throbber
From:
`To:
`Subject:
`Date:
`Attachments:
`
`Richard Chen
`John West; Carol Tillis; Christian Haudenschild; Eliane Sousa
`Final Board Slides
`Tuesday, July 17, 2012 5:05:11 PM
`board.07.18.12.v6.roc.ppt
`
`Includes change suggested by John. Ready for print.
`
`-Rich
`
`Personalis EX2070
`
`

`

`Research and Development
`
`Personalis, Inc.
`07.18.2012
`
`Richard Chen, CSO
`
`7/18/12
`
`Personalis, Inc. Proprietary and Confidential
`
`1
`
`Personalis EX2070
`
`

`

`R&D Overview
`
`• Hires
`• Product Development
`– Genome Pipeline Service
`– Disease Variant Discovery Service
`– Genome Interpretation Service
`• Content Development
`• Research Collaborations
`• Computing Infrastructure
`
`7/18/12
`
`Personalis, Inc. Proprietary and Confidential
`
`2
`
`Personalis EX2070
`
`

`

`R&D Hiring Update
`
`•
`•
`
`•
`
`Slower hiring ramp than plan, looking for great hires
`New R&D Hires
`• Daniel Newburger (Pipeline R&D, started mid-June)
`•
`Shujun Luo (Accuracy R&D, started mid-June)
`Near Term Open Positions
`•
`Linux systems admin – hired new recruiter, looking for consulting help
`• Test/Build Engineer
`• Applications Engineer
`• BI Pipeline Engineer
`
`Pipeline Mgr
`(Hugo Lam)
`
`BI Pipeline
`Engineer
`(Dan
`Newburger)
`
`BI Pipeline
`Engineer
`
`Build/Test
`Engineer
`
`BI Analyst
`(Gabor
`Bartha)
`
`R&D
`
`BI Apps &
`Research
`Mgr
`(Rong Chen)
`
`Mol Bio/Lab
`(Shujun Luo)
`
`BI App
`Scientist
`(Michael
`Clark)
`
`BI App
`Engineer
`
`Director
`Accuracy
`R&D
`(Mark Pratt)
`
`BI Tools
`(Jason
`Harris)
`
`Original Team
`
`New hires (started)
`
`New hires (not yet started)
`
`Near Term Open Positions
`
`Scientific
`Content &
`Curation
`Mgr
`
`Sr Project
`Mgr
`(Scott Kirk)
`
`Linux
`Systems
`Admin
`
`Genomics
`Counselor
`(G.
`Chandratilla
`ke)
`
`Genomics
`Counselor
`(Sarah
`Garcia)
`
`5 Part Time
`Curation
`Scientists
`
`7/18/12
`
`Personalis, Inc. Proprietary and Confidential
`
`3
`
`Personalis EX2070
`
`

`

`Summary of Resource Allocation
`
`Accuracy R&D
`Mark Pratt
`Gabor Barth
`Jason Harris
`Shujun Luo
`
`Pipeline R&D
`Hugo Lam
`Daniel Newburger
`
`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
`
`7/18/12
`
`Personalis, Inc. Proprietary and Confidential
`
`4
`
`Personalis EX2070
`
`

`

`R&D Roadmap
`
`•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
`
`7/18/12
`
`Personalis, Inc. Proprietary and Confidential
`
`5
`
`Personalis EX2070
`
`

`

`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
`
`Genome
`Interpretation Service
`
`Feasibility Assess
`
`Spec & Resource
`
`Prototype Testing
`w/ Collaborator
`v1 Development
`
`v1 Testing
`
`v1 Launch
`
`Prototype Development
`
`Prototype Testing w/ Collaborator
`
`v1 Dev
`
`Prototype Development
`
`Prototype Testing w/ Collaborator
`
`7/18/12
`
`Personalis, Inc. Proprietary and Confidential
`
`6
`
`Personalis EX2070
`
`

`

`Update: Genome Pipeline Service
`• R&D team focus on development of the prototype Pipeline Service
`• Successful move to new location with minimal impact to R&D
`• Key development milestones
`• HugeSeq pipeline component updates
`• Ethnicity specific genomes used for alignment
`• Variant annotation engine completed
`• Case/control analysis methodology for key use cases developed
`•
`First prototype output reports being generated
`• Remain on track for testing prototype with collaborators in Aug 2012
`• Risks/Challenges
`• Hiring – working aggressively with recruiter for scientific computing and BI hires, further delay in
`hires could affect schedule
`• Computing infrastructure – rackspace contraints relieved with move to new building, looking to
`install scalable storage solutions for R&D, additional computing capacity installed
`Licensing of 3rd party tools and content
`Identifying friendly research collaborators to work with in August
`
`•
`•
`
`7/18/12
`
`Personalis, Inc. Proprietary and Confidential
`
`7
`
`Personalis EX2070
`
`

`

`Update: DVDS and GIS
`
`•
`
`Success of Pipeline and Accuracy efforts are critical for these products
`
`• Resources focused on pipeline development, but working concurrently
`with SAB/Founder working groups on defining and spec’ing components
`of DVDS and GIS
`• Key software modules for DVDS already being developed through SAB consulting arrangement
`• GIS Complex disease report, Mendelian disease report, and PGx specs being developed by
`working groups
`
`Founder/SAB Lead
`Working Group
`Mike, Carlos
`Pipeline
`Mike, Carlos
`Accuracy
`Atul
`GIS: Complex Dz
`Euan/Rick
`GIS: Mendelian Dz
`GIS: Pharmacogenomics Russ
`DVDS
`Euan/Rick
`
`Personalis Lead
`Hugo, Scott
`John, Mark
`Rong/Sarah/Gemma
`Sarah/Gemma
`Rich
`Michael
`
`7/18/12
`
`Personalis, Inc. Proprietary and Confidential
`
`8
`
`Personalis EX2070
`
`

`

`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)
`
`7/18/12
`
`Personalis, Inc. Proprietary and Confidential
`
`9
`
`Personalis EX2070
`
`

`

`VarimedDB Dashboard
`
`7/18/12
`
`Personalis, Inc. Proprietary and Confidential
`
`10
`
`Personalis EX2070
`
`

`

`Scientific Computing Infrastructure
`
`•
`•
`
`Increased our genome processing capability to 240 cores
`Looking to add ~120TB usable storage for R&D
`– Fielded NAS options from NetApp, Hitachi, Isilon, Dell
`– Most competitive offers from Hitachi and NetApp
`• Met with Amazon, Clikr regarding cloud options (referred from MDV)
`•
`Increasing speed of internal network to 10G
`•
`Server backup planning initiated
`• Continuing search for Linus/Unix sys admin
`
`7/18/12
`
`Personalis, Inc. Proprietary and Confidential
`
`11
`
`Personalis EX2070
`
`

`

`Overall R&D Risks and Mitigation
`
`Risk
`• R&D hiring delay of BI engineers and Unix sys admin.
`May impact schedule
`
`• 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
`
`• Product Differentiation
`
`• Identifying high quality collaborators for testing our
`services. Potentially long lead time.
`
`Mitigation
`• New IT recruiters now involved for Unix sys admin
`hire
`• Redoubled efforts on BI hires (new process,
`conferences, networking)
`• Started dev on those items with long lead times to
`develop concurrently with Pipeline (MendelDB, etc)
`• Systematically reviewing and applying for licenses
`for key content and algorithms
`• 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
`• Begin to identify collaborators for each of the
`services to get IRB/ethical legal framework in place
`
`7/18/12
`
`Personalis, Inc. Proprietary and Confidential
`
`12
`
`Personalis EX2070
`
`

`

`Next Steps & Priorities
`
`•
`
`•
`
`•
`
`•
`
`•
`
`•
`
`•
`
`Continuing hiring for open positions
`
`Continue focus on Pipeline Service development with Aug 2012 prototype target
`
`Identify friendly collaborators for testing Pipeline Service Prototype
`
`Continue to define specs and plan around Disease Variant Discovery Service and
`Genome Interpretation Service
`
`Expand computing storage capabilities
`
`Continue to execute on content priorities, develop longer term content strategy
`
`Continue to execute on Accuracy objectives and integration with laboratory
`capabilities
`
`7/18/12
`
`Personalis, Inc. Proprietary and Confidential
`
`13
`
`Personalis EX2070
`
`

This document is available on Docket Alarm but you must sign up to view it.


Or .

Accessing this document will incur an additional charge of $.

After purchase, you can access this document again without charge.

Accept $ Charge
throbber

Still Working On It

This document is taking longer than usual to download. This can happen if we need to contact the court directly to obtain the document and their servers are running slowly.

Give it another minute or two to complete, and then try the refresh button.

throbber

A few More Minutes ... Still Working

It can take up to 5 minutes for us to download a document if the court servers are running slowly.

Thank you for your continued patience.

This document could not be displayed.

We could not find this document within its docket. Please go back to the docket page and check the link. If that does not work, go back to the docket and refresh it to pull the newest information.

Your account does not support viewing this document.

You need a Paid Account to view this document. Click here to change your account type.

Your account does not support viewing this document.

Set your membership status to view this document.

With a Docket Alarm membership, you'll get a whole lot more, including:

  • Up-to-date information for this case.
  • Email alerts whenever there is an update.
  • Full text search for other cases.
  • Get email alerts whenever a new case matches your search.

Become a Member

One Moment Please

The filing “” is large (MB) and is being downloaded.

Please refresh this page in a few minutes to see if the filing has been downloaded. The filing will also be emailed to you when the download completes.

Your document is on its way!

If you do not receive the document in five minutes, contact support at support@docketalarm.com.

Sealed Document

We are unable to display this document, it may be under a court ordered seal.

If you have proper credentials to access the file, you may proceed directly to the court's system using your government issued username and password.


Access Government Site

We are redirecting you
to a mobile optimized page.





Document Unreadable or Corrupt

Refresh this Document
Go to the Docket

We are unable to display this document.

Refresh this Document
Go to the Docket