DIYgenomics: an open platform for citizen science

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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

  1. DIYgenomics: an open platform for citizen science Melanie Swan Founder DIYgenomics +1-650-681-9482 @DIYgenomics www.DIYgenomics.org [email_address] July 21, 2010, OSCON, Portland OR Slides: http://slideshare.net/LaBlogga
  2. About Melanie Swan <ul><li>Founder, DIYgenomics </li></ul><ul><li>Futurist, entrepreneur, risk manager </li></ul><ul><li>MBA, Wharton; BA, Georgetown Univ.; Instructor, Singularity University </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. 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 21, 2010 DIYgenomics.org
  3. Agenda <ul><li>Context for DIYgenomics </li></ul><ul><ul><li>Open source, open science, citizen science </li></ul></ul><ul><li>Motivation for DIYgenomics </li></ul><ul><ul><li>DNA sequencing – 10x/yr improvements </li></ul></ul><ul><li>Activities of DIYgenomics </li></ul><ul><ul><li>Personal genome apps </li></ul></ul><ul><ul><li>Citizen science research studies </li></ul></ul>July 21, 2010 DIYgenomics.org
  4. Open source: literal and conceptual July 21, 2010 DIYgenomics.org Software <ul><li>Data (and analysis) </li></ul><ul><li>1 million member biobanks </li></ul><ul><li>Individual-contributed health data </li></ul><ul><li>Activities: science </li></ul><ul><li>Long-tail medicine </li></ul><ul><li>Preventive medicine </li></ul>
  5. Open science / citizen science ecosystem July 21, 2010 DIYgenomics.org Traditional science research Open science DIYbio Citizen science: 200+ organizations 1 1 http://scienceforcitizens.net/
  6. Agenda <ul><li>Context for DIYgenomics </li></ul><ul><ul><li>Open source, open science, citizen science </li></ul></ul><ul><li>Motivation for DIYgenomics </li></ul><ul><ul><li>DNA sequencing – 10x/yr improvements </li></ul></ul><ul><li>Activities of DIYgenomics </li></ul><ul><ul><li>Personal genome apps </li></ul></ul><ul><ul><li>Citizen science research studies </li></ul></ul>July 21, 2010 DIYgenomics.org
  7. We are standing in a new era July 21, 2010 DIYgenomics.org April 1, 2010 Image credit: http://pubs.acs.org/cen/_img/87/i50/8750cover2_law.gif Dec. 14, 2009
  8. 3 rd and 4 th generation sequencing arrives July 21, 2010 DIYgenomics.org 3 rd Gen: Sequencing by Synthesis 2 nd Gen: Parallelized sequencing 1 st Gen: Sanger Sequencing 4 th 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 <ul><li>Synthetic chromosome created </li></ul><ul><li>Bacterial genome built from scratch and booted to life </li></ul>July 21, 2010 DIYgenomics.org 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 July 21, 2010 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.
  11. Agenda <ul><li>Context for DIYgenomics </li></ul><ul><ul><li>Open source, open science, citizen science </li></ul></ul><ul><li>Motivation for DIYgenomics </li></ul><ul><ul><li>DNA sequencing – 10x/yr improvements </li></ul></ul><ul><li>Activities of DIYgenomics </li></ul><ul><ul><li>Personal genome apps </li></ul></ul><ul><ul><li>Citizen science research studies </li></ul></ul>July 21, 2010 DIYgenomics.org
  12. DIYgenomics model <ul><li>Problem: lack of predictive health self-management tools </li></ul>July 21, 2010 DIYgenomics.org 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 apps 1. 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)
  13. Agenda <ul><li>Open source, open science, citizen science </li></ul><ul><ul><li>Context for DIYgenomics </li></ul></ul><ul><li>DNA sequencing – 10x/yr improvements </li></ul><ul><ul><li>Motivation for DIYgenomics </li></ul></ul><ul><li>DIYgenomics </li></ul><ul><ul><li>Personal genome apps </li></ul></ul><ul><ul><li>Citizen science research studies </li></ul></ul>July 21, 2010 DIYgenomics.org
  14. Apps - Android <ul><li>Side-by-side comparison of consumer genomic services by loci and variants for top 20 conditions </li></ul>July 21, 2010 DIYgenomics.org Application developed by: Michael Kolb, Lawrence S. Wong, Melanie Swan
  15. Apps - iPhone July 21, 2010 DIYgenomics.org <ul><li>Side-by-side comparison of consumer genomic services by loci and variants for top 20 conditions </li></ul>Application developed by: Ted Odet, Greg Smith (ManyFriends.com)
  16. Apps – web based personal genome tools July 21, 2010 DIYgenomics.org <ul><li>Health risk </li></ul>Risk for top 20 Health Conditions Response to 250 Drugs
  17. Apps – MySNPs July 21, 2010 DIYgenomics.org <ul><li>FILEfox extension </li></ul><ul><ul><li>Private, local data viewing </li></ul></ul>Response to 250 Drugs Marat Nepomnyashy; https://addons.mozilla.org/en-US/firefox/addon/156946/ 1. 2. 3.
  18. Apps – web based personal genome tools July 21, 2010 DIYgenomics.org <ul><li>Drug response: Side-by-side comparison of locus, gene and variant information for 250 drugs </li></ul><ul><li>* indicates that the FDA has validated genomic markers for this drug </li></ul>Risk for top 20 Health Conditions Response to 250 Drugs
  19. Agenda <ul><li>Context for DIYgenomics </li></ul><ul><ul><li>Open source, open science, citizen science </li></ul></ul><ul><li>Motivation for DIYgenomics </li></ul><ul><ul><li>DNA sequencing – 10x/yr improvements </li></ul></ul><ul><li>Activities of DIYgenomics </li></ul><ul><ul><li>Personal genome apps </li></ul></ul><ul><ul><li>Citizen science research studies </li></ul></ul>July 21, 2010 DIYgenomics.org
  20. DIYgenomics citizen science studies <ul><li>Goal: preventive medicine </li></ul><ul><ul><li>Establish baseline measures of wellness and pre-clinical interventions </li></ul></ul><ul><li>Model: integrate health data streams </li></ul><ul><ul><li>Available now: genotype, phenotype and intervention data </li></ul></ul><ul><ul><li>Vis-à-vis traditional model: immediate, prospective, longitudinal, systems-level approach </li></ul></ul><ul><li>Health genomics studies </li></ul><ul><ul><li>Aging </li></ul></ul><ul><ul><li>Pre-diabetes </li></ul></ul><ul><ul><li>Macular degeneration </li></ul></ul><ul><ul><li>Neuroplasticity </li></ul></ul><ul><li>Behavioral genomics studies </li></ul><ul><ul><li>Productivity, concentration and focus </li></ul></ul><ul><ul><li>Personality predisposition </li></ul></ul><ul><ul><li>Risk-taking/novelty-seeking behavior </li></ul></ul>July 21, 2010 DIYgenomics.org Image credit: http://www.tigerteamconsulting.com/TTC_Site/sectors_binf.jsp Source: http://diygenomics.pbworks.com
  21. DIYgenomics study #1: MTHFR <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 (methylenetetrahydrofolate reductase) 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 </li></ul><ul><ul><li>Risk: nutritional deficiencies and symptoms associated with diabetes complications, including vascular damage and nerve damage </li></ul></ul><ul><li>50% or more of the population may have some form of MTHFR polymorphism </li></ul>July 21, 2010 DIYgenomics.org Source: http://diygenomics.pbworks.com/MTHFR
  22. MTHFR pathway diagram July 21, 2010 DIYgenomics.org Aaron Vollrath; http://bit.ly/cHRzS8
  23. DIYgenomics MTHFR study protocol July 21, 2010 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>
  24. MTHFR pilot study – in-process results July 21, 2010 DIYgenomics.org <ul><li>Average drug store vitamin (Centrum multivitamin) reduced homocysteine levels for 4/5 participants </li></ul>Blood Test # 2. Homocysteine levels DIYgenomics MTHFR citizen science study 1 1. Genotype profiles Baseline LMF Source: http://diygenomics.pbworks.com/MTHFR_Results 1 Results are not statistically significant and are intended as a pilot demonstration of citizen science as a model Baseline + LMF Centrum Homocysteine umol/l Centrum
  25. Innovating the research model July 21, 2010 DIYgenomics.org Institutional PI (principal investigator) Traditional Research Model Citizen Science Research Model Research subjects Citizen scientists Investigators = Participants Institutional Review Board (IRB) Citizen ethicists FAQs Grant funding Journal publication Self publishing Patient advocacy groups Research foundations Social VC Crowd-sourcing
  26. DIYgenomics study #2: Aging <ul><li>Gene expression data: assess physiological vs. biological age </li></ul><ul><li>Top ten genomic mechanisms of aging </li></ul><ul><ul><li>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 </li></ul></ul><ul><li>Top ten phenotypic biomarkers of aging </li></ul><ul><ul><li>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 </li></ul></ul><ul><li>Corresponding interventions </li></ul><ul><li>Longitudinal analysis </li></ul>July 21, 2010 DIYgenomics.org Image credit: http://reisearch.net/biotech_page/dna_horizontal.gif Source: http://diygenomics.pbworks.com
  27. DIYgenomics Citizen Science – Join Us! <ul><li>Participate in a study </li></ul><ul><li>Join the DIYgenomics open source software community </li></ul><ul><li>Organize a study on our platform </li></ul><ul><li>Contribute your data </li></ul><ul><li>Contribute financial support </li></ul>July 21, 2010 DIYgenomics.org Image credit: http://www.uchsc.edu/vivat/2006/September2006/images/DNA_strand.jpg http://diygenomics.pbworks.com/DIYgenomics_software
  28. Thank you! Melanie Swan Founder DIYgenomics +1-650-681-9482 @DIYgenomics www.DIYgenomics.org [email_address] 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 trials Personal genome apps

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