Athurva Gore/LabNotes/2009-9-9
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Exome Resequencing
PGP4, 6, and 10
- Wanted to see if using a 5 bp throwout range works well with these libraries
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