Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes

Question

[David]

Hello,

I'm working with genomic coordinates derived from differentially accessible regions (DARs) in ATAC-seq data analysis. I aim to investigate whether any mutations within these regions are associated with various cancers. To accomplish this, I believe I need access to a cancer genome database that includes mutation information.

Could anyone recommend databases or resources where I can find mutation datasets for these comparisons? Any guidance on how to proceed with this analysis would be greatly appreciated!

Thank you in advance for your help

Answer 1

[LChart]

Step 1: Go to TCGA in the GDC and open the Cohort Builder

https://portal.gdc.cancer.gov/analysis_page?app=CohortBuilder&tab=general

Step 2: Use the Cohort Builder (simplest: General Diagnosis > Tissue or Organ of Origin) to select a broad cancer type (other fields can make this far narrower)

Step 3: Click on Repository, and under "Data Type" select "Masked Somatic Mutation"

Step 4: Click "Add All to Cart"

Step 5: Download your mutation files