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Patient-Organized Genomic Research Studies Melanie Swan, MBA  Founder DIYgenomics +1-650-681-9482 @DIYgenomics   www.DIYgenomics.org   [email_address] March 3, 2011, Scripps, La Jolla CA The Future of Genomic Medicine IV conference Slides: http://slideshare.net/LaBlogga Personal genome apps Crowd-sourced clinical trials
Agenda ,[object Object],[object Object],[object Object],[object Object],March 3, 2011 DIYgenomics.org Image credit: Getty Images
About Melanie Swan ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],March 3, 2011 DIYgenomics.org
Numerous useful applications of genomics ,[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],March 3, 2011 DIYgenomics.org Image credit:  http://bit.ly/fovpJc
Agenda ,[object Object],[object Object],[object Object],[object Object],March 3, 2011 DIYgenomics.org Image credit: Getty Images
DIYgenomics philosophy March 3, 2011 DIYgenomics.org ,[object Object],[object Object],[object Object],[object Object],Source: http://diygenomics.pbworks.com/MTHFR Genotype Phenotype Intervention Outcome + + =
DIYgenomics study design template: MTHFR March 3, 2011 DIYgenomics.org Source:  http://diygenomics.pbworks.com/ http://diygenomics.pbworks.com/w/file/36469280/DIYgenomics+study+design+template+blank.doc Cyanocobalamin Image credit: http://wikimedia.org
Homocysteine metabolism pathway March 3, 2011 DIYgenomics.org Source: Swan, M., Hathaway, K., Hogg, C., McCauley, R., Vollrath, A. Citizen science genomics as a model for crowdsourced preventive medicine research. J Participat Med. 2010 Dec 23; 2:e20.
MTHFR pilot study results March 3, 2011 DIYgenomics.org ,[object Object],Blood Test # 2. Homocysteine levels DIYgenomics MTHFR Vitamin B deficiency study 1 1. Genotype profiles Baseline LMF Source: Swan, M., Hathaway, K., Hogg, C., McCauley, R., Vollrath, A. Citizen science genomics as a model for crowdsourced preventive medicine research. J Participat Med. 2010 Dec 23; 2:e20.   1 Results are not statistically significant and are intended as a pilot demonstration of patient-organized genomic studies Baseline + LMF Centrum  Homocysteine umol/l Centrum  LMF = L-methylfolate
DIYgenomics studies March 3, 2011 DIYgenomics.org Image credit: http://www.narsad.org/?q=node/11245 Study Status 1. MTHFR/Vitamin B Pilot complete, open enrollment 2. Memory filtering In design (Q1/Q2) 3. Aging Open enrollment 4. Vitamin D In design (Q2) 5. Mental performance In design (Q3) 6. Metabolism/cholesterol mgt In design (Q3) 7. Citizen scientist proposed… Ongoing
Memory filtering study March 3, 2011 DIYgenomics.org ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Image credit: http://bit.ly/g2DIcW
Aging (genomic markers) ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],March 3, 2011 DIYgenomics.org Image credit: http://reisearch.net/biotech_page/dna_horizontal.gif Source: DIYgenomics Aging GWAS Database: http://bit.ly/fDobgO
Aging (phenotypic markers) ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],March 3, 2011 DIYgenomics.org Image credit: http://reisearch.net/biotech_page/dna_horizontal.gif Source: DIYgenomics Aging Study,  http://diygenomics.pbworks.com/w/page/30326105/Aging
Aging (interventions) ,[object Object],[object Object],[object Object],March 3, 2011 DIYgenomics.org Image credit: http://reisearch.net/biotech_page/dna_horizontal.gif Source: DIYgenomics Aging Study,  http://diygenomics.pbworks.com/w/page/30326105/Aging
Innovating the research model March 3, 2011 DIYgenomics.org Institutional PI (principal  investigator) Traditional Research Model Patient-organized Research Model Research subjects Citizen scientists*  Investigators = Participants *Self-selection bias: 100,000 consumer genomics customers Institutional Review Board (IRB) IRBs, FAQs, Citizen ethicists Grant funding Journal publication Self publishing Patient advocacy groups Research foundations Social VC Crowd-sourcing
Genomic study platform: Genomera March 3, 2011 DIYgenomics.org
Agenda ,[object Object],[object Object],[object Object],[object Object],March 3, 2011 DIYgenomics.org Image credit: Getty Images
Ranking variant quality ,[object Object],[object Object],[object Object],[object Object],March 3, 2011 DIYgenomics.org Source: DIYgenomics Image credit: http://www.evexiscy.com
Athletic performance March 3, 2011 DIYgenomics.org Image credit: http://www.istockphoto.com V = number of variants; % = ratio of favorable polymorphisms to total alleles for a sample individual; S = number of studies Source: Swan, M. Applied genomics: personalized interpretation of athletic performance GWAS. 2011 Jan. Submitted.   Category Genes V % S Endurance, power, and energy Endurance ACE, ACTN3, ADRB2/ ADRB3, BDKRB2, COL5A1, GNB3 7 50 22 Power ACE, ACTN3, AGT 3 50 8 Energy HIF1A, PPARGC1A  3 25 9 Musculature, and heart and lung capacity Muscle fatigue and repair HNF4A, NAT2 and IL-1B 5 40 4 Strength HFE, HIF1A, IGF1, MSTN GDF8  5 17 15 Heart and lung capacity  CREB1, KIF5B, NOS3, NPY and ADRB1, APOE, NRF1  9 36 11 Metabolism, recovery, and other    Metabolism  AMPD1, APOA1, PPARA, PPARD  5 50 9 Recovery  CKMM/CKM, IL6  2 50 5 Ligament and tendon strength   Ligament strength  COL1A1, COL5A1, CILP  3 50 4 Tendon strength  COL1A1, COL5A1, GDF5, MMP3  7 63 5
OTC product response, toxin processing ,[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],March 3, 2011 DIYgenomics.org Source: DIYgenomics Image credit: http://sciencephoto.com
Predictive wellness profiling: cancer ,[object Object],March 3, 2011 DIYgenomics.org Source: DIYgenomics Image credit: http://utmb.edu TP53:  cell cycle arrest, PTEN: cell cycle progression modulator, MYC: cell cycle regulator
Lung cancer risk and drug response ,[object Object],March 3, 2011 DIYgenomics.org Source: Swan, M. Review of cancer risk prediction in direct-to-consumer genomic services. (poster) Canary Foundation Early Detection Symposium, May 25-27, 2010, Stanford University, Stanford CA. Image credit: http://www.xianet.net
Wellness profiling: immune system ,[object Object],[object Object],[object Object],March 3, 2011 DIYgenomics.org Source: DIYgenomics Image credit: http://www.iayork.com CTLA4: T-cell inhibition; IL3: growth-promoting cytokine
Agenda ,[object Object],[object Object],[object Object],[object Object],March 3, 2011 DIYgenomics.org Image credit: Getty Images
4,000+ mobile app downloads ,[object Object],[object Object],[object Object],[object Object],March 3, 2011 DIYgenomics.org Android development: Michael Kolb, Lawrence S. Wong, Laura Klemme, Melanie Swan iPhone development: Ted Odet, Greg Smith, Laura Klemme, Melanie Swan “ genomics” “ genomics”
Multi-view web app with private data upload March 3, 2011 DIYgenomics.org Private data upload: Marat Nepomnyashy; https://addons.mozilla.org/en-US/firefox/addon/156946
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:   Lorenzo Albanello Cindy Chen John Furber Hong Guo Kristina Hathaway Laura Klemme Priya Kshirsagar  Lucymarie Mantese Raymond McCauley Marat Nepomnyashy Ted Odet Roland Parnaso William Reinhardt Greg Smith Aaron Vollrath Lawrence S. Wong  International collaborations: JST and Rikengenesis Takashi Kido Minae Kawashima Jin Yamanaka University Hospitals of Geneva Louis Nahum Armin Schnider Personal genome apps Crowd-sourced clinical trials

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Patient-Organized Genomic Research Studies Drive New Models of Citizen Science

  • 1. Patient-Organized Genomic Research Studies Melanie Swan, MBA Founder DIYgenomics +1-650-681-9482 @DIYgenomics www.DIYgenomics.org [email_address] March 3, 2011, Scripps, La Jolla CA The Future of Genomic Medicine IV conference Slides: http://slideshare.net/LaBlogga Personal genome apps Crowd-sourced clinical trials
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  • 7. DIYgenomics study design template: MTHFR March 3, 2011 DIYgenomics.org Source: http://diygenomics.pbworks.com/ http://diygenomics.pbworks.com/w/file/36469280/DIYgenomics+study+design+template+blank.doc Cyanocobalamin Image credit: http://wikimedia.org
  • 8. Homocysteine metabolism pathway March 3, 2011 DIYgenomics.org Source: Swan, M., Hathaway, K., Hogg, C., McCauley, R., Vollrath, A. Citizen science genomics as a model for crowdsourced preventive medicine research. J Participat Med. 2010 Dec 23; 2:e20.
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  • 10. DIYgenomics studies March 3, 2011 DIYgenomics.org Image credit: http://www.narsad.org/?q=node/11245 Study Status 1. MTHFR/Vitamin B Pilot complete, open enrollment 2. Memory filtering In design (Q1/Q2) 3. Aging Open enrollment 4. Vitamin D In design (Q2) 5. Mental performance In design (Q3) 6. Metabolism/cholesterol mgt In design (Q3) 7. Citizen scientist proposed… Ongoing
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  • 15. Innovating the research model March 3, 2011 DIYgenomics.org Institutional PI (principal investigator) Traditional Research Model Patient-organized Research Model Research subjects Citizen scientists* Investigators = Participants *Self-selection bias: 100,000 consumer genomics customers Institutional Review Board (IRB) IRBs, FAQs, Citizen ethicists Grant funding Journal publication Self publishing Patient advocacy groups Research foundations Social VC Crowd-sourcing
  • 16. Genomic study platform: Genomera March 3, 2011 DIYgenomics.org
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  • 19. Athletic performance March 3, 2011 DIYgenomics.org Image credit: http://www.istockphoto.com V = number of variants; % = ratio of favorable polymorphisms to total alleles for a sample individual; S = number of studies Source: Swan, M. Applied genomics: personalized interpretation of athletic performance GWAS. 2011 Jan. Submitted. Category Genes V % S Endurance, power, and energy Endurance ACE, ACTN3, ADRB2/ ADRB3, BDKRB2, COL5A1, GNB3 7 50 22 Power ACE, ACTN3, AGT 3 50 8 Energy HIF1A, PPARGC1A 3 25 9 Musculature, and heart and lung capacity Muscle fatigue and repair HNF4A, NAT2 and IL-1B 5 40 4 Strength HFE, HIF1A, IGF1, MSTN GDF8 5 17 15 Heart and lung capacity CREB1, KIF5B, NOS3, NPY and ADRB1, APOE, NRF1 9 36 11 Metabolism, recovery, and other   Metabolism AMPD1, APOA1, PPARA, PPARD 5 50 9 Recovery CKMM/CKM, IL6 2 50 5 Ligament and tendon strength  Ligament strength COL1A1, COL5A1, CILP 3 50 4 Tendon strength COL1A1, COL5A1, GDF5, MMP3 7 63 5
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  • 26. Multi-view web app with private data upload March 3, 2011 DIYgenomics.org Private data upload: Marat Nepomnyashy; https://addons.mozilla.org/en-US/firefox/addon/156946
  • 27. 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: Lorenzo Albanello Cindy Chen John Furber Hong Guo Kristina Hathaway Laura Klemme Priya Kshirsagar Lucymarie Mantese Raymond McCauley Marat Nepomnyashy Ted Odet Roland Parnaso William Reinhardt Greg Smith Aaron Vollrath Lawrence S. Wong International collaborations: JST and Rikengenesis Takashi Kido Minae Kawashima Jin Yamanaka University Hospitals of Geneva Louis Nahum Armin Schnider Personal genome apps Crowd-sourced clinical trials