Genomic Biomarkers Agenda

Registration

Identifying Biomarkers of Synergy for Combination Therapy in Cancer
Yair Benita, Senior Computational Biologist, Merck Research Laboratories, United States of America

Cancer is a complex disease requiring combination therapy. I will discuss strategies for identifying synergistic drug combinations and associated genomic biomarkers. I will focus on the complexity of defining combination therapy biomarkers and the key differences compared to defining biomarkers for single agent therapy.

Next Generation X-Aptamers for Identification of Personalized Biomarkers in Cancer
David Gorenstein, Associate Dean for Research/Founder AM, The University of Texas Health Science Center, United States of America

We have developed both in vitro enzymatic combinatorial selection and split-synthesis chemical combinatorial methods to identify phosphorothioate-modified oligonucleotide “thioaptamers” and next-gen “X”-aptamers to a number of different protein targets for both proteomics and biomarker discovery in cancer.

Coffee Break and Networking in Exhibition Hall

Applications of Cancer Genomics and Nextgen Sequencing in Cancer Biomarker Research
Han Chang, Principal Scientist, Bristol-Myers Squibb, United States of America

Identification of alterations in the cancer genome is essential for cancer biomarker research, and nextgen sequencing technologies can provide comprehensive views of the cancer genome.  I will present an example using integrated analysis of cancer genomic data to elucidate mechanisms of acquired resistance in a pre-clinical model.  The impact of nextgen sequencing technologies on cancer genomics and oncology R&D will also be discussed.

Plasma Tumor DNA Biomarkers: Applications and Implications for Breast Cancer Therapy
Ben Park, Associate Professor, Johns Hopkins University, United States of America

The identification of somatic genomic alterations present in a patient’s breast cancer allows for the development of DNA biomarkers that are unique for every individual’s tumor. We can assess these DNA biomarkers in the plasma of breast cancer patients by quantitative PCR. This allows us to determine whether the presence or absence of plasma tumor DNA correlates with disease burden, response to therapy and ultimately clinical benefit for the patient.

Lunch Break and Networking in Exhibition Hall

Poster Viewing Session

Genotyping Assay in Digital PCR Conditions for the Detection of IDH1 Mutation in Plasma
Yannick Marie, Platform Manager, Universite Pierre et Marie Curie, France

The use of circulating tumor DNA as a biomarker is a challenge, particularly in regards to brain tumors. Through the use of COLD PCR and digital PCR, we were able not only to highlight the presence of circulating tumor DNA in patients with gliomas, but also  to validate the presence of the most frequent mutation in this disease. The strong prognostic impact of this change now allows us to propose an alternative technique for imaging in terms of diagnostics, but also for the prognosis of these tumors.

Biomarkers to Predict the Response to Rituximab
Cornelis Verweij, Professor, VU University Medical Centre, Netherlands

The presentation highlights the outcome of biomarker discovery research, which adds new information to our understanding of the mechanism of action of B-cell depletion therapy, and demonstrates clinically useful biomarkers for response prediction, taking the paradigm of personalized medicine one step further.

Coffee Break and Networking in Exhibition Hall

Discovery of Predictive Biomarkers of Drug Response using In Vitro and In Vivo Models of Cancer
Adam Pavlicek, Senior Principal Scientist in Computational Biology, Pfizer, United States of America

Identification of predictive biomarkers of response is essential for the success of targeted cancer therapies in clinical trials. I will present specific cases of pre-clinical studies with Xalkori , IGF1R and gamma-secretase inhibitors, and compare the different approaches used. Key computational and statistical considerations of experimental design and data analysis will be mentioned.

PIK3CA Gene Alterations in Bladder Cancer
Marta Dueñas Porto, Senior Researcher, CIEMAT, Spain

Study of mutations and copy number in PIK3CA gene as well as mRNA expression levels in samples of human bladder cancer and paired normal tissue. This results support that PIK3CA may constitute a good prognostic tool for bladder cancer.

Antibody-Based Proteomics: Fast-Tracking Molecular Diagnostics in Oncology
William Gallaghr, Chief Scientific Officer/Professor, OncoMark Limited/University College Dublin, Ireland

This presentation will cover the utility of antibody-based profiling using tissue microarrays and associated digital pathology approaches to expedite the transition from biomarker discovery to validation in oncology. Case studies covering a range of cancer and biomarker types will be outlined.

Immunosignaturing as a Fundamentally New Approach to Diagnosis and Diagnostic Discovery
Stephen Johnston, Director, Arizona State University, United States of America

Splaying the antibody repertoire on a complex peptide surface is remarkably informative as a diagnostic platform. It allows new opportunities for early diagnosis and rethinking the paradigm for diagnostic discovery.

Drinks Reception

Methylation Patterns in Cell-Free Circulating DNA from Blood for Detection and Diagnosis of Disease
Victor Levenson, Associate Professor, Rush University Medical Center, United States of America

Using our MethDet technology for methylome analysis in very small samples for proof-of-principle studies, we established the feasibility of methylation biomarkers for disease detection, diagnosis, and monitoring of treatment. The modified technology allows analysis of methylation events on a genome-wide scale using cell-free DNA from blood. Development and validation of the first clinical-grade biomarker will be presented.

Epigenomic Biomarkers in Huntington's Disease
Hoon Ryu, Associate Professor, Boston University School of Medicine, United States of America

Deregulation of chromatin remodeling is linked to the pathogenesis of Huntington’s disease but the mechanism is elusive. In order to identify how genomes are deregulated by heterochromatin, we performed ChIP genome-wide sequencing combined with RNA-sequencing followed by platform integration analysis.

Coffee Break and Networking in Exhibition Hall

Toward Personalized Medicine in ICU
Wenzhong Xiao, Assistant Professor, Massachusetts General Hospital, United States of America

Inflammation is one of the most common conditions of human diseases. Severe inflammatory stresses produce a similar “genomic storm” in blood leukocytes of surgical ICU patients, suggesting common underlying molecular mechanisms of systemic inflammation regardless of initiating etiology. Comparisons of patients with and without complications reveal genomic biomarkers for potential targeted treatments.

Technology Assessment for Evaluation of microRNAs as Biomarkers
Shidong Jia, Scientist, Genentech Inc, United States of America

Dr. Jia’s lab has developed working procedures to evaluate microRNA as biomarker for cancer prognosis, prediction and patient stratification. In particular, their work has refreshed current practice and demonstrated a new approach for measuring microRNA signature in FFPE samples.

Lunch Break and Networking in Exhibition Hall

Poster Viewing Session

Translating Prognostic and Predictive Biomarkers into Clinic
Mao Mao, Research Fellow, Pfizer Global Research and Development, United States of America

The ongoing efforts for biomarker discovery, validation and translation, and several successes that have guided clinical practice including MammaPrint testing for breast cancer prognosis and ALK fusion screening as companion diagnostics for Crizotinib treatment will be discussed.

Biomarkers for Transplantation
Robert McMaster, Executive Director/Professor, University of British Columbia, Canada

The aim of this study is to derive genomic and plasma protein diagnostic markers for acute heart and kidney graft rejection. We propose a computational biomarker pipeline, founded on advanced statistical methodologies, to identify and validate blood derived biomarkers.

Coffee Break and Networking in Exhibition Hall

A Novel Genome-Wide Assay Identifies Chromatin Biomarkers that Control Stem Cell Behavior
Steven Okino, Staff Scientist, Bio-Rad Laboratories, United States of America

We present a novel assay that maps accessible chromatin genome wide. We used this assay to identify chromatin regions that control stem cell behavior. This assay can be used to identify chromatin biomarkers associated with specific biological or pathological states.

Design and Analysis of Biomarker Panels
Craig Nelson, Associate Professor, University of Connecticut , United States of America

The MUMP pipeline is a cost-effective method for the design of biomarker panels combined with statistical interpretation of gene expression data that will move the field of biomarker analysis from manual curation to computationally supported rational design.

Close of Conference