Athurva Gore/LabNotes/2009-8-13: Difference between revisions

From ZhangLabWiki
Jump to navigation Jump to search
>Ajgore
(New page: =Probe Generation= * '''DONE''' ** KKESH72 ** CpG-SNP set (with 80 bp gap) * '''CURRENTLY RUNNING:''' ** FlyDup901 ** FlyDup936 ** RPLCACRD ** FlyDup5279 * '''TO RERUN:''' ** LeeCancer (on...)
 
>Ajgore
 
(7 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{ 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=
=Probe Generation=
* '''DONE'''
* '''DONE'''
Line 8: Line 13:
** RPLCACRD
** RPLCACRD
** FlyDup5279
** 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:'''
* '''TO RERUN:'''
** LeeCancer (on opposite strand to target cDNA)
** LeeCancer (on opposite strand to target cDNA)
Line 13: Line 21:
** ZhangSNP (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?)
** 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.

Latest revision as of 22:38, 13 August 2009

Navigation[edit]

NEW LAB NOTEBOOK NAVIGATION BAR[edit]

  • Can now start each page with the following:
{{ AGLabEntry|PREVIOUSDATE|NEXTDATE }}
  • Where date format is YYYY-M-DD

Probe Generation[edit]

  • 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[edit]

  • 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.