Location: E2-599, UCSC Campus When: Wednesday September 20, 2017 3:30-4:30 PM Speaker: Anthony Schweitzer

Abstract:

Technologies such as next generation sequencing are showing us brief glimpses of the enormous complexities within our cells transcriptomes.  Non-coding RNAs and alternative splicing events are new sources of biomarker development.  These biomarkers help identify risk for disease, diagnose disease, guide treatment strategies, and monitor patient responses to therapy.  Robustly identifying these transcriptome changes are difficult without careful consideration of the variances and challenges inherent to the technology.  The United States FDA Sequencing Quality Control, or SEQC has been investigating technical variance associated with RNA sequencing.  Detailed analysis on precision and accuracy can provide insight and clarity on the power and limitations of RNA-seq.  Historically, expression microarray data has been affected by signal and fold-change compression.  RNA-seq workflows often overinflate fold-change.  This has limited the ability to directly compare data from different platforms.

When considering both RNA-seq and whole transcriptome microarrays utilizing the same RNA controls, performance comparisons between RNA-seq and microarrays demonstrate that deep sequencing is required to measure low abundance transcripts.  Additionally exon level measurements are more costly to obtain using RNA-seq.  As a result of this, researchers are routinely missing important changes easily accessible on microarrays.  When used in a clinical research setting the added variance from samples and the challenges associated with whole transcriptome profiling of blood or FFPE tissue can also impair the ability discover clinically associated events.  Here in this talk we will explore fundamental differences between arrays and RNA-seq for deep exploration of the transcriptome.

About Anthony Schweitzer:

Anthony Schweitzer

Anthony (Tony) Schweitzer is a Principal Scientist and Director of Bioinformatics for Expression Microarrays at Thermo Fisher Scientific. He provides expertise globally across the organization and has responsibilities in sales, marketing, product support and R&D.  He manages the Expression Bioinformatics Team and designs and develops next generation expression solutions.  He actively participates in the US FDA SEQC/MAQC-III consortium and educates on the power and limitations of RNA-seq.  He has given lectures and seminars worldwide sharing insights on transcriptomics, biomarker discovery and clinical use of microarrays for personalized medicine.  He has developed a passion for aiding investigators with their research and clinical needs and empowering them with tools and insight normally beyond their capabilities.

Tony began his career in Columbus Ohio working on large scale genomic efforts including progenitor stem cell research and pathogen detection.  In 1997 he relocated to the San Francisco bay area and worked on clinical target discovery programs for large pharma and biotech in the areas of Asthma and Diabetes.  In 1999 Tony became the Director of Bioinformatics and IT for Metabolex Inc. and began working with Affymetrix to develop custom Affymetrix expression arrays.  In 2004 he brought his bioinformatics skills and knowledge to Affymetrix laboratories heading up the Expression R&D informatics team and worked extensively on developing whole transcriptome expression microarrays.