Interactive Workshops

Tuesday, 24th September 2013

9.00am – 12.00pm
Workshop A: Approaches in Analyzing Next-Generation Sequencing Data for the Purposes of Functional Genomics and Translational Research

The course will provide insight into best-practice methods and common tools which are critical for interpreting meaningful biological results from a nextgeneration sequencing dataset.

Next-generation sequencing technologies have become the gold-standard for cutting edge basic, translational, and clinical research. Sequencing methods have proven useful for uncovering differential gene/transcript expression, indels, SNVs, CNV, gene fusions, chromosomal translocations, methylation, and epigenetic markers such as microRNAs. The purpose of this course is to provide insight into the computational resources (cluster computing, disk arrays, cloud computing), tools (BowTie/Tophat, BWA, GATK, BioConductor), and algorithms available for interpreting meaningful results from data that can span multiple terabytes in size.

Dr. Gregory Miles will describe the analysis of RNA-Seq data as well as other kinds of NGS technologies. He will also provide a deeper understanding of standard workflows, in-silico protocols, and common pitfalls that are critical to the successful analysis of NGS data.

Leave the workshop with:

• An understanding of how to get biologically meaningful results from the analysis of NGS data

• An understanding of the infrastructure necessary to analyze NGS data

• Answers to common questions/issues that bioinformaticians run into on a daily basis

• Gain hands-on experience in applying tools to analyze NGS data

Workshop leader

Gregory Miles, Senior Bioinformatics Scientist, Cancer Institute of New Jersey

Greg graduated with a Ph.D in Bioinformatics from Boston University. His technical expertise includes programming in C++, Java, Perl/CGI, PHP, R (Bioconductor), and Oracle/MySQL. He has performed Bioinformatics research and programming at Binghamton University, Boston University and the NIH and has extensive expertise in both Next-Generation Sequencing and gene expression/microarray data analysis. Before joining the CIC, he consulted and developed Java software for a small biotech company and provided bioinformatics support for industry customers. His current projects at the CIC include numerous microarray/ pathway analysis projects, exploring G-quadriplex-related differentially expressed genes and the development of novel bioinformatics methods for determining microRNA/mRNA dysregulations in cancer and their subtypes.

1.00pm – 4.00pm
Workshop B: Next-Generation Genomics Enabling Next Generation Medicine: the Promise and the Challenges

This workshop takes an in-depth look at the challenges and opportunities in applying next-generation sequencing to the genomic characterization of solid tumors and hematological malignancies in a clinical laboratory setting.

NGS has enabled a leap forward in the molecular testing of cancer. Using data from a series of assay validations, we will discuss the pros and cons of different target enrichment strategies, sequencing platforms, data analysis methods and validation strategies.

Participants will have the opportunity to share their own experiences and learn from others. This workshop will provide you with the following information you need to make decisions about implementing NGS assays and working with the resulting data:

• NGS assay design and validation

• Regulation of NGS-based molecular testing

• Current laboratory NGS guidelines

• The important role of molecular testing in clinical trials

Leave this workshop with a complete understanding of the resources available to help the oncologist who is faced with interpreting a complex diagnostic report and how NGS testing is being used for patient stratification for clinical trials.

Workshop leader

Cyrus Hedvat, Director, Diagnostic Molecular, Pathology Laboratory, Memorial Sloan-Kettering Cancer Center

Cyrus is a pathologist at Memorial Sloan Kettering Cancer Center who specializes in molecular pathology and hematopathology. He is actively involved in the molecular testing of a high volume of hematological malignancies and solid tumors in the Diagnostic Molecular Pathology Laboratory. He has led efforts to implement next generation sequencing tests in the clinical lab, now a routine part of clinical testing. His own research focuses on the identification of clinically relevant genomic abnormalities in acute myeloid leukemia and myeloproliferative neoplasms. The goal of these studies is to use advanced technologies to identify molecular targets that can be used to improved diagnosis and treatment of cancer.

4.30pm – 7.30pm
Workshop C: Development and Application of More Integrated Analyses of Cancer Genomic Data to Help Identify New Somatic 
Mutations, and Discover Clinically Relevant Cancer Targets - cancelled