Bio IT World Expo 2016  
Bio IT World Expo 2016
Archived Content

Molecular Diagnostics Informatics 

Final Agenda


7:00 am Workshop Registration and Morning Coffee

8:00 am - 4:00 pm Pre-Conference Workshops*

*Separate Registration Required

2:00- 7:00 pm Main Conference Registration

4:00 Event Chairperson's Opening Remarks

Cindy Crowninshield, RD, LDN, Conference Director, Cambridge Healthtech Institute

4:05 Keynote Introduction

Sanjay Joshi, Solutions Architect, Life Sciences, EMC Isilon Storage Division



Martin LeachMartin Leach, Ph.D., CIO, Broad Institute of MIT and Harvard


Jill MesirovJill P. Mesirov, Ph.D., Associate Director and Chief Informatics Officer; Director, Computational Biology and Bioinformatics, Broad Institute of MIT and Harvard


Hitachi Data Systems5:00 - 7:00 Welcome Reception in the Exhibit Hall with Poster Viewing

Drop off a business card at the CHI Sales booth for a chance to win 1 of 2 iPod touches® or 1 of 2 Xbox 360s®*!

*Apple® is not a sponsor or participant in this program




7:00 am Registration and Morning Coffee

7:55 Chairperson's Opening Remarks

Phillips Kuhl, Co-Founder and President, Cambridge Healthtech Institute

8:00 Keynote Introduction

Bas Burger, President, Global Commerce, BT Global Services



Eric PerakslisEric D. Perakslis, Ph.D., CIO and Chief Scientist of Informatics, U.S. Food and Drug Administration


8:45 Benjamin Franklin Award & Laureate Presentation

9:10 Best Practices Award Program

Cycle Computing small9:45 Coffee Break in the Exhibit Hall with Poster Viewing


MDx Enabled Personalized Care 

10:50 Chairperson's Remarks

Kevin Krenitsky, M.D., COO, Foundation Medicine

11:00 DNA Testing While You Wait: the Promise of Nanowire Diagnostics

Sir John Burn, MD, FMedSci, Professor of Clinical Genetics, Institute of Genetic Medicine, Newcastle University, UK; Genetics Lead, National Institute of Health Research, UK; Medical Director, QuantuMDx Ltd

A major barrier preventing genomic knowledge being translated into routine tests with real clinical utility  is the cost and complexity of DNA analysis.  The current crop of devices has cut cost per base  and improved turnaround but capital costs are restrictive and their design relies on centralised sample processing.  We have developed, in an academic/commercial partnership, a novel method of performing genotyping and sequencing which involves a simple DNA filtration system, a microfluidic PCR followed by use of nanowires as field effect transistors to detect binding of heavily charged nucleotides to single stranded DNA bound by linker molecules to the nanowires.  The result is a feasible method of providing handheld, targeted DNA sequencing for diagnostics at the point of need. We will manufacture a cell phone sized, portable device which will provide, using disposable cassettes, a sample to result output in around 20 minutes for around 20 dollars. We will explore real-time infectious disease epidemiology combining local DNA analysis on multiple  portable DNA Sequencers linked to cloud based analysis and transmission to centres of research excellence, allowing for the monitoring of emerging infections and/or drug resistance. Furthermore we predict  routine use of molecular pathology and primary care based pharmacogenetics to target medications in addition to more traditional genetic diagnostic applications. Affordable DNA testing "while you wait" anywhere on the planet and in real-time, is within reach.

11:30 Genomic Analysis Goes to the Clinic: An Intuitive Interface for a Complex Challenge

Kevin Krenitsky, M.D., COO, Foundation Medicine

When a physician reads a thermometer or blood pressure gauge the results inform their diagnosis almost intuitively. For genomic sequencing advanced computational biology can identify medically relevant mutations out of miles of base pairs, but applying this complex analysis to routine care is far from intuitive. This talk will take us from computational biology to an elegant clinical interface, showing how physicians are now using genomic analysis seamlessly in practice to provide the best possible treatment for individual patients.

12:00 pm Biomarker Discovery by NextGen Sequencing of Immune Repertoire

Jian Han, Ph.D., Faculty Investigator, Hudson Alpha Institute for Biotechnology

This presentation describes the Repertoire 10K or R10K project – a new method for analysis of the immune repertoire by high-throughput sequencing and informatics, and a new index for measurement of health status and disease prognosis. This method is based on semi-quantitative and comprehensive analysis of the T cell receptor beta CDR3 sequences present in peripheral blood.

12:30 Luncheon Presentation (Sponsorship Opportunity Available) or Lunch on Your Own


Clinical Applications of MDx 

1:40 Chairperson's Remarks

William G. Loudon, M.D., Ph.D., Assistant Professor, Neurosurgery, University of California Irvine; Section Chief, Neurosurgery, Children’s Hospital of Orange County

1:45 Challenges for Clinical Acceptance and Application of Cutting Edge Molecular Diagnostic and Therapeutics by the Medical Community

William G. Loudon, M.D., Ph.D., Assistant Professor, Neurosurgery, University of California Irvine; Section Chief, Neurosurgery, Children’s Hospital of Orange County

2:15 Clinical Genomicist Workstation:  Analyze, Interpret, and Report NextGen-Based Molecular Diagnostic Studies

Rakesh Nagarajan, Ph.D., Asst Professor, Pathology & Immunology, Washington University

The advent of genome-wide profiling technologies and their routine use in basic science and translational research is now promoting their application in the clinical setting.  However, there are several potent informatics barriers that must be overcome before clinical sequencing can become routine.  Good Laboratory Practice-based quality assurance metrics must be established to guarantee the accuracy required to make medical decisions.  Genetic variants identified by sequencing must be systematically annotated and interpreted so that a clinical genomicist can decide which are medically actionable.  Software applications and technologies are required to facilitate reporting of genomic results and to transmit these data to the electronic health record (EHR). To address these issues, we have developed the Clinical Genomicist Workstation (CGW), which is a 'soup-to-nuts' solution for processing clinical sequencing orders from specimen accessioning to report finalization, sign out, and submission to the EHR.

2:45 Genalysis: Semiconductor Based True Point-of-Care Nucleic Acid Testing for the Real World

Yan Lin Lye, Business Development Associate, DNA Electronics Ltd.

When it comes to nucleic acid testing, the industry has historically been unable to bring technologies out of the lab to enable rapid, simple, and portable point-of-care testing. That is until now.  DNA Electronics has developed Genalysis(R), a true point-of-care, sample-to-answer in 30 minutes USB based platform for nucleic acid testing that requires no expensive instrumentation like heat blocks, optics, or cameras. Moreover since DNA Electronics was established with the goal of bringing the innovation, user friendliness and connectivity of consumer electronics to the life sciences, the entire process only requires simple manual steps that deskills a once arduous process to only 1 minute of hands on time. All this is possible, through our proprietary DNA Logic and CMOS based platform which has already revolutionized the sequencing industry by licensing to Ion Torrent and partnering with Roche 454 for their semiconductor based platforms. DNAe's Genalysis platform is poised to bring an equally significant revolution to the molecular diagnostics industry.

3:15 Refreshment Break in the Exhibit Hall with Poster Viewing

3:45 The Role of Evidence Based Medicine in the Adoption of Molecular Diagnostics

Katherine Tynan, Ph.D., Business Development & Strategic Consulting for Diagnostics Companies, Tynan Consulting LLC

The enthusiasm with which personalized medicine is being embraced by healthcare providers, payers and patients is testament to the potential of molecular diagnostics to transform the practice of medicine and thereby improve patient outcomes and healthcare cost-effectiveness. This presentation will present the barriers to realize this potential as well as the different stakeholder perspectives, the levels of evidence that can be generated for molecular diagnostics and how they can drive change in the healthcare system will be discussed.

4:15 Panel Discussion:Clinical Adoption of NGS - Where Rubber Meets the Ground

Moderator: Katherine Tynan, Ph.D., Business Development & Strategic Consulting for Diagnostics Companies, Tynan Consulting LLC
William G. Loudon, M.D., Ph.D., Assistant Professor, Neurosurgery, University of California Irvine; Section Chief, Neurosurgery, Children’s Hospital of Orange County
Rakesh Nagarajan, Ph.D., Asst Professor, Pathology & Immunology, Washington University
Stan Letovsky, Ph.D., Vice President and CIO, SynapDx Corporation


Massively parallel sequencing platforms will have a profound impact on how we diagnose cancer, inherited genetic disease and infectious disease going forward.  In the context of inherited genetic disease genome sequencing reveals thousands of sequence variants for every patient.   Mendelian diseases although individually rare are collectively responsible for considerable childhood morbidity and mortality.  Traditionally the majority of patients have gone undiagnosed - whole exome and whole genome sequencing are profoundly impacting the diagnostics yields for these tests. (Rare diseases account for 20‐30% of all infant deaths, 15% of pediatric hospital admissions and 80% of rare diseases have a genetic cause, 3-6% of children worldwide are affected by a rare genetic disease).

1) How can informatics facilitate the processing and annotation of NGS data to support clinical interpretation and reporting?
2) How can informatics support access to the most up-to-date information from genome annotation databases and medical literature knowledge bases?
3) How applicable will some of the IT tools developed for Mendelian traits be for Complex disease traits where traditionally both the sheer volume of data and low predictive power have not made it worthwhile for practitioners to invest time grappling with the information.

4:45 Biomarkers for Predicting Exacerbations in COPD Patients

Raymond Ng, Ph.D., Chief Informatics Officer, Computer Science, Proof Centre of Excellence, University of British Columbia

By employing a computationally-driven biomarker discovery approach on a cohort of 240 patients, clinical as well as genomic and proteomic biomarkers were identified that can predict who will have frequent exacerbations. The area under the receiver operating characteristic curve (AUC) of these biomarkers is between 0.70 and 0.80. Such biomarkers, when validated, will provide valuable information to clinicians for managing COPD patients.

5:15 Best of Show Awards Reception in the Exhibit Hall

6:15 Exhibit Hall Closes





Genomic and Clinical data Integration and Open Platform 

8:40 Chairperson's Opening Remarks

Eric Neumann, Ph.D., CTO, PanGenX

8:45 A Fully Automated, Open Platform for Molecular Differential Diagnoses

Jian Han, Ph.D., President and CSO, iCubate

We ( have developed a patented mPCR (multiplex PCR) technology; a fully integrated molecular diagnostic system, the iCubate system, that can perform extraction, amplification, and detection steps, multiplexed, automatically, and in a closed cassette; and established an open business model, iCubate 2.0 (

9:15 Clinical Diagnostics Testing with Next Generation Sequencing: Challenges and Opportunities

Eric W. Klee, Ph.D., Assistant Professor of Medical Informatics, Division of Biomedical Informatics and Statistics, Mayo Clinic Rochester

The emergence of next generation sequencing has opened numerous opportunities to the field of clinical diagnostic testing, but with it also comes the formidable challenge of managing, processing, and interpreting the data. This deluge of data has resulted in the need for bioinformatics expertise to assist in interpretation of NGS results, and innovative systems to aggregate and integrate disparate data sources for the purpose of the resulting variants.  This presentation will discuss the challenges and opportunities we have faced in implementing an NGS based clinical diagnostic test at the Mayo Clinic.

9:45 Linking Together Pharmacogenomics Knowledge: Enabling Diagnostic to be Actionable

Eric Neumann, Ph.D., CTO, PanGenX

10:15 Coffee Break in the Exhibit Hall and Poster Competition

10:45 Plenary Keynote Panel Chairperson's Remarks

Kevin Davies, Ph.D., Editor-in-Chief, Bio-IT World

10:50 Plenary Keynote Panel Introduction

Geoffrey Noer, Senior Director, Product Marketing, Panasas


11:00 Plenary Keynote Panel:
A special plenary session featuring trends and challenges in cancer research:

Julian Adams, Ph.D., President, Research and Development, Infinity Pharmaceuticals, Inc.

Jose Baselga, M.D., Ph.D., Chief and Bruce A. Chabner Chair, Division of Hematology/Oncology, Massachusetts General Hospital; Associate Director, Massachusetts General Hospital Cancer Center; Professor of Medicine, Harvard Medical School

Sir John Burn, MD, FMedSci, Professor of Clinical Genetics, Institute of Genetic Medicine, Newcastle University, UK; Genetics Lead, National Institute of Health Research, UK; Medical Director, QuantuMDx Ltd

John Quackenbush, Ph.D., Professor, Biostatistics and Computational Biology, Cancer Biology Center for Cancer Computational Biology, Dana-Farber Cancer Institute

12:15 Luncheon in the Exhibit Hall with Poster Viewing


MultipleX Assay Accuracy and Test Result Interpretation 

1:55 Chairperson's Remarks

Alex Bangs, CIO, Crescendo Bioscience, Inc.

2:00 Personalized Patient Care through the Use of Multi-Biomarker Diagnostics and Novel Software Applications

Alex Bangs, CIO, Crescendo Bioscience, Inc.

A multi-biomarker blood test has been developed to more comprehensively measure disease activity in RA patients, and provide an objective, quantitative complement to traditional patient and physician assessments. These efforts are complemented by tools that enable physicians to track disease trajectory over time and take a more quantitative and personalized approach to patient care.

2:30 Comparing RNASeq Algorithms for Blood Gene Expression

Stan Letovsky, Ph.D., Vice President and CIO, SynapDx Corporation

Different expression quantitation algorithms for RNASeq data can give suprisingly different results. Here we report on comparisons of several algorithms run on the same dataset. We describe the impact of algorithmic choices on reproducibility and sensitivity to detect expression changes.

3:00 Accelerated Development of Diagnostic Assays Using NGENix™ in silico Powered Design

Richard Del Mastro, Ph.D., Vice President, Research and Development, IntelligentMDx

IMDx's proprietary NGENix™ bioinformatics platform powers the design process to rapidly develop qualitative and quantitative multiplexed real time PCR-based solutions to detect all strains of pathogens. NGENix™ utilizes modules that identify unique regions within sequenced genomes, designs oligonucleotide solutions, assesses the thermodynamics of the DNA multiplex and reviews cross-reactivity to other genomes. The process is efficient at generating accurate diagnostic assays with continued clinical relevancy.

3:30 Cloud-Based Development of Molecular Diagnostics Tests for Cancer

Ljubomir Buturovic, Ph.D., Vice President and Chief Scientist, Informatics, Pathwork Diagnostics, Inc.

Development of maximally informative genomics-based cancer diagnostics tests can present informatics challenges due to conceptual and computational complexity of analyzing the high-dimensional genomics data. Pathwork Diagnostics developed a cloud-based software solution to this problem. The system had been used to develop informatics for the FDA-cleared Tissue of Origin cancer classification test currently marketed for clinical use, and can be applied to other prognostic and predictive diagnostic tests.

4:00 Conference Adjourns


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