D., Ph.D., Professor of Pathology, Harvard Medical School; Associate Director, Wellman Center for Photomedicine, Massachusetts General Hospital 

Endoscopic microscopy is a new field where microscopic images are obtained from living patients. This capability opens up possibilities for obtaining histopathologic diagnoses from tissues that are difficult or unsafe to sample, screening entire organs for occult microscopic disease, and understanding disease mechanisms in vivo. In this talk, I will describe some endoscopic microscopy techniques developed, including optical coherence tomography (OCT), optical coherence microscopy (OCM), and confocal microscopy (CM) and will discuss how these methods can potentially impact patient care.

Feasibility of Confocal Fluorescence Microscopy for The Evaluation and Differentiation of Benign and Malignant Human Breast Tissue 

Wei Tse Yang, M.D., Professor and Chief, Section of Breast Imaging Deputy Chairman, Department of Diagnostic Radiology The University of Texas, M.D. Anderson Cancer Center 

Confocal fluorescence microscopy has the potential to be a valuable imaging technique to acquire high resolution images of fresh tissue when used in conjunction with an optical contrast agent such as proflavine.  Proflavine is a topical fluorescent antiseptic which rapidly stains cell nuclei.  In a pilot study, confocal fluorescence images of fresh human breast tissue specimens were visually compared to conventional histo-pathological slides. Findings were categorized as normal, benign lesions, and malignant in situ and invasive tumors. Breast tissue features in confocal fluorescence microscopy were interpreted using the criteria: 1) cell architecture and orientation, 2) nuclear spacing, 3) nuclear size, 4) staining patterns. Confocal fluorescence microscopy and standard histo-pathological preparation show histological features of breast tissue that are comparable in appearance. This optical imaging technique is rapid, inexpensive, and does not require extensive specimen preparation. 

Label-Free Structural and Molecular Optical Coherence Imaging for Intraoperative Guidance in Breast Cancer Surgery 

Stephen A. Boppart, M.D., Ph.D., Bliss Professor of Engineering, Departments of Electrical and Computer Engineering, Bioengineering, and Medicine, Beckman Institute for Advanced Science and Technology, University of Illinois 

Rapid label-free approaches for structural and molecular imaging and histopathology have been developed based on broadband coherence imaging. Optical Coherence Tomography (OCT) provides images of microstructure based on backscattered light, while Nonlinear Interferometric Vibrational Imaging (NIVI) provides molecular histopathology images from vibrational signatures generated by coherent anti-Stokes Raman scattering (CARS). These coherence imaging technologies offer real-time intraoperative feedback, an alternative to traditional post-operative histological staining, and the potential for future in vivo label-free molecular histopathology. 

Rapid Cancer Detection by Topically Spraying an Activatable Fluorescent Probe during the Surgery and Endoscopy Procedures 

Hisataka Kobayashi, M.D., Ph.D., Chief Scientist, Molecular Imaging Program, NCI, NIH 

In this talk, we will discuss the potential of fluorescence-guidance during surgery or endoscopy that will strongly assist defining the tiny cancer or the clear border between cancer and normal tissue for successful sampling of biopsy specimen and total resection of cancer. Additionally, a newly developed activatable probe, which can be activated within a minute after hitting cancer cells (and is therefore a good spraying application) will be introduced. 

Panel Discussion: Intra-Operative Optical Imaging and In Vivo Microscopy: Trends and Applications 

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