From:
`To:
`Subject:
`Date:
`Attachments:
`
`Richard Chen
`John West; Carol Tillis; Christian Haudenschild
`Final board slides
`Wednesday, December 12, 2012 4:52:53 PM
`board.12.14.12.v5.roc.ppt
`
`My final board slides attached
`
`Personalis EX2105
`
`
`To:
`Subject:
`Date:
`Attachments:
`
`Richard Chen
`John West; Carol Tillis; Christian Haudenschild
`Final board slides
`Wednesday, December 12, 2012 4:52:53 PM
`board.12.14.12.v5.roc.ppt
`
`My final board slides attached
`
`Personalis EX2105
`
`
`
`R&D Update
`
`Personalis, Inc.
`12.14.2012
`
`Richard Chen, CSO
`
`© Personalis, Inc. All Rights Reserved. COMPANY CONFIDENTIAL.
`
`12/14/12
`
`1
`
`Personalis EX2105
`
`
`
`R&D Overview
`
`• Product Development
`• Content Development
`• Computing Infrastructure
`• Hiring
`
`© Personalis, Inc. All Rights Reserved. COMPANY CONFIDENTIAL.
`
`12/14/12
`
`2
`
`Personalis EX2105
`
`
`
`Product Roadmap
`
`Clinical Dx Services & Genome
`Interpretation Services
`What are the disease risks?
`Which drugs should be avoided
`or dosed differently?
`
`Disease Variant Discovery Services (DVDS)
`
`What is the causative
`Genetic Variant?
`
`Personalis Genome Services (PGS)
`
`Sample Collection &
`DNA Extraction
`
`TTAGC…
`Whole
`Genome/Exome
`Sequence
`
`Alignment and
`Variant Calling
`
`Genes
`
`Pathways &
`Networks
`Diseases
`
`Drugs
`
`Prototype
`development
`ongoing
`
`Focus on V1 PGS
`development
`
`Clinical Dx
`
`Clinical
`Research
`(IRB)
`
`Discovery
`Research
`
`© Personalis, Inc. All Rights Reserved. COMPANY CONFIDENTIAL.
`
`12/14/12
`
`3
`
`Personalis EX2105
`
`
`
`Personalis Genome Services for Research
`• Currently focused on PGS v1 development
`– ~80 features/enhancements, ~370 tasks, including features required for VA project
`– v1 key differentiating features: Exome+, accuracy, SV detection, analytics leveraging
`proprietary content, unique visualization and enhanced reporting
`– Improving overall system performance optimization
`
`• Biological testing is critical
`– Obtaining both known and unknown disease data sets to test our algorithms
`– Initiating new collaborations with Dr. Aaron Gilter at Stanford for ALS and Dystonia
`• Objective is to test our algorithms and co-author papers if successful
`– Moyamoya 132 cases sequenced, analyzed with pipeline, now being interpreted
`– GOAL: success stories we can talk about with customers, publish on
`
`•
`
`Extending SAB to cover key product areas
`– Prof. Bob Nussbaum UCSF: Recognized world expert in medical genetics, rare pediatric
`syndromes
`
`• PGS v1 service on track to launch at AGBT conference Feb 2013
`– 3 abstracts accepted to AGBT to support the PGS launch
`– Topics focus on key differentiators including accuracy, proprietary content, and “success
`stories” applying our technology
`
`© Personalis, Inc. All Rights Reserved. COMPANY CONFIDENTIAL.
`
`12/14/12
`
`4
`
`Personalis EX2105
`
`
`
`Exome Plus
`Review of Key Goals & Milestones
`
`• Goal is to fix problems with standard exome sequencing
`– Typical exome sequencing misses a lot of exome (GC regions, etc)
`– Lots of biomedically interpretable content missed on standard exomes
`– The Personalis Exome Plus aims to solve these issues by augmenting standard
`exomes with custom pullout data
`• Milestones
`– Designed and Received Enrichment Probes/Kits from Agilent
`– Prelim analysis shows encouraging results
`– Now working on second iteration of Exome Plus
`• Anticipate that this will be launched in 2 phases:
`– Targeting the first release as part of the PGS v1 launch in Feb 2013.
`– More research intensive parts of Exome Plus will be part of a 2nd release in 2013.
`
`© Personalis, Inc. All Rights Reserved. COMPANY CONFIDENTIAL.
`
`12/14/12
`
`5
`
`Personalis EX2105
`
`
`
`Extending PGS to Rare Pediatric Syndromes
`(DVDS)
`
`• Extending PGS capability to address another key research use case:
`Rare Pediatric Syndrome Trios/Large Pedigrees
`• Consists of new analysis modules built on top of the same
`sequencing, alignment, variant calling, and annotation pipeline
`used for PGS
`• Near term goal to test our capabilities on real biological examples,
`and to understand requirements for product
`• Biological testing on known and unknown samples including
`– Dystonia family
`– MoyaMoya family
`– Miller syndrome
`– Initiating discussion with Jon Bernstein from Stanford Med Genetics
`– Others
`
`© Personalis, Inc. All Rights Reserved. COMPANY CONFIDENTIAL.
`
`12/14/12
`
`6
`
`Personalis EX2105
`
`
`
`Summary of High-Level Timelines
`
`Jun
`
`Jul
`
`Aug
`
`Sept
`
`Oct
`
`Nov
`
`Dec
`
`2012
`May
`
`Spec
`
`PGS v1
`Launch
`
`(Original
`May 8,2012
`BOD
`projection)
`
`2013
`Jan
`
`Feb
`
`Mar
`
`Apr
`
`Prototype Development
`
`Personalis Genome
`Services
`
`Feasibility
`
`Disease Variant
`Discovery Service
`
`v1 Development
`
`Exome Plus
`Moyamoya Proj
`
`v1 Testing
`
`Launch
`
`Spec & Resource
`
`Prototype Dev
`Prototype Test
`
`VA Proj
`
`v1 Dev
`
`© Personalis, Inc. All Rights Reserved. COMPANY CONFIDENTIAL.
`
`12/14/12
`
`7
`
`Personalis EX2105
`
`
`
`Personalis Genome Services for Research
`Key customer use cases addressed in PGS v1 Release
`
`Standard Seq & Pipeline
`
`Seq
`
`Lab
`
`Align
`
`Var
`Call
`
`DB
`Anno
`
`CLIA Seq and Pipeline
`
`Seq
`
`Lab
`
`Align
`
`Var
`Call
`
`DB
`Anno
`
`Population Case/Ctrl Studies
`
`Disease Cohort Study
`
`Complex Dz Case/Ctrl Study
`
`Pharma Case/Ctrl Study
`
`Tumor vs Normal Paired Case/Ctrl Studies
`
`Mendelian Dz Case/Ctrl Study
`
`Mendelian Multiple Trios Study
`
`Mendelian Large Pedigree
`Rare Pediatric Syndromes Dx
`(Trio etc)
`
`Diagnostic Panels
`
`PGS v1 Release
`DVDS Prototype Features
`
`Genome Screening & Interpretation Service
`
`© Personalis, Inc. All Rights Reserved. COMPANY CONFIDENTIAL.
`
`12/14/12
`
`Discovery
`Research
`
`Clinical
`Research
`
`Clinical
`Diagnostics
`
`8
`
`Personalis EX2105
`
`
`
`Content: Personalis Genome Library
`
`• Gained access to genomes from large public sequencing projects to
`include as part of our genome “library” including
`– UK10K : 4000 genomes, 6000 exomes, > $16 M investment from Wellcome Trust
`– NHLBI GO Exome Sequencing Project: ~500 exomes: Heart, Lung, Blood Dz
`– 1000 Genomes (exomes)
`– dbGAP data – Kabuki syndrome, Miller syndrome exomes
`– Represents > 2.5 PB of data in total and > $20M in research grants to date
`• Sequencing exomes/whole genomes in-house with latest chemistries
`to also serve as potential controls
`– Centenarians
`– 1000 genomes
`• These genomes enable us to
`– Establish population allele frequencies to enable filtering of disease causing var
`– Provide potential control sets when customers don’t have controls for comparison
`– Establish normal ranges for genomes for quality control purposes
`– Validate our pipeline and algorithms
`
`© Personalis, Inc. All Rights Reserved. COMPANY CONFIDENTIAL.
`
`12/14/12
`
`9
`
`Personalis EX2105
`
`
`
`Content: MendelDB
`Curation
`
`QC Stats
`
`# phenotypes
`
`phenotypes remaining for QC
`
`# genes (blue) # variants (red)
`
`productivity (phenotypes/hour)
`
`•
`
`•
`
`•
`
`•
`
`High quality curated DB of
`Mendelian phenotypes and
`their variants
`– Managed by Sarah Garcia
`and Gemma
`Chandratillake, both
`Genetics Ph.D. & Genetic
`Counselors
`
`Critical content to support
`Disease Variant Discovery
`Service and Genome
`Interpretation Service
`
`Finished (~560) GeneReviews >
`600 common Mendelian
`disease phenotypes
`
`Now finishing QC of that data
`
`• Will then continue phenotype
`curation and variant curation
`from other sources
`
`•
`
`Flexible workforce for other
`curation tasks in the future
`
`productivity (rows/hr)
`
`# errors/entry
`
`© Personalis, Inc. All Rights Reserved. COMPANY CONFIDENTIAL.
`
`12/14/12
`
`10
`
`Personalis EX2105
`
`
`
`261,861 variants
`
`Content: VarimedDB
`
`300,000
`
`250,000
`
`200,000
`
`150,000
`
`100,000
`
`50,000
`
`0
`
`Numbre of distinct variants
`
`723,195 relationships
`
`11/27/2012
`10/27/2012
`9/27/2012
`8/27/2012
`7/27/2012
`6/27/2012
`5/27/2012
`4/27/2012
`3/27/2012
`2/27/2012
`1/27/2012
`12/27/2011
`11/27/2011
`10/27/2011
`9/27/2011
`8/27/2011
`7/27/2011
`6/27/2011
`5/27/2011
`4/27/2011
`3/27/2011
`2/27/2011
`1/27/2011
`12/27/2010
`11/27/2010
`10/27/2010
`9/27/2010
`8/27/2010
`7/27/2010
`6/27/2010
`5/27/2010
`4/27/2010
`3/27/2010
`2/27/2010
`1/27/2010
`
`11/27/2012
`10/27/2012
`9/27/2012
`8/27/2012
`7/27/2012
`6/27/2012
`5/27/2012
`4/27/2012
`3/27/2012
`2/27/2012
`1/27/2012
`12/27/2011
`11/27/2011
`10/27/2011
`9/27/2011
`8/27/2011
`7/27/2011
`6/27/2011
`5/27/2011
`4/27/2011
`3/27/2011
`2/27/2011
`1/27/2011
`12/27/2010
`11/27/2010
`10/27/2010
`9/27/2010
`8/27/2010
`7/27/2010
`6/27/2010
`5/27/2010
`4/27/2010
`3/27/2010
`2/27/2010
`1/27/2010
`
`Date
`
`5,510 phenotypes
`
`Date
`
`13,919 papers
`
`11/27/2012
`9/27/2012
`
`7/27/2012
`5/27/2012
`3/27/2012
`1/27/2012
`11/27/2011
`9/27/2011
`
`7/27/2011
`5/27/2011
`3/27/2011
`1/27/2011
`11/27/2010
`9/27/2010
`
`7/27/2010
`5/27/2010
`3/27/2010
`1/27/2010
`
`Date
`
`14,500
`
`12,500
`
`10,500
`
`8,500
`
`6,500
`
`4,500
`
`2,500
`
`Numbre of papers
`
`800,000
`
`700,000
`
`600,000
`
`500,000
`
`400,000
`
`300,000
`
`200,000
`
`100,000
`
`0
`
`Number of rows
`
`6,000
`
`5,000
`
`4,000
`
`3,000
`
`2,000
`
`1,000
`
`0
`
`Numbre of phenotypes
`
`11/27/2012
`10/27/2012
`9/27/2012
`8/27/2012
`7/27/2012
`6/27/2012
`5/27/2012
`4/27/2012
`3/27/2012
`2/27/2012
`1/27/2012
`12/27/2011
`11/27/2011
`10/27/2011
`9/27/2011
`8/27/2011
`7/27/2011
`6/27/2011
`5/27/2011
`4/27/2011
`3/27/2011
`2/27/2011
`1/27/2011
`12/27/2010
`11/27/2010
`10/27/2010
`9/27/2010
`8/27/2010
`7/27/2010
`6/27/2010
`5/27/2010
`4/27/2010
`3/27/2010
`2/27/2010
`1/27/2010
`
`Date
`
`© Personalis, Inc. All Rights Reserved. COMPANY CONFIDENTIAL.
`
`12/14/12
`
`11
`
`Personalis EX2105
`
`
`
`Scientific Computing Infrastructure
`
`• Milestones
`– Installed another 107TB of Hitachi HNAS Storage
`– New backup system currently being installed including disk to disk backup and
`disk to tape archiving
`– Currently evaluating cost/benefit of cloud implementation with CLIQR
`
`• Hiring is a key challenge:
`– Director of High Performance Computing and Architecture
`– Linux Systems Admin
`
`• Doing a reassessment of scientific computing needs (storage, CPUs)
`for next 12 months because of recent (good) developments:
`– Ops: VA project (processing >300 genomes every 2 months)
`– Ops: Moyamoya and customer projects
`– R&D: Access to very large public genome/exome databases R&D: General R&D
`needs
`
`© Personalis, Inc. All Rights Reserved. COMPANY CONFIDENTIAL.
`
`12/14/12
`
`12
`
`Personalis EX2105
`
`
`
`Hiring Update
`
`• Open Positions
`•
`Director of High Performance Computing and Architecture
`•
`Linux systems admin
`
`Pipeline Mgr
`(Lam)
`
`BI Pipeline
`Engineer
`(Newburge)
`
`BI Pipeline
`Engineer
`(Wang)
`
`Test/Build
`Engineer
`(Ming Li)
`
`BI Analyst
`(Bartha)
`
`R&D (Chen)
`
`Director
`Accuracy
`R&D
`(Pratt)
`
`BI Tools
`(Harris)
`
`Mol Bio/Lab
`(Luo)
`
`BI App
`Scientist
`(Clark)
`
`Original Team
`
`New hires (started)
`
`BI Apps &
`Research
`Mgr
`(Chen)
`
`BI App
`Engineer
`(Patwardhan
`)
`
`Scientific
`Content &
`Curation
`Mgr
`
`Sr Project
`Mgr
`(Kirk)
`
`BI Scientist
`(Chervitz)
`
`Genomics
`Counselor
`(Chandratilla
`ke)
`
`Genomics
`Counselor
`(Garcia)
`
`5 Part Time
`Curation
`Scientists
`
`9/5/12
`© Personalis, Inc. All Rights Reserved. COMPANY CONFIDENTIAL.
`
`12/14/12
`
`13
`
`Personalis EX2105
`
`
`
`ASHG Takeaways
`
`• Huge shift in past year to NGS as the primary discovery research
`platform in medical genetics community (previously genotyping)
`
`•
`
`Increased awareness that having accuracy standards for NGS is
`critical
`– NIST/FDA (Genome in a Bottle Consortium), CDC, NCBI, CAP
`
`• Also, a large interest in using NGS for clinical
`– Taking place in CLIA certified labs
`– Rare pediatric syndromes most common use case
`– Increasing interest in using NGS to replace current gene panels.
`
`© Personalis, Inc. All Rights Reserved. COMPANY CONFIDENTIAL.
`
`12/14/12
`
`14
`
`Personalis EX2105
`
`
`
`Risks and Mitigation
`
`Risk
`• Aggressive timeline
`
`• Pipeline performance risk
`
`• Product Differentiation
`
`• Exome plus costs, may limit margins on product
`• Hiring of Unix sys admin and director of high
`performance computing.
`• Long lead time content curation and content
`quality items for GIS and DVDS
`• Licensing of applications and content for analysis
`
`• Ethical use of Genomes for R&D
`
`Mitigation
`• Minimized “research” features that could result in product
`delay, focused on achievable, differentiated features for v1
`• Able to reduce run time per genome from 2 days down to 17
`hrs by stacking runs
`• Assess how we can address with more hardware, cloud
`
`• Prioritized differentiation in three key product areas: Exome+ ,
`SV’s, accuracy/quality, content, visualization
`• Giving conference talks at AGBT to discuss differentiation, 3
`abstracts accepted
`• Actively working on cost model and ways to reduce cost
`• Redoubled efforts with in-house recruiter to identify more
`leads
`• Started dev on those items with long lead times to develop
`concurrently with Pipeline (MendelDB, etc)
`• Have systematically reviewing and applied for licenses for key
`content and algorithms
`• Ethics board approval for all Genomes used for R&D
`• Part of orientation training
`
`© Personalis, Inc. All Rights Reserved. COMPANY CONFIDENTIAL.
`
`12/14/12
`
`15
`
`Personalis EX2105
`
`
`
`Next Steps & Priorities
`
`•
`
`•
`
`•
`
`•
`
`•
`
`•
`
`•
`
`Continue development on PGS v1 priorities with goal of Feb 2013 launch at AGBT
`
`Execute on product features required for VA project, enable success
`
`Run biological test cases with the goal of creating success stories for publication,
`discussion with customers
`
`Continue implementing DVDS prototype and early test cases/collaborations
`
`Continue Hiring for open scientific computing positions
`
`Continue to execute on content priorities, develop longer term content strategy
`
`Continue to work with OPS team to deliver successes with early customers and
`collaborators
`
`© Personalis, Inc. All Rights Reserved. COMPANY CONFIDENTIAL.
`
`12/14/12
`
`16
`
`Personalis EX2105
`
`
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