BioInfo SIG: A Bioinformatics Perspective on Affymetrix Microarrays



  • Monthly Meeting of the Bioinformatics SIG



    Alan J. Williams, Ph.D. (bio) – Director, Chip Design; Affymetrix, Inc.

    Presentation Overview

    DNA microarrays allow for the simultaneous interrogation of many nucleic acid substrings. In the case of Affymetrix’s most recent mRNA expression monitoring chip, the HG-U133 Plus 2.0, over one million 25-base substrings are interrogated by an approximately 1.5 cm2 chip. Twenty-two separate interrogations of the same mRNA sequence fragment are combined to generate signal estimates which are proportional to the actual concentration of that mRNA transcript in a complex sample. This allows for robust expression monitoring of over 50,000 distinct mRNA fragments. While this presentation will focus on the application of microarrays for mRNA expression monitoring, it should be noted that alternative probe tiling strategies allow for genotyping, resequencing, genome architecture and transcript discovery applications. In the context of mRNA expression monitoring, the chip design goal is to identify a set of independent 25-base substrings (probes) which will hybridize to a specific mRNA transcript (target). This generally involves the non-trivial tasks of assembling a complete set of transcript annotations, selecting regions within the transcripts to target, and selecting probes that will hybridize specifically to the target region and have binding affinities which are responsive to changes in target concentration. This presentation will provide an overview of the technology and will discuss the biological and computational challenges and approaches in designing expression monitoring arrays.


    About the Presenter


    Alan J. Williams, Ph.D.

    Dr. Williams is Director of Chip Design for Affymetrix, Inc. the leading DNA microarray company located in Santa Clara. His bioinformatics team which designs content for mRNA expression monitoring and DNA genotyping microarrays is split between the Emeryville and Santa Clara sites. He received a B.S. degree in Plant Biology in 1995 from the University of California at Davis, and his Ph.D. in Molecular, Cellular, and Developmental Biology from the University of California at Riverside in 2001. He joined a small Berkeley bioinformatics start-up, Neomorphic, in 2000 as a computational biologist. Neomorphic was later acquired by Affymetrix, Inc.


    Event Logistics:



    Hanson Bridgett

    333 Market Street, 21st Floor

    San Francisco, CA, 94105

    Note: Location provided courtesy of Hanson, Bridgett, Marcus, Vlahos, Rudy, LLP.


    6:30 - 7:00 p.m. Registration and Networking

    7:00 - 9:00 p.m. Presentation



    $15 at the door for non-SDForum members

    No charge for SDForum members

    Please call 408.494.8378 for student memberships

    Registration NOT required

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