29
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchCreated page with "'''One day: Thursday, September 13, 2018, 8:30 am - 3:00 pm ?''' Perhaps 4 1/3 total hours of presentations, if lunch is brought in. (If you think I'm a bit optimistic o..."
'''One day: Thursday, September 13, 2018, 8:30 am - 3:00 pm ?'''
Perhaps 4 1/3 total hours of presentations, if lunch is brought in.
(If you think I'm a bit optimistic on the timings, I'd have to agree with you.)
= Draft Agenda =
== Introduction and Overview of TOPMed data resources and services (30 minutes) ==
''Goncalo Abecasis will present overview of IRC activies''
* Introduce IRC personnel and their expertise
* Sequence for 130,000+ participants
* Variant calls and genotypes, phased and unphased
* Structural variant calls in progress
* BRAVO variant browser
* ENCORE analysis server
* TOPMed imputation reference panel
* Main developments in the past year, including security improvements, Manual, etc.
== Characteristics of variants in data freeze 6 (20 minutes) ==
''Hyun Min Kang and Jonathan LeFaive will present this section''
* Overall numbers
* Differences by ancestry, study and sequencing center
* Allele frequencies of deleterious variants
* Genotype accuracy
* Compare harmonized versus sequencing center mappings
* Process for variant calling, genotyping, filtering, phasing and distribution
* Process for interim 'snapshot' genotypes
== Calling structural variants (20 minutes) ==
''Our colleagues at Baylor will present this section. William Salerno?''
* Procedures and plans for structural variant calling
* Benefits of ensemble approach
* Initial results
* Data access mechanisms
* Anticipated data size
* Coordination with SNPs and indels
== BRAVO variant browser helps to assess variant quality (20 minutes) ==
''Daniel Taliun will present this section''
* Purpose
* Which studies are included
* Usage / main features
* Both rare and common variants
* Improvements in the last year
* Access via an applications programming interface (API)
* View all information used in filtering
* Coordination with gnomAD
* Potential plans for PheWeb integration
== Break (30 minutes) ==
== ENCORE analysis server (15 minutes) ==
''Matthew Flickinger will present this section''
* Principle of operation
* Releases only aggregate data summaries
* Visualizations help to assess results
* Data sharing and collaboration tools
* Capability to re-run previous jobs with new data
* SAIGE analysis gives accurate results in case-control studies
* Usage statistics comparing last 12-months to previous 12-months
* Some highlights from user survey results
== Improved results from the latest TOPMed imputation panel (15 minutes) ==
''Goncalo Abecasis will present this, unless Lukas Forrer is available. Ketian to prepare summaries of imputation quality''
* Principle of operation
* Measuring imputation quality in different populations
* Pushing the low frequency boundary
* Improved accuracy for African American and Latino samples
* Challenges and opportunities from collaboration and integration with NIH Commons / NHLBI Stage
== Potential Population Genetics Update (15 minutes) ==
'' Check with Sebastian Zoellner''
== Manuscript support (30 minutes) ==
''Albert Vernon Smith will present overview for this section''
* How can and how is the IRC supporting TOPMed manuscripts and discoveries?
* Overall TOPMed landmark paper
* Analysis of telomere length
* Mitochondrial DNA copy number
* Lipids analysis using TOPMed imputed genotypes
* UK BioBank with TOPMed imputation
* Context specific mutation rates
* Data sharing with Centers for Common Disease Genetics
== Lunch (45 minutes) ==
== Interactions with outside groups (30 minutes) ==
''Albert Vernon Smith to take the lead on this section''
* NIH Data Commons
* NHLBI Data STAGE
* NHGRI Centers for Common Disease Genetics
* Global Alliance for Genomics and Health (GA4GH)
* NIMH Parkinsons Disease Consortium
== Cloud access to TOPMed sequence data (15 minutes) ==
''Tom Blackwell to take the lead on this section''
* NCBI's 'Fusera' controlled access mechanism
* User perspective -- involves a Google or Amazon billing project
* What is needed for users to have a great overall experience?
* Education and training for users
== Feedback from NHLBI (60 minutes) ==
Perhaps 4 1/3 total hours of presentations, if lunch is brought in.
(If you think I'm a bit optimistic on the timings, I'd have to agree with you.)
= Draft Agenda =
== Introduction and Overview of TOPMed data resources and services (30 minutes) ==
''Goncalo Abecasis will present overview of IRC activies''
* Introduce IRC personnel and their expertise
* Sequence for 130,000+ participants
* Variant calls and genotypes, phased and unphased
* Structural variant calls in progress
* BRAVO variant browser
* ENCORE analysis server
* TOPMed imputation reference panel
* Main developments in the past year, including security improvements, Manual, etc.
== Characteristics of variants in data freeze 6 (20 minutes) ==
''Hyun Min Kang and Jonathan LeFaive will present this section''
* Overall numbers
* Differences by ancestry, study and sequencing center
* Allele frequencies of deleterious variants
* Genotype accuracy
* Compare harmonized versus sequencing center mappings
* Process for variant calling, genotyping, filtering, phasing and distribution
* Process for interim 'snapshot' genotypes
== Calling structural variants (20 minutes) ==
''Our colleagues at Baylor will present this section. William Salerno?''
* Procedures and plans for structural variant calling
* Benefits of ensemble approach
* Initial results
* Data access mechanisms
* Anticipated data size
* Coordination with SNPs and indels
== BRAVO variant browser helps to assess variant quality (20 minutes) ==
''Daniel Taliun will present this section''
* Purpose
* Which studies are included
* Usage / main features
* Both rare and common variants
* Improvements in the last year
* Access via an applications programming interface (API)
* View all information used in filtering
* Coordination with gnomAD
* Potential plans for PheWeb integration
== Break (30 minutes) ==
== ENCORE analysis server (15 minutes) ==
''Matthew Flickinger will present this section''
* Principle of operation
* Releases only aggregate data summaries
* Visualizations help to assess results
* Data sharing and collaboration tools
* Capability to re-run previous jobs with new data
* SAIGE analysis gives accurate results in case-control studies
* Usage statistics comparing last 12-months to previous 12-months
* Some highlights from user survey results
== Improved results from the latest TOPMed imputation panel (15 minutes) ==
''Goncalo Abecasis will present this, unless Lukas Forrer is available. Ketian to prepare summaries of imputation quality''
* Principle of operation
* Measuring imputation quality in different populations
* Pushing the low frequency boundary
* Improved accuracy for African American and Latino samples
* Challenges and opportunities from collaboration and integration with NIH Commons / NHLBI Stage
== Potential Population Genetics Update (15 minutes) ==
'' Check with Sebastian Zoellner''
== Manuscript support (30 minutes) ==
''Albert Vernon Smith will present overview for this section''
* How can and how is the IRC supporting TOPMed manuscripts and discoveries?
* Overall TOPMed landmark paper
* Analysis of telomere length
* Mitochondrial DNA copy number
* Lipids analysis using TOPMed imputed genotypes
* UK BioBank with TOPMed imputation
* Context specific mutation rates
* Data sharing with Centers for Common Disease Genetics
== Lunch (45 minutes) ==
== Interactions with outside groups (30 minutes) ==
''Albert Vernon Smith to take the lead on this section''
* NIH Data Commons
* NHLBI Data STAGE
* NHGRI Centers for Common Disease Genetics
* Global Alliance for Genomics and Health (GA4GH)
* NIMH Parkinsons Disease Consortium
== Cloud access to TOPMed sequence data (15 minutes) ==
''Tom Blackwell to take the lead on this section''
* NCBI's 'Fusera' controlled access mechanism
* User perspective -- involves a Google or Amazon billing project
* What is needed for users to have a great overall experience?
* Education and training for users
== Feedback from NHLBI (60 minutes) ==
