Transcript DIY Genomics_ an open platform for citizen science

DIYgenomics: an open
platform for citizen science
July 21, 2010 OSCON, Portland OR
Slides: http://slideshare.net/LaBlogga/slideshows
Melanie Swan
Founder
DIYgenomics
415-505-4426
@DIYgenomics
www.DIYgenomics.org
[email protected]
About Melanie Swan

Founder, DIYgenomics
 Futurist & serial entrepreneur
 MBA, Wharton; BA, Georgetown
 Sample publications

Swan, M. Multigenic Condition Risk Assessment in
Direct-to-Consumer Genomic Services. Genet.
Med. 2010, May;12(5):279-88.
 Swan, M. Translational antiaging research.
Rejuvenation Res. 2010, Feb;13(1):115-7.
 Swan, M. Emerging patient-driven health care
models: an examination of health social networks,
consumer personalized medicine and quantified
self-tracking. Int. J. Environ. Res. Public Health
2009, 2, 492-525.
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Agenda
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Open source, open science, citizen science: context for
DIYgenomics
DNA sequencing – 10x/yr improvements
DIYgenomics
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Personal genome apps
Citizen science research studies
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Open source: literal and conceptual
Activities: science
Open science, citizen science
• Long-tail medicine
• Preventive medicine
Data (and analysis)
• 1 million member biobanks
• Individual-contributed health data
Software
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Open science / citizen science ecosystem
Traditional science
research
Open
science
DIYbio
Citizen
science: 200+
organizations
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Agenda
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
Open source, open science, citizen science: context for
DIYgenomics
DNA sequencing – 10x/yr improvements
DIYgenomics


Personal genome apps
Citizen science research studies
July 21, 2010
DIYgenomics.org
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We are standing in a new era
April 1, 2010
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Image credit: http://pubs.acs.org/cen/_img/87/i50/8750cover2_law.gif
Dec. 14, 2009
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3rd and 4th generation sequencing arrives
1st Gen: Sanger Sequencing
3rd Gen: Sequencing by Synthesis
2nd Gen: Parallelized sequencing
4th Gen: Electronic Sequencing
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Sources: http://www.genomicseducation.ca/files/images/information_articles/sequencing.gif,
http://www.wellcome.ac.uk/News/2009/Features/WTX056032.htm,
http://www.pacificbiosciences.com/video_lg.html, http://www.nanoporetech.com/sequences
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Unbounded opportunity: read and write DNA
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Synthetic chromosome created
Bacterial genome built from
scratch and booted to life
Image credit: http://www.guardian.co.uk/science/2010/may/20/craig-venter-synthetic-life-form
May 22, 2010
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DIYgenomics.org
Source: Gibson DG et al. Creation of a Bacterial Cell Controlled by a Chemically Synthesized
Genome. Science. 2010 May 20.
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New concept of health self-management
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DIYgenomics.org
Source: Extended from Swan, M. Emerging patient-driven health care models: an examination of health social networks, consumer
personalized medicine and quantified self-tracking. Int. J. Environ. Res. Public Health 2009, 2, 492-525, Figure 1.
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Agenda



Open source, open science, citizen science: context for
DIYgenomics
DNA sequencing – 10x/yr improvements
DIYgenomics


Personal genome apps
Citizen science research studies
July 21, 2010
DIYgenomics.org
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DIYgenomics model
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Problem: lack of predictive self-health management tools
1. Patient-driven clinical trials/research studies
2. Personal genome apps
1. Supplement efficacy
1. Health condition risk
2. Drug efficacy, dosage & side effects
2. Drug response
3. General longitudinal studies
3. Athletic performance
Health genomics studies
• MTHFR mutation/Vit B-12 deficiency
• Aging
• Cancer analysis
• Cholesterol management
• Macular degeneration
• Neuroplasticity
Behavioral genomics studies
• Productivity & attention
• Personality predisposition
• Risk-taking behavior
4. Personal care products
5. Diseaseome
6. Vitamin supplement efficacy
7. Nutrigenomics
Additional genomic studies
• Copy-number variation
• Gene expression
• Diseasome
8. Pet genomics
9. Overall report (all of the above)
Open-source software
• Web & mobile applications
Provided by partner
company: Genomera
(Advisory Board: George Church,
Hugh Rienhoff)
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3. Citizen science community platform (Facebook/eBay of genomics)
• Interaction and study design & operation
•Biobank for genotyping files & EMR import
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Apps - Android
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Side-by-side comparison of consumer genomic services
by loci and variants for top 20 conditions
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Apps - iPhone
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Apps – web based personal genome tools
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Health risk
Risk for top 20 Health Conditions
Response to 250 Drugs
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Apps – MySNPs
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FILEfox extension
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Private, local
Response to 250 Drugs
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Marat Nepomnyashy; https://addons.mozilla.org/en-US/firefox/addon/156946/
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Apps – web based personal genome tools
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Drug response: Side-by-side comparison of locus, gene
and variant information for 250 drugs Risk for top 20 Health Conditions
* indicates that the FDA has validated genomic markers
for this drug
Response to 250 Drugs
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Agenda



Open source, open science, citizen science: context for
DIYgenomics
DNA sequencing – 10x/yr improvements
DIYgenomics


Personal genome apps
Citizen science research studies
July 21, 2010
DIYgenomics.org
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DIYgenomics citizen science studies
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Model: integrate health data streams for preventive medicine
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Available now: genotype, phenotype & intervention data
 Vis-à-vis traditional model: immediate, prospective, longitudinal,
systems-level approach
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Health genomics
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Aging
 Pre-diabetes
 Macular degeneration
 Neuroplasticity
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Behavioral genomics
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Productivity, concentration and focus
 Personality predisposition
 Risk-taking/novelty-seeking behavior
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DIYgenomics.org
Image credit: http://www.tigerteamconsulting.com/TTC_Site/sectors_binf.jsp
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DIYgenomics study #1: MTHFR/Vit B12
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Do common mutations in the MTHFR gene keep vitamin B from
working?
Can a group of ordinary people come together to find out? And
maybe find a treatment?
In the MTHFR gene (methylenetetrahydrofolate reductase), 2 small
variations in DNA (SNPs rs1801133/C677T & rs1801131/A1298C)
keep vitamin B9 (or folic acid) from being metabolized into its active
form (folate).
Without this form of vitamin B, homocysteine may accumulate. This
may lead to nutritional deficiencies and symptoms associated with
diabetes complications, including vascular damage and nerve
damage. This is also associated with blood clots and pregnancy
loss.
Up to 60% of people may have some form of MTHFR mutation.
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DIYgenomics study #1: MTHFR/Vit B12
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We aim to:
 Find people with MTHFR mutations - by collecting
genotype data from volunteers who have used genetic
testing services like 23andMe.
 Try simple interventions - like special vitamin B
supplements available over-the-counter.
 See if they work - by asking participants to share results
from blood tests performed at commercial labs.
 Drug companies won't do this type of study -- there's
little money to be made in over-the-counter treatments.
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MTHFR pathway diagram
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DIYgenomics MTHFR study structure
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Investigate genotype-phenotype linkage and apply
interventions to improve phenotypic outcomes
Genotype
Phenotype
MTHFR gene SNPs:
Blood tests:
1.
B-complex
rs1801133 (A/G)
B-12 and
2.
L-methylfolate
rs1801131 (A/G)
Homocysteine
3.
B-complex + Lmethylfolate
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Intervention
Findings
Analyze, explore,
implement, share,
and publish
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MTHFR study – preliminary results
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Average drug store vitamin (Spectrum multivitamin)
reduced homocysteine levels for 4/5 participants
DIYgenomics citizen science study:
Homocysteine Levels
Homocysteine umol/l
Blood Test #
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DIYgenomics Citizen Science – Join Us!
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Participate in a study
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Organize a study on our platform
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Contribute your data
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Innovate blood tests 2.0 and
interventions 2.0 (synthetic biology)
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Collaborate: Japan, South Africa
Image credit: http://www.uchsc.edu/vivat/2006/September2006/images/DNA_strand.jpg
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Collaborators:
Cindy Chen
Priya Kshirsagar
Lucymarie Mantese
Raymond McCauley
Marat Nepomnyashy
Roland Parnaso
Aaron Vollrath
Thank you!
Lawrence S. Wong
Slides: http://slideshare.net/LaBlogga/slideshows
Creative Commons 3.0 license
Melanie Swan
Founder
DIYgenomics
415-505-4426
@DIYgenomics
www.DIYgenomics.org
[email protected]