Colon CIMP

The project began in February 2012

The goal: investigation of CIMP (CpG methylator phenotype) in Colon Cancer using 450k Illumina Human Methylation arrays

Project team: Vitalina Komashko, Justin Guinney, Jonathan Derry

Table of contents:

1. Project proposal
2. Literature
   
   1. MINT markers
   2. Shen, 2007 CIMP CpGs on 450k platform
   3. Laird (2006, 2011) markers
   4. Hinoue 2012: re-analysis
3. Platforms
   
   1. IlluminaHumanMethylation450k.db Bioconductor package
   2. 27k platform: how I removed probes that overlap with SNPs and repetitive regions
4. Clinical information
   
   1. Correlation with technical variables (processing batch/slide): 450k platform
   2. Correlation with the batch with clinical variables in CRC dataset (148 patients): 27k
   3. Correlation of processing batch with clinical variables in colon cancer: 27k
   4. Clinical variables of interest
5. DNA methylation
   
   1. 27k array platform
      
      1. Normalization
      2. Shen, 2007: attempt to reproduce results
      3. Laird 2006, 2011 markers: attempt to reproduce results
      4. Forcing CIMP clusters (using K means) and correlation with mutational status
         
         1. Colon cancer: Shen and Laird markers
         2. Colorectal cancer: Shen and Laird markers
      5. De novo discovery of clusters (based on Hinoue 2012 methodology) in TCGA CRC and correlation with mutational status
   2. 450k array platform
      
      1. Reading raw data files (.idat)
      2. Relationship between various types of batches in the data
      3. Normalization
      4. Shen, 2007: attempt to reproduce the results using TCGA data
6. more