personal health citzenship
DESCRIPTION
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. - PowerPoint PPT PresentationTRANSCRIPT
Personal health citzenship
Huntington's Chorea Nancy Wexler’s family
AdrenoleukodystrophyAugusto Odone’s son
Doug Melton’s son, Sam, has diabetes
Parkison’s DiseaseMichael J. Fox
Cancer, substance
abuseBetty Ford
Hugh Rienhoff
PersonalGenome.org
PersonalGenome.org Project Goals
1) Active subject participation, informed redactions2) Entrance exam to ensure highly informed consent3) 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, donations6) Highly integrated, holistic, systems-biology
7) Subjects informed enough to “opt-out”8) Life-impacting info can reach subjects9) Cells available for personal functional genomics
Reducing costs via open-sourcehardware, software, wetware, ELSware
Factor • 30 Equipment speed: 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
G
A
C
T
Multiplex Cyclic Sequencing by Synthesis (Next-gen, polonies on slides or beads)
Polymerase -or- LigaseShendure,
Porreca, et al. 2005 Science
Illumina, IBS
AB-SOLiD, CGI
Mitra, et al. 2003 Analyt.
Biochem.1999NAR
PersonalGenome.org
G.007 Hardware open-CAD
• 30 msec move/settle• 42 kbp/sec• 10-60 Gbp/run• $124,000
EM-CCD Camera
Xenon Light
Fluidics
Autofocus
Objective
Stage
3U Imaging2U Sequencing
G.007-HardwareNikon, Hamamatsu, Alcott, Prior, Sutter, Bioptechs, PI, Uniblitz, Superlogics
Shendure, Porreca et al. 2005
Danaher, Hamamatsu, Nikon$124K with computer & 1 yr serviceContact:[email protected]
Rich Terry et al. 2007
DIY
PersonalGenome.org
36 Flowcells G007
PersonalGenome.org
Gel array, 12M beadsShendure, Porreca et al. 2005
Glass array, 60M beadsKim, Porreca et al. 2007
1.6M reads 12M reads(M. Umbarger)
Higher density & accuracy
PGP & G.0072005 2007 2008
Bases per run 30 Mbp 11 Gbp 30 Gbp
Bases per read 26 26 36
Cost per megabase $80 $2.88 $0.50
Cost per 1% diploid (20x 30Mbp)
$37,000 $1,800 $300
Reagent Volume Street price Bulk
T4 ligase 10 ml $26,000 $1,700
Hot-start Taq 50 ml $60,700 $2,000
Nonamers 40 ml $41,500 $1,600
Nucleotides 120 ml $29,000 $3,500
Beads 54 ml $6,000 $1,000?
Monthly reagent usagePersonalGenome.org