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 protected]

July 21, 2010, OSCON, Portland OR

Slides: http://slideshare.net/LaBlogga

2July 21, 2010DIYgenomics.org

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.


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


Open source: literal and conceptual

Software

Data (and analysis)• 1 million member biobanks

• Individual-contributed health data

Activities: science• Long-tail medicine

• Preventive medicine


Open science / citizen science ecosystem

Traditional science research

Open science

DIYbio

Citizen science: 200+ organizations1

1http://scienceforcitizens.net/


Agenda





We are standing in a new era

April 1, 2010 Image credit: http://pubs.acs.org/cen/_img/87/i50/8750cover2_law.gif Dec. 14, 2009


3rd and 4th generation sequencing arrives3rd Gen: Sequencing by Synthesis

2nd Gen: Parallelized sequencing

1st Gen: Sanger Sequencing

4th 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

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

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.


Agenda





DIYgenomics model

Problem: lack of predictive health self-management tools

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 apps1. 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


Apps - Android

Side-by-side comparison of consumer genomic services by loci and variants for top 20 conditions

Application developed by: Michael Kolb, Lawrence S. Wong, Melanie Swan


Apps - iPhone

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

Health risk

Risk for top 20 Health Conditions

Response to 250 Drugs


Apps – MySNPs

FILEfox extension Private, local data viewing


Marat Nepomnyashy; https://addons.mozilla.org/en-US/firefox/addon/156946/

1.

2.

3.


Apps – web based personal genome tools

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



Agenda





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 Image credit: http://www.tigerteamconsulting.com/TTC_Site/sectors_binf.jsp



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

Source: http://diygenomics.pbworks.com/MTHFR


MTHFR pathway diagram

Aaron Vollrath; http://bit.ly/cHRzS8


DIYgenomics MTHFR study protocol

1. Genotype

MTHFR gene SNPs:

rs1801133 (A/G)

rs1801131 (A/G)

2. Phenotype

Blood tests:

B-12 and

Homocysteine

3. Intervention

(2 week periods)

1. B-complex

2. L-methylfolate

3. B-complex + L-methylfolate

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


MTHFR pilot study – in-process results

Average drug store vitamin (Centrum multivitamin) reduced homocysteine levels for 4/5 participants

Blood Test #

2. Homocysteine levels

DIYgenomics MTHFR citizen science study1

1. Genotype profiles

Baseline LMF

Source: http://diygenomics.pbworks.com/MTHFR_Results

1Results 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

Institutional PI (principal

investigator)

Traditional Research Model Citizen Science Research Model

Research subjects

Citizen scientists

Investigators = Participants

Institutional Review Board

(IRB)

Citizen ethicistsFAQs

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

Image credit: http://reisearch.net/biotech_page/dna_horizontal.gif



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 supportImage credit: http://www.uchsc.edu/vivat/2006/September2006/images/DNA_strand.jpg

http://diygenomics.pbworks.com/DIYgenomics_software

Thank you!

Melanie SwanFounder

DIYgenomics+1-650-681-9482

@DIYgenomicswww.DIYgenomics.org

[email protected]

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 trialsPersonal genome apps

diygenomics: an open platform for citizen science

Technology