John West
`Christian Haudenschild
`chaudenschild@personalis.com; Mark Pratt; Carol Tillis; Richard Chen
`Confidential : Personalis laboratory plans
`Monday, April 2, 2012 9:12:57 AM
`
`From:
`To:
`Cc:
`Subject:
`Date:
`
`Hi Christian,
`
`Part of Personalis' plan is to be able to
`accept samples from customers, sequence them, and provide the medical analysis of the genomes.
`The lab analysis may include multiple assays from the same sample, both NGS and other (e.g. Electrophoretic
`fragment analysis, arrays, FISH, etc).
`Our goal is to be accurate, comprehensive and validated.
`To that end, our NGS may include both whole genome and deeper sequencing of some regions selected by pull out.
`Mark Pratt is working on lists of regions we may want to pull out. Some of the pullout may be to sequence with a
`second paired-end insert length (likely quite long).
`
`We are also thinking about how to incorporate RNAseq (Mark Pratt can get you a copy of the recent "Snyderome"
`paper, for some of our thinking on that.
`
`We expect to outsource the whole genome NGS, but might want to do the targeted sequencing ourselves. We have
`budgeted a MiSeq for that, both to be able to look at smaller amounts of sequence and for the longer reads.
`
`As far as arrays go, we are interested in fluorescence intensities, not just genotypes, for validation of structural
`variants. We have been thinking about use of the Illumina 5M and exome arrays. We are also thinking about a
`custom array based on the content in our highly curated databases. Arrays are inexpensive relative to whole genome
`sequencing, so even if we need more than one array type per sample, it could be OK.
`
`For all this, we will need an ability to receive samples and divide them up both for the initial assays but also for
`follow on validation. This means we will need a system to handle, QC, track and store samples. Initially we expect
`these may be DNA or cell lines (e.g. Coriell) but later these to include blood and saliva samples. Initially we may
`outsource a lot and then selectively pull more in house, especially our proprietary assays.
`
`We will need to practice on samples and have been thinking about a few projects for this:
`
`1. Craig Venter's DNA, available through Coriell, as the only single-person whole genome Sanger sequence, for
`genome-wide comparison of NGS vs Sanger.
`
`2. A large family or two, with at least 4 children / family and all four grandparents. This is to use Mendelian
`Inheritance as a check for the results obtained from the individual genomes. We have data from one family quartet
`now, but the data is from late 2009. We would like modern data from individuals who have no relationship with the
`company.
`
`3. Samples with triplet repeat expansions already validated by electrophoresis fragment analysis (e.g. Huntington's
`samples from Coriell). We have ideas for how to sequence these with NGS.
`
`Can you please work with Carol, Mark & Rich, cc'ed here, to develop a plan for this, including facilities, staffing,
`CapEx, IT, potential outsource partner labs, what needs to be CLIA and how we can be CLIA if we outsource,
`HIPPA, etc. There will be many specifics to be worked out and I look forward to discussing this with you more.
`
`Thanks and again, Welcome on board.
`
`John West
`
`Cell (408) 836-5586
`
`Personalis EX2036.1
`
`

`

`john.west@Personalis.com
`
`On Apr 1, 2012, at 1:36 PM, Christian Haudenschild <chaudenschild@sonic.net> wrote:
`
`> Excellent have a nice trip and enjoy the snow.
`> Christian
`
` Sent from my iPhone
`
` On Apr 1, 2012, at 7:48, John West <john.west@personalis.com> wrote:
`
`>>>
`
`>>
`
`>>
`
`> Hi Christian,
`>>
`>> Welcome on Board !
`>>
`>> My son's high school has spring break
`>> this week so we will be away at
`>> Whistler skiing. I will be on email
`>> by iPhone early each morning and
`>> each evening and will be back in the
`>> office Monday next week (April 9th).
`>> I apologize for being away your first
`>> week, but look forward to catching up
`>> next week.
`>>
`>> I will send you a number of emails
`>> with background reading, etc.
`>>
`>> Carol Tillis has been making arrangements for your office, computer, etc, and will have your on-boarding
`papers. FYI we will be moving fairly soon, so we expect
`>> to have better offices shortly.
`>>
`>> I have asked Mark Pratt to look out
`>> for you and to introduce you to some
`>> of what we are doing.
`>>
`>> As you may know, Scott Kirk (also ex-
`>> Illumina Hayward) will also be starting
`>> tomorrow, working for Rich Chen in a
`>> role related to R&D project management.
`>>
`>> You also have a Personalis email
`>> account, which I am cc'ing here.
`>> You should already be able to
`>> access it, but in case not, Carol should
`>> be able to help.
`>>
`>> Again, I apologize for not being there
`>> this week, but I look forward to seeing
`>> you on the 9th.
`>>
`>> John West
`>>
`>> Cell (408) 836-5586
`>> john.west@Personalis.com
`
`Personalis EX2036.2
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`

`

`>>
`>>
`>>
`>>
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`Personalis EX2036.3
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`Personalis EX2036.3
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`