2013 Archived Content
Thursday, June 27
7:30 am Morning Coffee
8:30 Chairperson’s Opening Remarks
Matthew E. Roth, Ph.D., Assistant Professor & Co-Director, Bioinformatics Research Lab, Baylor College of Medicine
8:35 Epigenetic Biomarkers as Cancer Diagnostic Tools
Mukesh Verma, Ph.D., Chief, Methods and Technologies Branch, Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, NIH
Alterations in epigenetic profiling may provide important insight into the etiology and natural history of cancer. Since several epigenetic changes occur before histopathological changes, they can serve as biomarkers for cancer diagnosis and risk assessment. Many cancers may remain asymptomatic until a relatively late stage; attempts should be made for early detection, accurate prediction of the disease progression, and frequent monitoring for the management of the disease. Epigenetic diagnostic markers of breast, colon, lung, and prostate cancer will be discussed.The importance of analytical and clinical validation of biomarkers, and the challenges and opportunities in this field are also discussed.
9:05 FEATURED PRESENTATION:
Lessons from Surveying the DNA Methylation "Cityscape" of Lethal Metastatic Prostate Cancer
Srinivasan (Vasan) Yegnasubramanian, M.D., Ph.D., Assistant Professor, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine
Alterations in DNA methylation are a hallmark of human cancers, including prostate cancer. We carried out genome-scale analyses of DNA methylation alterations in multiple metastases from each of 13 men that died of metastatic prostate cancer and created DNA methylation cityscapes to visualize these complex data. These analyses revealed that each individual developed a unique DNA methylation signature that was largely maintained across all metastases within that individual. By analyzing their frequency, clonal maintenance, and correlation with expression, we nominated potential "driver" DNA methylation alterations that could be prioritized for development as epigenetic biomarkers and therapeutic targets.
9:35 Selected Presentation: Development of a Non-Invasive Test for Early Detection of Colorectal Tumors
Guro Elisabeth Lind, Ph.D., Head, Epigenetics, Department of Cancer Prevention, Institute for Cancer Research, Oslo University Hospital
We have identified altogether 12 epigenetic biomarkers for early detection of colorectal cancer. A panel of six of these epi-markers was positive in 94% of cancers, 93% of adenomas and in only 2% of normal mucosa samples. In a direct comparison using the same protocol and the same series of tissue samples we recently demonstrated that the six-gene panel could outperform several previously published epi-markers, including VIM and SEPT9 which are included in commercial tests for early detection of colorectal cancer using stool and blood, respectively.
9:50 Selected Presentation: Single-Base Resolution Mapping of DNA Epigenetic Marks in Parallel
Michael Booth, Research Scientist, Balasubramanian Lab, Department of Chemistry, University of Cambridge
Aberrant DNA methylation is central to the pathogenesis of cancer and has also been implicated in several other diseases. Although recent evidence strongly suggests that the different classes of methylated cytosines (e.g. methyl, hydroxymethyl, formyl) are functionally distinct, traditional tools cannot accurately distinguish between these modifications, confounding analysis. We have developed two novel techniques to quantitatively measure 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC) and 5-formylcytosine (5fC) at single-base resolution. In addition to our previously published oxidative bisulfite sequencing (oxBS-Seq), we now introduce reduced bisulfite sequencing (redBS-Seq) to map 5fC. These new methods will advance translational research by allowing the study of these DNA modifications accurately and in parallel.
10:05 Coffee Break in the Exhibit Hall with Poster Viewing
10:45 Analysis of DNA Cytosine Methylation in Human Hematopoietic Stem Cell Differentiation and Relevance in Hematological Malignancy
Boris Bartholdy, Ph.D., Assistant Professor, Research, Department of Cell Biology, Albert Einstein College of Medicine
Leukemias are malignant diseases characterized by the disruption of genetic and epigenetic programs occurring during hematopoietic differentiation, resulting in a differentiation block and accumulation of immature cells. Using a modified HELP technique we analyzed DNA methylation changes concomitant with differentiation of highly purified human hematopoietic stem and myeloid progenitor cells from healthy human individuals, and identified a commitment-associated methylation signature. We subsequently tested this signature as a classifier in patients with acute myeloid leukemia (AML). This signature proved to be a significant and robust survival classifier in several large cohorts of AML patients, independent of the treatment regimen and known epigenetic and other prognostic mutations.
11:15 Epigenomics of Chronic Lymphocytic Leukemia
Huidong Shi, Ph.D., Associate Professor, Biochemistry and Molecular Biology, Medical College of Georgia, Georgia Health Sciences University Cancer Center, Georgia Regents University
Chronic lymphocytic leukemia (CLL) is a biologically and clinically heterogeneous disease. Using genome-wide bisulfite sequencing, we analyzed the DNA methylomes of IGHV-mutated and unmutated CLL patients and of normal B-cell subpopulations at single base resolution. The DNA methylation landscape in CLL patients indicates that CLL B-cells possess an active B-cell phenotype; at the same time, the two molecular subtypes have unique DNA methylation patterns that seem to represent epigenetic imprints from distinct normal B-cell subpopulations. The epigenomic analysis identified novel epigenetic changes that can be potentially developed into biology-based prognostic indicators for CLL. The results will advance our understanding of the epigenetic contribution to molecular heterogeneity in CLL.
11:45 Close of Session
11:55 Lunch on Your Own
1:15 pm Chairperson’s Opening Remarks
(Sponsorship Opportunities Available)
The success of producing As, Cs, Gs, and Ts at exponentially lower costs, along with longer and more accurate reads is revolutionizing genomic diagnostic medicine. Thus, the promise of next-generation sequencing has shifted from discovery to clinical utility. Now the question is: how do we best use this sequence information in patient care? Hear first-hand from the companies that continue to drive the genomics revolution.
1:20 - 1:35 Interpreting Molecular Data from Sequencing Platforms with Leading Edge Knowledge for Treatment and Diagnostic Options
Jennifer Carter, Founder & CMO, N-of-One, Inc.
Physicians, labs, institutions and patients can efficiently make the best diagnostic and treatment choices, The PrecisionWorks framework enables experts to translate molecular data specific to each patient and the extensive available knowledge for each cancer type into state-of-the-art, clinically actionable insights and therapeutic options focused at the point of care.
1:35 - 2:05 Clinical Interpretation of Genomes in Healthy Individuals
Carri-Lyn Mead, Ph.D., Scientist 2, Illumina, Inc.
2:05 - 2:35 Finally! Easy Access to Whole Human Genomes
Julie Adams, Vice President, Product Management, Complete Genomics
Complete is developing software to deliver genomic information from any and all sources in an actionable, personalized form. As a first step,Genome Voyager™ is now available as an educational tool that enables researchers and academics to gain first-hand experience analyzing whole human genomes. After joining the Genome Voyager community, users can visualize and explore published whole human genomes. Users also have the opportunity to collaborate with colleagues and discuss their findings.
2:35 - 3:05 The Pursuit of Higher Accuracy and Precision in Clinical Next Generation Sequencing – the SmartChip TE™ Target Enrichment System
Jude Dunne, Ph.D., Vice President, Product Development, WaferGen
The clinical sequencing community has been grappling with the transfer of ngs sequencing tests from development into the clinic. Recommendations from working groups have highlighted accuracy and precision as key attributes for successful introduction of tests into the clinical CLIA environment. To meet this challenge WaferGen has developed the high-density SmartChip TE System. Practical benefits of this methodology include flexibility in panel development, improved accuracy and precision with a simple, intuitive, lab-friendly workflow.
3:05 - 3:35 Integrated NGS Sequencing and Reporting Using the Ion Torrent Platform
Mike Lelivelt, Ph.D., Director, Bioinformatics & Software Products, Ion Torrent, part of Life Technologies
As next generation sequencing prepares for a move from the research bench to future clinical applications, Ion Torrent is building systems to support the routine acquisition of sequencing data. Torrent Suite Software is designed for easy, routine control of the Ion Torrent Personal Genome Machine as well as monitoring data quality control covering the fundamentals of sequencing performance. Following acquisition read data in Torrent Suite Software, data can be transferred to Ion Reporter Software in a streamlined automated manner. Ion Reporter Software offers both mapping and variant calling using a controlled, role-based workflow with integrated audit trails. Variants called within Ion Reporter are labeled with rich annotation sources from public repositories. Easy to use filters enable data to be reduced done to the variants of greatest impact. Decision support functionality within Ion Reporter Software allows technicians to classify variants into a formal report structure. External annotation sources, such as Ingenuity and Compendia Cancer Annotations, are integrated into Ion Reporter to allow increased variant knowledge to be directly available for incorporation into variant reports.
3:35 Refreshment Break in the Exhibit Hall with Poster Viewing
4:00 Harnessing Position-Dependent Co-Methylation in Clinical Epigenome-Wide Association Studies (EWAS)
Mei-Lyn Ong, Ph.D., Research Scientist, Agency of Science, Technology and Research (ASTAR), Singapore Institute for Clinical Sciences (SICS)
Studies conducted by us suggest that statistical power can be improved by using the intrinsic properties of DNA methylation, including position-dependent co-methylation to group CpGs by chromosomal location and restriction of the analyses to inter-individual variably methylated regions, and hence reduce both the false positive rate and the huge multiple testing problem inherent in these studies. We are applying the method to our Singapore-based birth cohort study to discover clinically relevant differentially methylated regions for diagnosis and intervention.
4:30 The Human Epigenome Atlas and Its Application to Understanding Human Disease
Matthew E. Roth, Ph.D., Assistant Professor & Co-Director, Bioinformatics Research Lab, Baylor College of Medicine
The Human Epigenome Atlas contains human reference epigenomes and data on locus-specific epigenomic states for a variety of tissues and cell types. The presentation will provide a brief overview of the epigenetic data residing within the Atlas and how this data can be used to further our understanding of physiological conditions and human disease. Methods for computational processing and comparison of methylomes using array technologies and genomic bisulfite sequencing will be highlighted.
5:00 FEATURED PRESENTATION:
DNA Methylation Detection using Nanopores
George Vasmatzis, Ph.D., Director, Biomarker Discovery Program, Center of Individualized Medicine; Consultant, Department of Molecular Medicine, Mayo Clinic and Foundation
I will discuss some of our latest work around integrating micro-fabrication and solid state technologies with biomarkers. In diagnostics, a biosensor that could look for subtle structural or sequence variations at the single molecule level would be extremely useful . Epigenetic modifications have been linked with cancer, and we have developed nanopore technology to detect the methylation profile of a single molecule. The challenges and the potential of such technology will be discussed.
5:30 Evening Reception
6:30 Close of TCEC: The Clinical Epigenome Conference