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Trends in Cancer Diagnostics

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Ensuring the Safety and Validity of Molecular Diagnostic Tests

AlbertoGutierrezAlberto Gutierrez, Ph.D., Deputy Director, OIVD, Office of in Vitro Diagnostic Device Evaluation and Safety, Food & Drug Administration






Bringing Point-of-Care HIV Diagnostics to Market: FDA Perspectives

ElliotCowanElliot Cowan, Ph.D., Chief, Product Review Branch, Division of Emerging and Transfusion Transmitted Diseases, FDA/CBER/OBRR






Distinguished Speaking Faculty:

Steven M. Anderson, Chief Scientific Officer and Vice President, LabCorp

Michal Daniely, Ph.D., Director for Research & Test Development, Biology, BioView Ltd.

Cynthia Gawron-Burke, Ph.D., Director, Scientific Liaison, External Scientific Affairs, Merck & Co., Inc.

Ingegerd Hellstrom, M.D., Ph.D., Professor Emeritus, Pathology, University of Washington

Akihiro Kondo, Ph.D., Professor, Graduate School of Medicine, Osaka University

Raphael Lehrer, Ph.D., Head, Personalized Oncology Services, CollabRx, Inc.

Neal Lindeman, M.D., Assistant Professor, Pathology, Harvard Medical School; Associate Pathologist, Pathology, Brigham and Women’s Hospital

Daniel E. Mercola, M.D., Ph.D., Professor, Pathology and Laboratory Medicine; Director, Translational Cancer Biology, University of California, Irvine

Charles Mullighan, MBBS(Hons), M.Sc., M.D., St. Jude Children’s Research Hospital

Lee N. Newcomer, M.D., Senior Vice President, Oncology, UnitedHealthcare

Michael Pisano, Ph.D., President and Chief Executive Officer, NextGen Sciences

Bruce Quinn, M.D., Ph.D., Senior Health Policy Specialist, Foley Hoag

Richard K. Wilson, Ph.D., Professor and Director, Genetics, The Genome Center, Washington University School of Medicine

Pre-conference Symposia



Scientific Advisory Board

Carlos Cordon-Cardo, M.D., Ph.D., Director, Molecular Pathology Center, Memorial Sloan Kettering Cancer Center, Columbia University Center

Harry Glorikian, Managing Partner, Scientia Advisors

Myla Lai-Goldman, M.D., Managing Partner, Personalized Science, LLC

Jorge A. León, Ph.D., President, Leomics Consulting

Franklyn G. Prendergast, M.D., Ph.D., Professor, Pharmacology, Biochemistry & Molecular Biology, Director of Center for Personalized Medicine, Mayo Clinic

Pre-Conference Symposia

Sunday, August 9

Click here for information about the Pre-Conference Symposia

Monday, August 10

7:30-8:30am Registration and Morning Coffee


8:30 Chairperson’s Opening Remarks

Jorge A. León, Ph.D., President, Leomics Consulting

8:40 Sequencing the Cancer Genome

Richard WilsonRichard K. Wilson, Ph.D., Professor and Director, Genetics, Genome Sequencing Center, Washington University

New technology recently has facilitated the complete sequencing of individual human genomes. As the cost and efficiency of this approach continues to improve, we can envision a powerful new means for the study of genes and other genome elements and mechanisms that underlie cancer and other human diseases. I will discuss some of the discoveries made to date with emerging genome sequencing technologies, and how these methods will allow us to better understand both basic biology and human disease.

9:10 Cancer Biomarkers to Predict Therapeutic Response

Cynthia Gawron BurkeCynthia Gawron-Burke, Ph.D., Director, Scientific Liaison, External Scientific Affairs, Merck & Co., Inc.

The discovery of  pharmacodynamic and patient stratification biomarkers will continue to have a profound effect on the research and development of targeted cancer therapeutics. Novel gene expression signatures that can be used to monitor tumorigenic pathway activity in human tumors have recently been reported.  The value of collaborative partnerships in realizing the potential of gene expression signature biomarkers for clinical use will be discussed.


9:40 Personalized Oncology Research: Applying Discovery Technologies in the Clinic Today

Raphael LehrerRaphael Lehrer, Ph.D., Head, Personalized Oncology Services, CollabRx, Inc.

We will describe an innovative personalized cancer research service that uses an unbiased analysis of whole-genome data to generate actionable therapeutic strategies to target the mechanisms driving an individual’s tumor.    The service is built on an open platform that can incorporate new technologies and approaches, which we are exploiting to augment our current expression and SNP/CNV methods with full-genome tumor sequencing.  Beyond delivery of care to late-stage patients, this approach has important implications to discovery of novel diagnostics and therapeutic combinations.

10:10 Networking Coffee Break, Exhibit and Poster Viewing


10:50 Chairperson’s Remarks

Arshad Ahmed, Partner & Co Founder, Scientia Advisors LLC

11:00 Prostate Cancer Microenvironment Biomarkers for Diagnosis and Prognosis

Daniel E. Mercola, M.D., Ph.D., Professor, Pathology and Laboratory Medicine; Director, Translational Cancer Biology, University of California, Irvine

We have previously developed methods for the extraction of cell-type specific gene expression values for the principal cell types occurring in tissue samples used for gene expression analysis, i.e., tumor epithelial cells, stroma cells, and the epithelial cells of BPH and dilated cystic glands. The method uses a linear combination model to express the observed microarray gene intensity as a sum of the individual cell contributions and, when combined with an estimate of percent cell composition, may be solved for gene expression of each gene of the array and for the four cell types. The method has been extended to define differential expression of cell-specific values for tumor compared to not tumor tissue and relapsed compared to nonrelapsed tumors. The results indicate that tumor-adjacent stroma exhibits dozens of significant differential gene expression changes that are potentially useful in diagnosis of prostate cancer and assignment of risk of relapse based solely on measurements of the tumor microenvironment. A multiplex PCR-based assay is being developed for general application to FFPE samples.

11:30 The Use of Genome-Wide Profiling of Genetic Alterations to Identify New Prognostic Markers and Therapeutic Targets in Acute Lymphoblastic Leukemia

Charles MullighanCharles Mullighan, MBBS(Hons), MSc, M.D., Assistant Member, Pathology, St. Jude Children’s Research Hospital

A substantial proportion of patients with acute lymphoblastic leukemia (ALL) experience treatment failure and relapse, which carries a poor prognosis. New tools to identify patients at high risk of relapse are needed, as well as novel targets for therapeutic intervention to improve outcome in high risk ALL. Recent studies have performed high resolution, genome-wide profiling of genetic alterations in ALL, and have identified multiple novel recurring genetic alterations that target key cellular pathways including lymphoid development, apoptosis, tumor suppressors and cell cycle regulation. Transcription factors regulating B lymphoid development are altered in over 60% of B-progenitor cases, and alteration of the IKZF1 gene, which encodes the early lymphoid transcription factor IKAROS, is associated with very poor outcome in ALL. Moreover, cases harboring IKZF1 alterations have a gene expression profile similar to BCR-ABL1 ALL, a subtype of ALL that also has IKZF1 alteration and poor outcome. Ongoing work has shown that poor outcome, IKZF1-altered (but BCR-ABL1 negative) cases harbor novel mutations in tyrosine kinases that are potentially “druggable”. These results demonstrate the power of integrated, cross-platform genomic analyses to identify novel prognostic markers and therapeutic targets in ALL.

TSG Partners12:00pm Sponsorship Presentation

The Road To Commercialization – Navigating The Critical Issue At the Convergence of Molecular Dx & Oncology
Panel Moderator:

Panna Sharma, CEO & Managing Partner, TSG


R.S.K. Chaganti, Ph.D., Founder & Chairman, Cancer Genetics, Inc.
John C. Schafer, CEO, Diagnocure


12:30 Luncheon Presentation Sponsored by NextgenNEW logo
New Method Provides the Solution for the Bottleneck in Protein Assay Development

Michael Pisano, Ph.D., President and Chief Executive Officer, NextGen Sciences

A new method used to develop protein assays, called peptide MRM, is rapidly being recognized as a solution to the current bottlenecks in protein biomarker development.    Is this method yet another ‘omics hype or will this method allow the production of assays for thousands of proteins in the next five years?  The National Cancer Institute’s Clinical Proteomic Technologies for Cancer Program has heavily invested in peptide MRM and the first wave of manuscripts have been prepared and submitted for publication.  The key bottlenecks with traditional protein assays are availability of assays (with high specificity) and the timeline and cost for developing assays.  Traditional protein assay are reliant on affinity reagents (e.g., antibodies) for quantitation of a protein.   Highly specific antibody-based assays exist for only about 500 of the 20,000 human proteins.  This new method does not use antibodies for quantitation of proteins and high specificity is determined prior to assay development.  Peptide MRM assays can even be designed to monitor specific post-translational modifications (e.g., phosphorylation).  Assay development time with peptide MRM assays range from a week to several months (not years) and can cost less than $2K per protein.  NextGen Sciences has been an early adopter of this method, has developed numerous peptide MRM assays and is testing large sample sets as a CRO for industry and academia.  This presentation will include an overview of peptide MRM method and cancer examples (including timelines) both the development of assays and their application to confirm biomarkers.


2:00 Chairperson’s Remarks

2:10 Novel Biomarkers Located at 3p22.1 And 10q22.3 Offer a Non-Invasive Diagnosis of Lung Cancer in Induced Sputum Samples by Combination of Cytology and Fluorescence in Situ Hybridization (FISH)

Michal Daniely, Ph.D., Director for Research & Test Development, Biology, BioView Ltd.

Lung cancer results from a series of genetic and epigenetic alterations. Recently, two biomarkers located at 3p22.1 and 10q22.3, were found to be altered in early stage lung cancer. The study was aimed to evaluate a new assay combining FISH and cytology for detection of lung cancer by induced sputum (IS). We blindly tested 83 IS samples from advanced and early stage lung cancer patients and from healthy smokers and non-smoking controls (19, 18, 36 and 10 samples, respectively). 36/37 lung cancer patients (97.37% sensitivity) were detected, with a specificity of 82.22%. In conclusion, combined analysis of cytology and FISH in IS samples can be used as a non-invasive diagnostic test for early detection of lung cancer.

2:40 Analysis of AFP-L3 in Hepatocellular Carcinoma Patients

Akihiro Kondo, Ph.D., Professor, Graduate School of Medicine, Osaka University

Alpha-fetoprotein (AFP) is an oncofetal glycoprotein that contains a single glycosylation site at the level of asparagine 232, and is a well-known tumor marker for hepatocellular carcinomas (HCC). Recently, the Lens culinaris agglutinin (LCA)-reactive fraction of AFP (AFP-L3) has been measured as a more specific marker for HCC. AFP-L3 reflects HCC-specific changes in the glycans of AFP. The N-glycan structures of the AFP-L3, a tumor marker of HCC, were analyzed in relationship to glycosyltransferases and LCA-affinity electrophoresis, using HPLC and MALDI-TOF MS.

3:10 Networking Refreshment Break, Exhibit and Poster Viewing

4:00 Break-out Sessions: Collaborating to Bring Novel Diagnostics to Market

Developing Gene Expression Signature Biomarkers for Clinical Use
Moderator: Myla Lai-Goldman, M.D., Managing Partner, Personalized Science, LLC

  • What are the obstacles to adoption of gene signatures in clinical practice?  Ie Technology, validation, reimbursement, regulatory, education
  • What are the "lessons learned" from the currently available gene signature assays in clinical practice?
  • How do we overcome the obstacles?

Personalizing Cancer Therapy
Moderator: Arshad Ahmed, Partner & Co Founder, Scientia Advisors LLC

• Why is personalized medicine important in cancer?
• To what extent is cancer medicine already personalized?
• Future of personalized medicine in cancer
• Challenges for achieving personalized medicine

Identifying Novel Prognostic Markers Using Genomic Analysis
Moderator: Charles Mullighan, MBBS(Hons), MSc, M.D., St. Jude Children’s Research Hospital

5:00 Networking Reception

6:00 Close of Day One


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