Maximum Parsimony Analysis of Gene Copy Number Changes in Tumor Phylogenetics

Friday, January 29, 2016 - 2:50am to 4:00pm
2A27 Swearingen Engineering Center

Friday, January 29, 2:50 - 4:05 PM, 2A27 Swearingen Engineering Center
Jijun Tang, University of South Carolina

Abstract: Evolution of cancer cells are characterized by large scale and rapid changes in the chromosomal landscape. The fluorescence in situ hybridization (FISH) technique provides a way to measure the copy numbers of preselected genes in a group of cells and has been found to be a reliable source of data to model the evolution of tumor cells. Chowdhury recently developed a theoretically sound and scalable model for tumor progression driven by gains and losses in cell count patterns obtained by FISH probes. Their model aims to find the Rectilinear Steiner Minimum Tree (RSMT) that describes progression of FISH cell count patterns over its branches in a parsimonious manner. This model is found to effectively model tumor evolution and is also useful in tumor classification. However the RSMT problem is NP--complete and efficient heuristics are necessary to obtain solutions, especially for large datasets. In this talk we will present a new algorithm for the RSMT problem, based on Maximum Parsimony phylogeny inference. Experimental results from both simulated and real tumor data show that our approach outperforms previous heuristics for the RSMT problem, thus obtaining better models for tumor evolution.

Bio: Jijun Tang is a professor in the department of Computer Science and Engineering, University of South Carolina, USA. He obtained his Master degree from Tianjin University China and PhD degree from the University of New Mexico, USA. His research interests include computational biology, algorithm design and computer game development, with focus on phylogenetic reconstruction and ancestral genome inference, using higher level genomic data such as genome rearrangements and copy number variations. He has coauthored more than 80 research papers in international conferences and journals. He was program co-chair of 2016 APBC and 2012 WABI conferences and was on the program committees of more than 50 international conferences.