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Life is the New Black / Genentech

Raymond McCauley presentation for Genentech, Charlotte, NC, November 2013, on digital biology, DNA sequencing, and the future of cancer research.
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Raymond McCauley

on 14 November 2013

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Transcript of Life is the New Black / Genentech

Your chance to try it...
Consumer access to research tool
"Recreational genomics"
Disease risk, carrier status, genealogy
Human Genome Project
2001, 13 years
~$2.7B

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

454 James Watson Genome
2007, ~2 months
$1M

Illumina Yoruban Trio
2008, 6 weeks
$100K

Illumina Consumer Sequencing
May 2009, 2 weeks
$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
Singularity
University

for your attention
raymond@raymondmccauley.net
DNA Structure
DNA Sequencing
Biology now falls under Moore's Law
Raymond McCauley
biochemistry
biophysics
electrical engineering
computer science
bioinformatics
nanotechnology
genetic engineering
DNA 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
DNA Sequencing Economics
Cost
Exponential Biosciences
systems
biology
DNA Sequencing Tech 5X ~ 10X

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

Current Research Areas:
Bioinformatics
Personal Genomics
Cancer Sequencing
2020
2016
2014
2020
=
=
=
=
Companies to Watch
Illumina
Complete Genomics
Ion Torrent / Life Technologies
Oxford Nanopore
Genia
DNAnexus
Invitae
NuMedii
Personalis
Station X *
Strand LS
SV Bio
Genentech
Genomic Health
Counsyl
Vecoy Nanomedicines
Verinata **
Second Genome
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
Writing DNA
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
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
Innovation 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
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
Closing Thoughts
In the future,
if it is made out of
atoms,

you will make it with
biology.
What does your industry
make or use?
DNA Origami
Genetic Engineering
Industrial
Human
Food
PGD
mitochondrial therapy
germ line therapy
Biology as Technology
Batten Disease Finding Ends a Diagnostic Odyssey for California Family
Bio-IT World January 24, 2013
Dylan
Jacob
Dietrich Stephan at
"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
Digital Agriculture
versus
Digital Agriculture
Okanagan Specialty Fruits
Aqua Bounty
Arcadia BioSciences
Hanahan & Weinberg

Hallmarks of Cancer:
The Next Generation

Cell, March 2011
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 1,200,000 SNPs
Gene Scan
Gene Sequence
most interesting/best known
1.2 million bases
0.04%
almost all
3.2 billion bases
100%
DNA Microarrays
Tools
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...
Try it...
So What?
Personal Example
When I first found out about
my AMD risk
it was
"
untreatable
" & "
incurable
"
but
Genentech

now has 2 treatments available
footnote
or need to unmake?
What's Next
People
Teams
Interdisciplinary
Innovation 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
Nothing fades faster than last year's technology
2008
$500K
Today
$1
People
Teams
Interdisciplinary
=
DNA sequencing
and synthesis prices
continue to plummet
Synthetic
Biology
*
Hype Cycle
but...
Metagenomics
Meta
Raymond McCauley
@raymondmccauley
+1-650-776-4561
Thank you
Peter DiLaura
Second Genome
New Yorker article
DNA has 521 year half-life
GMO
Anxiously watching
IP
Hopefully watching
Crowdfunding
Democratization
*
Democratization
of
Biotechnology
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

Located in Sunnyvale, California

501c3 all-volunteer community lab, supported by monthly memberships and classes
Let's do that for biotech
iGEM 2004
international
Genetically
Engineered
Machines
competition
iGEM World Jamboree 2010
Who wants to be a
Genetic Engineer?
We teach
classes...
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,
31 startup companies
have done work
and recruited partners
at BioCurious
We build
community
BioCurious/FBI
Joint Conference on
Biohacking
June 12-16, 2012
http://openpcr.org/
Garage Labs
When we talk about garage labs
in Silicon Valley, we aren't kidding...
Helixis Real Time PCR
Industry: $30,000
Helixis: $13,900
How does
$599
sound?
The Biotech
Revolution
is Here!
If you've got:
Who wants to build something?
Dremelfuge
Centrifuge
=
$57
>$500
on Shapeways
used, on eBay
Research Tools
Better, Cheaper, Faster
US$750000,
a PhD in molecular biology,
and a fully equipped lab
Edge
Indicators
What do
we do?
iGEM Inaugural Competition, 2004
More tools in more hands
=
More Breakthroughs
Watching in
rearview mirror
Regulatory
Covers
Disease risk, carrier status,
genealogy, random stuff

What do
you
want to know?
Some of your info also applies to
family...

Privacy:
to share or not to share?
Do you want to be found by long-lost relatives?
Health insurance
protected by law

(GINA)
Life insurance, long-term disability is
not
Human
Prenatal Genetic Dx
Mitochondrial therapy
Germ line therapy
"Redneck Genetic Engineering"

bone marrow replacement
HIV cure
Nic Volker cure
Gene doping
How long until
genetic engineering
for
adults
?
Rare Disease
is the
Long Tail
of human health...
Coming Soon!
epigenomics
regulomics
environomics
metagenomics
your name here + omics
from a research lab near you!
metagenomics
Peter DiLaura, CEO
Practical Advice
Use antibiotics wisely
Eat like ancestors
Get a dog
metagenomics
market segmentation
for your bacteria
=
Crowd-Sourced
Metagenomics
New Engineering School at Stanford
Bioengineering
Big Deal?
What was the
last new school
at Stanford
?
Hint: established
1965
Answer: Department of
Computer Science
Graduates built
Silicon Valley

& triggered the
computer revolution
We are
everywhere
...
currently tracking
23 community labs
200+ individual labs
on 6 continents
Algae Chassis Project
DNA
Origami
a new kind of
Pharma Deal
Collgard Biopharmaceuticals
licensed compound halofuginone (
HT-100
)
to
Halo Therapeutics
for
$1M
Duchenne
Muscular Dystrophy
(DMD)
Meet the Halo board of directors...
The Seckler
Family
the Wicka
Family
DIY Drug Development
Orphan Drug status in US
Thumbs up from EU's Treat-NMD
Clinical trials start 2013
“We are ready to be the ones who get to make the decision of go or no go on this one." - Thomas Wicka
You let
kids go hands-on
with blowtorches?!?
Why, yes!
Yes we do!
5 year old Harlan
makes Calcium burn
red
.
If it's so great,
why doesn't my doctor have it?
sequencing =
easy
interpretation =
hard
DNA Synthesis
is now as easy as typing
Do you
believe?
$300M
2001
=
+
2013
=
2007
=

Covers
Disease risk, carrier status, genealogy

What do
you
want to know?
Some of your info also applies to
family...

Privacy:
to share or not to share?
Do you want to be found by long-lost relatives?
In US,
Health insurance
protected by law

(GINA)
Life insurance, long-term disability is
not
Eye Problems
Genetic
Nearsightedness
Farsightedness
Color blindness
Retinitis pigmentosa
Genetic + Environmental
Glaucoma
AMD
Amblyopia / “lazy eye”
Strabismus
More genetic discoveries all the time...
March 2013: 24 new genes associated with
refractive error / nearsightedness
Virginie Verhoven, Erasmus Med Center, Genome-wide meta-analyses of multiancestry cohorts identify multiple new susceptibility loci for refractive error and myopia
FFPE
FF
Formalin Fixed
Paraffin Embedded
Fresh
Frozen
versus
This could save your life...
from Eric Topol, MD
Synthetic
Biology
*
Hype Cycle
Scaling Problems
Cells are
not

computers
FF v. FFPE
Action Items
Embrace genetic info for preventive health
If you get cancer,
remember
Fresh
Frozen
Formalin Fixed Parrafin Embedded
good preview
of things to come
Encourage gene scans in corporate wellness programs
Insurance changes forever
in the biotech 21st century
Absolute
Privacy , Data
Escrow
Expose your kids (& yourself) to biotechnology
Raymond McCauley
+1-650-776-4561
Build a
biohacker
space
Get a Book
The Stuff of Life
by Mark Schultz
Illustrated by
Zander Cannon
& Kevin Cannon
Try it
3D printed
pipetter
+ straw
+ spring from PEZ dispenser
DNA Sequencing Economics
Cost
Time
Yovivo! Yogurt
gene-hacked yogurt + resveratrol
food as a hackable nutraceutical platform
yovivoyogurt.com
from Radiant Genomics
ApE = A Plasmid Editor
Hacking DNA
latest
Looking for innovation in biotech?
Look in a garage near you...
Food & Synthetic Biology
Sample6
Modern Meadows *
Evolva
Best Conference
Future of Genomic Medicine
Dr. Eric Topol, Scripps Health
March 6&7 2014
Clinicians - Keep Learning
Vanillin
$300M
Genentech
rDNA human insulin
made in E. Coli
1978
Itakura, Riggs, Goeddel, and Crea, at City of Hope Medical Research Center
Ambitious
Timothy Ray Brown
HIV diagnosed 1995
AML diagnosed 2006
CCR5Δ32 stem cell transplant
HIV-free since 2009
Blood, March 10, 2011, vol. 117, no. 10, 2791-2799
MIT Technology Review, Susan Young, September 30, 2013
Genetic Engineering
& Viral Vaccines
Molecular Machines
Regulatory
Genome Collections
Systems Biology
Personalized
Medicine
Intellectual
Property
Medical Informatics
Future of
Deep
Sequencing
Cell Free DNA
Early Diagnostics
Adaptive
Clinical Trials
Access to
Sequencing
Treating a patient for
a particular
lung cancer

becomes

Treating a patient for
cancer of the PI3K pathway
Hanahan & Weinberg

Hallmarks of Cancer:
The Next Generation

Cell, March 2011
FFPE
FF
Formalin Fixed
Paraffin Embedded
Fresh
Frozen
versus
This could save your life...
from Eric Topol, MD
Cancer
Sequencing
If it's so great,
why doesn't my doctor have it?
sequencing =
easy
interpretation =
hard
Cancer Treatment
Photo: Peter Rigaud, for Stern, 2010
Timothy Ray Brown
HIV diagnosed 1995
AML diagnosed 2006
CCR5Δ32 stem cell transplant / "redneck genetic engineering"
HIV-free since 2009
Blood, March 10, 2011, vol. 117, no. 10, 2791-2799
Photo: Peter Rigaud, for Stern, 2010
&
personal
very personal
Cancer Treatment Reviews, Volume 37, Issue 8, December 2011, Pages 618–632
oncolytic viral therapy
virus infects tissue target
inhibited in normal cells
proliferates in cancer cells
kills cancer cells
attracts immune response
virus seeks new tumor sites
Innovation
Drivers
Funding
Sources
1. Reform regulatory review of tumor biomarker tests
2. Increase reimbursement for tumor biomarker tests that are proven to help determine which therapies will or are working
3. Increase investment for tumor biomarker research so it's comparable to new drug research
4. Increase the rigor for peer review of tumor biomarker publications
5. Include only proven biomarker tests in evidence-based care guidelines
Tumor Biomarkers Undervalued
1 Aug 2013: http://www.sciencedaily.com/releases/2013/08/130801125133.htm
Station X
Cancer
Informatics
General
Informatics
Foundation Medicine
Video for Prospective Patients
Foundation Medicine
Video for Clinicians
Paving the Way for Personalized Medicine:
FDA’s Role in a New Era
of Medical Product Development
Released 1 Nov 2013
FDA Breakthrough Therapy Designation
quicker review for worthy drugs
awards "outside the box" thinking
first approval granted to CLL drug Nov 2013
Cancer pharmacogenomics
Therapeutic cancer vaccines
Cancer sequencing
Cancer companion diagnostics
Adaptive clinical trials
I-SPY 2 Trial
new clinical trial model, begun 2010
genetics, imaging & drugs for breast cancer
tumor biomarkers and personal treatment
adaptive trial design *
20 centers participating, public/private

Crizotinib
cancer: lung (NSCLC)
gene: EML4-ALK fusion
approved: Aug 2011
Vemurafenib
cancer: melanoma
gene: BRAF V600E mutation
approved: June 2011
Dabrafenib
cancer: melanoma
gene: BRAF V600E mutation
approved: May 2013
Trametinib
cancer: melanoma
gene: BRAF V600E/K mutation
approved: May 2013
Targeted
cancer therapies
approved in
last 2 years
ACLU v. Myriad Genetics
Cell Spot Microarrays
siRNA for personal cancer
diagnostics & treatment
Rantala et al. BMC Genomics 2011 12:162 doi:10.1186/1471-2164-12-162
VTT Technical Research Centre of Finland
McCauley
Full transcript