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

Genomic self-hacking: citizen science and the realization of personalized medicine Melanie Swan Genome Geek 650-681-9482 @DIYgenomics www.DIYgenomics.org [email_address] Quantified Self Meetup Group NASA AMES - July 19, 2011 Slides: http://slideshare.net/LaBlogga

Future health: layers of preventive medicine July 19, 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

New concept of health self-management July 19, 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.

Genome hacking philosophy July 19, 2011 DIYgenomics.org
Goal: preventive medicine
Realize preventive medicine by establishing baseline markers of wellness and pre-clinical interventions
Generalized hypothesis
One or more polymorphisms may result in out-of-bounds baseline levels of phenotypic markers. These levels may be improved through personalized intervention.
Source: http://diygenomics.pbworks.com/MTHFR Genotype Phenotype Intervention Outcome + + =

DTC genomics – interpretation variance July 19, 2011 DIYgenomics.org Private data upload: Marat Nepomnyashy; https://addons.mozilla.org/en-US/firefox/addon/156946

Open-source mobile apps (5,000+ downloads)
Health condition, drug response, athletic performance
23andMe data upload
Android
iPhone
July 19, 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” T T T T T T T C C

Vitamin B deficiency / MTHFR mutation
Do common mutations in the MTHFR gene prevent vitamin B from working correctly?
Test whether 2 variations in the MTHFR gene 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 of cardiovascular disease, etc.)
50% or more of the population may have some form of MTHFR polymorphism
July 19, 2011 DIYgenomics.org Source: http://diygenomics.pbworks.com/MTHFR

Homocysteine metabolism pathway July 19, 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 19, 2011 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

Vitamin B / MTHFR pilot study results July 19, 2011 DIYgenomics.org
Drug store vitamin (Centrum) reduced homocysteine levels for 6/7 participants
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

Athletic performance July 19, 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

Preventive wellness
Personal uses of the personal genome
Ancestry
Carrier status
Disease risk profiling
Drug response
Athletic performance capability
Product response
Wellness profiling
Cancer
Immune system
Aging
July 19, 2011 DIYgenomics.org

Predictive wellness profiling: cancer
Proto-oncogene/tumor suppressor gene polymorphisms
July 19, 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
Risk and drug response for specific cancers
July 19, 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
Immune system genomic wellness profiling
Immune response: T-cell activation
CTLA4, CD226, CD86, IL3
July 19, 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 19, 2011 DIYgenomics.org
Herbal supplement TA-65 (astragalus root) taken by 1000 people worldwide. Telomere and immune system benefits in humans published Mar 2011. 1
TERC (RNA gene that extends telomeres) SNPs:
rs10511887, rs12696304, rs16847897, rs2293607, rs610160
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 19, 2011 DIYgenomics.org 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.

Personal health collaboration studies July 19, 2011 DIYgenomics.org More information: www.DIYgenomics.org www.DIYgenomics.org/DIYgenomics_poster.ppt

Study design template: MTHFR example July 19, 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

Health hackers need Blood Tests 2.0
Low-cost home-administered self-read finger-stick blood, urine, saliva tests:
Traditional blood tests (Homocysteine, Vitamin B-12, Folate, Vitamin D, Creatinine, eGFR, Cortisol, Calcium, Iron, Aldosterone)
Hormones (Estrogen, Progesterone, Testosterone, Estradiol)
Immune system: CD4, CD8/CD28 ratio, IL-1, IL-6
Chemical / h eavy metal burden: mercury, cadmium, lead, tin

Towards an epistemology of citizen science
Provide a structure and context for self-derived health knowledge
Q1: Are new kinds of knowledge are being formed through group collaborations such as wikipedia and health social networks?
Q2: Are there differences in the types of knowledge generated by traditional medicine, self-experimentation, and health collaboration communities?

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

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