Short Tandem Repeat (STR) Profiler

Short tandem repeat (STR) profiling is commonly performed for authentication of biomedical models of human origin. Members of PDXNet assisted in the development of STRprofiler, a Python package, command line tool, and Shiny application, which provides methods for STR profile comparison and cross-contamination detection. STRprofiler is pre-populated with a database containing STR profiles from The Jackson Laboratory PDX Program and the NCI's Patient-Derived Model Repository. The tool can also be run with custom databases or used to query against the Cellosaurus cell line database.

Access the STRprofiler Shiny application here: https://pdxnet.shinyapps.io/strprofiler/

See the associated publication for more details: Jared M Andrews, Michael W Lloyd, Steven B Neuhauser, Margaret Bundy, Emily L Jocoy, Susan D Airhart, Carol J Bult, Yvonne A Evrard, Jeffrey H Chuang, Suzanne Baker, STRprofiler: efficient comparisons of short tandem repeat profiles for biomedical model authentication, Bioinformatics, Volume 40, Issue 12, December 2024, btae713, https://doi.org/10.1093/bioinformatics/btae713

STRprofiler Landing Page

Funding is provided by the NIH to the PDXNet Data Commons and Coordination Center (NCI U24-CA224067), and to the PDX Development and Trial Centers (NCI U54-CA224076, NCI U54-CA224083, NCI U54-CA224070, NCI U54-CA283759, NCI U54-CA283766, and U54-CA283762)