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{{ AGLabEntry|2009-9-8|2009-9-10 }} =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... ===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== * 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
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