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= |
Revision as of 23:51, 9 September 2009
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