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DIYgenomics (www.DIYgenomics.org) is a new platform bringing citizen scientists together to run peer cohort research studies and conduct novel research linking genetic data and physical biomarkers. Some norms are developing in response to the variety of community-based research issues that arise such as adaptive studies, informed consent, security, anonymity, and study design.
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DIYgenomics: an open platform for citizen science
Melanie Swan Founder
DIYgenomics+1-650-681-9482
@DIYgenomics www.DIYgenomics.org
July 21, 2010, OSCON, Portland OR
Slides: http://slideshare.net/LaBlogga
2July 21, 2010DIYgenomics.org
About Melanie Swan
Founder, DIYgenomics Futurist, entrepreneur, risk manager MBA, Wharton; BA, Georgetown Univ.;
Instructor, Singularity University 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.
3July 21, 2010DIYgenomics.org
Agenda
Context for DIYgenomics Open source, open science, citizen science
Motivation for DIYgenomics DNA sequencing – 10x/yr improvements
Activities of DIYgenomics Personal genome apps Citizen science research studies
4July 21, 2010DIYgenomics.org
Open source: literal and conceptual
Software
Data (and analysis)• 1 million member biobanks
• Individual-contributed health data
Activities: science• Long-tail medicine
• Preventive medicine
5July 21, 2010DIYgenomics.org
Open science / citizen science ecosystem
Traditional science research
Open science
DIYbio
Citizen science: 200+ organizations1
1http://scienceforcitizens.net/
6July 21, 2010DIYgenomics.org
Agenda
Context for DIYgenomics Open source, open science, citizen science
Motivation for DIYgenomics DNA sequencing – 10x/yr improvements
Activities of DIYgenomics Personal genome apps Citizen science research studies
7July 21, 2010DIYgenomics.org
We are standing in a new era
April 1, 2010 Image credit: http://pubs.acs.org/cen/_img/87/i50/8750cover2_law.gif Dec. 14, 2009
8July 21, 2010DIYgenomics.org
3rd and 4th generation sequencing arrives3rd Gen: Sequencing by Synthesis
2nd Gen: Parallelized sequencing
1st Gen: Sanger Sequencing
4th Gen: Electronic Sequencing
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
9July 21, 2010DIYgenomics.org
Unbounded opportunity: read and write DNA
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
Source: Gibson DG et al. Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome. Science. 2010 May 20.
10July 21, 2010DIYgenomics.org
New concept of health self-management
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.
11July 21, 2010DIYgenomics.org
Agenda
Context for DIYgenomics Open source, open science, citizen science
Motivation for DIYgenomics DNA sequencing – 10x/yr improvements
Activities of DIYgenomics Personal genome apps Citizen science research studies
12July 21, 2010DIYgenomics.org
DIYgenomics model
Problem: lack of predictive health self-management tools
Health genomics studies• MTHFR mutation/Vit B-12 deficiency• Aging • Cancer analysis• Cholesterol management• Macular degeneration• Neuroplasticity
1. Supplement efficacy
2. Drug efficacy, dosage & side effects
3. General longitudinal studies
1. Health condition risk
2. Drug response
3. Athletic performance
4. Personal care products
5. Diseaseome
6. Vitamin supplement efficacy
7. Nutrigenomics
8. Pet genomics
9. Overall report (all of the above)
2. Personal genome apps1. Crowd-sourced research studies
3. Citizen science community platform (Facebook/eBay of genomics)• Citizen scientists post and operate research studies
• Individual-shared biobank of genotyping & EMR files
Provided by partner company: Genomera
(Advisory Board: George Church, Hugh Rienhoff)
Behavioral genomics studies• Productivity & attention• Personality predisposition• Risk-taking behavior
Additional genomic studies• Copy-number variation• Gene expression• Diseasome
(open-source web/mobile software)
Source: http://diygenomics.pbworks.com
(define baseline of wellness)
13July 21, 2010DIYgenomics.org
Agenda
Open source, open science, citizen science Context for DIYgenomics
DNA sequencing – 10x/yr improvements Motivation for DIYgenomics
DIYgenomics Personal genome apps Citizen science research studies
14July 21, 2010DIYgenomics.org
Apps - Android
Side-by-side comparison of consumer genomic services by loci and variants for top 20 conditions
Application developed by: Michael Kolb, Lawrence S. Wong, Melanie Swan
15July 21, 2010DIYgenomics.org
Apps - iPhone
Side-by-side comparison of consumer genomic services by loci and variants for top 20 conditions
Application developed by: Ted Odet, Greg Smith (ManyFriends.com)
16July 21, 2010DIYgenomics.org
Apps – web based personal genome tools
Health risk
Risk for top 20 Health Conditions
Response to 250 Drugs
17July 21, 2010DIYgenomics.org
Apps – MySNPs
FILEfox extension Private, local data viewing
Response to 250 Drugs
Marat Nepomnyashy; https://addons.mozilla.org/en-US/firefox/addon/156946/
1.
2.
3.
18July 21, 2010DIYgenomics.org
Apps – web based personal genome tools
Drug response: Side-by-side comparison of locus, gene and variant information for 250 drugs
* indicates that the FDA has validated genomic markers for this drug
Risk for top 20 Health Conditions
Response to 250 Drugs
19July 21, 2010DIYgenomics.org
Agenda
Context for DIYgenomics Open source, open science, citizen science
Motivation for DIYgenomics DNA sequencing – 10x/yr improvements
Activities of DIYgenomics Personal genome apps Citizen science research studies
20July 21, 2010DIYgenomics.org
DIYgenomics citizen science studies
Goal: preventive medicine Establish baseline measures of wellness and pre-clinical
interventions Model: integrate health data streams
Available now: genotype, phenotype and intervention data Vis-à-vis traditional model: immediate, prospective, longitudinal,
systems-level approach Health genomics studies
Aging Pre-diabetes Macular degeneration Neuroplasticity
Behavioral genomics studies Productivity, concentration and focus Personality predisposition Risk-taking/novelty-seeking behavior Image credit: http://www.tigerteamconsulting.com/TTC_Site/sectors_binf.jsp
Source: http://diygenomics.pbworks.com
21July 21, 2010DIYgenomics.org
DIYgenomics study #1: MTHFR
Do common mutations in the MTHFR gene prevent vitamin B from working correctly?
Test whether 2 variations in the MTHFR gene (methylenetetrahydrofolate reductase) keep vitamin B9 (folic acid) from being metabolized into its active form (folate) rs1801133/C677T rs1801131/A1298C
Without this form of vitamin B, homocysteine may accumulate Risk: nutritional deficiencies and symptoms associated with diabetes
complications, including vascular damage and nerve damage 50% or more of the population may have some form of MTHFR
polymorphism
Source: http://diygenomics.pbworks.com/MTHFR
22July 21, 2010DIYgenomics.org
MTHFR pathway diagram
Aaron Vollrath; http://bit.ly/cHRzS8
23July 21, 2010DIYgenomics.org
DIYgenomics MTHFR study protocol
1. Genotype
MTHFR gene SNPs:
rs1801133 (A/G)
rs1801131 (A/G)
2. Phenotype
Blood tests:
B-12 and
Homocysteine
3. Intervention
(2 week periods)
1. B-complex
2. L-methylfolate
3. B-complex + L-methylfolate
Investigate genotype-phenotype linkage and apply interventions to improve phenotypic outcomes
Protocol confirmed with two separate experts in the field
Source: http://diygenomics.pbworks.com/MTHFR
24July 21, 2010DIYgenomics.org
MTHFR pilot study – in-process results
Average drug store vitamin (Centrum multivitamin) reduced homocysteine levels for 4/5 participants
Blood Test #
2. Homocysteine levels
DIYgenomics MTHFR citizen science study1
1. Genotype profiles
Baseline LMF
Source: http://diygenomics.pbworks.com/MTHFR_Results
1Results are not statistically significant and are intended as a pilot demonstration of citizen science as a model
Baseline+ LMF
Centrum
Homocysteine umol/l
Centrum
25July 21, 2010DIYgenomics.org
Innovating the research model
Institutional PI (principal
investigator)
Traditional Research Model Citizen Science Research Model
Research subjects
Citizen scientists
Investigators = Participants
Institutional Review Board
(IRB)
Citizen ethicistsFAQs
Grant funding
Journal publication
Self publishing
Patient advocacy
groups
Research foundations
Social VC
Crowd-sourcing
26July 21, 2010DIYgenomics.org
DIYgenomics study #2: Aging
Gene expression data: assess physiological vs. biological age Top ten genomic mechanisms of aging
Neurodegenerative disease, osteoporosis, IGF-1/Insulin signaling, lipoprotein metabolism, inflammation, immune system function, DNA damage repair, telomere length, transcription, catabolism, mitochondrial health, cell cycle/stem cell health, protein function, blood operations
Top ten phenotypic biomarkers of aging Blood pressure and hypertension, cholesterol (HDL / LDL /
triglycerides; LDL particle size), BMI, Framingham Risk Score, VO2 max, erythrocyte glycoslyation, telomere length, lymphocyte growth capability, granulocyte strength
Corresponding interventions Longitudinal analysis
Image credit: http://reisearch.net/biotech_page/dna_horizontal.gif
Source: http://diygenomics.pbworks.com
27July 21, 2010DIYgenomics.org
DIYgenomics Citizen Science – Join Us!
Participate in a study
Join the DIYgenomics open source software community
Organize a study on our platform
Contribute your data
Contribute financial supportImage credit: http://www.uchsc.edu/vivat/2006/September2006/images/DNA_strand.jpg
http://diygenomics.pbworks.com/DIYgenomics_software
Thank you!
Melanie SwanFounder
DIYgenomics+1-650-681-9482
@DIYgenomicswww.DIYgenomics.org
Slides: http://slideshare.net/LaBlogga
Creative Commons 3.0 license
Collaborators:
Cindy Chen
Priya Kshirsagar
Lucymarie Mantese
Raymond McCauley
Marat Nepomnyashy
Ted Odet
Roland Parnaso
Greg Smith
Aaron Vollrath
Lawrence S. Wong
Crowd-sourced clinical trialsPersonal genome apps