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DIYgenomics: an open platform for citizen science

DIYgenomics: an open platform for citizen science. Melanie Swan Founder DIYgenomics 415-505-4426 @DIYgenomics www.DIYgenomics.org studies@DIYgenomics.org. July 21, 2010 OSCON, Portland OR Slides: http://slideshare.net/LaBlogga/slideshows. About Melanie Swan. Founder, DIYgenomics

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DIYgenomics: an open platform for citizen science

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  1. DIYgenomics: an open platform for citizen science Melanie Swan FounderDIYgenomics415-505-4426@DIYgenomicswww.DIYgenomics.orgstudies@DIYgenomics.org July 21, 2010 OSCON, Portland OR Slides: http://slideshare.net/LaBlogga/slideshows

  2. 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 Health2009, 2, 492-525.

  3. Agenda • Open source, open science, citizen science: context for DIYgenomics • DNA sequencing – 10x/yr improvements • DIYgenomics • Personal genome apps • Citizen science research studies

  4. 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

  5. Open science / citizen science ecosystem Traditional science research DIYbio Open science Citizen science: 200+ organizations

  6. Agenda • Open source, open science, citizen science: context for DIYgenomics • DNA sequencing – 10x/yr improvements • DIYgenomics • Personal genome apps • Citizen science research studies

  7. 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

  8. 3rd and 4th generation sequencing arrives 1st Gen: Sanger Sequencing 3rd Gen: Sequencing by Synthesis 2nd Gen: Parallelized 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

  9. 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.

  10. 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.

  11. Agenda • Open source, open science, citizen science: context for DIYgenomics • DNA sequencing – 10x/yr improvements • DIYgenomics • Personal genome apps • Citizen science research studies

  12. DIYgenomics model • Problem: lack of predictive self-health management tools 2. Personal genome apps 1. Patient-driven clinical trials/research studies 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) 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 Additional genomic studies • Copy-number variation • Gene expression • Diseasome Open-source software • Web & mobile applications Provided by partner company: Genomera (Advisory Board: George Church, Hugh Rienhoff) 3. Citizen science community platform (Facebook/eBay of genomics) • Interaction and study design & operation •Biobank for genotyping files & EMR import

  13. Apps - Android • Side-by-side comparison of consumer genomic services by loci and variants for top 20 conditions

  14. Apps - iPhone

  15. Apps – web based personal genome tools • Health risk Risk for top 20 Health Conditions Response to 250 Drugs

  16. Apps – MySNPs • FILEfox extension • Private, local Response to 250 Drugs Marat Nepomnyashy; https://addons.mozilla.org/en-US/firefox/addon/156946/

  17. 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

  18. Agenda • Open source, open science, citizen science: context for DIYgenomics • DNA sequencing – 10x/yr improvements • DIYgenomics • Personal genome apps • Citizen science research studies

  19. DIYgenomics citizen science studies • Model: integrate health data streams for preventive medicine • Available now: genotype, phenotype & intervention data • Vis-à-vis traditional model: immediate, prospective, longitudinal, systems-level approach • Health genomics • Aging • Pre-diabetes • Macular degeneration • Neuroplasticity • Behavioral genomics • Productivity, concentration and focus • Personality predisposition • Risk-taking/novelty-seeking behavior Image credit: http://www.tigerteamconsulting.com/TTC_Site/sectors_binf.jsp

  20. DIYgenomics study #1: MTHFR/Vit B12 • 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.

  21. DIYgenomics study #1: MTHFR/Vit B12 • 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.

  22. MTHFR pathway diagram

  23. Genotype Phenotype Intervention Findings MTHFR gene SNPs: rs1801133 (A/G) rs1801131 (A/G) Blood tests: B-12 and Homocysteine • B-complex • L-methylfolate • B-complex + L-methylfolate Analyze, explore, implement, share, and publish DIYgenomics MTHFR study structure • Investigate genotype-phenotype linkage and apply interventions to improve phenotypic outcomes

  24. MTHFR study – preliminary results • Average drug store vitamin (Spectrum multivitamin) reduced homocysteine levels for 4/5 participants DIYgenomics citizen science study: Homocysteine Levels Homocysteine umol/l Blood Test #

  25. DIYgenomics Citizen Science – Join Us! • Participate in a study • Organize a study on our platform • Contribute your data • Innovate blood tests 2.0 and interventions 2.0 (synthetic biology) • Collaborate: Japan, South Africa Image credit: http://www.uchsc.edu/vivat/2006/September2006/images/DNA_strand.jpg

  26. Collaborators: Cindy Chen Priya Kshirsagar Lucymarie Mantese Raymond McCauley Marat Nepomnyashy Roland Parnaso Aaron Vollrath Lawrence S. Wong Thank you! Melanie SwanFounderDIYgenomics415-505-4426@DIYgenomicswww.DIYgenomics.orgstudies@DIYgenomics.org Slides: http://slideshare.net/LaBlogga/slideshows Creative Commons 3.0 license

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