Bioinformatics Core

简介:

Summary: The Bioinformatics Core is the primary data management and analysis arm of the UP-PDTC. Of note, the Bioinformatics Core will include biostatistics, bioinformatic and data management. The Bioinformatics Core enhances the productivity of the proposed project investigators, PDX Core and, eventually the PDXNet by providing them access to a statistical/bioinformatics/data management team who possess expertise in study design and conduct, and data analysis in patient derived xenotransplantation studies including the analysis of genomic, proteomic and RNA sequencing data. Timely and in-depth collaboration ensures that the proposed studies are designed, managed, analyzed, and reported to the highest standard and provide valid and robust answers to the scientific questions that the U54 project seeks to address. Importantly, Bioinformatics Core personnel will work with other experts in PDXNet to ensure a consensus of tumor and response measurement which can be widely used across the network. The Core is located within the Department of Biostatistics, Epidemiology and Informatics, and the Institute for Biomedical Informatics (IBI) at Penn Perelman School of Medicine. The DBEI and IBI are interdisciplinary homes for faculty, staff and students specialized in biostatistics, epidemiology, and clinical/bioinformatics research on campus. Furthermore, Dr. Long is a Professor of Biostatistics and Director of the Biostatistics and Informatics Core for the Abramson Cancer Center. Through his roles, Dr. Long has substantial experience addressing clinically relevant endpoints for pre-clinical studies which will be necessary for development of XP2 trials using biomarkers to guide development of expected human Phase 2 trials. Dr. E. Paul Wileyto is an experienced biostatistician with expertise in pre-clinical study design including tumor measurements and appropriate study design. Dr. Taehyong Kim is Interim Director of Bioinformatics Core at the Penn Institute for Biomedical Informatics with extensive experience in analysis of NGS data, RNA sequencing and other omic data. This team has already contributed to definitions of tumor volume and growth in PDX models as well as to planned XP2 studies in Projects 1 and 2. Importantly, a major role of the Bioinformatics Core will be studies of tumor changes during serial transplantation. These studies will involve multi-omics analysis for Project Two and the development of novel potential biomarkers using artificial intelligence. Project One will work closely with Bioinformatics personnel to apply recently developed techniques to study leukemia cell phenotypic evolution using deconvolution of RNA seq data using CIBERSORTx. This novel approach will help define leukemic cell evolution in vivo to a degree never previously done.