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| − | '''One day: Thursday, September 13, 2018, 8:30 am - 4:00 pm ?'''
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| | | | |
| − | Perhaps 5 1/2 total hours of presentations.
| + | '''Successfully occurred on Thursday September 13, 2018''' |
| − | | |
| − | = Draft Agenda =
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| − | | |
| − | == Introduction and Overview of TOPMed data resources and services (30 minutes) ==
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| − | | |
| − | ''Goncalo Abecasis will present overview of IRC activies'' | |
| − | | |
| − | * Introduce IRC personnel and their expertise
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| − | * Sequence for 130,000+ participants
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| − | * Variant calls and genotypes, phased and unphased
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| − | * Structural variant calls in progress
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| − | * BRAVO variant browser
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| − | * ENCORE analysis server
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| − | * TOPMed imputation reference panel
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| − | * Main developments in the past year, including security improvements, Manual, etc.
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| − | == Characteristics of variants in data freeze 6 (20 minutes) ==
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| − | | |
| − | ''Hyun Min Kang and Jonathan LeFaive will present this section''
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| − | | |
| − | * Overall numbers
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| − | * Differences by ancestry, study and sequencing center
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| − | * Allele frequencies of deleterious variants
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| − | * Genotype accuracy
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| − | * Compare harmonized versus sequencing center mappings
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| − | * Process for variant calling, genotyping, filtering, phasing and distribution
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| − | * Process for interim 'snapshot' genotypes
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| − | | |
| − | == Calling structural variants (20 minutes) ==
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| − | | |
| − | ''Our colleagues at Baylor will present this section. William Salerno?''
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| − | | |
| − | * Procedures and plans for structural variant calling
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| − | * Benefits of ensemble approach
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| − | * Initial results
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| − | * Data access mechanisms
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| − | * Anticipated data size
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| − | * Coordination with SNPs and indels
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| − | | |
| − | == BRAVO variant browser helps to assess variant quality (20 minutes) ==
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| − | | |
| − | ''Daniel Taliun will present this section''
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| − | | |
| − | * Purpose
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| − | * Which studies are included
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| − | * Usage / main features
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| − | * Both rare and common variants
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| − | * Improvements in the last year
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| − | * Access via an applications programming interface (API)
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| − | * View all information used in filtering
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| − | * Coordination with gnomAD
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| − | * Potential plans for PheWeb integration
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| − | | |
| − | == Break (30 minutes) ==
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| − | | |
| − | == Summary of contract spending to date (20 minutes) ==
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| − | | |
| − | ''Denise Bianchi and Goncalo Abecasis will present this section''
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| − | | |
| − | * Broad subdivisions: personnel, cloud storage, cloud computing, hardware
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| − | * Divided between Task 1 and Task 2
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| − | | |
| − | == Improved results from the latest TOPMed imputation panel (20 minutes) ==
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| − | | |
| − | ''Goncalo Abecasis will present this, unless Lukas Forer is available. Ketian Yu to prepare summaries of imputation quality''
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| − | | |
| − | [[Media:nhlbi.4761.imputation.accuracy.2018aug31.pptx|'''(slides)''']]
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| − | | |
| − | * Principle of operation
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| − | * Measuring imputation quality in different populations
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| − | * Pushing the low frequency boundary
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| − | * Improved accuracy for African American and Latino samples
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| − | * Challenges and opportunities from collaboration and integration with NIH Commons / NHLBI Stage
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| − | | |
| − | == Potential Population Genetics Update (20 minutes) ==
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| − | | |
| − | '' Check with Sebastian Zoellner''
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| − | | |
| − | == Cloud access to TOPMed sequence data (20 minutes) ==
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| − | | |
| − | ''Tom Blackwell to take the lead on this section''
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| − | | |
| − | [[Media:nhlbi.4768.fusera.slides.01.pdf|'''(slides)''']]
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| − | | |
| − | * NCBI's 'Fusera' controlled access mechanism
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| − | * User perspective -- involves a Google or Amazon billing project
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| − | * What is needed for users to have a great overall experience?
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| − | * Education and training for users
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| − | | |
| − | == Lunch (70 minutes) ==
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| − | | |
| − | == ENCORE analysis server (20 minutes) ==
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| − | | |
| − | ''Matthew Flickinger will present this section''
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| − | | |
| − | * Principle of operation
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| − | * Releases only aggregate data summaries
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| − | * Visualizations help to assess results
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| − | * Data sharing and collaboration tools
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| − | * Capability to re-run previous jobs with new data
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| − | * SAIGE analysis gives accurate results in case-control studies
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| − | * Usage statistics comparing last 12-months to previous 12-months
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| − | * Some highlights from user survey results
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| − | | |
| − | == Manuscript support (30 minutes) ==
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| − | | |
| − | ''Albert Vernon Smith will present overview for this section''
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| − | | |
| − | * How can and how is the IRC supporting TOPMed manuscripts and discoveries?
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| − | | |
| − | * Overall TOPMed landmark paper
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| − | * Analysis of telomere length
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| − | * Mitochondrial DNA copy number
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| − | * Lipids analysis using TOPMed imputed genotypes
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| − | * UK BioBank with TOPMed imputation
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| − | * Context specific mutation rates
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| − | * Data sharing with Centers for Common Disease Genetics
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| − | | |
| − | == Interactions with outside groups (30 minutes) ==
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| − | | |
| − | ''Albert Vernon Smith to take the lead on this section''
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| − | | |
| − | * NIH Data Commons
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| − | * NHLBI Data STAGE
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| − | * NHGRI Centers for Common Disease Genetics
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| − | * Global Alliance for Genomics and Health (GA4GH)
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| − | * NIMH Parkinsons Disease Consortium
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| − | | |
| − | == Break (20 minutes) ==
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| − | | |
| − | == Future plans for the next Task Order (30 minutes) ==
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| − | | |
| − | == Feedback from NHLBI (40 minutes) ==
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| − | | |
| − | == Finish (3:50 pm) ==
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