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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
  3. Platform
    1. IlluminaHumanMethylation450k.db Bioconductor package
  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
    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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