TOPMed Site Visit 2018 - Revision history

Tblackw: Replaced content with " '''Successfully occurred on Thursday September 13, 2018'''"

2018-09-28T14:14:36Z

Replaced content with " '''Successfully occurred on Thursday September 13, 2018'''"

← Older revision		Revision as of 10:14, 28 September 2018
Line 1:		Line 1:
	~~'''One day: Thursday, September 13, 2018, 8:30 am - 4:00 pm ?'''~~

	~~Perhaps 5 1/2 total hours of presentations.~~		'''Successfully occurred on Thursday September 13, 2018'''

	~~= 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) ==~~

	~~== Summary of contract spending to date (20 minutes) ==~~

	~~''Denise Bianchi and Goncalo Abecasis will present this section''~~

	* Broad subdivisions: personnel, cloud storage, cloud computing, hardware
	* Divided between Task 1 and Task 2

	~~== Improved results from the latest TOPMed imputation panel (20 minutes) ==~~

	~~''Goncalo Abecasis will present this, unless Lukas Forer is available. Ketian Yu to prepare summaries of imputation quality''~~

	~~[[Media:nhlbi.4761.imputation.accuracy.2018aug31.pptx\|'''(slides)''']]~~

	* 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 (20 minutes) ==~~

	~~'' Check with Sebastian Zoellner'~~'

	~~== Cloud access to TOPMed sequence data (20 minutes) ==~~

	~~''Tom Blackwell to take the lead on this section''~~

	~~[[Media:nhlbi.4768.fusera.slides.01.pdf\|'''(slides)''']]~~

	* 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

	~~== Lunch (70 minutes) ==~~

	~~== ENCORE analysis server (20 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

	~~== 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

	~~== 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

	~~== Break (20 minutes) ==~~

	~~== Future plans for the next Task Order (30 minutes) ==~~

	~~== Feedback from NHLBI (40 minutes) ==~~

	~~== Finish (3:50 pm) ==~~

Tblackw at 15:43, 4 September 2018

2018-09-04T15:43:55Z

← Older revision		Revision as of 11:43, 4 September 2018
Line 1:		Line 1:
	'''One day: Thursday, September 13, 2018, 8:30 am - 3:00 pm ?'''		'''One day: Thursday, September 13, 2018, 8:30 am - 4:00 pm ?'''

	Perhaps 4 1/3 total hours of presentations~~, if lunch is brought in~~.		Perhaps 5 1/2 total hours of presentations.

	~~(If you think I'm a bit optimistic on the timings, I'd have to agree with you.)~~

	= Draft Agenda =		= Draft Agenda =
Line 59:		Line 57:
	== Break (30 minutes) ==		== Break (30 minutes) ==

	== ~~ENCORE analysis server~~ (15 minutes) ==		== Summary of contract spending to date (20 minutes) ==

	''~~Matthew Flickinger~~ will present this section''		''Denise Bianchi and Goncalo Abecasis will present this section''

			* Broad subdivisions: personnel, cloud storage, cloud computing, hardware
			* Divided between Task 1 and Task 2

	* Principle of operation		== Improved results from the latest TOPMed imputation panel (20 minutes) ==
	* 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 Forer is available. Ketian Yu to prepare summaries of imputation quality''

	''~~Goncalo Abecasis will present this, unless Lukas Forrer is available. Ketian to prepare summaries of imputation quality~~''		[[Media:nhlbi.4761.imputation.accuracy.2018aug31.pptx\|'''(slides)''']]

	* Principle of operation		* Principle of operation
Line 82:		Line 76:
	* Challenges and opportunities from collaboration and integration with NIH Commons / NHLBI Stage		* Challenges and opportunities from collaboration and integration with NIH Commons / NHLBI Stage

	== Potential Population Genetics Update (15 minutes) ==		== Potential Population Genetics Update (20 minutes) ==

	'' Check with Sebastian Zoellner''		'' Check with Sebastian Zoellner''

			== Cloud access to TOPMed sequence data (20 minutes) ==

			''Tom Blackwell to take the lead on this section''

			[[Media:nhlbi.4768.fusera.slides.01.pdf\|'''(slides)''']]

			* 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

			== Lunch (70 minutes) ==

			== ENCORE analysis server (20 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

	== Manuscript support (30 minutes) ==		== Manuscript support (30 minutes) ==
Line 99:		Line 119:
	* Context specific mutation rates		* Context specific mutation rates
	* Data sharing with Centers for Common Disease Genetics		* Data sharing with Centers for Common Disease Genetics

	~~== Lunch (45 minutes) ==~~

	== Interactions with outside groups (30 minutes) ==		== Interactions with outside groups (30 minutes) ==
Line 112:		Line 130:
	* NIMH Parkinsons Disease Consortium		* NIMH Parkinsons Disease Consortium

	== ~~Cloud access to TOPMed sequence data~~ (15 minutes) ==		== Break (20 minutes) ==

	~~''Tom Blackwell to take~~ the ~~lead on this section''~~		== Future plans for the next Task Order (30 minutes) ==

	* NCBI's 'Fusera' controlled access mechanism		== Feedback from NHLBI (40 minutes) ==
	* 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~~) ==		== Finish (3:50 pm) ==

Tblackw: Created 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..."

2018-08-29T18:18:18Z

Created 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..."

New page

'''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) ==