GCAT Update June 2013 @ The Clinical Genome Conference

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GCAT Update June 2013 @ The Clinical Genome Conference

  1. 1. GCAT: Genome Comparison and Analytic Testing Update June 2013 David Mittelman, Ph.D. Virginia Bioinformatics Institute at Virginia Tech @evolvability #TCGC #GCAT
  2. 2. How do we build the most accurate model or representation of a patient’s genome? Question:
  3. 3. This was supposed to be the future... where is my $1000 genome? Hall, N., Genome Biology. 2013.
  4. 4. Lots of platforms and sequencing applications
  5. 5. Even more ways to analyze the data Fonseca, N.A., et. al., Bioinformatics. 2012.
  6. 6. What standards do we use? How do we measure performance? http://xkcd.com/927/
  7. 7. http://xkcd.com/927/ @parkertm What standards do we use? How do we measure performance?
  8. 8. http://www.bioplanet.com/gcat • Free to use for everyone • A platform to benchmark NGS methods • A collaboration effort for standards and metrics • A common playground for experimentation • An effort to accelerate NGS adoption • A work in progress… we need your help What is GCAT?
  9. 9. http://www.bioplanet.com/gcat What is GCAT?
  10. 10. Mapping algorithms continue to improve read alignments 100bp PE
  11. 11. Mapping quality performance is an important feature 100bp PE
  12. 12. The performance of mappers affect which variants are called
  13. 13. The performance of mappers affects variants discovery Mutation Recall: Genome in a Bottle Zook, J., et. al, in preparation. 2013.
  14. 14. Variant discovery is also greatly affected by variant callers Mutation Recall: Genome in a Bottle Zook, J., et. al, in preparation. 2013.
  15. 15. We launched GCAT to standardize genome analysis • Launched April 7, 2013 at the Bio-IT World Conference. • GCAT has been viewed more than 20,000 times from visitors across 144 countries. • Our users have processed 500+ reports and more than 900 million bases. • The GCAT cloud has processed 24 million variant calls and 1.6 billion alignments. • All the data in GCAT is freely available for realtime filtering, comparing and sharing. http://www.bioplanet.com/gcat
  16. 16. New features in development for GCAT • Lots of new features already available since our last presentation at Bio-IT World. For example data sharing via social media and advanced data filtering options. • We will be imminently releasing new functionality to compare variant calls against the NIST Genome-in-a-Bottle “truth set”. • Lots more validation data to come from Illumina’s Platinum Genome Project, as well as orthogonal sequencing methods such as PacBio and Sanger. • We are building support for somatic variant detection, whole genome sequencing, and RNAseq. • New testing category: de novo assembly. http://www.bioplanet.com/gcat

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