Athurva Gore/LabNotes/2009-9-9

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Revision as of 23:51, 9 September 2009 by >Ajgore (→‎Exome Resequencing)
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Exome Resequencing

PGP4, 6, and 10

  • Dr. Zhang pointed out that PGP4, 6, and 10 used size-selected libraries
  • Wanted to see if using a 5 bp throwout range works well with these libraries
  • For all three, success!
    • 10% false call rate with PGP10
    • 5% non-dbSNP rate with PGP4 and PGP6
  • Can therefore use a 5bp trimming due to size-selection; as expected.
  • Compute statistics, insert here
  • RESULTS:
    • ADD HERE

IPS and Cancer

LOH Mutations

  • Need to check LOH mutations; is the new variant the damaging one? Or the old one?
    • If nondamaging version is lost, this is not actually harmful to the cell...
    • Modified SIFT input to have fibroblast first, IPS second
    • Can now easily check if damage is gained or lost.
  • ALL DAMAGING MUTATIONS: The non-damaging variant was lost via LOH!
    • True for most (all but 3) tolerated mutations as well
    • Strange. Will need to investigate with Primers...

PCR Primers for target Genes

  • Need to use Primer3 to obtain PCR primers for regions of interest.
    • Have five regions of interest: 2 from GOH, 3 from LOH
    • Get book on DNA methods? Or talk to Alice or Ida about it
    • Pull out sequences of an optimal length around SNP plus flanking regions