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Welcome to the BBCAR project wiki! Here, I document the most up-to-date workflow of the project.

Project goals

• Characterization of genomic aberrations that distinguishes individuals by risk for breast cancer.
• Development of risk stratification multi-view ML model.

Data description

Sequencing reads files

• Sequencing data location:
  • BBD tissue: /projects/b1122/saya/raw/bbb_tissue/
  • Germline: /projects/b1122/saya/raw/germline/
• Originally taken from:
  • Tumor tissue: /projects/b1122/Zexian/Alignment/BBCAR/RAW_data/
  • Germline: /projects/b1122/Zexian/Alignment/Germline_37/RAW_data/

Clinical data files

• Clinical data location: /projects/b1131/saya/bbcar/data/clinical/
• Originally taken from:
  • Gannon shared local file with me: /Users/sayadennis/Projects/bbcar_project/GATK_Analysis_Sample_Status.xlsx
  • Files with names starting with BBCaRDatabaseNU09B2-* are downloaded from the BBCAR REDCap database. NOTE: the outcome labels of REDCap is apparently not always correct!!! Gannon and Natalie double-checked the outcomes for each patient and correctly labeled with bbcar_label_studyid_from_gatk_filenames.csv.

Sequencing metadata files

• A subset of samples were sequenced at University of Chicago, and the rest were sequenced at Indiana.
  • Which samples were sequenced at Indiana?
    • Sample IDs can be found at /projects/b1131/saya/bbcar/data/sample_ids_uchicago.txt
  • What's the difference?
    • U Chicago samples: Uses Exome intervals /projects/b1122/gannon/bbcar/RAW_data/int_lst/SureSelect_v5/
    • Indiana samples: Uses Exome intervals /projects/b1122/gannon/bbcar/RAW_data/int_lst/SureSelect_v6/

Workflow

1. Process data
   • Process mutations
   • Process copy number variations
   • Process clinical
2. Create data summary
3. Statistical characterization of features
4. Predict breast cancer risk