ICSB3: DRPM Measures

Report
Little Data: NextGen Info Storage in DNA
3:55-4:50 PM CBA 7-Mar-2013 12:12-12:21 PM
Thanks to:
.gov
NHGRI
|| NIGMS
||
.edu
||
ArmRev.org
||
Oppenheimer
.org
Foundation
||
||
.com
Azco
||
||
Read
LSRF
Gen9
= = = = = = = = I/O = = = = = = = Write
Next-generation Digital Information Storage in DNA
1. Read/write DNA 10-fold/yr: Next = FISSeq
2. E.coli & human genome engineering
3. DNA data archiving
4. Brain Activity Map I/O: Polymerase
Biologically Inspired Engineering
From $3 ‘Optimistic’ exponential extrapolation
billion to an
affordable
genome
DNA sequencing
1E+13
1E+12
1E+11
When?
1E+10
1E+9
1E+8
6 decades
& Moore's law
1.5x/yr for
electronics
1E+7
1E+6
1E+5
1E+4
1E+3
1965 1970 1975 1980 1985 1990 1995 2000 2005 2010 2015 2020 2025 2030 2035 2040
3
From $3
billion to an
affordable
genome
Early arrival
1E+13
1E+12
1E+11
When?
1E+10
1E+9
1E+8
6 years
DNA sequencing
& Moore's law
1.5x/yr for
electronics
1E+7
1E+6
1E+5
1E+4
1E+3
1965 1970 1975 1980 1985 1990 1995 2000 2005 2010 2015 2020 2025 2030 2035 2040
4
Fluorescent in situ Sequencing (FISSEQ)
60 cycles x 4 colors
Single base
differences
Lee, Yang, Terry, Nilsson, Church et al.
5
Next-generation Digital Information Storage in DNA
1. Read/write DNA 10-fold/yr: Next = FISSeq
2. E.coli & human genome engineering
3. DNA data archiving
4. Brain Activity Map I/O: Polymerase
Biologically Inspired Engineering
113 kbp DNA 151 genes
Smaller.
Higher speed &
accuracy requires
a few extra genes
(E.coli 20 min.
doubling)
Reconstituted
ribosomes:
Jewett & Church
Pure translation:
Forster & Church
MSB ’05
GenomeRes.’06
Shimizu, Ueda ’01
7
First Genomically Recoded Organism (GRO)
3 New Biological Functions
Metabolic dependence
Safety
4.7 Mbp
New Amino Acids
Lajoie MJ, Rovner AJ, Goodman DB, Aerni HR, Haimovich AD,
Mercer JA, Wang HH, Carr PA, Mosberg JA, Rohland N, Schultz PG,
Jacobson JM, Rinehart J, Church GM, Isaacs FI
Virus resistance
Safety
Multiplex Assembly Genome Engineering (MAGE)
#1: ss-90mer x ds-Circle
#2: ss-Mb x ds-Circle conjugation
Costantino &Court PNAS’03 Isaacs et al., Science ‘11
Wang et al., Nature '09
CAGE
MAGE
200 kbp BAC
#3: CRISPR
#4: 10 Mbp Microcell-Mediated
Chromosome Transfer (MMCT)
9
Targeted Gene Therapy
ZnF nuclease CCR5 double
null in T-cells Sangamo
Phase 2 clinical trial (AIDS
treatment)
2007 Leukemia & AIDS:
Timothy Ray Brown
Next: CRISPR RNA guided Nucleases
10
Next-generation Digital Information Storage in DNA
1. Read/write DNA 10-fold/yr: Next = FISSeq
2. E.coli & human genome engineering
3. DNA data archiving
4. Brain Activity Map I/O: Polymerase
Biologically Inspired Engineering
1977: 3- & 4-way DNA. 2009: caDNAno.org
2012: Douglas, Bachelet, Church. Science
Nanorobot: Sensors, Logic, Actuators
DNA+mAb
Next-Gen Synthesis
12K CustomArray Electrolytic
55K Agilent Ink-jet
80K LCSci/Mycroarray Photo-Acid
6.3M Roche Photo 5’ protection
($0.2K-$13K / chip)
Amplify pools with flanking universal primers
Paths to error correction
1.Hyb-Select: Tian et al. 2004 Nature
2. MutS: Carr & Jacobson 2004 NAR
3. MutHLS: Smith & Modrich 1997 PNAS
4. Endo/Exonuclease : Bang Nat Meth. 2008
5. Errase
6. Sequencing
13
Archival DNA.
Zettabyte/kg
Images  Camera  Computer  Inkjet  DNA  Polymerase
Text
printer
copying
Images  RNA Polymerase
DMD + Nitrobenzyl
2012 Church, et al
2013 Goldman et al.
1986 Davis, et al.
Digital Inkjet 2012
DNA-video 2013
Kosuri
15
Next-generation Digital Information Storage in DNA
1.
2.
3.
4.
Read/write DNA 8-fold/yr
Fluorescent In Situ Sequencing (FISSeq)
Nanorobots & DNA data archiving
Brain Activity Map I/O: Polymerase
Biologically Inspired Engineering
Brain Activity Map (BAM)
Sep 2011: Kavli, Gatsby, Allen: Chun
Imaging: Greenspan, Yuste, Zhaung, Reid
Optical fibers: Roukes, Boyden, Scherer
Nano: Alivisatos, Park, Weiss, McEuen
Stimulation: Donoghue, Deisseroth
Computation: Kording, Sejnowski
Polymerase: Zamft, Marblestone, Schmidt, Tyo,
Martín-Alarcón, Marcus
17
Epilepsy & Images via Electrode Wires
Quiroga et al. 2005 Nature. Invariant
visual representation by single neurons in
the human brain (left posterior hippocampus)
18
Number of Simultaneously Recorded Neurons
Scaling of Brain Mapping Technologies
Konrad Kording
Polymerase
7e25 Op/kWh
IC energy
efficiency
1.5x /yr
economist.com/node/215
20
1350
Ions to DNA
Light to DNA
ATP to DNA
DNA
Pol
Ions to DNA
Zamft, Marblestone
et al. PLoS One 2012
DNA
Pol
Dpo4 Pol
.
.
Brain Activity Map I/O
Why?
Blindness, deafness, stroke,
traumatic brain injuries, spinal cord injuries, Parkinson’s,
chronic pain, depression, locked-in syndrome, dystonia,
essential tremor, epilepsy,
neurodegenerative diseases.
Alivisatos, Chun, Church, Donoghue, Greenspan, Roukes,
Yuste; The Brain Activity Map Project and the Challenge
of Functional Connectomics. Neuron 2012
25
Brain Activity
Map I/O
Ju Lu, Harvard University
26
Miesenböck Science 2009
Wireless molecular I/O. 100M Neural cells
27
Next-generation Digital Information Storage in DNA
1.
2.
3.
4.
Read/write DNA 8-fold/yr
Fluorescent In Situ Sequencing (FISSeq)
Nanorobots & DNA data archiving
Brain Activity Map I/O: Polymerase
Biologically Inspired Engineering
.
Zorzos et al 2012 Optics Letters
42nm spacing fluorescent barcodes. Nature Chem 2012
Lin, Jungmann, Leifer, Li, Levner, Church, Shih, Yin
Fluorescent
In situ
Sequencing
FISSEQ
RNA & DNA
Jay Lee
Evan Daugharthy
Reza Kalhor
Jonathan Scheiman
Michael Sismour
Joyce Yang
John Aach
Kun Zhang
Yoav Mayshar
Polonator & Advanced
Technology Team:
Nicholas Conway
Daniel Levner
Chao Li
Richard Terry
Brian Turczyk
Frederick Vigneault
Generic Health Advice
•Exercise
•Drink your milk
•Eat your grains
• & beans
• & iron
• & meat
•Get more rest
UNLESS …
•Exercise
•Drink your milk
•Eat your grains
• & beans
• & iron
• & meat
•Get more rest
HCM (cardiac arrest)
MCM6 (gastric distress)
HLA-DQ2 (diarrhoea)
G6PD (red cell lysis)
HFE (Liver damage)
LDLR (clogged arteries)
HLA-DR2 (excessive sleep)
Most new Sequencing = single-molecule imaging
1. Danaher
MA
2. Roche-454
CT
3. AB-SOLiD
MA
4. Illumina
UK,CA
5. CGI/BGI
CA
6. Helicos
MA
7. Pacific Bio
CA
8. IBS/Qiagen
MA
9. Ion Torrent
CT
17. LightSpeed
CA
10. Genapsys
CA
11. Electronic Biosci CA
12. Nabsys
RI
13. OxfordNanopore UK
14. Genia
CA
15. IBM-Roche
NY
16. NobleGen
MA
18. GnuBio
MA
19. Bionanomatrix
PA
20. Halcyon
CA
21. ZS Genetics
NH
22. Electron Optica
CA
23. Genizon BioSci QC
24. LaserGen
TX
25. GE Global
NY
26. Stratos Genomics WA
27. Reveo
NY
28. Firebird
FL
29. Zeiss
MA
30. Lucigen
WI
31. Adv. Liquid Logic NC
32. Caerus Molec Diag CA
33. Nanophotonics Biosci CA
34. Network Biosystems MA
35. SeiraD
NM
36. Affymetrix
CA
37. Population Gen Tech UK
38. AQI Sciences
AZ
39. Base4innovation
UK
40. Li-Cor
NE
41. U.S. Genomics
MA
42. Mobious Genomics UK
43. Visigen
TX
44. Starlight
CA
34
http://arep.med.harvard.edu/gmc/nexgen.html
Nanopore : Polymer vs Monomer vs NanoTag
1988-1995:
Church,
Deamer,
Branton,
Baldarelli,
Kasianowicz.
GG
2012: Oxford & Genia
AAA
TTT CCC
2009 Clarke, Bayley, et al
2010 Derrington, Gundlach, et al
2012 Cherf, Akeson, et al
5′ GCAACAGAGCCAGC CCC
35
GCAACAGAGCCAGC AAA GCAACAGAGCCAGC CCC
GCAACAGAGCCAGC TTT GCAACAGAGCCAGC GG A A15 3′.
Nanopore: Polymer vs Monomer vs NanoTag
“accuracy better than
1 in 5x108 events”
A
C
G T
Oxford, Genia
PEG-Labeled PP: Ju, Kasianowicz, et al.
Scientific Reports 2012

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