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Genomic Know-How® Webinar Series

With industry expertise and Genomic Know-How, EA|Quintiles advances science from understanding the human genome and disease biology to detecting the effects of therapies and creating opportunities for those who can leverage new techniques and technologies. With over 500 collective years of genomic experience, 94 publications, FDA collaborations and participation in standardized initiatives, EA|Quintiles has upheld its market position as a leading provider of genomics services in clinical trials and research. Attend our webinar series to tap into our Genomic Know-How.

This program will benefit Discovery and Development Scientists from large pharmaceutical and small-midsize biotechnology companies.

April 25, 2014 (archived): Best Practices for Obtaining RNA Sequencing Data from Formalin-fixed Paraffin-embedded (FFPE) Samples

May 28, 2014 (archived): Targeted Oncology Biomarker Solutions in the Elucidation of Inflammatory Breast Cancer Mechanisms

June 25, 2014 (archived): Exome Sequencing and Analysis: Considerations for Sample Input, Capture Techniques and Pipelines related to Variant Detection

July 25, 2014 (archived): Sources of Error and the Role of Replicates in NGS

August 22, 2014 (archived): The Evolution of RNA-Sequencing

WEBINAR #1

Best Practices for Obtaining RNA Sequencing Data from Formalin-fixed Paraffin-embedded (FFPE) Samples

This webinar is intended to help genomic researchers better understand technical hurdles in the analysis of FFPE-derived RNA to:

  • Learn how EA has overcome challenges inherent in FFPE samples
  • Gain insight into experimental design considerations
  • Learn how to exploit your collection of FFPE material

By attending the webinar you will learn:

  • How RNA sequencing data derived from fresh frozen and FFPE material can be compared
  • How to design experiments that obtain meaningful data from your FFPE samples

Date:
April 25, 2014

Speaker:
Patrick Hurban, PhD, Global Head of Genomic Research and Development, EA | Quintiles

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WEBINAR #2

Targeted Oncology Biomarker Solutions in the Elucidation of Inflammatory Breast Cancer Mechanisms

This webinar is intended to help cancer researchers and clinicians alike, better understand how genomic data can be used to gain insights into drug resistance, and will focus specifically on resistance and response in a specific subtype of breast cancer.

Next generation sequencing (NGS) has posed new challenges and opportunities in cancer treatment and drug development. These technologies have enabled clinicians and researchers the capability to identify variants in cancer pathways that may be predictive of response, and resistance to oncology therapeutics. However, NGS outputs are typically large & complex datasets that present challenges in interpretation.

During the webinar, the presenters will describe:

  • Targeted sequencing solutions
  • The analysis of NGS data generated using a targeted cancer sequencing panel from a multi-sample cohort of patients
  • How this data has led to new insights into drug resistance and response in a specific breast cancer subtype

Particular emphasis will be placed on contextualization of variants with respect to biological pathways.

By attending this webinar, the audience can expect to gain insights into translational approaches that may be used to understand the biological implications of genomic variants and their interaction with drug response.

Date: May 28, 2014

Speakers:
Sarah Bacus, PhD, Senior VP and Chief Scientific Officer, Translational R&D Oncology, Quintiles
Jeff Fitzgerald, Director, Personalized Medicine Integration, EA | Quintiles

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WEBINAR #3

Exome Sequencing and Analysis: Considerations for Sample Input, Capture Techniques and Pipelines related to Variant Detection

Exome Sequencing has become the leading tool for discovery-based research in pre-clinical settings for DNA aberrations.

It is important to understand how various molecular factors affect the underlying variant representation to ensure proper experimental techniques enhance biomarker discovery.

This webinar will focus on oncology or complicated admixed tissues where very low frequency alleles are under investigation, and will cover topics including:

  • Effects of sample input (intact DNA, FFPE, ultra-low quantity) and recommendations for input
  • Contrasting different target enrichment protocols and describing capture bias
  • Determining the appropriate amount of sequencing coverage needed for your genetic problem
  • Best practices for determining variants and deriving limit of detection

Date: June 25, 2014

Speaker:
Vic Weigman, PhD, Associate Director of Translational Genomics, EA | Quintiles

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WEBINAR #4

Sources of Error and the Role of Replicates in Next Generation Sequencing (NGS)

Advances in next-generation sequencing (NGS) technologies have rapidly improved sequencing fidelity and substantially decreased sequencing error rates. However, given that there are billions of nucleotides in a human genome, even low experimental error rates yield many errors in variant calls. Erroneous variants can mimic true somatic and rare variants, thus requiring costly confirmatory experiments to minimize the number of false positives.

In this webinar, learn more about the sources of experimental errors in NGS (e.g.Sample Preparation, Library Preparation, Sequencing and imaging) and better understand how replicates can be used to abate such errors in reducing the noise in data processing and in downstream analysis.

Date: July 25, 2014

Speaker:
Kim Robasky, PhD, Associate Director, Bioinformatics, EA | Quintiles

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WEBINAR #5

The Evolution of RNA-Sequencing

Although RNA-Seq is a relatively new methodology, with some of the first transcriptome-wide analyses appearing around 2008, RNA-Seq has rapidly evolved to become a standard assay for RNA measurement. In the last several years, assays have improved to be high throughput, more specific, work with smaller input amounts, process degraded RNA, and perform well with special tissues (eg, blood samples). On the bioinformatics side, there have been improvements in references, alignment, quantitation, and variant detection methods, and the development of specialized methods, such as transcriptome assembly, fusion discovery, infectious agent detection, and metagenomic expression.

Viewers will learn about the many RNA-Seq related improvements, as well as some of the current limitations in inferences and precision. Some examples of improvements and new capabilities that will be discussed include:

  • strand precision
  • the ability to measure RNA from a small number of cells
  • new protocols for degraded RNA
  • and the ability to sequence samples at great depths (up to 1B paired reads) extending the dynamic range to over 6 orders of magnitude.

The presenter will also examine some current limitations including that due to specific biases inherent to each protocol, we cannot make inferences about absolute copy number of a particular RNA species with any precision, only relative copy number, despite the omnipresence of normalization measures such as FPKM that imply otherwise. In addition, until we have technologies that provide full-length sequencing, we will be unable to discern potentially important quantitative and qualitative differences in highly similar isoforms.

Through this webinar viewers will have a much more comprehensive understanding of the types of biological questions and problems RNA-Seq can address fully or be a key aid in addressing, and those it cannot.

Date: August 22, 2014

Speaker:
Wendell Jones, PhD, Global Head, Genomic Bioinformatics, EA | Quintiles

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ABOUT THE SPEAKERS

Patrick Hurban, PhD, Global Head of Genomic Research and Development, EA | Quintiles

Dr. Hurban joined Quintiles in 2012 as Global Head of Genomic Research and Development, upon the acquisition of Expression Analysis by Quintiles. He is responsible for the identification and implementation of new genomic capabilities, for consulting on special projects, and for the development and validation of genomic assays. These include broad-based screening assays such as exome and RNA sequencing, as well as microarray-based expression profiling and genotyping, to highly targeted assays. Dr. Hurban has over 25 years of experience in molecular genetics, including over 15 years in positions of increasing responsibility in high-profile genomics-focused organizations. His research interests have focused on the genetic control of gene expression and have spanned diverse fields such as toxicology, developmental and cancer biology.

Following a Bachelor’s degree in Biology from the University of North Carolina at Chapel Hill, he earned his Ph.D. in Human Genetics from the University of Utah in Salt Lake City before serving as a Postdoctoral Research Fellow of the American Cancer Society in the Department of Developmental Biology at Stanford University.

Sarah Bacus, PhD, Senior VP and Chief Scientific Officer, Translational R&D Oncology, Quintiles

Sarah Bacus is the Senior Vice President, Translational R&D - Oncology, Innovation and Chief Scientific Officer at Quintiles. Dr. Bacus has over 30 years of experience in basic and applied research in oncology drug development and diagnostics. Prior to her role at Quintiles, Dr. Bacus founded and sold four successful companies in the oncology field that were all focused on diagnostic and pre-clinical work for personalized medicine in oncology – CAS (Sold to Becton Dickinson); QDL (Sold to Ventana); TMD (Sold to Quintiles), and Oncotest (Sold to TEVA). Work performed by these companies revolutionized tissue imaging, facilitated accelerated approval of drugs such as lapatinib and established novel treatment strategies still currently in use today. Dr. Bacus has noteworthy accomplishments in preclinical drug development, applied and basic oncology research, personalized medicine and development of diagnostics and biomarkers which culminated in over 120 peer review papers, multiple worldwide patented biomarkers, and worldwide recognition as a leader in personalized medicine. Dr. Bacus holds professorships at Duke University and University of Illinois at Chicago. Dr. Bacus earned a BSc in Physics and Mathematics, M.Sc. in Biophysics and a PhD in Medical Physics at the Hebrew University in Israel.

Jeff Fitzgerald, Director, Personalized Medicine Integration, EA | Quintiles

Jeff brings to EA | Quintiles over a decade of successful sales and support experience in the genomics tools sector. In his current position he supports the integration of genomic technologies to address biomarker analysis in sponsors’ clinical trials.

Previously while at RainDance Technologies he cultivated new business opportunities in research and clinical markets through the use of its sequence enrichment solutions in conjunction with various next generation sequencing platforms. In previous sales and support roles at Affymetrix, he supported key genome and academic research centers in the use of expression, resequencing, and genotyping microarrays. Prior to his commercial experience, Jeff sought to identify molecular markers responsible for tumor progression while performing research in the Department of Pathology at Brigham and Women’s Hospital and Harvard Medical School.

Jeff holds a Bachelor of Science from the University of Vermont in Microbiology and Molecular Genetics.

Vic Weigman, PhD, Associate Director of Translational Genomics, EA | Quintiles

Dr. Weigman has been involved in genomic research for the past 13 years, primarily in data interpretation and algorithm development. Through work at UNC Lineberger Cancer Center under Charles Perou, he worked on developing mechanisms for integrating murine and human drug response data and developed new copy number biomarkers for subtypes of breast cancer. While at EA | Quintiles, he helped cultivate the expansion of the next gen sequencing infrastructure to support pre-clinical research into biomarker identification. Currently he directs the Translational Genomics Group at EA | Quintiles, whose goal is continue biomarker discovery for drug development along with constructing assays and informatics tools necessary to support market-ready products used for genomic profiling of cancer.

Kim Robasky, PhD, Associate Director, Bioinformatics, EA | Quintiles

Dr. Robasky received her Ph.D. in bioinformatics from Boston University, with a research appointment in the Church Lab at the Department of Genetics at Harvard Medical School in 2013. Kimberly’s publications include analyses of whole genome and targeted sequencing data via phasing, haplotyping and variant interpretation with a focus on characterizing error to improve accuracy and clinical understanding. Kimberly is currently Associate Director of Bioinformatics for Expression Analysis, a Quintiles Company, in Durham, NC, where she has brought to bear her previous experience as a financial consulting software architect to institute and support best practices for software engineering and genomic data annotation. Kimberly’s current focus is on surveying existing datasets, including The Cancer Genome Atlas data, for clinically relevant features and cancer drug targets.

Wendell Jones, PhD, Global Head, Genomic Bioinformatics, EA | Quintiles

Wendell currently heads the genomic bioinformatics organization at EA/Quintiles and has been a part of the EA team for over 12 years. His general interests are bioinformatics, statistical analysis and modeling, statistical graphics, and analyzing large datasets. Wendell has participated in several working groups and consortiums including the Sequencing Quality Control project (SEQC) and was heavily involved in the Microarray Quality Control (MAQC) project, serving as co-chair of the Clinical Working Group in MAQC Phase II. Phase II examined the capabilities of microarrays for predicting preclinical and clinical outcomes in complex diseases. Wendell's current research interests include sequencing-based studies and clinical applications of RNA, miRNA, and DNA in addition to other genomics technologies. Wendell supports student research in biology and genetics as a faculty adjunct within the School of Medicine at University of North Carolina at Chapel Hill.

ABOUT EA | QUINTILES

EA | Quintiles provides cutting-edge genomic sequencing, gene expression, genotyping, and bioinformatics services to pharmaceutical companies, diagnostic test developers, government agencies, and academic labs. EA | Quintiles conducts projects under clinical-grade quality control and offers bioinformatics expertise and computational infrastructure to process genomic data with consistency and speed.

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