Genomic self-hacking: citizen science and the realization of personalized medicine


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Quantified self ignite talk. Redesigning biology may be man's ultimate artistic and scientific exploit. The first steps are reading and writing genetic data with DNA sequencing and synthetic biology. Already human genome sequencing costs have declined such that individuals worldwide are accessing their own genomic data, and can explore it through open-source science communities such as DIYgenomics.

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Genomic self-hacking: citizen science and the realization of personalized medicine

  1. 1. Genomic self-hacking: citizen science and the realization of personalized medicine Melanie Swan Genome Geek 650-681-9482 @DIYgenomics [email_address] Quantified Self Meetup Group NASA AMES - July 19, 2011 Slides:
  2. 2. Future health: layers of preventive medicine July 19, 2011 Individual 2. Preventive Care Health Social Networks Citizen Science Studies Health Advisors 3. Traditional health care system and physicians 1. Automated digital health monitoring
  3. 3. New concept of health self-management July 19, 2011 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.
  4. 4. Genome hacking philosophy July 19, 2011 <ul><li>Goal: preventive medicine </li></ul><ul><ul><li>Realize preventive medicine by establishing baseline markers of wellness and pre-clinical interventions </li></ul></ul><ul><li>Generalized hypothesis </li></ul><ul><ul><li>One or more polymorphisms may result in out-of-bounds baseline levels of phenotypic markers. These levels may be improved through personalized intervention. </li></ul></ul>Source: Genotype Phenotype Intervention Outcome + + =
  5. 5. DTC genomics – interpretation variance July 19, 2011 Private data upload: Marat Nepomnyashy;
  6. 6. Open-source mobile apps (5,000+ downloads) <ul><li>Health condition, drug response, athletic performance </li></ul><ul><li>23andMe data upload </li></ul><ul><li>Android </li></ul><ul><li>iPhone </li></ul>July 19, 2011 Android development: Michael Kolb, Lawrence S. Wong, Laura Klemme, Melanie Swan iPhone development: Ted Odet, Greg Smith, Laura Klemme, Melanie Swan “ genomics” “ genomics” T T T T T T T C C
  7. 7. Vitamin B deficiency / MTHFR mutation <ul><li>Do common mutations in the MTHFR gene prevent vitamin B from working correctly? </li></ul><ul><li>Test whether 2 variations in the MTHFR gene keep vitamin B9 (folic acid) from being metabolized into its active form (folate) </li></ul><ul><ul><li>rs1801133/C677T </li></ul></ul><ul><ul><li>rs1801131/A1298C </li></ul></ul><ul><li>Without this form of vitamin B, homocysteine may accumulate (risk of cardiovascular disease, etc.) </li></ul><ul><li>50% or more of the population may have some form of MTHFR polymorphism </li></ul>July 19, 2011 Source:
  8. 8. Homocysteine metabolism pathway July 19, 2011 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.
  9. 9. Vitamin B / MTHFR study protocol July 19, 2011 <ul><li>Investigate genotype-phenotype linkage and apply interventions to improve phenotypic outcomes </li></ul><ul><li>Protocol confirmed with two separate experts in the field </li></ul>Source: 1. Genotype MTHFR gene SNPs: rs1801133 (A/G) rs1801131 (A/G) 2. Phenotype Blood tests: B-12 and Homocysteine 3. Intervention <ul><li>(2 week periods) </li></ul><ul><li>B-complex </li></ul><ul><li>L-methylfolate </li></ul><ul><li>B-complex + L-methylfolate </li></ul>
  10. 10. Vitamin B / MTHFR pilot study results July 19, 2011 <ul><li>Drug store vitamin (Centrum) reduced homocysteine levels for 6/7 participants </li></ul>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
  11. 11. Athletic performance July 19, 2011 Image credit: 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
  12. 12. Preventive wellness <ul><li>Personal uses of the personal genome </li></ul><ul><ul><li>Ancestry </li></ul></ul><ul><ul><li>Carrier status </li></ul></ul><ul><ul><li>Disease risk profiling </li></ul></ul><ul><ul><li>Drug response </li></ul></ul><ul><ul><li>Athletic performance capability </li></ul></ul><ul><ul><li>Product response </li></ul></ul><ul><li>Wellness profiling </li></ul><ul><ul><li>Cancer </li></ul></ul><ul><ul><li>Immune system </li></ul></ul><ul><ul><li>Aging </li></ul></ul>July 19, 2011
  13. 13. Predictive wellness profiling: cancer <ul><li>Proto-oncogene/tumor suppressor gene polymorphisms </li></ul>July 19, 2011 Source: DIYgenomics Image credit: TP53: cell cycle arrest, PTEN: cell cycle progression modulator, MYC: cell cycle regulator
  14. 14. Lung cancer risk and drug response <ul><li>Risk and drug response for specific cancers </li></ul>July 19, 2011 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:
  15. 15. Wellness profiling: immune system <ul><li>Immune system genomic wellness profiling </li></ul><ul><li>Immune response: T-cell activation </li></ul><ul><ul><li>CTLA4, CD226, CD86, IL3 </li></ul></ul>July 19, 2011 Source: DIYgenomics Image credit: CTLA4: T-cell inhibition; IL3: growth-promoting cytokine
  16. 16. Aging: TA-65, telomere length & TERC mutation July 19, 2011 <ul><li>Herbal supplement TA-65 (astragalus root) taken by 1000 people worldwide. Telomere and immune system benefits in humans published Mar 2011. 1 </li></ul><ul><li>TERC (RNA gene that extends telomeres) SNPs: </li></ul><ul><ul><li>rs10511887, rs12696304, rs16847897, rs2293607, rs610160 </li></ul></ul>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.
  17. 17. Aging: applied healthspan engineering July 19, 2011 Source: Larrick JW, Mendelsohn A. Applied Healthspan engineering. Rejuvenation Res. 2010 Apr-Jun;13(2-3):265-80, Table 2. Legend: ACE, angiotensin converting enzyme; ARBs, angiotensin receptor blockers; EGCG, epigallocatechin 3-gallate; mTOR, mammalian target of rapamycin.
  18. 18. Personal health collaboration studies July 19, 2011 More information:
  19. 19. Study design template: MTHFR example July 19, 2011 Source: Cyanocobalamin Image credit:
  20. 20. Health hackers need Blood Tests 2.0 <ul><li>Low-cost home-administered self-read finger-stick blood, urine, saliva tests: </li></ul><ul><li>Traditional blood tests (Homocysteine, Vitamin B-12, Folate, Vitamin D, Creatinine, eGFR, Cortisol, Calcium, Iron, Aldosterone) </li></ul><ul><li>Hormones (Estrogen, Progesterone, Testosterone, Estradiol) </li></ul><ul><li>Immune system: CD4, CD8/CD28 ratio, IL-1, IL-6 </li></ul><ul><li>Chemical / h eavy metal burden: mercury, cadmium, lead, tin </li></ul>July 19, 2011
  21. 21. Towards an epistemology of citizen science <ul><li>Provide a structure and context for self-derived health knowledge </li></ul><ul><li>Q1: Are new kinds of knowledge are being formed through group collaborations such as wikipedia and health social networks? </li></ul><ul><li>Q2: Are there differences in the types of knowledge generated by traditional medicine, self-experimentation, and health collaboration communities? </li></ul>July 19, 2011