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. Correlation of processing batch with clinical variables: colon cancer
      3. Shen, 2007: attempt to reproduce results
      4. Laird 2006, 2011 markers: attempt to reproduce results
      5. Forcing CIMP clusters and correlation with mutational status
         
         1. Colon cancer: Shen and Laird markers
         2. Colorectal cancer: Shen and Laird markers
   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