Giab workshop update mar2019
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Giab workshop update mar2019
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Giab workshop update mar2019
- 2. March 28, 2019 Genome in a Bottle Consortium Update
- 3. Welcome
- 5. The Joint Initiative for Metrology in Biology is a platform for us to work together. • Collaborative home for measurement science and standards for ‘omics and synthetic biology • NIST, Stanford University, and private sector • operated by SLAC • Watch for series of workshops in measurement science, measurement tool, and standards development
- 6. Workshop Hygiene • Plenary sessions (not Thinkshops) can be considered as public information unless the speaker specifically requests differently – Open for tweeting • Please include @GenomeInABottle
- 7. What’s Genome in a Bottle? • Authoritative Characterization of Human Genomes – enduring commitment to resource availability • Samples • Data – widely available open resources – all data made available without embargo • Enable technology and tool-building with benchmark samples and methods for… – development – optimization – demonstration • Germline samples available now • Developing capacity for somatic sample development
- 8. What GIAB Isn’t • Population genetics • Disease-specific • Many clinical samples • Non-human • Genome, not transcriptome, epigenome, proteome, metabolome…
- 11. Small Variant Publications Zook, J.M. et al. An open resource for accurately benchmarking small variant and reference calls. Nature Biotechnology https://doi.org/10.1038/s41587-019-0074-6 (2019). In Press – coming soon!
- 12. GIAB Products are being used Statistics • GIAB Papers >600 Citations • 1245 NIST RM Units sold Two anecdotes • When should clinical labs confirm variants • Training AI methods
- 13. When should clinical variants be confirmed?
- 14. Training & testing AI/deep learning methods
- 15. Open consent enables secondary reference samples • >50 products now available based on broadly-consented, well- characterized GIAB PGP cell lines • Genomic DNA + DNA spike-ins – Clinical variants – Somatic variants – Difficult variants • Clinical matrix (FFPE) • Circulating tumor DNA • Stem cells (iPSCs) • Genome editing • …
- 16. GIAB Developing New Data • PacBio Sequel of Chinese trio with Mt Sinai – New data paper: https://doi.org/10.1101/562611 • PacBio CCS of HG002 – New analysis paper: https://doi.org/10.1101/519025 – Plans for 30x Sequel II CCS of all GIAB samples • Oxford Nanopore – JIMB/NIST/Birmingham/ Nottingham Ultra-long reads – UCSC Promethion • Strand-seq – Collaboration with Lansdorp lab
- 17. GIAB Developing New Data • PacBio Sequel of Chinese trio with Mt Sinai – New data paper: https://doi.org/10.1101/562611 • PacBio CCS of HG002 – New analysis paper: https://doi.org/10.1101/519025 – Plans for 30x Sequel II CCS of all GIAB samples • Oxford Nanopore – JIMB/NIST/Birmingham/ Nottingham Ultra-long reads – UCSC Promethion • Strand-seq – Collaboration with Lansdorp lab
- 18. Goals for This Workshop Update consortium and onboard new members Coordinate with related efforts Considerations for cell-based reference samples Roadmap for new data and methods Difficult small variants Structural variants Strategy for product development How can GIAB be used to benchmark human assemblies?
- 19. Workshop Agenda THURSDAY, MARCH 28, 2019 Welcome, Onboarding, and GIAB Progress Update Break How GIAB fits in the Rest Of the World Lunch Thinkshop: Cells as “packaging” for GIAB Genomes New Data from GIAB Genomes Break New Methods to Characterize GIAB Genomes GIAB Product and Tool Roadmap Reception FRIDAY, MARCH 29, 2019 Product Development Strategy Break Thinkshop: Benchmarking Assemblies GIAB Steering Committee Meeting See http://jimb.stanford.edu/ for detailed agenda.
- 20. Steering Committee Agenda • Policy – Samples, consents, repository relationships • Does NIST need to stand up a repository? • Are NIST RMs needed? – Cells instead of DNA • GIAB Imprimatur – Publications – Communications • Strategy – Roadmap – Prioritizing partnerships – Next 2-3 workshops – Resourcing GIAB work – Research v. Standards-making – Tool development vs reference sample development
- 21. GIAB Roadmap
- 22. • Develop open-access samples and data for broad uses in industry, academia, and government • Convene community of experts to characterize genomes -> GIAB/NIST integrates results to form benchmarks • Develop benchmarking tools Unique GIAB roles in genomics
- 24. • New sequencing data • Trying to develop NIST repository to host GIAB products • New GIAB logo • Publications about benchmark set and benchmarking methods in press in Nature Biotech Progress Update • Development of NIST repository • Developing cancer samples for somatic benchmarking • Draft publication about SV Benchmark Set Ongoing and Future Work
- 25. New Repository for GIAB/PGP Samples • Trying to develop NIST repository to host GIAB products – Ensure long-term open dissemination of GIAB products – Working to assure continuity with existing products – Developing business case and model • Recognized as NIST strategic opportunity – Identified 6 admixed PGP cell lines – Potential home for tumor/normal samples
- 26. New logo and trademark New GIAB Logo GIAB Trademark • NIST pursuing trademark for “Genome in a Bottle” and logo
- 28. • Draft HG002 SV benchmark met design goals • Writing publication • Evaluating “straw man” difficult small variant set • Nate Olson and Justin Wagner on-boarded Progress Update • Characterize remaining ~15% of genome • Integration pipeline development • Assembly metrology • New methods for reference characterization of somatic genomes Ongoing and Future Work Benchmarking assemblies thinkshop Friday morning
- 29. • GIAB Analysis Team focused on SVs and difficult to map small variants Progress Update • Individual collaborations exploring expanding calls for other variant types Ongoing and Future Work
- 30. • Analysis Team evaluated v0.6 benchmark -> met design goals • Drafting Publication Progress Update • Finish manuscript • Integration pipeline development for GRCh38 and all 7 genomes • Resolve clusters of variants • Integrate new technologies and methods Ongoing and Future Work
- 32. • Used 10x and PacBio CCS to expand to difficult to map regions • Evaluating draft v4alpha difficult small variant benchmark set Progress Update • Release v4 benchmark set • Integration pipeline and data development for GRCh38 and all 7 genomes • Write manuscript Ongoing and Future Work
- 33. • Developing methods to detect mosaic/somatic variants in normal cell lines • Compare parents vs. child • Compare blood to cell line Progress Update • Illumina plans to sequence blood in next 2 months • Find regions in normal samples with no mosaic variants • Develop integration methods for somatic variants Ongoing and Future Work
- 35. • “Best practices for benchmarking germline small-variant calls in human genomes” in Nat. Biotech. • https://rdcu.be/bqpDT • Two new tools for SV benchmarking Progress Update • Interpreting stratified performance metrics • Best practices for structural variant benchmarking • Using GIAB to benchmark assemblies • Somatic benchmarking tools Ongoing and Future Work
- 36. The road ahead... 2019 Integration pipeline development for small and structural variants Manuscripts for small and structural variants 2020 Difficult large variants Somatic sample development Germline samples from new ancestries Diploid assembly 2021+ Somatic integration pipeline Somatic structural variation Large segmental duplications Centromere/ telomere ...
- 37. Next Workshop Date April 1-2, 2020 at Stanford