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 Founder, DIYgenomics Futurist, entrepreneur, risk manager MBA, Wharton; BA, Georgetown Univ.; Instructor, Singularity University 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. July 21, 2010 DIYgenomics.org

Agenda Context for DIYgenomics Open source, open science, citizen science Motivation for DIYgenomics DNA sequencing – 10x/yr improvements Activities of DIYgenomics Personal genome apps Citizen science research studies July 21, 2010 DIYgenomics.org

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

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 Synthetic chromosome created Bacterial genome built from scratch and booted to life 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 Problem: lack of predictive health self-management tools 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)

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

Apps - Android Side-by-side comparison of consumer genomic services by loci and variants for top 20 conditions July 21, 2010 DIYgenomics.org Application developed by: Michael Kolb, Lawrence S. Wong, Melanie Swan

Apps - iPhone July 21, 2010 DIYgenomics.org Side-by-side comparison of consumer genomic services by loci and variants for top 20 conditions Application developed by: Ted Odet, Greg Smith (ManyFriends.com)

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

Apps – MySNPs July 21, 2010 DIYgenomics.org FILEfox extension Private, local data viewing 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 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

DIYgenomics citizen science studies Goal: preventive medicine Establish baseline measures of wellness and pre-clinical interventions Model: integrate health data streams Available now: genotype, phenotype and intervention data Vis-à-vis traditional model: immediate, prospective, longitudinal, systems-level approach Health genomics studies Aging Pre-diabetes Macular degeneration Neuroplasticity Behavioral genomics studies Productivity, concentration and focus Personality predisposition Risk-taking/novelty-seeking behavior 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 Do common mutations in the MTHFR gene prevent vitamin B from working correctly? Test whether 2 variations in the MTHFR gene (methylenetetrahydrofolate reductase) 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: nutritional deficiencies and symptoms associated with diabetes complications, including vascular damage and nerve damage 50% or more of the population may have some form of MTHFR polymorphism 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 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 1. Genotype MTHFR gene SNPs: rs1801133 (A/G) rs1801131 (A/G) 2. Phenotype Blood tests: B-12 and Homocysteine 3. Intervention (2 week periods) B-complex L-methylfolate B-complex + L-methylfolate

MTHFR pilot study – in-process results July 21, 2010 DIYgenomics.org Average drug store vitamin (Centrum multivitamin) reduced homocysteine levels for 4/5 participants 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 Gene expression data: assess physiological vs. biological age Top ten genomic mechanisms of aging 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 Top ten phenotypic biomarkers of aging 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 Corresponding interventions Longitudinal analysis 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! Participate in a study Join the DIYgenomics open source software community Organize a study on our platform Contribute your data Contribute financial support 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