march 2013 introduction
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Genome-in-a-Bottle Consortium
Reference Materials for Clinical Applications of Human Genome Sequencing
Marc Salit, Ph.D. and Justin Zook, Ph.DNational Institute of Standards and Technology
VisionReference Samples
Variant List, Performance
Metrics
SamplePreparation
Sequencing
Bioinformatics
NIST in partnership with FDA
• FDA calls for NIST RMs for WGS– “An RM from NIST has great
potential to facilitate FDA's regulatory approach to WGS, and would help provide assurance that different sequencers at different locations had a particular level of ongoing performance.”• Elizabeth Mansfield, Director,
Personalized Medicine Staff, OIVD/CDRH/FDA
• FDA funding work at NIST to develop reference materials suitable to support regulatory oversight– materials to be used as
part of evaluation of technical performance of sequencing instruments as devices
Value of a NIST RM• NIST commitment to:
– Maintain availability of RM– Maintain data on RM – ongoing
aggregation of sequence data to increase accuracy and minimize biases
– Be a neutral arbiter in aggregation of data from different platforms
• NIST infrastructure to distribute RM• NIST investment in genomic
measurement science• NIST imprimatur as an
internationally recognized source of “higher order” RMs for regulatory and commercial purposes
Why a consortium?
Genome in a Bottle Consortium Development
• NIST met with sequencing technology developers to assess standards needs– Stanford, June 2011
• Open, exploratory workshop– ASHG, Montreal, Canada– October 2011
• Small, invitational workshop at NIST to develop consortium for human genome reference materials– FDA, NCBI, NHGRI, NCI, CDC, Wash
U, Broad, technology developers, clinical labs, CAP, PGP, Partners, ABRF, others
– developed draft work plan– April 2012
• Open, public meeting at NIST to formally establish consortium, present draft work plan– formed working groups– identified candidate genomes– established principles of:
• reference material selection• characterization• informatics• performance metrics
– August 2012
• Expect to be sequencing candidate genomes Q4 2012– developing large RM batches to
characterize in 2013
• Website– www.genomeinabottle.org
Genome in a Bottle Working Groups
Reference Material Selection& Design
Andrew Grupe,Celera
•Develop prioritized list of whole human genomes for Reference Materials
• Identify candidate approaches and materials for artificial RMs•Develop prioritized list
Meaurements for Reference Material Characterization
Elliott Margulies & Mike Eberle, Illumina
•Develop consensus plan for experimental characterization of Reference Materials
Bioninformatics, Data Integration, and Data Representation
Steve Sherry, NCBI
•Develop plan for integrating experimental data and forming consensus variant calls and confidence estimates
•Develop consensus plan for data representation
Performance Metrics & Figures of Merit
Justin Johnson, EdgeBio
•User interface to the Genome-in-a-Bottle Reference Material• “Dashboard”•what an end user will
see and report to understand and describe the performance of their experiment• variant call accuracy•process performance
measures to enable optimization
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