Scaling citizen science genomics

DIYgenomics Open-source preventive medicine and scaling citizen science genomics Melanie Swan Founder DIYgenomics 650-681-9482 @DIYgenomics www.DIYgenomics.org [email_address] July 28, 2011, OSCON, Portland OR Slides: http://slideshare.net/LaBlogga

About Melanie Swan
Founder DIYgenomics, hedge fund manager, futurist, entrepreneur
Current projects: MelanieSwan.com
Work experience: Fidelity, JP Morgan, Arthur Andersen, iPass, RHK/Ovum
Education: MBA Finance, Wharton; BA French/Economics, Georgetown Univ
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. Engineering Life into Technology: the Application of Complexity Theory to a Potential Phase Transition of Intelligence. Symmetry 2010 , 2, 150:183.
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.
July 28, 2011 DIYgenomics.org Source: http://melanieswan.com/publications.htm

Biology is an information technology July 28, 2011 DIYgenomics.org Image credit: http://pubs.acs.org/cen/_img/87/i50/8750cover2_law.gif I hate you 010010010010000001101 0 000110 000 1011101000110010100100000011110010110111101110101 I love you 01001001001000000110110001101111011101100110010100100000011110010110111101110101 Image credit: http://www.nanoporetech.com/sequences 4th Gen: Electronic Sequencing

Biology is the information technology July 28, 2011 DIYgenomics.org Image credit: J. Craig Venter Institute Image credit: Anthony Atala lab Image credit: Thomas Matthiesen Artificial cell booted to life Algal biofuel Image credit: http://www.rexresearch.com Whole organ decellularization and recellularization (heart) Organ regeneration (urethra) DNA nanotechnology latch box for drug delivery Image credit: Aarhus University

Agenda July 28, 2011 DIYgenomics.org Citizen science progress to date Scaling citizen science Grand vision next steps Image credit: http://www.gettyimages.com

Citizen science definition July 28, 2011 DIYgenomics.org Institutional science research DIYbio Citizen science: 200+ organizations 1 1 http://scienceforcitizens.net/finder
Investigation without professional training

Politics of personalized genomics
U.S. Genetic Information Nondiscrimination Act (GINA) 2008
Our world is not Gattaca
Genomic test regulation expected
Genomic rights and petitions
Petition for Access to Genetic Information http://www.thepetitionsite.com/1/mydna
Petition for Health Data Rights http://www.healthdatarights.org
Health as a currency
Health as a human right
July 28, 2011 DIYgenomics.org Image credit: http://www.sonypictures.com Image credit: http://sciencephoto.com

Consumer genomics test landscape July 28, 2011 DIYgenomics.org Single/few condition Multiple condition Whole genome Cost 1 Lower cost with family group or medical condition Service Breadth Public studies Matchmaking ScientificMatch $1,995 GenePartner $10-$99 Paternity Genelex $200-$475 Identigene $149-$399 Pregnancy Screening Counsyl $349 Nutrigenomics APO E Gene Diet $389 Inherent Health $99 Coriell 15 conditions Scripps (Navigenics) 28 conditions Pers. Genome Proj. Conditions undisclosed Harvard Med. Sch. Genetic disorders, Predisposition DNA Direct $200-$3,500 Matrix Genomics $199-$799 Drug sensitivity, $ Exome 23andme 201 conditions Navigenics* 40 conditions deCODEme 49 conditions $1,000 $99 $299 Genomics 71 conditions Pathway* $2,500 $999 $2,000 $985 *Must be physician-ordered Knome EdgeBio $6,000 $19,500 Knome Illumina $48,000 $350,000 $99,500 $68,500 $5,000 1 $39,500

Genomics comparison scorecard July 28, 2011 DIYgenomics.org 1 Conditions, genes, variants, underlying research references, and methodology white paper(s) available on public website
Which service to buy?
*Physician prescription required Consumer genomic service # Cond-itions Cost Report Data access Visible research quality 1 Updates deCODEme 49 $2,000  +   +  23andme 201 $99     + Navigenics* 40 $999    Pathway Genomics* 71 $299  Coriell (10,000 partic. 7/11) 15 public study PGP (Personal Genome Project) n/a public study

Consumer genomics: interpretation variance July 28, 2011 DIYgenomics.org Source: www.DIYgenomics.org and Swan, M. Multigenic Condition Risk Assessment in Direct-to-Consumer Genomic Services. Genet. Med. 2010, May;12(5):279-88. Private data upload: Marat Nepomnyashy

Open-source mobile apps (5,000+ downloads)
Health condition, drug response, athletic performance
23andMe data upload
Android
iPhone
July 28, 2011 DIYgenomics.org Android development: Michael Kolb, Lawrence S. Wong, Laura Klemme, Melanie Swan iPhone development: Ted Odet, Greg Smith, Laura Klemme, Melanie Swan “ genomics” 4,000+ downloads “ genomics” 1,000+ downloads T T T T T T T C C

Citizen science health landscape July 28, 2011 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. Health collaboration communities Health social networks

Lifecycle of a health condition July 28, 2011 DIYgenomics.org Pre-clinical (80%) Clinical (20%) Preventive medicine Long-tail medicine Self-tracking Wellness profiling Health community collaboration Applied healthspan engineering Traditional medicine Disease treatment Medical expertise Emergency Exceptions Time # conditions becoming clinical Goal: decrease in clinical conditions over time

Genome hacking philosophy July 28, 2011 DIYgenomics.org
Goal: preventive medicine
Realize preventive medicine by establishing baseline markers of wellness and pre-clinical interventions
Generalized hypothesis
One or more polymorphisms may result in out-of-bounds baseline levels of phenotypic markers. These levels may be improved through personalized intervention.
Source: http://diygenomics.pbworks.com/MTHFR Genotype Phenotype Intervention Outcome + + =

Vitamin B deficiency / MTHFR mutation
Do common mutations in the MTHFR gene prevent vitamin B from working correctly?
Test whether 2 variations in the MTHFR gene 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 of cardiovascular disease, etc.)
50% or more of the population may have some form of MTHFR polymorphism
July 28, 2011 DIYgenomics.org Source: http://diygenomics.pbworks.com/MTHFR

Homocysteine metabolism pathway July 28, 2011 DIYgenomics.org Source: Swan, M., Hathaway, K., Hogg, C., McCauley, R., Vollrath, A. Citizen science genomics as a model for crowdsourced preventive medicine research. J Participat Med. 2010 Dec 23; 2:e20.

Vitamin B / MTHFR study protocol July 28, 2011 DIYgenomics.org
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 1. Genotype MTHFR gene SNPs: rs1801133 (A/G) rs1801131 (A/G) 2. Phenotype Blood tests: B-12 and Homocysteine 3. Intervention
(2 week periods)
B-complex
L-methylfolate
B-complex + L-methylfolate

Vitamin B / MTHFR pilot study results July 28, 2011 DIYgenomics.org
Drug store vitamin (Centrum) reduced homocysteine levels for 6/7 participants
Blood Test # 2. Homocysteine levels DIYgenomics MTHFR Vitamin B deficiency study 1 1. Genotype profiles Baseline LMF Source: Swan, M., Hathaway, K., Hogg, C., McCauley, R., Vollrath, A. Citizen science genomics as a model for crowdsourced preventive medicine research. J Participat Med. 2010 Dec 23; 2:e20. 1 Results are not statistically significant and are intended as a pilot demonstration of citizen science genomic studies Baseline + LMF Centrum Homocysteine umol/l Centrum LMF = L-methylfolate

Personal health collaboration studies July 28, 2011 DIYgenomics.org More information: www.DIYgenomics.org www.DIYgenomics.org/DIYgenomics_poster.ppt

Scaling citizen science
Engaging participants and building trust
Innovating the Institutional Review Board
Accessing blood tests 2.0
Developing a philosophy of epistemology of citizen science
July 28, 2011 DIYgenomics.org Image credit: http://slobodkina.com

Engaging personal health collaborators
Participation must be fun and easy
Relevant value proposition to target market
Nomenclature framing: enhancement, optimization
Crowdsourcing the value chain: data, questions, financing, analysis
July 28, 2011 DIYgenomics.org Image credit: http://www.superstock.com

Athletic performance July 28, 2011 DIYgenomics.org Image credit: http://www.istockphoto.com V = number of variants; % = ratio of favorable polymorphisms to total alleles for a sample individual; S = number of studies Source: Swan, M. Applied genomics: personalized interpretation of athletic performance GWAS. Jan 2011. Category Genes V % S Endurance, power, and energy Endurance ACE, ACTN3, ADRB2/ ADRB3, BDKRB2, COL5A1, GNB3 7 50 22 Power ACE, ACTN3, AGT 3 50 8 Energy HIF1A, PPARGC1A 3 25 9 Musculature, and heart and lung capacity Muscle fatigue and repair HNF4A, NAT2 and IL-1B 5 40 4 Strength HFE, HIF1A, IGF1, MSTN GDF8 5 17 15 Heart and lung capacity CREB1, KIF5B, NOS3, NPY and ADRB1, APOE, NRF1 9 36 11 Metabolism, recovery, and other Metabolism AMPD1, APOA1, PPARA, PPARD 5 50 9 Recovery CKMM/CKM, IL6 2 50 5 Ligament and tendon strength Ligament strength COL1A1, COL5A1, CILP 3 50 4 Tendon strength COL1A1, COL5A1, GDF5, MMP3 7 63 5

Study design template: MTHFR example July 28, 2011 DIYgenomics.org Source: http://diygenomics.pbworks.com http://diygenomics.pbworks.com/w/file/36469280/DIYgenomics+study+design+template+blank.doc Cyanocobalamin Image credit: http://wikimedia.org

DIYgenomics study ecosystem – CRO 2.0 July 28, 2011 DIYgenomics.org Sponsors Funders Study manager Graduate student partner* Study operation platform (Genomera) Study advisors* Participants Oversight (IRB) * Domain expert

Health hackers need Blood Tests 2.0
Low-cost home-administered self-read finger-stick blood, urine, saliva tests:
Traditional blood tests (Homocysteine, Vitamin B-12, Folate, Vitamin D, Creatinine, eGFR, Cortisol, Calcium, Iron)
Hormones (Estrogen, Progesterone, Testosterone, Estradiol)
Immune system: CD4, CD8/CD28 ratio, IL-1, IL-6
Chemical / h eavy metal burden: mercury, cadmium, lead, tin
July 28, 2011 DIYgenomics.org OrSense continuous non-invasive glucose monitoring Cholestech LDX home cholesterol test

Towards an epistemology of citizen science
Provide a structure and context for self-derived health knowledge
Q1: Are new kinds of knowledge are being formed through group collaborations such as wikipedia and health social networks?
Q2: Are there differences in the types of knowledge generated by traditional medicine, self-experimentation, and health collaboration communities?
July 28, 2011 DIYgenomics.org Image credit: http://inkingrey.com

Ontological shift
Old thinking:
My health is the responsibility of my physician
New thinking:
My health is my responsibility
… and I have the tools to make it fun and easy
July 28, 2011 DIYgenomics.org Image credit: http://efx3.com

Personal genome applications
Ancestry
Carrier status
Disease risk profiling
Drug response
Athletic performance capability
Product response
Wellness profiling
Cancer
Immune system
Aging
July 28, 2011 DIYgenomics.org

Predictive wellness profiling: cancer
Proto-oncogene/tumor suppressor gene polymorphisms
July 28, 2011 DIYgenomics.org Source: DIYgenomics Image credit: http://utmb.edu TP53: cell cycle arrest, PTEN: cell cycle progression modulator, MYC: cell cycle regulator

Lung cancer risk and drug response
Risk and drug response for specific cancers
July 28, 2011 DIYgenomics.org Source: Swan, M. Review of cancer risk prediction in direct-to-consumer genomic services. (poster) Canary Foundation Early Detection Symposium, May 25-27, 2010, Stanford University, Stanford CA. Image credit: http://www.xianet.net

Wellness profiling: immune system
Immune system genomic wellness profiling
Immune response: T-cell activation
CTLA4, CD226, CD86, IL3
July 28, 2011 DIYgenomics.org Source: DIYgenomics Image credit: http://www.iayork.com CTLA4: T-cell inhibition; IL3: growth-promoting cytokine

Aging: TA-65, telomere length & TERC mutation July 28, 2011 DIYgenomics.org
Herbal supplement TA-65 (astragalus root) taken by 1000 people worldwide. Telomere and immune system benefits in humans published Mar 2011 1
TERC (RNA gene that extends telomeres) SNPs:
rs10511887, rs12696304, rs16847897, rs2293607, rs610160
1 Source: Harley CB, et al. A natural product telomerase activator as part of a health maintenance program. Rejuvenation Res. 2011 Feb;14(1):45-56.

Aging: applied healthspan engineering July 28, 2011 DIYgenomics.org Source: Larrick JW, Mendelsohn A. Applied Healthspan engineering. Rejuvenation Res. 2010 Apr-Jun;13(2-3):265-80, Table 2.
Aging studies need not be longitudinal, current improvements to known biomarkers of aging can be measured
Image credit: http://www.gettyimages.com Legend: ACE, angiotensin converting enzyme; ARBs, angiotensin receptor blockers; EGCG, epigallocatechin 3-gallate; mTOR, mammalian target of rapamycin.

Circles of preventive medicine July 28, 2011 DIYgenomics.org Individual 2. Preventive Care Health Social Networks Citizen Science Studies Health Advisors 3. Traditional health care system and physicians 1. Automated digital health monitoring 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.

Health self-management July 28, 2011 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.

Thank you! Melanie Swan Founder DIYgenomics 650-681-9482 @DIYgenomics www.DIYgenomics.org [email_address] Slides: http://slideshare.net/LaBlogga Creative Commons 3.0 license Collaborators: Lorenzo Albanello Janet Chang Cindy Chen Jon Dekay John Furber Eri Gentry Kristina Hathaway Takashi Kido Laura Klemme Lucymarie Mantese Raymond McCauley Louis Nahum Marat Nepomnyashy Ted Odet Roland Parnaso William Reinhardt Greg Smith Aaron Vollrath Lawrence S. Wong Crowd-sourced clinical trials Personal genome apps

Scaling citizen science genomics

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