From:
`To:
`Subject:
`Date:
`Attachments:
`
`Richard Chen
`John West; Carol Tillis
`updated board slides
`Monday, June 11, 2012 4:03:47 PM
`board.06.05.12.v3.roc.ppt
`
`Latest version
`
`Personalis EX2062
`
`
`To:
`Subject:
`Date:
`Attachments:
`
`Richard Chen
`John West; Carol Tillis
`updated board slides
`Monday, June 11, 2012 4:03:47 PM
`board.06.05.12.v3.roc.ppt
`
`Latest version
`
`Personalis EX2062
`
`
`
`Research and Development
`
`Personalis, Inc.
`06.05.2012
`
`Richard Chen, CSO
`
`2/7/12
`
`Personalis, Inc. Proprietary and Confidential
`
`1
`
`Personalis EX2062
`
`
`
`R&D Overview
`
`• Hires
`• Product Development
`– Genome Pipeline Service
`– Disease Variant Discovery Service
`– Genome Interpretation Service
`• Content Development
`• Research Collaborations
`• Computing Infrastructure
`
`2/7/12
`
`Personalis, Inc. Proprietary and Confidential
`
`2
`
`Personalis EX2062
`
`
`
`R&D Hiring Update
`
`•
`
`•
`
`New R&D Hires
`•
`Jason Harris (Accuracy R&D, started late May)
`• Daniel Newburger (Pipeline R&D, starting mid-June)
`
`Near Term Open Positions
`• Scientific Computing Mgr – increased computing needs, size of R&D team making this more critical
`• Test/Build Engineer
`• Applications Engineer
`
`Pipeline Mgr
`(Hugo Lam)
`
`Director
`Accuracy R&D
`(Mark Pratt)
`
`R&D
`
`Bioinformatics
`Applications &
`Research Mgr
`(Rong Chen)
`
`BI Pipeline
`Engineer
`(Dan
`Newburger)
`
`Build/Test
`Engineer
`
`BI Analyst
`(Gabor Bartha)
`
`BI Tools
`(Jason Harris)
`
`BI Applications
`Scientist
`(Michael Clark)
`
`BI Applications
`Engineer
`
`Scientific
`Content &
`Curation Mgr
`
`Sr Project Mgr
`(Scott Kirk)
`
`Scientific
`Computing
`Mgr
`
`Genomics
`Counselor
`(G.
`Chandratillake
`)
`
`Genomics
`Counselor
`(Sarah Garcia)
`
`5 Part Time
`Curation
`Scientists
`
`Original Team
`
`New hires (started)
`
`New hires (not yet started)
`
`Near Term Open Positions
`
`3
`
`Personalis EX2062
`
`
`
`Product Dev: Summary of Resource
`Allocation
`Pipeline R&D
`Hugo Lam
`Daniel Newburger (Start 7/15)
`
`Accuracy R&D
`Mark Pratt
`Gabor Barth
`Jason Harris
`
`Apps R&D
`Rong Chen
`Michael Clark
`
`Content R&D
`Sarah Garcia
`Gemma Chandratillake
`PT Curators
`
`Pipeline Service
`
`Disease Variant
`Discovery
`Service
`Genome
`Interpretation
`Service
`
`Research
`Collaborations
`Ethics Board
`
`2/7/12
`
`Personalis, Inc. Proprietary and Confidential
`
`4
`
`Personalis EX2062
`
`
`
`Founder/SAB Working Groups
`
`•
`
`Formed small dev teams engaging with a specific founder/SAB member on
`an key part of our product roadmap
`•
`Small group weekly meetings (2-4 hrs)
`• All groups convene every 4-5 weeks for review and updates
`
`Working Group
`
`Founder/SAB Lead
`
`Personalis Lead
`
`Mike, Carlos
`Pipeline
`Mike, Carlos
`Accuracy
`Atul
`GIS: Complex Dz
`Euan/Rick
`GIS: Mendelian Dz
`GIS: Pharmacogenomics Russ
`DVDS
`Euan/Rick
`
`Hugo, Scott
`John, Mark
`Rong/Sarah/Gemma
`Sarah/Gemma
`Rich
`Michael
`
`2/7/12
`
`Personalis, Inc. Proprietary and Confidential
`
`5
`
`Personalis EX2062
`
`
`
`R&D Update
`
`•Moving forward on
`all three services.
`
`•Current dev focus
`is on Genome
`Pipeline Service.
`
`•Specing out and
`planning for DVDS
`and GIS.
`
`•As resources
`allow, starting dev
`on long lead items
`for DVDS and GIS
`
`Genome Interpretation Service (GIS)
`
`What are the disease risks?
`Which drugs should be avoided
`or dosed differently?
`
`Disease Variant Discovery Service (DVDS)
`
`What is the causative
`Genetic Variant?
`
`Genome Pipeline Service (PS)
`
`Sample Collection &
`DNA Extraction
`
`TTAGC…
`Whole
`Genome/Exome
`Sequence
`
`Alignment and
`Variant Calling
`
`Genes
`
`Pathways &
`Networks
`Diseases
`
`Drugs
`
`Clinical
`Research
`(IRB)
`Growing clinical
`opportunity
`
`Discovery
`Research
`
`2/7/12
`
`Personalis, Inc. Proprietary and Confidential
`
`6
`
`Personalis EX2062
`
`
`
`Product Dev: Summary of Estimated
`Timelines
`
`Mar
`
`Apr
`
`May
`
`Jun
`
`Jul
`
`Aug
`
`Sept
`
`Oct
`
`Nov
`
`Dec
`
`Jan
`
`Feb
`
`Genome Pipeline
`Service
`
`Spec & Resource
`
`Prototype Development
`
`Disease Variant
`Discovery Service
`
`Feasibility Assess
`
`Spec & Resource
`
`Prototype Testing w/ Collaborator
`
`v1 Development
`
`v1 Testing
`
`v1 Launch
`
`Prototype Development
`
`Prototype Testing w/ Collaborator
`
`Genome
`Interpretation Service
`
`Feasibility Assess
`
`Spec & Resource
`
`Prototype Development
`
`Prototype Testing w/ Collaborator
`
`2/7/12
`
`Personalis, Inc. Proprietary and Confidential
`
`7
`
`Personalis EX2062
`
`
`
`Update: Genome Pipeline Service
`• Team focused on development of the prototype Pipeline Service
`• On track for testing prototype with “friendly” collaborators in
`Aug 2012
`• Agile development/Scrum (2-3 week cycles) Dev Process
`• Development environment in place:
`•
`JIRA (for project management, collaboration)
`• GIT (version control system)
`• Confluence (JIRA plug-in for internal WIKI)
`• Key Risks/Challenges
`• Product differentiation through accuracy and content – actively managing and iterating on
`features/product design to maximize differentiation/value
`• Hiring – working aggressively with recruiter for scientific computing and BI hires, delay in hires
`could affect schedule
`• Computing infrastructure - currently contrained by rackspace at Regus, with move, now working to
`address computing CPUs, storage, network speed needs
`• Move to new office –move plan minimizes disruption, should impact the schedule < 3-5 days
`•
`Licensing of 3rd party tools and content
`•
`Identifying friendly research collaborators to work with in August – need time to put IRB and
`collaboration agreements in place
`
`2/7/12
`
`Personalis, Inc. Proprietary and Confidential
`
`8
`
`Personalis EX2062
`
`
`
`Update: DVDS and GIS
`
`•
`
`Success of Pipeline and Accuracy efforts are critical for these products
`
`• Resources focused on pipeline development, but working concurrently on
`defining and spec’ing the DVDS and GIS
`
`• Completed first draft of functional spec and sample report for DVDS, now
`in project planning and resourcing phase
`
`2/7/12
`
`Personalis, Inc. Proprietary and Confidential
`
`9
`
`Personalis EX2062
`
`
`
`MendelDB Dashboard
`
`•
`
`•
`
`•
`
`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
`
`On track to finish all (~560) GeneReviews by Aug
`2012, corresponding to >200 common
`Mendelian disease phenotypes
`
`• Will then continue phenotype curation and
`variant curation from other sources
`
`•
`
`Flexible workforce for other curation tasks in the
`future
`
`# phenotypes
`
`# genes (blue)
`# variants (red)
`
`productivity
`(rows/hr)
`
`Raw error rate
`(# errors/row)
`(prior to QC)
`
`2/7/12
`
`Personalis, Inc. Proprietary and Confidential
`
`10
`
`Personalis EX2062
`
`
`
`VarimedDB Dashboard
`
`2/7/12
`
`Personalis, Inc. Proprietary and Confidential
`
`11
`
`Personalis EX2062
`
`
`
`Supercentenarian Collaboration
`
`• Completed IRB and Stanford Collaboration Agreement with Dr. Stuart Kim
`and Stanford
`• Moving forward with research collaboration
`• Goal: To uncover genetic factors that permit extreme longevity
`• Do supercentenarians have fewer overall risk alleles for common diseases that help them avoid
`disease?
`• Do supercentenarians have protective alleles that allow them to avoid aging/disease?
`• Do supercentenarians have CNVs that provide protection against or promote aging/disease?
`• Details:
`• >=110 yrs old, 71 such people in the world, most female
`• ~17 supercentenarians (>=110 years old) have been sequenced (CG)
`• Analyzing variants using our content/algorithms
`• Benefits:
`• Potentially high profile, impact publication
`• Will showcase the power of our content from Varimed
`• Research experience with genomes from extremely healthy, long lived people
`• Test case for our Pipeline product
`
`2/7/12
`
`Personalis, Inc. Proprietary and Confidential
`
`12
`
`Personalis EX2062
`
`
`
`Scientific Computing Infrastructure
`
`•
`
`Increased needs from:
`– Accuracy and R&D effort
`• processing and reprocessing of numerous genomes has increased computing requirements
`substantially
`
`• Additional New hardware geared at:
`•
`Increasing our genome processing capability
`– Dell R910 servers x 4 (for total of 6)
`– Dell R710 servers x 5
`Increasing our overall storage to enable development work, download of numerous genomes
`for development and testing work requires more storage
`– NAS (100 to 150TB of storage needed)
`Increasing speed of network
`– 10G switches
`
`•
`
`•
`
`• Other items
`•
`Server backup planning
`• Move to new location
`
`2/7/12
`
`Personalis, Inc. Proprietary and Confidential
`
`13
`
`Personalis EX2062
`
`
`
`Overall R&D Risks and Mitigation
`
`Risk
`
`Mitigation
`
`• Hiring great people takes time. If not hired on schedule, may
`impact schedule
`• Numerous development tasks are still research in nature
`making timeline more difficult to estimate
`
`• Long lead time content curation and content quality items for
`GIS and DVDS
`• Product dev process
`
`• Licensing of applications and content for analysis
`• Ethical use of Genomes for R&D
`
`• Product Differentiation
`
`• Scalability of products and services
`
`• Recruiters now involved, behind on scientific computing
`• Web site careers posting
`• Continue rapid prototyping to resolve, get visibility on some
`key technical risks to plan appropriately, especially with
`Accuracy effort, GIS product and report generation
`• Started on those items with long lead times to develop
`concurrently with Pipeline (MendelDB, etc)
`• Basic Project Mgmt infrastructure deployed including JIRA,
`GIT, JIRA, etc to enhance efficiency
`
`• Systematically reviewing and applying for licenses.
`• Ethics board approval for all Genomes used for R&D
`• Part of orientation training
`• Continuing to push differentiation in three key areas:
`Accuracy/Quality, Content, Features
`• Prioritize resources towards demonstrating value with our
`services, then scaling once that is demonstrated
`
`• Identifying high quality collaborators for testing our services.
`Potentially long lead time.
`
`• Begin to identify collaborators for each of the services to get
`IRB ethical legal framework in place
`
`2/7/12
`
`Personalis, Inc. Proprietary and Confidential
`
`14
`
`Personalis EX2062
`
`
`
`Next Steps & Priorities
`
`• Continuing hiring for open positions
`
`• Continue focus on Pipeline Service development with Aug 2012 prototype
`target
`
`• Begin to identify friendly collaborators for testing Pipeline Service Prototype
`
`•
`
`Further refine specs and project plan around Disease Variant Discovery
`Service and Genome Interpretation Service
`
`• Continue to execute on content priorities, develop longer term content
`strategy
`
`• Continue to execute on Accuracy objectives and integration with laboratory
`capabilities
`
`2/7/12
`
`Personalis, Inc. Proprietary and Confidential
`
`15
`
`Personalis EX2062
`
`
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