Genomic analysis of decreased DNA repair at TF-binding sites.
The full report can be found here: Creating and Measuring Mutation Profiles Within TFBSs
🏁 This independent research project was started on Jan. 20, 2020, under the guidance of Dr. Raluca Gordân and Harshit Sahay at Duke University.
✅ This project was finished on May 3, 2020.
Somatic mutation data is from ICGC DCC Data Release 28, published by the International Cancer Genome Consortium Data Portal.
I used the following cancer type datasets:
| Cancer Type | Projects |
|---|---|
| BLCA | BLCA-CN (bladder cancer – CN) BLCA-US (bladder urothelial cancer – TCGA, US) |
| BRCA | BRCA-EU (breast ER+ and HER2- cancer – EU/UK) BRCA-FR (breast cancer – FR) BRCA-KR (breast cancer – very young women – KR) BRCA-UK (breast triple negative/lobular cancer – UK) BRCA-US (breast cancer – TCGA, US) |
| COAD | COAD-US (colon adenocarcinoma – TCGA, US) |
| COCA | COCA-CN (colorectal cancer – CN) |
| HNSC | HNSC-US (head and neck squamous cell carcinoma – TCGA, US) |
| LUAD | LUAD-US (lung adenocarcinoma – TCGA, US) |
| LUSC | LUSC-CN (lung cancer – CN) LUSC-KR (lung cancer – KR) LUSC-US (lung squamous cell carcinoma – TCGA, US) |
| MELA | MELA-AU (skin cancer – AU) |
| READ | READ-US (rectum adenocarcinoma – TCGA, US) |
| SKCA | SKCA-BR (skin adenocarcinoma – BR) |
| SKCM | SKCM-US (skin cutaneous melanoma – TCGA, US) |
Active transcription factor-binding site data is that used by the Barcelona Biomedical Genomics Lab in their Sabarinathan et al., 2016 study.
I paired the following active TFBS (DHS) datasets with the following somatic mutation datasets:
| TFBSs | Mutations |
|---|---|
| Proximal BRCA (breast) | BRCA |
| Proximal BLCA (bladder) | BLCA |
| Proximal CRC (colorectal) | COAD, COCA, READ |
| Proximal HNSC (head and neck squamous cell carcinoma) | HNSC |
| Proximal LUAD/LUSC (lung adenocarcinoma, lung squamous cell carcinoma) | LUAD, LUSC |
| Proximal SKCM (melanoma) | MELA, SKCA, SKCM |
| Distal SKCM (melanoma) | MELA, SKCA, SKCM |