throbber
From:
`To:
`Cc:
`Subject:
`Date:
`Attachments:
`
`John West
`russ.altman@stanford.edu
`Richard Chen; John West
`Re: USE THIS ONE: my edits/slides v2
`Monday, August 20, 2012 6:26:50 AM
`Personalis El Camino 20Aug2012 Final.ppt
`
`The Final slides are attached.
`I accepted essentially all of Rich's suggestions.
`I am printing out a couple of copies to hand them.
`
`John
`
`On Mon, Aug 20, 2012 at 6:15 AM, Russ B Altman <russ.altman@stanford.edu> wrote:
`Yes, this is a very important point.
`
`Russ
`
`On Aug 20, 2012, at 6:12 AM, John West wrote:
`
`> We should also ask about turn-around-time for these tests needed by El Camino.
`> HiSeq-2000 runs take almost 2 weeks, plus sample prep and analysis time. Also queue
`time if we need to batch up a lot of samples into one HiSeq run.
`> The MiSeq is faster (1-2 days) and much lower capacity, so one run could be a single
`sample or just a few, but it's cost per base is about 6x.
`> The HiSeq-2500 is faster (also 1-2 days) but at >100Gbases / run, would also need a
`number of exome samples to fill it, and Illumina is pricing its consumables higher.
`> This may not be an issue, but by comparison, a real time PCR microfluidic card
`(competitive) solution can be run in a few hours after sample prep.
`
`>>
`
`>>
`
` John West
`
` On Sun, Aug 19, 2012 at 10:28 PM, John West <john.west@personalis.com> wrote:
`> If we can all be there a little early, we could discuss how to split up the process of
`presenting.
`> I'll see you in the morning.
`
`>>
`
`>>>
`
` John
`
`On Sun, Aug 19, 2012 at 10:25 PM, Russ B Altman <russ.altman@stanford.edu> wrote:
`> My only worry is that it is a lot of slides. I am hoping we can go through all those slides
`quickly, so that we can listen to them and their needs. I would limit it to 15 minutes, if
`possible. The stuff of greatest interest to them is really the last 4-5 slides.
`
`>>
`
`>>
`
`>>
`
` I also favor "genome-guided medicine"
`
` I will also try to get there early.
`
` Russ
`
`Personalis EX2082
`
`

`

`>>>
`
`>>
`
`On Aug 19, 2012, at 10:22 PM, John West wrote:
`
` > Thanks Rich,
`> >
`> > This looks fine and I will take a final pass through it in the morning before heading over
`there.
`> >
`> > John
`> >
`> > On Sun, Aug 19, 2012 at 9:23 PM, Richard Chen <richard.chen@personalis.com>
`wrote:
`> > HI John, Russ, my edits, john take or leave as you see fit. This
`> > includes stats from Russ.
`> >
`> > added 3 slides regarding PGx and Rare Pediatric Syndromes
`> >
`> > slide 12: Under work reported in, do we want to mention New York
`> > Times (the Mike Snyder thing which i believe mentioned us), and also
`> > the scientific papers that the company is based on (Lancet, Nature
`> > Biotech, PloS Genetics, etc)
`> >
`> > slide 14: Russ, ok with the stats/numbers? please edit/add to this
`> > slide as you see fit.
`> >
`> > I changed order of slides 12-16 (thought it might work better, but you
`> > can decide if you like it John)
`> >
`> > slide 17: I changed title by taking out "progressive"
`> >
`> > slide 17: changed "Staged development of clinical experience:" to
`> > "Staged development of clinical services:"
`> >
`> > slide 18 changed "broader" to "broad"
`> >
`> > slide 18 last line: "As the database builds, Personalis & El Camino
`> > assess the potential for a broader genome-scale joint diagnostic
`> > business" ... sounds like we're buidling a joint business, is this
`> > what you meant? If not I would suggest changing to "As the database
`> > grows, Personalis & El Camino jointly assess the potential for a
`> > broader genome-scale diagnostic opportunities"
`> >
`> > BTW, "Genomic Medicine" has been used quite a bit recently... I'm
`> > wondering if we should use that instead of "Genome Guided Medicine"?
`> >
`> > putting kids to bed, will revisit slides afterwards.
`> >
`> > Also I plan to leave here around 6:30am tomorrow to avoid potential
`> > traffic... most likely i'll arrive early (~7:30) so we could talk some
`
`Personalis EX2082
`
`

`

`> > in the morning...
`> >
`> > -Rich
`> >
`
`>>>
`
`Personalis EX2082
`
`

`

`Introduction to Personalis
`
`John West, CEO
`Richard Chen MD, CSO
`Russ Altman MD, Founder (Stanford)
`Monday Aug 20, 2012
`
`Personalis Confidential 8/20/2012
`
`1
`
`Personalis EX2082
`
`

`

`Rapidly Decreasing Sequencing Costs Drive
`Exponential Growth in Genomes Sequenced
`
`Personalis EX2082
`
`

`

`The Bottleneck
`
`Interpreting the genome – what does it all mean?
`
`Personalis EX2082
`
`

`

`El Camino Hospital, Leading in Genomics Since 2009
`
`Nov 16, 2009: Sample collection, Illumina whole genome sequencing, family of four.
`
`4
`
`Personalis EX2082
`
`

`

`April 16, 2010
`April 16, 2010
`
`i | | U mM | Nn a
`
`Print Page Close Window
`
`Illumina AnnouncesIts First Full Coverage DNA Sequencing of a Named Family
`SAN DIEGO, Apr 16, 2010 (BUSINESS WIRE) --Illumina, Inc. (NASDAQ:ILMN) today announcedthat it has
`sequenced the DNA of John, Judy, Anne and Paul West, the first publicly named family to have their DNA
`sequenced to full coverage by the company. The service was completed in Illumina’s CLIA certified and
`CAP accredited laboratory utilizing Illumina's Genome Analyzer technology and following the established
`process shownat http://www.everygenome.com/.
`
`“We are excited to work with the Wests to produce our first named family DNA sequence," said Jay
`Flatley, president and CEO ofIllumina. "John West has been a leader in this field for almost 30 years,
`including his tenure as CEO of Solexa prior to that company's acquisition by Illumina in 2007. We're
`delighted to welcome him back as a customer, and appreciate the vote of confidence in selecting Illumina
`to provide his family's sequencing. This represents an important step forward for genetic research as
`sequencing moves from single individuals to full families. More comprehensive information about a family's
`genetic makeup will lead to greater understanding of the human genome and help physicians make better
`healthcare decisions for their patients in the future."
`
`Solexa
`
`Personalis EX2082
`
`“4 Personalis
`
`Personalis EX2082
`
`

`

`May 1, 2010
`
`Groundbreaking publication by Stanford researchers
`Identified novel SNP’s predisposing to sudden cardiac death,
`and others guiding pharmaceutical therapy.
`
`Personalis EX2082
`
`

`

`Lancet annotation:
`Potential advice on hundreds of diseases & drugs.
`
`Personalis EX2082
`
`

`

`Sept 16, 2011
`
`Whole genome sequencing of families &
`technologies to dramatically improve accuracy
`
`Personalis EX2082
`
`

`

`December 18, 2011
`
`The top two DNA sequencing platforms, analyzing the same
`person, differ by > 300,000 SNP’s and at 70% of insertion &
`deletion variants. Accuracy is crucial for clinical interpretation.
`
`Personalis EX2082
`
`

`

`August 25, 2011
`
`Personalis exclusive license to 16 dockets of Stanford IP:
`Databases & methods for human genome interpretation
`
`Personalis EX2082
`
`

`

`Scientific / Medical Founders
`(Stanford University)
`
`Michael Snyder, PhD
`Chair, Department of Genetics
`Director, Center for Genomics and
`Personalized Medicine
`
`Russ Altman, MD, PhD
`Chair, Department of Bioengineering
`Director, Biomedical Informatics Program
`
`Euan Ashley, MRCP, DPhil
`Director, Center for Inherited
`Cardiovascular Disease
`
`Atul Butte, MD, PhD
`Asst Professor of Pediatrics (Systems
`Medicine) and Medicine (Informatics)
`
`2 Dept. Chairs
`3 MD’s
`1st to publish a
`clinical assessment
`based on an
`individual’s genome
`Leaders in genetic
`analysis technology,
`bioinformatics, and
`curation.
`
`Personalis EX2082
`
`

`

`Personalis Corporate
`
`• Headquartered in Menlo Park
`• No seed financing; direct to $20.5M Series-A
`– 3 top Sand Hill Road VC firms: Abingworth, MDV, Lightspeed
`– Stanford 10% participation per licensing agreement
`• First employees Nov 2011
`– Stanford MD CSO
`– 2 Stanford PhD genetic counselors
`– PhD researchers previously in Stanford founder labs
`– CEO & PhD researchers previously at Illumina
`• Top DNA sequencing platform provider
`– On track for 25-30 employees in 2012, 50-60 in 2013
`• Work already reported in:
`– Wall Street Journal & NY Times
`– Technology Review (MIT)
`– Business Week (on-line)
`– Wall Street analyst reports
`
`Personalis EX2082
`
`

`

`Personalis Summary
`
`• Sequencing & serious medical interpretation of human genomes
`• Working with the medical system:
`– Physicians, Genetic Counselors, Regulators
`• Accuracy at the laboratory level :
`– Rigorous assessment of NGS accuracy, then sample prep improvements
`– Using Stanford-developed methodology reduces the number of variants
`detected by approx. 700,000 (>20%)
`• Accuracy in medical interpretation:
`– Exclusive commercial license to Stanford-developed databases
`– Rigorous QC’ed manual curation of the literature (> 10,000 articles so far)
`– Stanford-developed methodology: 1st to combine multiple risk alleles in
`complex disease
`• Focus on a medical perspective:
`– Reports align with established medical specialties & are designed to work
`with hospital organizations
`• State of the art equipment – Lab & computation
`
`Personalis EX2082
`
`

`

`Pharmacogenomics :
`Exclusive Commercial License to PharmGKBTM database
`
`• Personalis’ pharmacogenomics service to clinicians focuses on delivering
`PGx based adverse event, dosing, efficacy reports for over 370 medications
`– These medications span multiple medical fields including cardiology,
`neurology, psychiatry, anesthesia/pain, oncology, rheumatology etc.
`• Personalis PGx analysis is powered by PharmGKB
`– World’s leading pharmacogenomics database, began in 2000 at
`Stanford (Dr. Russ Altman’s lab)
`– NIH funded with over $30M in funding to date, large development effort
`– Personalis has negotiated exclusive commercial license to the database
`content
`– Over 370 medications with pharmacogenomic data for
`increased/decreased adverse events, dosing, efficacy
`
`– Over 60 medications with detailed dose recommendations from CPIC or
`DPWG
`
`Personalis Confidential 8/20/2012
`
`14
`
`Personalis EX2082
`
`

`

`Rare Pediatric Syndromes
`
`• 8 million children a year world wide are born with genetic syndrome
`(prevalence 1-3%)
`• Patients can endure a frustrating series of specific “one-off” genetic tests
`over years often without yielding a diagnosis (“Diagnostic Odyssey”)
`• Personalis provides services to enable exome and/or whole genome
`sequencing for rare variant discovery
`• Physicians will be able to submit blood samples from a single patient or
`trios (patient + 2 parents) for diagnosis
`
`Personalis Confidential 8/20/2012
`
`15
`
`Personalis EX2082
`
`

`

`Rare Pediatric Syndromes
`Personalis is uniquely poised to deliver a superior service to clinicians:
`
`•Service developed in conjunction with MD’s, scientists, and genetic
`counselors that understand the key clinical and technical challenges
`•Best-in-class pipeline for identifying candidate variants from exome and
`whole genome sequencing
`•Best-in-class, highly accurate proprietary database of disease variants
`powering our analysis and interpretation
`– Databases (such as HGMD, OMIM) used by other service providers
`contain significant errors
`•State of the art proprietary algorithms
`– For differentiating de novo mutations from sequencing errors
`– For incorporating phenotype information into searches for novel trait
`associated alleles
`– For identifying true alleles that are IBD
`•Ability to interpret variants in intergenic regions, not just exonic regions
`
`Personalis Confidential 8/20/2012
`
`16
`
`Personalis EX2082
`
`

`

`Building towards
`Genome Guided Medicine
`
`• Solid base in medical genetics research:
`
`– Continue to build publication base & recognition
`– Experience with large number of genomes
`
`• Staged development of clinical services:
`
`– Focused tests to meet immediate medical needs in:
`• Pharmacogenomics
`• Rare Mendelian disorders
`
`– Build towards exome & whole genome
`• Data from early focused tests document the potential for
`broader benefits of the genome
`
`Personalis EX2082
`
`

`

`Proposed timing, financial & other terms
`
`• Pilot phase prior to Personalis CLIA certification, anticipated early
`2013
`• Personalis & El Camino define an expanding menu of focused
`genetic tests, and target test volumes
`• El Camino pays just for the tests ordered
`• At its own cost, Personalis implements the tests through broad
`genetic assays (e.g. exome & even whole genome)
`– Delivers focused results to El Camino promptly
`– Builds a database of broader results
`– Critical adjunct findings communicated to El Camino on an individual
`basis
`– As the database builds, Personalis & El Camino assess the potential for a
`broader genome-scale joint diagnostic business
`
`Personalis EX2082
`
`

`

`Proposed Working Relationship
`
`• El Camino & Personalis work as a team
`– El Camino nominates a lead physician in each area of specialty
`– Personalis provides specialty-specific training on its genome interpretation
`– Team sets joint goals, periodically reviews metrics
`– El Camino provides Personalis with patient medical data as needed for
`regulatory filings
`
`• El Camino has full medical & regulatory leadership & liability
`
`• El Camino physicians & genetic counselors have full responsibility for the
`patient interface, medical records & consents
`
`Personalis Confidential 8/20/2012
`
`19
`
`Personalis EX2082
`
`

`

`Regulatory Issues
`
`• We work through physicians & genetic counselors, not direct to consumer
`• Applied for CLIA approval of our laboratory and will seek CAP accreditation
`• Our services are “high-complexity laboratory developed tests”
`• Our interpretations will be physician consults, each signed by an MD
`• Personalis has discussed its plans informally with FDA staff and been
`encouraged in our efforts to improve and document next-gen DNA
`sequencing accuracy
`• Personalis is participating in a voluntary NIST consortium to develop US
`national standard reference materials for human genome sequencing.
`These may be used for NGS proficiency testing.
`• Seeking a high-level clinical center to partner with:
`– Build success cases and document results for later regulatory base
`– Stanford hospital conflict-of-interest due to founders & investment
`
`Personalis Confidential 8/20/2012
`
`20
`
`Personalis EX2082
`
`

`

`Genome Guided Medicine
`
`Personalis EX2082
`
`

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