Six Myths about Ontologies: The Basics of Formal Ontology
GCAT Update June 2013 @ The Clinical Genome Conference
1. GCAT: Genome Comparison and Analytic Testing
Update June 2013
David Mittelman, Ph.D.
Virginia Bioinformatics Institute at Virginia Tech
@evolvability #TCGC #GCAT
2. How do we build the most accurate model or representation of
a patient’s genome?
Question:
3. This was supposed to be the future...
where is my $1000 genome?
Hall, N., Genome Biology. 2013.
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?
13. The performance of mappers affects variants discovery
Mutation Recall: Genome in a Bottle
Zook, J., et. al, in preparation. 2013.
14. Variant discovery is also greatly affected by variant callers
Mutation Recall: Genome in a Bottle
Zook, J., et. al, in preparation. 2013.
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. 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