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| '''One day: Thursday, September 13, 2018, 8:30 am - 3:00 pm ?'''
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| Perhaps 4 1/3 total hours of presentations, if lunch is brought in.
| | '''Successfully occurred on Thursday September 13, 2018''' |
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| (If you think I'm a bit optimistic on the timings, I'd have to agree with you.)
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| = 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'' | |
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| * 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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| == ENCORE analysis server (15 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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| == Improved results from the latest TOPMed imputation panel (15 minutes) ==
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| ''Goncalo Abecasis will present this, unless Lukas Forrer is available. Ketian to prepare summaries of imputation quality''
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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 (15 minutes) ==
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| '' Check with Sebastian Zoellner''
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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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| == Lunch (45 minutes) ==
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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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| == Cloud access to TOPMed sequence data (15 minutes) ==
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| ''Tom Blackwell to take the lead on this section''
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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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| == Feedback from NHLBI (60 minutes) ==
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Successfully occurred on Thursday September 13, 2018
