Aug2013 NIST program slides
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The Genome-in-a-Bottle Consortium was established to develop reference materials for clinical applications of human genome sequencing. The National Institute of Standards and Technology (NIST) has been working with various organizations to obtain and characterize reference genomes. The current plan is to use the NA12878 genome as a pilot sample and 8 trios from the Personal Genome Project as a more complete set. Working groups were formed to address reference material selection, characterization measurements, bioinformatics/data integration, and performance metrics. The consortium discussed obtaining consent for reference genomes, the scope of work, and how decisions will be made regarding new reference materials and policies.
Aug2013 NIST program slides
- 1. Genome-in-a-Bottle Consortium August 2013 Reference Materials for Clinical Applications of Human Genome Sequencing Marc Salit, Ph.D. and Justin Zook, Ph.D National Institute of Standards and Technology
- 2. 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 • Open, public workshop at XGen Congress – March 2013 • Website – www.genomeinabottle.org
- 3. Well-characterized, stable RMs • Obtain metrics for validation, QC, QA, PT • Determine sources and types of bias/error • Learn to resolve difficult structural variants • Improve reference genome assembly • Optimization – integration of data from multiple platforms – sequencing and analysis • Enable regulated applications Comparison of SNP Calls for NA12878 on 2 platforms, 3 analysis methods
- 4. Measurement Process Sample gDNA isolation Library Prep Sequencing Alignment/Mapping Variant Calling Confidence Estimates Downstream Analysis • gDNA reference materials will be developed to characterize performance of a part of process – materials will be certified for their variants against a reference sequence, with confidence estimates genericmeasurementprocess
- 5. • NIST working with GiaB to select genomes • Current plan – NA12878 HapMap sample as Pilot sample • part of 17-member pedigree – trios from PGP as more complete set • 8 trios, focus on children • varying biogeographic ancestry 12889 12890 12891 12892 12877 12878 12879 12880 12881 12882 12883 12884 12885 1288712886 12888 12893 CEPH Utah Pedigree 1463 Putting “Genomes” in Bottles 11 children, Birth Order Redacted
- 6. 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 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 •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
- 7. Agenda Thursday Welcome and Intro Integrating large scale sequencing into clinical practice Heidi Rehm Personal Genomics Michael Snyder Break/Poster Session Update on GIAB Progress Marc Salit Comparison of NIST, Platinum Genomes, and other NA12878 call-sets to understand sequencing performance Justin Zook Presentations from related projects Platinum Genomes Michael Eberle NA12878 Trio Analysis Francisco De La Vega GeT-RM Project and Genome Browser Deanna Church Lunch (on your own in NIST cafeteria) Working Group Meetings Reference Material Selection & Design (Lecture Room E) Measurements for Reference Material Characterization (Dining Room A&B) Bioinformatics, Data Integration, and Data Representation (Lecture Room A) Performance Metrics and Figures of Merit (Lecture Room C) Friday Discussion between working groups Working group reports (Green Auditorium) Workplan refinement, timeline Lunch (on your own in NIST cafeteria) Discussion: Scope of consortium, how to make decisions Resource needs, how to meet them, and next steps
- 8. Agenda Thursday Welcome and Intro Integrating large scale sequencing into clinical practice Heidi Rehm Personal Genomics Michael Snyder Break/Poster Session Update on GIAB Progress Marc Salit Comparison of NIST, Platinum Genomes, and other NA12878 call-sets to understand sequencing performance Justin Zook Presentations from related projects Platinum Genomes Michael Eberle NA12878 Trio Analysis Francisco De La Vega GeT-RM Project and Genome Browser Deanna Church Lunch (on your own in NIST cafeteria) Working Group Meetings Reference Material Selection & Design (Lecture Room E) Measurements for Reference Material Characterization (Dining Room A&B) Bioinformatics, Data Integration, and Data Representation (Lecture Room A) Performance Metrics and Figures of Merit (Lecture Room C) Friday Discussion between working groups Working group reports (Green Auditorium) Workplan refinement, timeline Lunch (on your own in NIST cafeteria) Discussion: Scope of consortium, how to make decisions Resource needs, how to meet them, and next steps Please Note The plenary sessions of this workshop are being webcasted (audio & slides) – please use the microphones when asking questions. Web attendees can ask questions with chat. Slides will be made available on SlideShare after the workshop (see genomeinabottle.org). Tweets are welcome unless the speaker requests otherwise. Please use #giab as the hashtag.
- 9. Status Update, Consortium Business Marc Salit and Justin Zook
- 10. Consenting Genomes for use as Reference Materials • Risk of re-identification – this is a real risk – privacy – implications for family members • Meaning of possibility of withdrawal • Commercial application – indirect, research – direct, derived products • PGP project currently state-of-art – broad and direct – test to demonstrate understanding • “Wild West”
- 11. NIST Reference Materials Pilot RM - NA12878 • 8300 10ug vials of NA12878 gDNA @ NIST 4/2013 – Available for sequencing by GIAB participants – target for release as NIST RM 2/2014 • SNPs, small indels • Will be sequenced at ~10 labs – ~4 technologies, multiple modes • Received “Human Subjects Approval” for release of NA12878 as NIST RM Personal Genome Project • Ashkenazim trio DNA expected ~Dec 2013 • Asian son DNA expected ~Dec 2013 – Parents’ cell lines in process at Coriell • “Human subjects review” close to approval for release of PGP genomes as NIST RMs • Plan is 5-6 additional trios of diverse ancestry – Ideally, african, asian, hispanic – What should we do if PGP doesn’t have trios from each of these groups?
- 12. Planned Measurements on NA12878 candidate RM • NIST – ~300x total 2x150bp Illumina over 6 vials of NA12878 – ~100x SOLiD 5500W 2x50bp coverage – ~50x SOLiD 5500W 2x50bp coverage of parents • Illumina – PCR-free – Mate-pair • Complete Genomics – Normal pipeline – LFR pipeline • NCI – Ion Proton – Illumina – Various libraries • Garvan – Illumina exome • Celera – Targeted panels • Cornell Weill – Illumina • MTAs pending – Univ. of Nebraska Medical – Univ. of Michigan
- 13. HOW DO WE WANT TO FUNCTION AS A CONSORTIUM? What’s our scope? How do we make decisions?
- 14. Spectrum of Possibilities • NIST develops and disseminated gDNA RMs with consortium input • Consortium functions as a Standards Body, with dynamic portfolio and broad influence
- 15. Spectrum of Possibilities NIST develops and disseminates gDNA RMs with consortium input Consortium functions as a Standards Body, with dynamic portfolio and broad influence
- 16. Scope Basic Scope • Develop/disseminate pilot genome and 8 trios as RMs – gDNA and reference data • Develop/disseminate “Performance Metrics Suite” – data repository? • Documentary Standards to describe methods? – through a clinical SDO? CLSI? IFCC? Extended Scope • Other RMs as part of GiaB portfolio? – tumor/normal pair – artifical spike-in controls • pDNA from NCI – derived commercial materials • Cell lines for which we have reference gDNA • Such cell lines embedded in FFPE – engineered cell lines • designed as controls for specific variants
- 17. Extended Scope • need process to include new material/product in portfolio – what does it mean to put the GiaB imprimatur on something? • some possible requirements – guidelines for usage – methods for characterization – conduct interlab studies to establish utility • how do we decide what to do? – need to be • open, transparent, public • form consensus – pragmatic consensus needs champion and commitment • e.g. proposer pilots interlab • consortium members participate in interlab • how do we decide policy matters? – see draft data release policy discussion on this tomorrow after lunch…