Athurva Gore/LabNotes/2009-9-9: Difference between revisions

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=Exome Resequencing=
=Exome Resequencing=
==PGP4, 6, and 10==
==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
* 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=
=IPS and Cancer=
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** True for most (all but 3) tolerated mutations as well
** True for most (all but 3) tolerated mutations as well
** Strange.  Will need to investigate with Primers...
** Strange.  Will need to investigate with Primers...
===Foreskin Fibroblast data===
* Recall that foreskin fibroblast clustered alone...and clustered together only when penalty for heterozygous mismatch was removed.
* Could fibroblast have a bunch of extra heterozygous calls for some reason?
** Check some of the LOH SNPs.  What is happening at these positions?
*** Quality issues?
*** One strand capturing well?
*** Maybe still issues near the 3' end?  Had to cut it down to 15 bp, recall...


==PCR Primers for target Genes==
==PCR Primers for target Genes==

Latest revision as of 23:53, 9 September 2009

Navigation[edit]

Exome Resequencing[edit]

PGP4, 6, and 10[edit]

  • 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[edit]

LOH Mutations[edit]

  • 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...

Foreskin Fibroblast data[edit]

  • Recall that foreskin fibroblast clustered alone...and clustered together only when penalty for heterozygous mismatch was removed.
  • Could fibroblast have a bunch of extra heterozygous calls for some reason?
    • Check some of the LOH SNPs. What is happening at these positions?
      • Quality issues?
      • One strand capturing well?
      • Maybe still issues near the 3' end? Had to cut it down to 15 bp, recall...

PCR Primers for target Genes[edit]

  • 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