Quantitative genomics 2016 - Fiona Nielsen - Repositive

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


The next big thing

http://www.cell.com/neuron/fulltext/S0896-6273(16)30126-X




The next big thing


The next big thing

7 cases, heterozygousFour healthy carriers


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

https://docs.google.com/viewer?a=v&pid=sites&srcid=ZGVmYXVsdGRvbWFpbnxkZ21hY2FydGh1cnxneDoyOTJlNzAxNDM1YjQyODlm

• 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?

http://exac.broadinstitute.org/variant/11-47290147-G-A

https://rvs.u.hpc.mssm.edu/

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 and bad news

Good news: Lots of different data sources

Assay Types

Dedicated to…

Good news: Lots of samples

0.2

2

20

200

2000

20000

200000

2000000

Chart Title

Sam

ple

# (L

og10

)

Top 5:GEO (1.8M)PMI Cohort Program (1M)Auria Biopankki (1M)EGA (~0.6M)SRA (~0.5M)

Bad news: Its rather confusing

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

http://repositive.io/

http://journals.plos.org/plosbiology/article?id=10.1371%2Fjournal.pbio.1002418

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

Your Research Breakthrough Makes Headlines - including data!

The Next Big thing in 2017?

Thanks for listening!Find us on Twitter @repositiveio and try our

platform at http://repositive.io

Quantitative genomics 2016 - Fiona Nielsen - Repositive

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