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Digital Biology for Genentech

"Life is the New Black" for Genentech Innovation Day in February 2013 at Dallas., Texas.
by Raymond McCauley on 25 February 2013

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Transcript of Digital Biology for Genentech

Digital Biology:
Life is the New Black Raymond McCauley
for Genentech Innovation Day
Feb 2013 What
are
your
questions? Thank you for your attention Raymond McCauley
raymond@raymondmccauley.net Zooming Presentation Software prezi.com

Peter Arvai
Adam Somlai-Fischer (alternative from Microsoft Labs: pptPlex) DNA Structure Sequencing Biology now falls under Moore's Law Raymond McCauley biochemistry
biophysics
electrical engineering
computer science bioinformatics
nanotechnology microarrays sequencing personalized health DISCLAIMER These are my opinions and are not intended to reflect the views of any group or organization with which I may be affiliated. Reading DNA twitter: @raymondmccauley
email: raymond@raymondmccauley.net DNA Sequencing Economics Cost Time Just remember...

All of this:
Cheap tools
Greater access
Better understanding

adds up to a future where
people can ask more questions Creative Commons 3.0 license
Attribution-NoDerivs 3.0 Exponential Biosciences Creative Commons 3.0 license
Attribution-NoDerivs 3.0 social
(and other biological)
networks DNA Sequencing Tech 5X ~ 10X

Computer Tech
1.5X ~ 2X past: Biotech Chair, Singularity U
Co-Founder, BioCurious
Principal, Exponential Biosciences

Current Research Areas:
Bioinformatics
Personal Genomics
Cancer Sequencing
Genetic Engineering Human Genome Project
2001, 13 years
~$300M

Celera Genome Project
2001, ~3 years
$70M+

James Watson Genome
2007, ~2 months
$1M

Illumina Yoruban Trio
2008, 6 weeks
$100K

Illumina Consumer Sequencing
May 2009, 1 week
$48K

Illumina Consumer Sequencing
June 2010, 1 week
$9500 = $19500


Illumina Consumer Sequencing
June 2011, 1 week
$5000

Personal Genome Project (Various)
Jan 2012, 3-7 days
$2000 } Retail 2020 2016 2014 2020 = = = = Companies to Watch Democratization
of
Biotechnology More tools in more hands
=
More Breakthroughs Illumina
Complete Genomics
Ion Torrent / Life Technologies Oxford Nanopore
Genia DNAnexus
Station X
Invitae
Personalis
SV Bio
NuMedii Genentech
Genomic Health
Counsyl
Vecoy Nanomedicines
Verinata ** Next Gen Sequencing Next Next Gen Sequencing Informatics Diagnostics/Treatment Watson, Crick & Franklin & a Garage Near You... Source: National Human Genome Research Institute, Exponential Biosciences Singularity
University Erez
Livneh Writing DNA DNA Synthesis Who will drive
the biotech revolution? What will we make? in 2008,
Illumina HiSeq
200+ gigabases of DNA
2 human genomes
in 5 days
less than $10,000 each Complete Genomics
Illumina
Life Technologies/Ion Torrent
Pacific Biosciences
and
Genia
GnuBio
NABsys
Oxford Nanopore Genomics'
Greatest Hits Pharmacogenomics Cancer Rare Disease Treating a patient for
a particular
lung cancer

becomes

Treating a patient for
cancer of the PI3K pathway Drugs 1578 approved drugs
240 with genetic information
Just 21 shown in 23andMe sources:
http://www.drugbank.ca/stats
http://www.pharmgkb.org/
http://www.23andme.com/ Drug:
Clopidogrel (Plavix)
Reduces blood clots. Treats heart attack and stroke

Genotypes:
rs4244285 = AG
rs4986893 = GG
rs28399504 = AA
rs41291556 = TT
rs12248560 = CC

Haplotype:
CYP2C19 *1/*2

Phenotype:
Reduced clopidogrel efficacy
(higher dosage needed).

Patient:
Me! CYP450 Cytochrome P450s ADME/Tox Absorption
Distribution
Metabolism
Excretion
TOXicology Longevity People who never got:
cancer
cardiovascular disease
neurological conditions Nicholas Volker's story
"One In A Billion:
A boy's life, a medical mystery" Milwaukee Wisconsin Journal Sentinel,
by Mark Johnson and Kathleen Gallagher Nic Volker Pharmacogenomics Cancer Rare Disease Longevity First Human
Saved by
DNA Sequencing Q: Best way to live a long time?

A: Pick good parents! Genetic Engineering
=
Software Development How fast can you get to
"Hello World"
with 2 guys & a laptop in a garage? a hackerspace for biotech

First and largest biohacker lab in the world

Committed to making biotech
accessible, affordable, and open to everyone

a place to "experiment with friends"

501c3 all-volunteer community lab, supported by monthly memberships and classes Let's do that for biotech Every Disease
is a
Rare Disease... Stephen Kingsmore &
Center for Pediatric Genomic Medicine prepare samples
sequence DNA
digital analysis 4.5 hrs
25.5 hrs
20.0 hrs ~ $10 000 per case
"very helpful" in 7 out of 9 cases so far Two Lessons
from being in
an exponential business Find an exponential trend,
then hitchhike A prototype beats a plan Product Development Process (PDP) typical product:
18 month development cycle,
9 month market life

make new & rev old products
core team leaders involved from start
phase-gated milestones
manage technical and business risk is now as easy as typing ...and about to get easier New Developments Nothing fades faster than last year's technology 2008
$500K Today
$1 marginal cost,
market segmentation
& value-added services 1 human genome + interpretation
= $5000 4 human genomes, raw data
= $6000

1 human exome
= $1000

1 human "gene scan"
= $99 iGEM 2004 Closing Thoughts If it is made out of atoms,
in the future,
you will make it with biology. Or if you
unmake it... What does your industry
make or use? Intellectual Property (IP) is a mess...
...and no one knows what happens next. IP drives innovation
IP kills innovation
Where's the balance? Mobile/Sensors DNA Origami "Junk DNA" Genetic Engineering Industrial Human Food Pieter van Boheemen PGD
mitochondrial therapy
germ line therapy Biology as History Biology as Economy Biology as Technology Taxonomy

Collecting,
Classifying,
Arranging... Biology lacked an
organizing principle

Without predictive theory,
this was the only way to deal with such a complex subject matter Until... Better Tools Appeared






Revealing complexity
but simplifying theory Natural History About time... 1/3 World Economy Medicine Agriculture Energy Manufacturing Batten Disease Finding Ends a Diagnostic Odyssey for California Family
Bio-IT World January 24, 2013 Dylan Jacob Dietrich Stephan at international
Genetically
Engineered
Machines
competition iGEM World Jamboree 2010 mobile qPCR device Smaller, faster, cheaper
HPLC
Mass Spectroscopy
Pocket sequencers
Nanopore proteomics "Redneck Genetic Engineering"

bone marrow replacement
HIV cure
Nic Volker cure
Gene doping "The GM debate is over... We no longer need to discuss whether or not it is safe — over a decade and a half with three trillion GM meals eaten, there has never been a single substantiated case of harm. You are more likely to get hit by an asteroid than to get hurt by GM food.” - Mark Lynas, GMO crop burning environmental activist "...There is no more risk
in GMO food than conventionally
farmed food." - Anne Glover,
European Commission’s
Chief Scientific Advisor Crowdfunding & Biotech promise
peril
mostly promise Who wants to be a Genetic Engineer? Classes &
Safety Training Democratizing
DNA GMO Digital Agriculture versus Digital Agriculture Okanagan Specialty Fruits
Aqua Bounty
Arcadia BioSciences How do you react to a future
where today's biowarfare project
is tomorrow's science fair project?

When tools that were in dozens of hands
are now in thousands of hands? bioprinter project We build things.. OpenPCR $599 DNA Copy Machine We mentor the
next generation
of scientists
and technologists We support inventors
and entrepreneurs We take safety
and security
seriously In the last year,
19 startup companies
have done work
and recruited partners
at BioCurious Hanahan & Weinberg

Hallmarks of Cancer:
The Next Generation

Cell, March 2011 We build
community BioCurious/FBI
Joint Conference on
Biohacking
June 12-16, 2012 Species Conservation Scientist seeks
"adventurous
human woman"
to have
Neanderthal baby :( :) Singularity
University Acromegaly ostreolin
peptide somatostatin analog
Genentech deal for $545M Underdiagnosed
Difficult to diagnose
Presents in adults Genetic cause!
aryl hydrocarbon receptor interacting protein (AIP)
chief cause? of pituary tumors Companion
Diagnostic? as part of full genome scan version 3:
Illumina Custom OmniExpress+ BeadChip
Assays about 1,000,000 SNPs Your chance to try it...
Consumer access to research tool
"Recreational genomics"
Disease risk, carrier status, genealogy Gene Scan Gene Sequence most interesting/best known
1.2 million bases
0.04% all
3 billion bases
100% Microarrays Tools This is all out of date
in the next 48 hours What can you do about
being at risk for
an unpreventable disease?!? It turns out, lots of things:

prevention - vitamins, avoid UV
testing - Amsler grid
new opthamologist
investigate clinical trials
support research
don't put off that trip to the Louvre until retirement... Try it... So What? Personal Example When I first found out about
my AMD risk
it was
"untreatable" & "incurable"
but Genentech
now has treatments available footnote
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