`To:
`Cc:
`Subject:
`Date:
`
`John West
`Scott Kirk
`Richard Chen; Mark Pratt; Christian Haudenschild
`Re: Sprint 2 overview
`Sunday, June 17, 2012 11:48:04 PM
`
`Scott, Mark, Rich, Christian,
`
`For the next sprint I would like to propose three main accuracy goals:
`
`1) Analyze the A/B comparison results (many still being generated) against regions of the
`genome being defined by the BAM crawler, e.g. directional coverage and raw Q-score
`depression, to create a quantitative view of what is causing the approx. 400k discrepancies
`when the same genome (Amy) is sequenced twice (e.g. by Broad). This should lead to a
`recommendation about what to prioritize in trying to reduce the error rate.
`
`2) Identify all the locations in the genome which could lead to raw Q-score and/or coverage
`depression, e.g. homopolymers, di/tri/quad nucleotide repeats, palindromes / hairpins; then
`compare those with the discrepancies found in the A/B studies to further help understand the
`mechanisms underlying the discrepancies.
`
`3) Investigate what the iteration cycle time can be for designing pull out oligo sets, getting
`them made, testing them, analyzing the results. Plan the first iteration of this and if practical,
`send out the first order for a custom pull-out set. With Shujun on board, I hope she can help
`us with this goal in particular.
`
`I would recommend goals for completing the move, in some more detail. Can we have the
`servers moved and operational by the end of this sprint ? Will we have received the MiSeq
`and be operational with it ?
`
`I recommend the next sprint be through Monday July 9th, since the prior week is partial and a
`number of people will be out. Also, I will be back from the UK then, and would like to hear
`about the results of the sprint in person, if possible.
`
`I would be happy to discuss this in more detail, but wanted to get you my overall thoughts in
`time for the Monday meeting.
`
`Thanks,
`
`John
`
`On Fri, Jun 15, 2012 at 3:36 PM, Scott Kirk <scott.kirk@personalis.com> wrote:
`
`Personalis EX2065
`
`
`
`Hi John,
`
`Attached is the overview list for Sprint 2 for you to review. I walked through this with
`Rich already, but looks like 300 didn't work today for the three of us to review.
`
`Let me know if you have any comments.
`
`Thanks,
`Scott
`
`Personalis EX2065
`
`
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