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{{ AGLabEntry|2009-8-12|2009-8-14 }} =NEW LAB NOTEBOOK NAVIGATION BAR= * Can now start each page with the following: :<nowiki>{{ AGLabEntry|PREVIOUSDATE|NEXTDATE }}</nowiki> * Where date format is YYYY-M-DD =Probe Generation= * '''DONE''' ** KKESH72 ** CpG-SNP set (with 80 bp gap) * '''CURRENTLY RUNNING:''' ** FlyDup901 ** FlyDup936 ** RPLCACRD ** FlyDup5279 ** A-to-I Probes for Erez and Billy; currently generating list of sites near splice junctions *** Can then generate list of nearby exons and probes *** Then run through scripts as before * '''TO RERUN:''' ** LeeCancer (on opposite strand to target cDNA) ** LeeXGenes (on opposite strand to target cDNA) ** ZhangSNP (on opposite strand to target cDNA) ** TDMR Set (Also check if out-of-memory happens again...maybe run on Miner?) =IPS and Cancer= * Used Dr. Zhang's scripts (see yesterday) on 090805_HL003 lane 1 and lane 3. ** Both lane 1 and lane 3 do not use size-selection, making them better comparisons. ** This would imply that lane 2 is missing alleles...not sure why this might happen. ** Should find discrepancies between the two sequences. * Took alleles present in Lane 1 in locations with differences; this allows analysis of homozygous->heterozygous SNPs (as this is what would be expected) ** Should probably also look at heterozygous->homozygous, as this is possible...but probably want to ignore homozygous->homozygous ** Data file is in genome-miner:/home/ajgore/ExomeReads/s1_vs_s3_variants.txt * Ran data through SIFT ** SIFT found: Number of coding variants: 226 Coding variants predicted: 53% (122) Tolerated: 47% (58) Damaging: 53% (64) Nonsynonymous: 56% (127) Synonymous: 44% (99) Novel: 181% (222) * After looking at the genes, ONE GENE was found to be present in the Sanger Cancer Gene Census gene set ** '''NTRK3''' ** These genes have been implicated as being causative. * Ten genes were also found to be present in the COSMIC set ** '''ZNF608''' ** '''AMELX''' ** '''ERBB4''' ** '''MC3R''' ** '''BUB1''' ** '''USP25''' ** '''NTRK3''' ** '''TRIP4''' ** '''MAP4K3''' ** '''IKBKE''' ** These mutations are commonly present in cancer, but are not necessarily causative.
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