bhklab / breastpdtx

BREAST CANCER PDTX

Bruna, A. et al. (2016). A biobank of breast cancer explants with preserved intra-tumor heterogeneity to screen anticancer compounds. Cell. 167(1):260-274.

Manuscript available here; dataset here.

This is a BHKLAB project focused on creating, standardizing, and automating a computational pipeline for a set of breast cancer patient-derived tumor xenograft (PDTX) models, as well as patient-derived tumor cells (PDTCs). This is the first PDTX/PDTC dataset in the laboratory. Please head over to the Wiki if you would like to follow along the detailed and reproducible workflow.

Each day, a massive amount of data is shared by the cancer research community (as well as the research community as a whole). Important discoveries are published based on these data, and we as scientists have the responsibility of verifying the results.

Thanks to the increased number of data sharing platforms, the storage and retrieval of data have been made simpler than ever before. However, the way in which these data are shared are still not intuitive and straightforward for someone fresh to sort through and do high-level analysis.

Generally, people ask for codes that have generated the published results. However, having the code available is completely different from someone actually working through the code in hopes of reproducing the same results. This is what this project aims to accomplish - a comprehensive step-by-step tutorial/guide for anyone in computational biology and cancer genomics to follow along and validate the findings.

Again, please take a look at the Wiki should you wish to see the pipeline documentation.