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It's my first time posting to this forum but was looking for some help on the data aspects of this project.

My tools of choice would be in python/R .

Goal: I'm looking to create a disease specific profile of just SNPs and SNPs in miRNAs and miRNA target sites.

PART 1: TCGA My first step is using TCGA data which lists a ton of harmful mutations in a LOH .txt format. I'd like to be able to map those mutations to SNPs or genes or miRNAs (whatever entities they belong to). The TCGA datasheet is here. Example data is here. for breast cancer. I guess I can use this miRNA and mRNA data as well.

Questions here:

  1. How to decipher the LOH data to figure out if it's meaningful and where it maps?
  2. Which Tools to use for mapping and what formats for final data ? Fasta ?

miRNA/Targets and SNPs Next up is getting cancer specific miRNAs and mRNAs and mapping SNPs to them? I'm assuming using dbSNP or Sanger miRNA databases to get miRNA/targets and seed sequences.

I'm a bit lost as how to combine all these pieces of information, what formats to use for output (linked to individual pieces) and which tools if any to use to gather all this data using python. This tool is useful tool mirdsnp.

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You can take a look at this tutorial to understand TCGA MAF files. And you can find a list of TCGA MAF files containing mutations mapped to genes and miRNA at https://www.synapse.org/#!Search:syn1710680

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