Athurva Gore/LabNotes/2009-8-13

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Revision as of 22:36, 13 August 2009 by >Ajgore
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NEW LAB NOTEBOOK NAVIGATION BAR

  • Can now start each page with the following:
{{ AGLabEntry|PREVIOUSDATE|NEXTDATE }}
  • 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 on 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.
  • 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.
  • The COSMIC Gene set (Genes mutated in cancer, but not necessarily causative) was also analyzed
    • 10 genes were found that matched the COSMIC set
    • ZNF608
    • AMELX
    • ERBB4
    • MC3R
    • BUB1
    • USP25
    • NTRK3
    • TRIP4
    • MAP4K3
    • IKBKE