DIYgenomics: an open platform for citizen science Melanie Swan Founder DIYgenomics 415-505-4426 @DIYgenomics [email protected].

DIYgenomics: an open platform for citizen science

Melanie Swan Founder

DIYgenomics415-505-4426

@DIYgenomics www.DIYgenomics.org

[email protected]

July 21, 2010 OSCON, Portland OR

Slides: http://slideshare.net/LaBlogga/slideshows

2July 21, 2010DIYgenomics.org

About Melanie Swan

Founder, DIYgenomics Futurist & serial entrepreneur MBA, Wharton; BA, Georgetown 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

Open source, open science, citizen science: context for DIYgenomics

DNA sequencing – 10x/yr improvements 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: scienceOpen science, citizen science

• Long-tail medicine• Preventive medicine


Open science / citizen science ecosystem

Traditional science research

Open science

DIYbio

Citizen science: 200+ organizations


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 self-health 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)

Open-source software• Web & mobile applications

2. Personal genome apps1. Patient-driven clinical trials/research studies

3. Citizen science community platform (Facebook/eBay of genomics)• Interaction and study design & operation

•Biobank for genotyping files & EMR import

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


Apps - Android

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


Apps - iPhone


Apps – web based personal genome tools

Health risk

Risk for top 20 Health Conditions

Response to 250 Drugs


Apps – MySNPs

FILEfox extension Private, local


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


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

Model: integrate health data streams for preventive medicine Available now: genotype, phenotype & intervention data Vis-à-vis traditional model: immediate, prospective, longitudinal,

systems-level approach Health genomics

Aging Pre-diabetes Macular degeneration Neuroplasticity

Behavioral genomics 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/Vit B12

Do common mutations in the MTHFR gene keep vitamin B from working?

Can a group of ordinary people come together to find out? And maybe find a treatment?

In the MTHFR gene (methylenetetrahydrofolate reductase), 2 small variations in DNA (SNPs rs1801133/C677T & rs1801131/A1298C) keep vitamin B9 (or folic acid) from being metabolized into its active form (folate).

Without this form of vitamin B, homocysteine may accumulate. This may lead to nutritional deficiencies and symptoms associated with diabetes complications, including vascular damage and nerve damage. This is also associated with blood clots and pregnancy loss.

Up to 60% of people may have some form of MTHFR mutation.


DIYgenomics study #1: MTHFR/Vit B12

We aim to: Find people with MTHFR mutations - by collecting

genotype data from volunteers who have used genetic testing services like 23andMe.

Try simple interventions - like special vitamin B supplements available over-the-counter.

See if they work - by asking participants to share results from blood tests performed at commercial labs.

Drug companies won't do this type of study -- there's little money to be made in over-the-counter treatments.


MTHFR pathway diagram


DIYgenomics MTHFR study structure

Genotype

MTHFR gene SNPs:

rs1801133 (A/G)

rs1801131 (A/G)

Phenotype

Blood tests:

B-12 and

Homocysteine

Intervention

1. B-complex

2. L-methylfolate

3. B-complex + L-methylfolate

Findings

Analyze, explore, implement, share,

and publish

Investigate genotype-phenotype linkage and apply interventions to improve phenotypic outcomes


MTHFR study – preliminary results

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

Blood Test #

Homocysteine umol/l

DIYgenomics citizen science study: Homocysteine Levels


DIYgenomics Citizen Science – Join Us!

Participate in a study

Organize a study on our platform

Contribute your data

Innovate blood tests 2.0 and interventions 2.0 (synthetic biology)

Collaborate: Japan, South AfricaImage credit: http://www.uchsc.edu/vivat/2006/September2006/images/DNA_strand.jpg

Thank you!

Melanie SwanFounder

DIYgenomics415-505-4426

@DIYgenomicswww.DIYgenomics.org

[email protected]

Slides: http://slideshare.net/LaBlogga/slideshows

Creative Commons 3.0 license

Collaborators:

Cindy Chen

Priya Kshirsagar

Lucymarie Mantese

Raymond McCauley

Marat Nepomnyashy

Roland Parnaso

Aaron Vollrath

Lawrence S. Wong

DIYgenomics: an open platform for citizen science Melanie Swan Founder DIYgenomics 415-505-4426 @DIYgenomics [email protected].

Documents

science open science

drugs slide

netlabloggaslideshows

apps iphone slide

public health

diygenomics dna sequencing

agenda open source

health conditions response