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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)
    2. Clinical variables of interest
  5. DNA methylation
    1. 27k array platform
      1. Normalization
      2. Correlation of processing batch with clinical variables
      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


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