1.
Secure the data – share the knowledge
DNAdigest.org
Open Research Cambridge
Fiona Nielsen, December 16, 2013

2.
Take home messages
• DNA sequencing = exciting new opportunities
+ new challenges
• Your genome is your data (like your EHR)
• Options for sharing today are limited mostly to
all-or-nothing
• Take the opportunity to voice your opinion
My aim with this talk: to give you a little view of how you can share genetic data today, and give
you an idea of the challenges involved.
I will end the presentation with a brief introduction to the DNAdigest project, and then open the
floor for questions and discussion.

3.
Data is donated to research
Individuals are offered to opt-in their consent for their
data to be used for research to aid development of
diagnostics and treatments for genetic diseases
Genetic data is needed for research into inborn illnesses, heriditary diseases, rare diseases and cancer.

4.
Genome research today
the patient
the researcher
the sample
the data
DNAdigest.org

5.
Direct-to-consumer
genetic testing
You can order your own personal genotyping kit online
for only $99 from http://23andme.com
You can assess your own carrier status for known
disease genes before you get pregnant, for example
https://www.counsyl.com/
You can obtain non-invasive pre-natal testing by
detecting foetus DNA in the mothers blood, example
http://www.verinata.com/
You can have your whole genome sequenced for about
$7,000 http://www.dnadtc.com/products.aspx

6.
Example: 23andme
Manuel Corpas used direct-to-consumer testing
for himself and his family

7.
The “Corpasome”
Family genome and analysis published open
access online
•
•
•
Deceased
1M 23andMe •
v3 SNP chip •
•
•
•
•
•
•
Age: 75
1M 23andMe v3 SNP chip
15,823,554 HiSeq Exome
PE Reads
Age: 51
1M 23andMe v3 SNP chip
14,123,580 HiSeq Exome PE
Reads
•
•
•
•
Age: 79
1M 23andMe v3 SNP chip
15,190,489 HiSeq Exome
PE Reads
Age: 36
0.5M 23andMe v2 SNP chip
32,116,828 HiSeq Exome SE Reads
Metagenomics

8.
The “Corpasome”
Family genome and analysis published open
access online
open access online as a free resource for research

9.
But what about privacy?
There is large variation between individuals,
and we are all unique
This means that your genome
sequence can identify you
- or your heritage
Similarly, your medical record
may contain information that is
unique to you
DNAdigest.org
3,000,000,000bp ~ 3billion basepairs
in the human genome

10.
Consent for research
The head of the research
project will create a
custom consent form:
- Purpose
- How, when and who
DNAdigest.org

11.
Consent forms vary
Guidelines from NHS on informed consent:
http://www.hra.nhs.uk/documents/2013/09/information-sheet-and-consent-form-guidance.pdf
DNAdigest.org

12.
Consent forms vary
Guidelines from NHS on privacy:
Example wordings
http://www.hra.nhs.uk/documents/2013/09/information-sheet-and-consent-form-guidance.pdf
DNAdigest.org

13.
Consent is obtained in the
interest of the patient
However,
Contact with patient may be lost after data
collection
The institution acts as the custodian of the
collected data,

14.
and data is locked up
Institutions do not freely share data because revealing
entire datasets breaches confidentiality
Data access is restricted if available at all
If available, access requires specific application per dataset per project

15.
Results are published
When sufficient data is collected for a project, an
analysis is made and a paper may be published
to report the results.
Results from confidential data are reported in
anonymized form
Anonymization = removal of identifiers
• Name, birthdate, NHS number, town of birth

16.
Published information
Level of data detail varies per project and per
publication.
Rare disease research usually includes family
pedigrees and detailed description of the
disease symptoms per individual
GWAS studies usually
include only aggregated
statistics

17.
Problem for data sharing
Trade-off: details are necessary for data re-use!
Restricted access
repositories
Completely public data
•
•
•
•
•
Advantage: access to
complete datasets of
genetics and medical
data
Disadvantage:
cumbersome,
timeconsuming and
slow processing of
application for access
Disadvantage:
difficult to discover the
data you need
•
•
Advantage: Easy
access
Disadvantage: if
medical data is
removed = no value for
research
Disadvantage: no
guarantee of privacy
Example: The Personal
Genomes Project

18.
Limitations of current mechanisms
• Not easy to discover data
• Not easy to apply for access to data
• Not easy to deal with bulk datasets
As a consequence:
•
•
•
•
Researchers do not cross-check their results
Data is not re-used for analysis
Researchers duplicate existing work
Results are published based on small sample sizes
DNAdigest.org

19.
What if?
•
•
•
•
Every individuals would be custodian of their own data?
What if there would be different ways of sharing data?
What if you could share just part of your data?
What if the consent form included options for the level
of sharing of the data?
• What if you gave patients the option to share their data
with no restrictions?
• What if you could share data in aggregate statistics?
• What if you could share your data today and change your
mind tomorrow?
DNAdigest.org

20.
New approaches
• Crowdsourcing of genetic testing results:
#freethedata for breast cancer genes BRCA1 and BRCA2
• Share your 23andme data with OpenSNP
• Control your EHR with PatientsKnowBest
• DNAdigest: Allow sharing of aggregated data to
enable discovery and faster access for research
DNAdigest.org

21.
Our mission
To create a self sustainable platform that supports the
widest possible sharing and access of genomic data in
accordance with patient consent.

22.
DNAdigest is designing an ethical
data sharing platform
Allowing hypothesis centered queries, returning
anonymised aggregated data by patented mechanism

23.
Results are delivered as
anonymised aggregated statistics
DEMO

24.
Further reading
•
•
•
•
•
What to consider before undergoing a DNA test
article in the Wall Street Journal
Manuel Corpas blog: http://manuelcorpas.com
Interview about the DNAdigest project on Open-Steps.org
Genetic Privacy Network (launched Dec 2013)
resources about the risks and legal issues for US residents
Anonymization and re-identification: Routes for breaching
and protecting genetic privacy by Erlich and Narayanan
DNAdigest.org

25.
Take home messages
• DNA sequencing = exciting new opportunities
+ new challenges
• Your genome is your data (like your EHR)
• Options for sharing today are limited mostly to
all-or-nothing
• Take the opportunity to voice your opinion
• It is question time!

26.
Thanks for listening
And thanks to OpenResCam and Panton Arms for hosting!
DNAdigest is a not-for-profit organisation, founded for the
purpose of enabling faster and easier access and sharing of
genomic data for research.
Please visit us at DNAdigest.org
and on twitter @dnadigest
Thank you!
DNAdigest.org