`To:
`Subject:
`Date:
`
`Scott Kirk
`John West
`Notes from the runs discussion
`Thursday, October 4, 2012 11:45:54 AM
`
`Notes on experimental plans for sequencing projects:
`
`Where are we on various projects:
`
`Ops:
`
`a. Get technical baseline and get data with modern seq biochem
`
`i. Standard WGS trio
`
`1. Sequencing done – amy good, father and son 2nd read ”passed”
`but not great.
`
`2. Working through issues in analysis.
`
`3. Can look at things like coverage, GC bias, other non-familial
`parameters.
`
`4. Shown we can get good data, but may not every time.
`
`5. Suspecting reagent issues.
`
`6. Do we need additional baseline work? Yes. We’re still working
`out our processes so we’re getting the same thing consistently.
`Amy runs more useful than phiX runs.
`
`7. Can continue with project data and still look at trends in the
`data.
`
`8. Need run tracking metrics consolidated for the runs that have
`been completed. (Rose)
`
`ii. Standard Exome:
`
`1. Running 24 (CEPH family + some others)
`
`2. We have half a run – R2 issues, but R1 looked good.
`
`3. Rerun starts 10/4 - 2x100 run (12 days)
`
`iii. 2nd HiSEQ
`
`Personalis EX2093
`
`
`
`1.
`
`finishing qualifying run.
`
`iv. Storage size – 30TB
`
`1. Can park data on HDs rather than deleting if need be.
`
`v. R&D objective for accuracy –
`
`1. get data with modern sequencing biochem (aka V3)
`
`2. profiling of one sample (AMY). Value is beginning to drop off.
`
`3. additional goal is a cross samples for concordance (across
`diversity panel?)
`
`4. duplicate library preps and pullouts
`
`5. could run with Moyamoya samples? Should have enough for 2
`or 3 attempts on each sample.
`
`6. Mark make a plan for replicates on this.
`
`vi. OPS objective for standardizing processes and getting lab up and running.
`
`b. CLIA validation -
`
`i. Need CLS person on-board before we can do validation
`
`ii. 24 CFTR samples – DNA is in house.
`
`iii. Only 2-3 libraries so far though.
`
`iv. Need clarification on whether we needto be CLIA for VA project. If
`nothing, we plan to pursue CFTR approach. First item to be approved
`on would be standard exome seq for the purpose of diagnosing CFTR.
`
`v. WGS of samples useful later for WG addition to our menu, but not on the
`to do now.
`
`vi. WGS of NIST aliquot – NA12878 for proficiency testing – unclear about
`consents.
`
`vii. CLIA validation in Nov.
`
`Customer projects:
`
`a. Moyamoya 132 exomes project
`
`i. Can be used for Mark’s coverage statistics.
`
`ii. MiSEQ run finished and looks good with test samples (one pool of six).
`On/off target ratios look good.
`
`Personalis EX2093
`
`
`
`iii. 1st Moyamoya run starts today (10/4) – 24 samples.
`
`iv. 2nd library prep under way – start run
`
`v. Thursday next week (10/11), 2nd Moyamoya run can start. -second batch
`of 48.
`
`vi. Would have 72 done in 3 weeks.(10/22)
`
`vii. On 10/22 start 48 more. – need to see if we can pull in library prep.
`
`viii. 10/25 could start final group plus any reruns and some replicates (for
`understanding variability).
`
`b. Moyamoya familial collection – additional samples from Stanford.
`
`i. Not until 132 exome project completed.
`
`c. VA 1M veterans project
`
`R&D projects:
`
`a. Testing pullouts for EXOME+, WGS+, Panels
`
`i. Need to figure out when to slot in experimental plan.
`
`b. Determining accuracy dependence on seq ops parameters
`
`c. Samples with known pathogenic STR variants
`
`Personalis EX2093
`
`
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