A novel HMM for analyzing chromosomal aberrations in heterogeneous tumor samples

Comprehensive detection and identification of copy number and LOH of chromosomal aberration is required to provide an accurate therapy of human cancer. As a cost-saving and high-throughput tool, SNP arrays facilitate analysis of chromosomal aberration throughout the whole genome. The performance of previous approaches has been limited to several critical issues such as normal cell contamination, aneuploidy and tumor heterogeneity. For these reasons we present a Hidden Markov Model (HMM) based approach called TH-HMM (Tumor Heterogeneity HMM), for simultaneous detection of copy number and LOH in heterogeneous tumor samples using data from Illumina SNP arrays. Through adopting an efficient EM algorithm, our method can correctly detect chromosomal aberration events in tumor subclones. Evaluation on simulated data series indicated that TH-HMM could accurately estimate both normal cell and subclone proportions, and finally recovery the aberration profiles for each clones.