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DIYgenomics Open-source preventive medicine and scaling citizen science genomics   Melanie Swan  Founder DIYgenomics 650-681-9482 @DIYgenomics   www.DIYgenomics.org   [email_address] July 28, 2011, 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],[object Object],[object Object],July 28, 2011 DIYgenomics.org Source: http://melanieswan.com/publications.htm
Biology is an information technology July 28, 2011 DIYgenomics.org Image credit: http://pubs.acs.org/cen/_img/87/i50/8750cover2_law.gif I hate you 010010010010000001101 0 000110 000 1011101000110010100100000011110010110111101110101 I love you 01001001001000000110110001101111011101100110010100100000011110010110111101110101 Image credit:  http://www.nanoporetech.com/sequences 4th Gen: Electronic Sequencing
Biology is  the   information technology July 28, 2011 DIYgenomics.org Image credit: J. Craig Venter Institute  Image credit: Anthony Atala lab Image credit: Thomas Matthiesen   Artificial cell booted to life Algal biofuel Image credit: http://www.rexresearch.com Whole organ decellularization and recellularization (heart) Organ regeneration (urethra) DNA nanotechnology latch box for drug delivery Image credit: Aarhus University
Agenda July 28, 2011 DIYgenomics.org Citizen science progress to date Scaling citizen science Grand vision next steps Image credit: http://www.gettyimages.com
Citizen science definition July 28, 2011 DIYgenomics.org Institutional science research DIYbio Citizen science: 200+ organizations 1 1 http://scienceforcitizens.net/finder ,[object Object]
Politics of personalized genomics ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],July 28, 2011 DIYgenomics.org Image credit: http://www.sonypictures.com Image credit: http://sciencephoto.com
Consumer genomics test landscape July 28, 2011 DIYgenomics.org Single/few condition Multiple condition  Whole genome Cost 1 Lower cost with family group or medical condition  Service Breadth Public studies  Matchmaking ScientificMatch $1,995 GenePartner $10-$99 Paternity Genelex $200-$475 Identigene $149-$399 Pregnancy Screening Counsyl $349 Nutrigenomics APO E Gene Diet $389 Inherent Health $99 Coriell 15 conditions Scripps (Navigenics) 28 conditions Pers. Genome Proj. Conditions undisclosed Harvard Med. Sch. Genetic disorders, Predisposition DNA Direct $200-$3,500 Matrix Genomics $199-$799 Drug sensitivity, $ Exome 23andme 201 conditions Navigenics* 40 conditions deCODEme 49 conditions $1,000 $99 $299 Genomics 71 conditions Pathway*  $2,500 $999 $2,000 $985 *Must be physician-ordered Knome EdgeBio $6,000 $19,500 Knome Illumina $48,000 $350,000 $99,500 $68,500 $5,000 1 $39,500
Genomics comparison scorecard July 28, 2011 DIYgenomics.org 1 Conditions, genes, variants, underlying research references, and methodology white paper(s) available on public website ,[object Object],*Physician prescription required Consumer genomic service # Cond-itions Cost Report Data access Visible research quality 1 Updates deCODEme 49 $2,000  +   +  23andme 201 $99     + Navigenics* 40 $999    Pathway Genomics* 71 $299  Coriell (10,000 partic. 7/11) 15 public study PGP (Personal Genome Project) n/a public study
Consumer genomics: interpretation variance July 28, 2011 DIYgenomics.org Source: www.DIYgenomics.org and Swan, M. Multigenic Condition Risk Assessment in Direct-to-Consumer Genomic Services. Genet. Med. 2010, May;12(5):279-88. Private data upload: Marat Nepomnyashy
Open-source mobile apps (5,000+ downloads) ,[object Object],[object Object],[object Object],[object Object],July 28, 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” 4,000+ downloads “ genomics” 1,000+ downloads T  T T T  T T T  C C
Citizen science health landscape July 28, 2011 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.   Health collaboration communities Health social networks
Lifecycle of a health condition July 28, 2011 DIYgenomics.org Pre-clinical (80%)  Clinical (20%)  Preventive medicine Long-tail medicine Self-tracking Wellness profiling Health community collaboration Applied healthspan engineering Traditional medicine Disease treatment Medical expertise Emergency Exceptions Time # conditions becoming  clinical Goal: decrease in clinical conditions over time
Genome hacking philosophy July 28, 2011 DIYgenomics.org ,[object Object],[object Object],[object Object],[object Object],Source: http://diygenomics.pbworks.com/MTHFR Genotype Phenotype Intervention Outcome + + =
Vitamin B deficiency / MTHFR mutation ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],July 28, 2011 DIYgenomics.org Source: http://diygenomics.pbworks.com/MTHFR
Homocysteine metabolism pathway July 28, 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.
Vitamin B / MTHFR study protocol July 28, 2011 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]
Vitamin B / MTHFR pilot study results July 28, 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 citizen science genomic studies Baseline + LMF Centrum  Homocysteine umol/l Centrum  LMF = L-methylfolate
Personal health collaboration studies July 28, 2011 DIYgenomics.org More information: www.DIYgenomics.org  www.DIYgenomics.org/DIYgenomics_poster.ppt
Agenda July 28, 2011 DIYgenomics.org Citizen science progress to date Scaling citizen science Grand vision next steps Image credit: http://www.gettyimages.com
Scaling citizen science  ,[object Object],[object Object],[object Object],[object Object],July 28, 2011 DIYgenomics.org Image credit: http://slobodkina.com
Engaging personal health collaborators ,[object Object],[object Object],[object Object],[object Object],July 28, 2011 DIYgenomics.org Image credit: http://www.superstock.com
Athletic performance July 28, 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. Jan 2011. 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
Study design template: MTHFR example July 28, 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
DIYgenomics study ecosystem – CRO 2.0 July 28, 2011 DIYgenomics.org Sponsors Funders Study manager Graduate student partner* Study operation platform (Genomera) Study advisors* Participants Oversight (IRB) * Domain expert
Health hackers need Blood Tests 2.0 ,[object Object],[object Object],[object Object],[object Object],[object Object],July 28, 2011 DIYgenomics.org OrSense continuous non-invasive glucose monitoring Cholestech LDX home cholesterol test
Towards an epistemology of citizen science ,[object Object],[object Object],[object Object],July 28, 2011 DIYgenomics.org Image credit: http://inkingrey.com
Ontological shift ,[object Object],[object Object],[object Object],[object Object],[object Object],July 28, 2011 DIYgenomics.org Image credit: http://efx3.com
Agenda July 28, 2011 DIYgenomics.org Citizen science progress to date Scaling citizen science Grand vision next steps Image credit: http://www.gettyimages.com
Personal genome applications ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],July 28, 2011 DIYgenomics.org
Predictive wellness profiling: cancer ,[object Object],July 28, 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],July 28, 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],July 28, 2011 DIYgenomics.org Source: DIYgenomics Image credit: http://www.iayork.com CTLA4: T-cell inhibition; IL3: growth-promoting cytokine
Aging: TA-65, telomere length & TERC mutation July 28, 2011 DIYgenomics.org ,[object Object],[object Object],[object Object],1 Source: Harley CB, et al. A natural product telomerase activator as part of a health maintenance program. Rejuvenation Res. 2011 Feb;14(1):45-56.
Aging: applied healthspan engineering July 28, 2011 DIYgenomics.org Source: Larrick JW, Mendelsohn A. Applied Healthspan engineering. Rejuvenation Res. 2010 Apr-Jun;13(2-3):265-80, Table 2.   ,[object Object],Image credit: http://www.gettyimages.com Legend: ACE, angiotensin converting enzyme; ARBs, angiotensin receptor blockers; EGCG, epigallocatechin 3-gallate; mTOR, mammalian target of rapamycin.
Circles of preventive medicine July 28, 2011 DIYgenomics.org Individual 2. Preventive Care Health Social Networks Citizen Science Studies Health Advisors 3. Traditional health care system and physicians 1. Automated digital health monitoring 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.
Health self-management  July 28, 2011 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.
Thank you! Melanie Swan Founder DIYgenomics 650-681-9482  @DIYgenomics www.DIYgenomics.org [email_address] Slides: http://slideshare.net/LaBlogga Creative Commons 3.0 license Collaborators:  Lorenzo Albanello Janet Chang Cindy Chen Jon Dekay John Furber Eri Gentry Kristina Hathaway Takashi Kido Laura Klemme Lucymarie Mantese Raymond McCauley Louis Nahum Marat Nepomnyashy Ted Odet Roland Parnaso William Reinhardt Greg Smith Aaron Vollrath Lawrence S. Wong  Crowd-sourced clinical trials Personal genome apps

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Scaling citizen science genomics

  • 1. DIYgenomics Open-source preventive medicine and scaling citizen science genomics Melanie Swan Founder DIYgenomics 650-681-9482 @DIYgenomics www.DIYgenomics.org [email_address] July 28, 2011, OSCON, Portland OR Slides: http://slideshare.net/LaBlogga
  • 2.
  • 3. Biology is an information technology July 28, 2011 DIYgenomics.org Image credit: http://pubs.acs.org/cen/_img/87/i50/8750cover2_law.gif I hate you 010010010010000001101 0 000110 000 1011101000110010100100000011110010110111101110101 I love you 01001001001000000110110001101111011101100110010100100000011110010110111101110101 Image credit: http://www.nanoporetech.com/sequences 4th Gen: Electronic Sequencing
  • 4. Biology is the information technology July 28, 2011 DIYgenomics.org Image credit: J. Craig Venter Institute Image credit: Anthony Atala lab Image credit: Thomas Matthiesen Artificial cell booted to life Algal biofuel Image credit: http://www.rexresearch.com Whole organ decellularization and recellularization (heart) Organ regeneration (urethra) DNA nanotechnology latch box for drug delivery Image credit: Aarhus University
  • 5. Agenda July 28, 2011 DIYgenomics.org Citizen science progress to date Scaling citizen science Grand vision next steps Image credit: http://www.gettyimages.com
  • 6.
  • 7.
  • 8. Consumer genomics test landscape July 28, 2011 DIYgenomics.org Single/few condition Multiple condition Whole genome Cost 1 Lower cost with family group or medical condition Service Breadth Public studies Matchmaking ScientificMatch $1,995 GenePartner $10-$99 Paternity Genelex $200-$475 Identigene $149-$399 Pregnancy Screening Counsyl $349 Nutrigenomics APO E Gene Diet $389 Inherent Health $99 Coriell 15 conditions Scripps (Navigenics) 28 conditions Pers. Genome Proj. Conditions undisclosed Harvard Med. Sch. Genetic disorders, Predisposition DNA Direct $200-$3,500 Matrix Genomics $199-$799 Drug sensitivity, $ Exome 23andme 201 conditions Navigenics* 40 conditions deCODEme 49 conditions $1,000 $99 $299 Genomics 71 conditions Pathway* $2,500 $999 $2,000 $985 *Must be physician-ordered Knome EdgeBio $6,000 $19,500 Knome Illumina $48,000 $350,000 $99,500 $68,500 $5,000 1 $39,500
  • 9.
  • 10. Consumer genomics: interpretation variance July 28, 2011 DIYgenomics.org Source: www.DIYgenomics.org and Swan, M. Multigenic Condition Risk Assessment in Direct-to-Consumer Genomic Services. Genet. Med. 2010, May;12(5):279-88. Private data upload: Marat Nepomnyashy
  • 11.
  • 12. Citizen science health landscape July 28, 2011 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. Health collaboration communities Health social networks
  • 13. Lifecycle of a health condition July 28, 2011 DIYgenomics.org Pre-clinical (80%) Clinical (20%) Preventive medicine Long-tail medicine Self-tracking Wellness profiling Health community collaboration Applied healthspan engineering Traditional medicine Disease treatment Medical expertise Emergency Exceptions Time # conditions becoming clinical Goal: decrease in clinical conditions over time
  • 14.
  • 15.
  • 16. Homocysteine metabolism pathway July 28, 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.
  • 17.
  • 18.
  • 19. Personal health collaboration studies July 28, 2011 DIYgenomics.org More information: www.DIYgenomics.org www.DIYgenomics.org/DIYgenomics_poster.ppt
  • 20. Agenda July 28, 2011 DIYgenomics.org Citizen science progress to date Scaling citizen science Grand vision next steps Image credit: http://www.gettyimages.com
  • 21.
  • 22.
  • 23. Athletic performance July 28, 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. Jan 2011. 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
  • 24. Study design template: MTHFR example July 28, 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
  • 25. DIYgenomics study ecosystem – CRO 2.0 July 28, 2011 DIYgenomics.org Sponsors Funders Study manager Graduate student partner* Study operation platform (Genomera) Study advisors* Participants Oversight (IRB) * Domain expert
  • 26.
  • 27.
  • 28.
  • 29. Agenda July 28, 2011 DIYgenomics.org Citizen science progress to date Scaling citizen science Grand vision next steps Image credit: http://www.gettyimages.com
  • 30.
  • 31.
  • 32.
  • 33.
  • 34.
  • 35.
  • 36. Circles of preventive medicine July 28, 2011 DIYgenomics.org Individual 2. Preventive Care Health Social Networks Citizen Science Studies Health Advisors 3. Traditional health care system and physicians 1. Automated digital health monitoring 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.
  • 37. Health self-management July 28, 2011 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.
  • 38. Thank you! Melanie Swan Founder DIYgenomics 650-681-9482 @DIYgenomics www.DIYgenomics.org [email_address] Slides: http://slideshare.net/LaBlogga Creative Commons 3.0 license Collaborators: Lorenzo Albanello Janet Chang Cindy Chen Jon Dekay John Furber Eri Gentry Kristina Hathaway Takashi Kido Laura Klemme Lucymarie Mantese Raymond McCauley Louis Nahum Marat Nepomnyashy Ted Odet Roland Parnaso William Reinhardt Greg Smith Aaron Vollrath Lawrence S. Wong Crowd-sourced clinical trials Personal genome apps