DIYgenomics: an open platform for citizen science

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

About Melanie Swan ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],July 21, 2010 DIYgenomics.org

Agenda ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],July 21, 2010 DIYgenomics.org

Open source: literal and conceptual July 21, 2010 DIYgenomics.org Software ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

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/

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

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

Unbounded opportunity: read and write DNA ,[object Object],[object Object],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.

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.

DIYgenomics model ,[object Object],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)

Apps - Android ,[object Object],July 21, 2010 DIYgenomics.org Application developed by: Michael Kolb, Lawrence S. Wong, Melanie Swan

Apps - iPhone July 21, 2010 DIYgenomics.org ,[object Object],Application developed by: Ted Odet, Greg Smith (ManyFriends.com)

Apps – web based personal genome tools July 21, 2010 DIYgenomics.org ,[object Object],Risk for top 20 Health Conditions Response to 250 Drugs

Apps – MySNPs July 21, 2010 DIYgenomics.org ,[object Object],[object Object],Response to 250 Drugs Marat Nepomnyashy; https://addons.mozilla.org/en-US/firefox/addon/156946/ 1. 2. 3.

Apps – web based personal genome tools July 21, 2010 DIYgenomics.org ,[object Object],[object Object],Risk for top 20 Health Conditions Response to 250 Drugs

DIYgenomics citizen science studies ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],July 21, 2010 DIYgenomics.org Image credit: http://www.tigerteamconsulting.com/TTC_Site/sectors_binf.jsp Source: http://diygenomics.pbworks.com

DIYgenomics study #1: MTHFR ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],July 21, 2010 DIYgenomics.org Source: http://diygenomics.pbworks.com/MTHFR

MTHFR pathway diagram July 21, 2010 DIYgenomics.org Aaron Vollrath; http://bit.ly/cHRzS8

DIYgenomics MTHFR study protocol July 21, 2010 DIYgenomics.org ,[object Object],[object Object],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 ,[object Object],[object Object],[object Object],[object Object]

MTHFR pilot study – in-process results July 21, 2010 DIYgenomics.org ,[object Object],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

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

DIYgenomics study #2: Aging ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],July 21, 2010 DIYgenomics.org Image credit: http://reisearch.net/biotech_page/dna_horizontal.gif Source: http://diygenomics.pbworks.com

DIYgenomics Citizen Science – Join Us! ,[object Object],[object Object],[object Object],[object Object],[object Object],July 21, 2010 DIYgenomics.org Image credit: http://www.uchsc.edu/vivat/2006/September2006/images/DNA_strand.jpg http://diygenomics.pbworks.com/DIYgenomics_software

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

DIYgenomics: an open platform for citizen science

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DIYgenomics: an open platform for citizen science