icg-11 - genomic data projects around the world - nov 5 2016
TRANSCRIPT
ICG-11: Genomic Data Projects around the World - How to find data for your research
Fiona Nielsen – November 4th 2016
We are always looking for data
Genetics, Cancer,
Rare diseaseresearch
We need access to the right data at the right time
DNA interpretation
requires lots of data
How much data do you need to publish a paper?
2001: 1 human genome
2012: 1000 Genomes (1092 genomes, since increased to ~2500)
2015: UK10K, Icelandic population (2,636 + 100k imputed), Cancer genome atlas ~11,000 genomes
?
2016:Exac consortium 65,000 exomesGnomAD ~126,000 exomes
2020:
Data is not easy to find and access
FRAGMENTEDPoor visibility of available
genomic data
ADMIN BURDENHuge overhead to manage
data access
BAD CULTURELack of data sharing habits in
research culture
Finding and accessing data can take months
< 1 week
1-3 months
+6 months
40%
48%
11%
Time spent data scouting per project
Why the barrier?
Barriers
• Difficult to find data, let alone find the RIGHT data
• Time-consuming and difficult to apply for access to data
• Complicated and labourious to submit data to public repositories
http://blog.repositive.io/tag/data-access/
http://blog.repositive.io/tag/data-sharing/
But where in the world is the data?
?
DATA is fragmented
How to make data easy to discover?
We have identified hundreds of data sources
Universities – Or repositories affiliated to a university.
Projects/Consortia – Has a specific purpose/aim. Often focussed on a specific research question or disease.
Public repositories – Allows download and upload of data from multiple institutions.
Companies – For profit organisations making data available for free or as a service.
Biobanks – many have sequence data of their biological samples.
Researchers know on
average 4-5 data sources
More data sources appear every day, to date we have identified 350+
Simpler workflowfor data access
And indexed them on a the Repositive platform
Discover and access
Efficient Search, see related results
Find colleagues & their data interests
Co-annotate data & community feedback
Free to use: http://discover.repositive.io
Platform launched in Sept 2016
Discover and access
Efficient Search, see related results
Find colleagues & their data interests
Co-annotate data & community feedback
1 Million+ Human genomic datasets indexed
Free to use: http://discover.repositive.io
Platform launched in Sept 2016
Discover and access
Efficient Search, see related results
Find colleagues & their data interests
Co-annotate data & community feedback
1 Million+ datasets indexed
Simpler workflowfor data access
177kWhole Exomes
213kWhole Genomes
240023andMe samples
Free to use: http://discover.repositive.io
Platform launched in Sept 2016
Discover and access
Efficient Search, see related results
Find colleagues & their data interests
Co-annotate data & community feedback
1 Million+ datasets indexed
Simpler workflowfor data access
61+Countries
426+Research organisations
Using Repositive
PDX ConsortiumWith AstraZeneca
Free to use: http://discover.repositive.io
Data sources across the globeGEO location of 278 data sources analysed.
Found by tracking IP address of the source.
These include:
Public Repositories
Universities
Companies
BioBanks
Research consortiums
Data source content
Assay Types
Dedicated to…
Sequenced ethnicities
Aboriginals
African Americans
Africans
Australians
Chinese
MalaysIndians
DanishDutch Estonian
Russian
European Ancestry
FinnishIcelandic
JapaneseKorean
Latin Americans
Saudi
Swedish
Machines & Data sources
9475600
88
660
26
68
5062
3
25
0
0
23 International
Interesting site to look at: http://omicsmaps.com/stats
• Repositive is supporting the whole research workflow
• Faster, more efficient data discovery• Streamlining data access applications • Developing technology for efficient data access• Setting up pre-competitive data sharing agreements• Running workshops and training programmes
More efficient data access
Read about our pre-competitive PDX data resource in collaboration with AstraZeneca http://repositive.io/pdx
Building upon best practices
MAKE DATA DISCOVERABLE
SIMPLIFY WORKFLOWS
CONTRIBUTE TOCOMMUNITY
DNAdigest and Repositive – Connecting the world of genomic datahttp://www.tinyurl.com/plos-biology-repositive
First 30 data sources listed here:
Connecting the world of genomic data
Visit us at: http://repositive.io Or tweet us @repositiveio Free to use: http://discover.repositive.io
Fiona Nielsen, CEO Email us: [email protected]