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DIYgenomics: an open platform for citizen science Melanie Swan Founder DIYgenomics

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Presentation on theme: "DIYgenomics: an open platform for citizen science Melanie Swan Founder DIYgenomics"— Presentation transcript:

1 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

2 1 July 21, 2010 DIYgenomics.org 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 Health 2009, 2, 492-525.

3 2 July 21, 2010 DIYgenomics.org Agenda Open source, open science, citizen science: context for DIYgenomics DNA sequencing – 10x/yr improvements DIYgenomics Personal genome apps Citizen science research studies

4 3 July 21, 2010 DIYgenomics.org Open source: literal and conceptual Software Data (and analysis) 1 million member biobanks Individual-contributed health data Activities: science Open science, citizen science Long-tail medicine Preventive medicine

5 4 July 21, 2010 DIYgenomics.org Open science / citizen science ecosystem Traditional science research Open science DIYbio Citizen science: 200+ organizations

6 5 July 21, 2010 DIYgenomics.org Agenda Open source, open science, citizen science: context for DIYgenomics DNA sequencing – 10x/yr improvements DIYgenomics Personal genome apps Citizen science research studies

7 6 July 21, 2010 DIYgenomics.org 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 7 July 21, 2010 DIYgenomics.org 3 rd and 4 th generation sequencing arrives 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 8 July 21, 2010 DIYgenomics.org 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 9 July 21, 2010 DIYgenomics.org 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 10 July 21, 2010 DIYgenomics.org Agenda Open source, open science, citizen science: context for DIYgenomics DNA sequencing – 10x/yr improvements DIYgenomics Personal genome apps Citizen science research studies

12 11 July 21, 2010 DIYgenomics.org DIYgenomics model Problem: lack of predictive self-health management tools 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) Open-source software Web & mobile applications 2. Personal genome apps 1. Patient-driven clinical trials/research studies 3. Citizen science community platform (Facebook/eBay of genomics) Interaction and study design & operation Biobank for genotyping files & EMR import 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

13 12 July 21, 2010 DIYgenomics.org Apps - Android Side-by-side comparison of consumer genomic services by loci and variants for top 20 conditions

14 13 July 21, 2010 DIYgenomics.org Apps - iPhone

15 14 July 21, 2010 DIYgenomics.org Apps – web based personal genome tools Health risk Risk for top 20 Health Conditions Response to 250 Drugs

16 15 July 21, 2010 DIYgenomics.org Apps – MySNPs FILEfox extension Private, local Response to 250 Drugs Marat Nepomnyashy; https://addons.mozilla.org/en-US/firefox/addon/156946/

17 16 July 21, 2010 DIYgenomics.org 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 17 July 21, 2010 DIYgenomics.org Agenda Open source, open science, citizen science: context for DIYgenomics DNA sequencing – 10x/yr improvements DIYgenomics Personal genome apps Citizen science research studies

19 18 July 21, 2010 DIYgenomics.org 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 19 July 21, 2010 DIYgenomics.org 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 20 July 21, 2010 DIYgenomics.org 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 21 July 21, 2010 DIYgenomics.org MTHFR pathway diagram

23 22 July 21, 2010 DIYgenomics.org DIYgenomics MTHFR study structure Genotype MTHFR gene SNPs: rs1801133 (A/G) rs1801131 (A/G) Phenotype Blood tests: B-12 and Homocysteine Intervention 1.B-complex 2.L-methylfolate 3.B-complex + L- methylfolate Findings Analyze, explore, implement, share, and publish Investigate genotype-phenotype linkage and apply interventions to improve phenotypic outcomes

24 23 July 21, 2010 DIYgenomics.org MTHFR study – preliminary results Average drug store vitamin (Spectrum multivitamin) reduced homocysteine levels for 4/5 participants Blood Test # Homocysteine umol/l DIYgenomics citizen science study: Homocysteine Levels

25 24 July 21, 2010 DIYgenomics.org 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 Thank you! Melanie Swan Founder DIYgenomics 415-505-4426 @DIYgenomics www.DIYgenomics.org studies@DIYgenomics.org Slides: http://slideshare.net/LaBlogga/slideshows Creative Commons 3.0 license Collaborators: Cindy Chen Priya Kshirsagar Lucymarie Mantese Raymond McCauley Marat Nepomnyashy Roland Parnaso Aaron Vollrath Lawrence S. Wong


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