Athurva Gore/LabNotes/2009-8-13: Difference between revisions
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** 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= | =IPS and Cancer= | ||
* Used Dr. Zhang's scripts on lane 1 and lane 3. | * 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. | ** 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. | ** 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) | * 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 | ** Should probably also look at heterozygous->homozygous, as this is possible...but probably want to ignore homozygous->homozygous | ||
Line 40: | Line 41: | ||
** '''NTRK3''' | ** '''NTRK3''' | ||
** These genes have been implicated as being causative. | ** These genes have been implicated as being causative. | ||
* | * Ten genes were also found to be present in the COSMIC set | ||
** '''ZNF608''' | |||
''' | ** '''AMELX''' | ||
** AMELX | ** '''ERBB4''' | ||
** ERBB4 | ** '''MC3R''' | ||
** MC3R | ** '''BUB1''' | ||
** BUB1 | ** '''USP25''' | ||
** USP25 | ** '''NTRK3''' | ||
** NTRK3 | ** '''TRIP4''' | ||
** TRIP4 | ** '''MAP4K3''' | ||
** MAP4K3 | ** '''IKBKE''' | ||
** IKBKE''' | ** These mutations are commonly present in cancer, but are not necessarily causative. |
Latest revision as of 22:38, 13 August 2009
[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.