Bladder cancer · Tumor heterogeneity · Clonal evolution · Tumor immune microenvironment cell-free DNA · WGS · Phylogenetics · Transcriptomics. Genomic profiling·
This repository contains code, data, and results associated with the manuscript on the analysis of clonal and genomic heterogeneity in metastatic bladder cancer. We integrate multi-tumors DNA(WGS/WES) sequencing and cell-free DNA to reconstruct subclonal architectures and infer patterns of tumor evolution across primary and metastatic sites.
The evolution and heterogeneity of lethal metastatic bladder cancer subtypes (2025).
Pushpa Itagi*, Samantha L. Schuster*, Sonali Arora, Thomas W. Persse, Michael Yang, Alan Min, Pooja Chandra, Mohamed Adil, Patricia C. Galipeau, Allie S. Kreitman, Yixin Lin, Minjeong Ko, Erolcan Sayar, Robert D. Patton, Lori Kollath, Abby Meis, Nathan Ji, Khursheed Ali, Hrishi Venkatesh, Claire B. Mills Manasvita Vashisth, Cynthia L. Wladyka, Rosa Nadal, Jessica Hawley, Todd Yezefski, Sarah P. Psutka, John L. Gore, Daniel W. Lin, Peter S. Nelson, Heather H. Cheng, Michael T. Schweizer, Lawrence Fong, John K. Lee, Evan Yu, Eva Corey, Colm Morrissey, Petros Grivas, Robert B. Montgomery, Jonathan L. Wright, Michael C. Haffner, Funda Vakar-Lopez1, Omar Y. Mian, Hung-Ming Lam†, Andrew C. Hsieh†, Gavin Ha†
├── data/ # Raw and processed sequencing data includes source data files
├── scripts/ # Analysis and visualization code for all downstream analysis. Each type if analysis has its own folder with a name that describes the analysis.
├── results/ # Output figures and tables. Along with the source data files used to generate figures in main figures.
├── pipelines/ # Used to share pipelines used for the project such as mutation callers and a shell scripts if a custom pipleline was utilized.
├── LICENSE
└── README.md
## Resources
The GRCh38 version used for this project is downloaded from the google bucket gs://genomics-public-data/resources/broad/hg38/v0/