throbber
From:
`To:
`Subject:
`Date:
`Attachments:
`
`John West
`Richard Chen; Scott Kirk; Mark Pratt; Christian Haudenschild
`Slide for accuracy requirements walkthrough meeting 3-5pm today
`Tuesday, October 9, 2012 1:58:57 PM
`Accuracy mtg 9Oct2012 JW.pptx
`
`All,
`
`I put together one slide which summarizes my understanding of where we are headed on
`accuracy and how that should tie in to the product specifications we have for upcoming
`versions. Perhaps we can start our 3-5pm meeting by discussing this framework ?
`
`Thanks,
`
`John
`
`Personalis EX2096
`
`

`

`JW Accuracy Overview
`
`CHARACTERIZING ERRORS
`# by type, mechanism, medical application
`
`Methods to identify errors:
` A / B repeatability or vs Gold Std
` MIE (need SV, not just SNP)
` Single genome methods:
` Tri-allelic loci
` Odd allele ratios at het loci
`Low / no coverage (WGS & exomes)
`Coverage variability sample to sample
`Particularly for SV detection in exomes
`
`Define regions linked to mechanisms
`Download from UCSC browser (mostly done)
`Run alignment degeneracy alg on MiSeq :
`Read lengths
`Molecule lengths
`Coverage statistics
`To define low or variable coverage regions
`
`Pareto analysis
`# errors by type, error mechanism
`Focus this by medical application
`
`Re-Do this with modern data
` v3 seq chemistry, gel & PCR-free WGS
`v3 seq chem exomes
` CEPH1463, Venter, Diversity panel
` Data purchased, downloaded, seqc’d
`
`FIXING ERRORS
`
`Bioinformatic approaches:
` Better reference (NEMAR, SV version, hg20)
`Improve SV algorithms (many parts)
`Upstream-only base call around homopolymers
`LobSTR
`Use of array data (Genotyping and SV)
` Better alignment algs (3rd party & ours)
`
`Lab & bioinformatic approaches
` Pullout & integration with regular data
`Exome supplement
`Long read / molecule (SD’s, compressions)
`High GC
`Optimize operation for accuracy vs $
`Novel Assays (Pulsed field, phasing, etc)
`
`Content development
` Data downloaded, purchased, seqc’d in-house
`e.g. for BreakSeq, norms, GT ever seen ?
`MAF for SV/CNV/InDel, ethnic controls
`
`FLAGGING ERRORS
`
`Descriptors, not just Q-Scores:
`Why we think the Q is low
`
`More accurate Q-Scores
` Difficult sell due to competitive noise
`
`PRODUCT SPEC / FEATURE
`
`Reduced error rates
`Focused on medical content
`Quantitative Personalis vs Standard
`By method to ID errors
` by variant type &mechanism:
`SNP
`NEMAR hg20 vs Public hg19
`Coverage filled in
` Homopolymer region caller
`Alignment degen w long reads
` Optimize for accuracy vs $
`STR’s, InDel’s
`SV’s
`Qualitative too:
`e.g. SV zygocity & in exomes
`e.g. STR analyzed at all
`e.g. Reporting tri-allelic loci
`
`More content covered
` Finished genes in exomes
`Medical content outside exons
`Whole genome isn’t:
`Degenerate alignment (e.g. HLA)
`Low coverage
`
`Flags which guide the type of
`validation / follow-up
`
`© Personalis, Inc. All Rights Reserved. COMPANY CONFIDENTIAL.
`
`1
`
`Personalis EX2096
`
`

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