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Personal health citzenship. Doug Melton ’s son, Sam, has diabetes. Huntington's Chorea Nancy Wexler ’s family. Adrenoleukodystrophy Augusto Odone ’s son. Cancer, substance abuse Betty Ford. Parkison’s Disease Michael J. Fox. Hugh Rienhoff. PersonalGenome.org.

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Personal health citzenship


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personal health citzenship
Personal health citzenship

DougMelton’s son, Sam, has diabetes

Huntington's Chorea

NancyWexler’s family

Adrenoleukodystrophy

AugustoOdone’s son

Cancer, substance abuse

BettyFord

Parkison’s

Disease

Michael J. Fox

Hugh Rienhoff

PersonalGenome.org

personalgenome org project goals
PersonalGenome.org Project Goals

1) Active subject participation, informed redactions

2) Entrance exam to ensure highly informed consent

3) Subject & public access (not just research elite)

4) Eliminate over-promising de-identification

5) Scaleable to millions of research subjects,

via inexpensive DNA/trait data, donations

6) Highly integrated, holistic, systems-biology7) Subjects informed enough to “opt-out”

8) Life-impacting info can reach subjects

9) Cells available for personal functional genomics

reducing costs via open source hardware software wetware elsware
Reducing costs via open-sourcehardware, software, wetware, ELSware
  • Factor
  • 30 Equipmentspeed: from 1 up to 30 Mpixels/sec camera
  • 4 Equipment cost: from $500K down to $124K (Danaher Inc)
  • 36 Parallelism: 36 flow-cells per camera, 60M beads each
  • 15 Flow cell volume: 1.5 mm down to 0.01 or 0.02 mm
  • 40 Kit costs: $2000 down to $50 at standard enzyme costs
  • 10 Enzymes: $4000/mg down to <$400 (Enzymatics Inc)
  • 50 Genomic subset enrichment (Exome – 1% genome)

Error rate: 3E-7 at >=3X coverage

PersonalGenome.org

multiplex cyclic sequencing by synthesis

A

G

C

T

Multiplex Cyclic Sequencing by Synthesis

(Next-gen, polonies on slides or beads)

Polymerase -or- Ligase

Shendure, Porreca, et al. 2005 Science

Mitra, et al. 2003 Analyt. Biochem.

1999

NAR

AB-SOLiD, CGI

Illumina, IBS

PersonalGenome.org

g 007 hardware open cad
G.007 Hardware open-CAD

Xenon Light

EM-CCD Camera

Fluidics

Autofocus

Objective

Stage

3U Imaging

2U Sequencing

30 msec move/settle

42 kbp/sec

10-60 Gbp/run

$124,000

g 007 hardware
G.007-Hardware

Nikon, Hamamatsu, Alcott, Prior, Sutter, Bioptechs, PI, Uniblitz, Superlogics

Shendure, Porreca et al. 2005

Danaher, Hamamatsu, Nikon

$124K with computer & 1 yr service

Contact:

kevin.mccarthy@danahermotion.com

Rich Terry et al. 2007

DIY

PersonalGenome.org

36 flowcells
36 Flowcells

G007

PersonalGenome.org

higher density accuracy
Higher density & accuracy

Glass array, 60M beads

Kim, Porreca et al. 2007

Gel array, 12M beads

Shendure, Porreca et al. 2005

12M reads

(M. Umbarger)

1.6M reads

pgp g 007
PGP & G.007

Monthly reagent usage

PersonalGenome.org