Athurva Gore/LabNotes/2009-9-9
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[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...
- Check some of the LOH SNPs. What is happening at these positions?
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