Scaling citizen science genomics

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Scaling citizen science genomics

  1. 1. 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
  2. 2. About Melanie Swan <ul><li>Founder DIYgenomics, hedge fund manager, futurist, entrepreneur </li></ul><ul><li>Current projects: MelanieSwan.com </li></ul><ul><li>Work experience: Fidelity, JP Morgan, Arthur Andersen, iPass, RHK/Ovum </li></ul><ul><li>Education: MBA Finance, Wharton; BA French/Economics, Georgetown Univ </li></ul><ul><li>Sample publications </li></ul><ul><ul><li>Swan, M. Multigenic Condition Risk Assessment in Direct-to-Consumer Genomic Services. Genet. Med. 2010 , May;12(5):279-88. </li></ul></ul><ul><ul><li>Swan, M. Translational antiaging research. Rejuvenation Res. 2010 , Feb;13(1):115-7. </li></ul></ul><ul><ul><li>Swan, M. Engineering Life into Technology: the Application of Complexity Theory to a Potential Phase Transition of Intelligence. Symmetry 2010 , 2, 150:183. </li></ul></ul><ul><ul><li>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. </li></ul></ul>July 28, 2011 DIYgenomics.org Source: http://melanieswan.com/publications.htm
  3. 3. 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
  4. 4. 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
  5. 5. Agenda July 28, 2011 DIYgenomics.org Citizen science progress to date Scaling citizen science Grand vision next steps Image credit: http://www.gettyimages.com
  6. 6. Citizen science definition July 28, 2011 DIYgenomics.org Institutional science research DIYbio Citizen science: 200+ organizations 1 1 http://scienceforcitizens.net/finder <ul><li>Investigation without professional training </li></ul>
  7. 7. Politics of personalized genomics <ul><li>U.S. Genetic Information Nondiscrimination Act (GINA) 2008 </li></ul><ul><li>Our world is not Gattaca </li></ul><ul><li>Genomic test regulation expected </li></ul><ul><li>Genomic rights and petitions </li></ul><ul><ul><li>Petition for Access to Genetic Information http://www.thepetitionsite.com/1/mydna </li></ul></ul><ul><ul><li>Petition for Health Data Rights http://www.healthdatarights.org </li></ul></ul><ul><li>Health as a currency </li></ul><ul><li>Health as a human right </li></ul>July 28, 2011 DIYgenomics.org Image credit: http://www.sonypictures.com Image credit: http://sciencephoto.com
  8. 8. 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
  9. 9. Genomics comparison scorecard July 28, 2011 DIYgenomics.org 1 Conditions, genes, variants, underlying research references, and methodology white paper(s) available on public website <ul><li>Which service to buy? </li></ul>*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
  10. 10. 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
  11. 11. Open-source mobile apps (5,000+ downloads) <ul><li>Health condition, drug response, athletic performance </li></ul><ul><li>23andMe data upload </li></ul><ul><li>Android </li></ul><ul><li>iPhone </li></ul>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
  12. 12. 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
  13. 13. 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
  14. 14. Genome hacking philosophy July 28, 2011 DIYgenomics.org <ul><li>Goal: preventive medicine </li></ul><ul><ul><li>Realize preventive medicine by establishing baseline markers of wellness and pre-clinical interventions </li></ul></ul><ul><li>Generalized hypothesis </li></ul><ul><ul><li>One or more polymorphisms may result in out-of-bounds baseline levels of phenotypic markers. These levels may be improved through personalized intervention. </li></ul></ul>Source: http://diygenomics.pbworks.com/MTHFR Genotype Phenotype Intervention Outcome + + =
  15. 15. Vitamin B deficiency / MTHFR mutation <ul><li>Do common mutations in the MTHFR gene prevent vitamin B from working correctly? </li></ul><ul><li>Test whether 2 variations in the MTHFR gene keep vitamin B9 (folic acid) from being metabolized into its active form (folate) </li></ul><ul><ul><li>rs1801133/C677T </li></ul></ul><ul><ul><li>rs1801131/A1298C </li></ul></ul><ul><li>Without this form of vitamin B, homocysteine may accumulate (risk of cardiovascular disease, etc.) </li></ul><ul><li>50% or more of the population may have some form of MTHFR polymorphism </li></ul>July 28, 2011 DIYgenomics.org Source: http://diygenomics.pbworks.com/MTHFR
  16. 16. 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.
  17. 17. Vitamin B / MTHFR study protocol July 28, 2011 DIYgenomics.org <ul><li>Investigate genotype-phenotype linkage and apply interventions to improve phenotypic outcomes </li></ul><ul><li>Protocol confirmed with two separate experts in the field </li></ul>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 <ul><li>(2 week periods) </li></ul><ul><li>B-complex </li></ul><ul><li>L-methylfolate </li></ul><ul><li>B-complex + L-methylfolate </li></ul>
  18. 18. Vitamin B / MTHFR pilot study results July 28, 2011 DIYgenomics.org <ul><li>Drug store vitamin (Centrum) reduced homocysteine levels for 6/7 participants </li></ul>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
  19. 19. Personal health collaboration studies July 28, 2011 DIYgenomics.org More information: www.DIYgenomics.org www.DIYgenomics.org/DIYgenomics_poster.ppt
  20. 20. Agenda July 28, 2011 DIYgenomics.org Citizen science progress to date Scaling citizen science Grand vision next steps Image credit: http://www.gettyimages.com
  21. 21. Scaling citizen science <ul><li>Engaging participants and building trust </li></ul><ul><li>Innovating the Institutional Review Board </li></ul><ul><li>Accessing blood tests 2.0 </li></ul><ul><li>Developing a philosophy of epistemology of citizen science </li></ul>July 28, 2011 DIYgenomics.org Image credit: http://slobodkina.com
  22. 22. Engaging personal health collaborators <ul><li>Participation must be fun and easy </li></ul><ul><li>Relevant value proposition to target market </li></ul><ul><li>Nomenclature framing: enhancement, optimization </li></ul><ul><li>Crowdsourcing the value chain: data, questions, financing, analysis </li></ul>July 28, 2011 DIYgenomics.org Image credit: http://www.superstock.com
  23. 23. 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
  24. 24. 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
  25. 25. 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
  26. 26. Health hackers need Blood Tests 2.0 <ul><li>Low-cost home-administered self-read finger-stick blood, urine, saliva tests: </li></ul><ul><ul><li>Traditional blood tests (Homocysteine, Vitamin B-12, Folate, Vitamin D, Creatinine, eGFR, Cortisol, Calcium, Iron) </li></ul></ul><ul><ul><li>Hormones (Estrogen, Progesterone, Testosterone, Estradiol) </li></ul></ul><ul><ul><li>Immune system: CD4, CD8/CD28 ratio, IL-1, IL-6 </li></ul></ul><ul><ul><li>Chemical / h eavy metal burden: mercury, cadmium, lead, tin </li></ul></ul>July 28, 2011 DIYgenomics.org OrSense continuous non-invasive glucose monitoring Cholestech LDX home cholesterol test
  27. 27. Towards an epistemology of citizen science <ul><li>Provide a structure and context for self-derived health knowledge </li></ul><ul><li>Q1: Are new kinds of knowledge are being formed through group collaborations such as wikipedia and health social networks? </li></ul><ul><li>Q2: Are there differences in the types of knowledge generated by traditional medicine, self-experimentation, and health collaboration communities? </li></ul>July 28, 2011 DIYgenomics.org Image credit: http://inkingrey.com
  28. 28. Ontological shift <ul><li>Old thinking: </li></ul><ul><li>My health is the responsibility of my physician </li></ul><ul><li>New thinking: </li></ul><ul><li>My health is my responsibility </li></ul><ul><li>… and I have the tools to make it fun and easy </li></ul>July 28, 2011 DIYgenomics.org Image credit: http://efx3.com
  29. 29. Agenda July 28, 2011 DIYgenomics.org Citizen science progress to date Scaling citizen science Grand vision next steps Image credit: http://www.gettyimages.com
  30. 30. Personal genome applications <ul><ul><li>Ancestry </li></ul></ul><ul><ul><li>Carrier status </li></ul></ul><ul><ul><li>Disease risk profiling </li></ul></ul><ul><ul><li>Drug response </li></ul></ul><ul><ul><li>Athletic performance capability </li></ul></ul><ul><ul><li>Product response </li></ul></ul><ul><ul><li>Wellness profiling </li></ul></ul><ul><ul><ul><li>Cancer </li></ul></ul></ul><ul><ul><ul><li>Immune system </li></ul></ul></ul><ul><ul><ul><li>Aging </li></ul></ul></ul>July 28, 2011 DIYgenomics.org
  31. 31. Predictive wellness profiling: cancer <ul><li>Proto-oncogene/tumor suppressor gene polymorphisms </li></ul>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
  32. 32. Lung cancer risk and drug response <ul><li>Risk and drug response for specific cancers </li></ul>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
  33. 33. Wellness profiling: immune system <ul><li>Immune system genomic wellness profiling </li></ul><ul><li>Immune response: T-cell activation </li></ul><ul><ul><li>CTLA4, CD226, CD86, IL3 </li></ul></ul>July 28, 2011 DIYgenomics.org Source: DIYgenomics Image credit: http://www.iayork.com CTLA4: T-cell inhibition; IL3: growth-promoting cytokine
  34. 34. Aging: TA-65, telomere length & TERC mutation July 28, 2011 DIYgenomics.org <ul><li>Herbal supplement TA-65 (astragalus root) taken by 1000 people worldwide. Telomere and immune system benefits in humans published Mar 2011 1 </li></ul><ul><li>TERC (RNA gene that extends telomeres) SNPs: </li></ul><ul><ul><li>rs10511887, rs12696304, rs16847897, rs2293607, rs610160 </li></ul></ul>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.
  35. 35. 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. <ul><li>Aging studies need not be longitudinal, current improvements to known biomarkers of aging can be measured </li></ul>Image credit: http://www.gettyimages.com Legend: ACE, angiotensin converting enzyme; ARBs, angiotensin receptor blockers; EGCG, epigallocatechin 3-gallate; mTOR, mammalian target of rapamycin.
  36. 36. 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.
  37. 37. 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.
  38. 38. 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

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