quantitative genomics 2016 - fiona nielsen - repositive
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Your next scientific breakthrough
Fiona NielsenLondon, June 6th 2016
Slides will be made available online Tweets welcome #quantgen16
Discover genetic mechanisms that cause or prevent a disease
The next big thing
http://www.cell.com/neuron/fulltext/S0896-6273(16)30126-X
Discover genetic mechanisms that cause or prevent a disease
The next big thing
http://www.cell.com/neuron/fulltext/S0896-6273(16)30126-X
Discover genetic mechanisms that cause or prevent a disease
The next big thing
http://www.cell.com/neuron/fulltext/S0896-6273(16)30126-X
Discover genetic mechanisms that cause or prevent a disease
The next big thing
7 cases, heterozygousFour healthy carriers
Discover genetic mechanisms that cause or prevent a disease
The next big thing
7 cases, heterozygousFour healthy carriers
21 healthy carriers in ExAC database
Age of MS onset: 25-48 years13 carriers in ExAC > 50 years
•The more surprising a results seems to be, the less likely it is to be true
Take home message
Face up to false positives – Nature July 2012
• Validate your results with external data• No excuse for not validating against publicly available data • Human genetics check out: ExAC and Reference Variant Store
What can you do?
• Validate your results with external data• No excuse for not validating against publicly available data • Human genetics check out: ExAC and Reference Variant Store
What can you do?
Choose the right data for validation
For each hypothesis to test, consider what is the right data to use
- Data from healthy individuals- Data from same disease- Data from other disease- same technology- other technology- Population- Assay type- etc
Good news: Lots of samples
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2000000
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Top 5:GEO (1.8M)PMI Cohort Program (1M)Auria Biopankki (1M)EGA (~0.6M)SRA (~0.5M)
Good news: We are here to help
• Platform in beta testing• Free to use• http://repositive.io
• We are here to help you find data!
See also our paper in PLoS Biology: http://journals.plos.org/plosbiology/article?id=10.1371%2Fjournal.pbio.1002418
Genomic data evidence is no longer optional
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 genomesExac consortium 65,000 exomes
?
2016: The Reference Variant Store 80,000 samples
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