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DIYgenomics Open-source preventive medicine and scaling citizen science genomics

DIYgenomics Open-source preventive medicine and scaling citizen science genomics. Melanie Swan Founder DIYgenomics 415-505-4426 @DIYgenomics www.DIYgenomics.org melanie@DIYgenomics.org. July 28, 2011, OSCON, Portland OR Slides: http://slideshare.net/LaBlogga. About Melanie Swan.

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DIYgenomics Open-source preventive medicine and scaling citizen science genomics

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  1. DIYgenomicsOpen-source preventive medicine and scaling citizen science genomics Melanie Swan FounderDIYgenomics415-505-4426@DIYgenomicswww.DIYgenomics.orgmelanie@DIYgenomics.org July 28, 2011, OSCON, Portland OR Slides: http://slideshare.net/LaBlogga

  2. 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. Symmetry2010, 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 Health2009, 2, 492-525. Source: http://melanieswan.com/publications.htm

  3. Biology is an information technology 011011000110111110111011001100101 – I love you 011011000110111110111010001100101 – I hate you Image credit: http://www.nanoporetech.com/sequences Image credit: http://pubs.acs.org/cen/_img/87/i50/8750cover2_law.gif Dec. 14, 2009

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

  5. Agenda Citizen science progress to date Scaling citizen science Grand vision next steps Image credit: http://www.gettyimages.com

  6. Citizen science definition • Investigation without professional training Traditional science research DIYbio Citizen science: 200+ organizations1 1http://scienceforcitizens.net/finder

  7. Politics of personalized genomics • Genetic Information Nondiscrimination Act (GINA) 2008 • Our world is not Gattaca • Genomic test regulation expected • Genomic rights • 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 Image credit: http://www.sonypictures.com

  8. Cost Knome $ Knome $350,000 $19,500 $99,500 EdgeBio Pathway* Navigenics* Genetic disorders, $6,000 Genomics 40 conditions Drug sensitivity, Illumina $68,500 71 conditions Predisposition $48,000 $39,500 23andme deCODEme DNA Direct $200-$3,500 49 conditions $10,0001 201 conditions Matrix Genomics $199-$799 Paternity $2,500 $2,000 Genelex $200-$475 Identigene $149-$399 $999 $1,000 $985 Pregnancy Screening $299 $99 Counsyl $349 *Must be physician-ordered Nutrigenomics APO E Gene Diet $389 Inherent Health $99 Public studies Harvard Med. Sch. Matchmaking Coriell Scripps (Navigenics) Pers. Genome Proj. ScientificMatch $1,995 15 conditions 28 conditions Conditions undisclosed GenePartner $10-$99 Exome Single/few condition Multiple condition Whole genome 1Lower cost with family group or medical condition Service Breadth Consumer genomics test landscape

  9. Genomics comparison scorecard • Which service to buy? 1Conditions, genes, variants, underlying research references, and methodology white paper(s) available on public website

  10. Consumer genomics: interpretation variance 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. T T T T T T T C C Open-source mobile apps (5,000+ downloads) • Health condition, drug response, athletic performance • 23andMe data upload • Android • iPhone “genomics” “genomics” Android development: Michael Kolb, Lawrence S. Wong, Laura Klemme, Melanie Swan iPhone development: Ted Odet, Greg Smith, Laura Klemme, Melanie Swan

  12. Citizen science health landscape Health social networks Health collaboration communities 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.

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

  14. Genotype Phenotype Intervention Outcome + + = Genome hacking philosophy • 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

  15. 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 Source: http://diygenomics.pbworks.com/MTHFR

  16. Homocysteine metabolism pathway 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. 1. Genotype 2. Phenotype 3. Intervention MTHFR gene SNPs: rs1801133 (A/G) rs1801131 (A/G) Blood tests: B-12 and Homocysteine • (2 week periods) • B-complex • L-methylfolate • B-complex + L-methylfolate Vitamin B / MTHFR study protocol • 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

  18. Vitamin B / MTHFR pilot study results • Drug store vitamin (Centrum) reduced homocysteine levels for 6/7 participants DIYgenomics MTHFR Vitamin B deficiency study1 1. Genotype profiles 2. Homocysteine levels Homocysteine umol/l Centrum Baseline Centrum LMF Baseline + LMF 1Results are not statistically significant and are intended as a pilot demonstration of citizen science genomic studies Blood Test # LMF = L-methylfolate 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.

  19. Personal health collaboration studies More information: www.DIYgenomics.org www.DIYgenomics.org/DIYgenomics_poster.ppt

  20. Agenda Citizen science progress to date Scaling citizen science Grand vision next steps Image credit: http://www.gettyimages.com

  21. 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 Image credit: http://slobodkina.com

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

  23. Athletic performance 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.

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

  25. DIYgenomics study ecosystem – CRO 2.0 Funders Sponsors Study advisors* Oversight Study manager Graduate student partner* Study operation platform (Genomera) Participants * Domain expert

  26. Innovating the research model Traditional Research Model Citizen Science Research Model Citizen ethicists FAQs Institutional Review Board (IRB) Institutional PI (principal investigator) Patient advocacy groups Research foundations Social VC Crowd-sourcing Citizen scientists Investigators = Participants Grant funding Journal publication Self publishing Research subjects

  27. 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, Aldosterone) • Hormones (Estrogen, Progesterone, Testosterone, Estradiol) • Immune system: CD4, CD8/CD28 ratio, IL-1, IL-6 • Chemical / heavy metal burden: mercury, cadmium, lead, tin

  28. 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? Image credit: http://inkingrey.com

  29. 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 Image credit: http://efx3.com

  30. Agenda Citizen science progress to date Scaling citizen science Grand vision next steps Image credit: http://www.gettyimages.com

  31. Preventive wellness • Personal uses of the personal genome • Ancestry • Carrier status • Disease risk profiling • Drug response • Athletic performance capability • Product response • Wellness profiling • Cancer • Immune system • Aging

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

  33. Lung cancer risk and drug response • Risk and drug response for specific cancers Image credit: http://www.xianet.net 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.

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

  35. Aging: TA-65, telomere length & TERC mutation • 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 1Source: Harley CB, et al. A natural product telomerase activator as part of a health maintenance program. Rejuvenation Res. 2011 Feb;14(1):45-56.

  36. Aging: applied healthspan engineering Source: Larrick JW, Mendelsohn A. Applied Healthspan engineering. Rejuvenation Res. 2010 Apr-Jun;13(2-3):265-80, Table 2.

  37. Circles of preventive medicine 1. Automated digital health monitoring 2. Preventive Care Health Social Networks Citizen Science Studies Health Advisors Individual 3. Traditional health care system and physicians 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.

  38. 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.

  39. Crowd-sourced clinical trials Personal genome apps Collaborators: Lorenzo Albanello Janet Chang Cindy Chen Jon Dekay John Furber Eri Gentry Kristina Hathaway Takashi Kido Laura Klemme Lucymarie Mantese Raymond McCauley Thank you! Louis Nahum Marat Nepomnyashy Ted Odet Roland Parnaso William Reinhardt Greg Smith Aaron Vollrath Lawrence S. Wong Melanie SwanFounderDIYgenomics415-505-4426@DIYgenomicswww.DIYgenomics.orgmelanie@DIYgenomics.org Slides: http://slideshare.net/LaBlogga Creative Commons 3.0 license

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