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.
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.
Wendell Jones, PhD, Global Head, Genomic Bioinformatics, EA
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.
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.