A hidden Markov model-based approach to reconstructing double minute chromosome amplicons

Double minute chromosomes (DMs) are circular fragments of extrachromosomal DNA. They cause extreme gene amplification in the cells of malignant tumours. Their existence correlates with malignant tumour cell behaviour and drug resistance. Locating DMs is important for informing precision therapy to cancer treatment. Furthermore, accurate detection of double minutes requires precise reconstruction of their amplicons, which are the highly-amplified gene-carrying contiguous segments that adjoin to form DMs. This work presents AmpliconFinder - a Hidden-Markov Model-based approach to detect DM amplicons. To assess its efficacy, AmpliconFinder was used to augment an earlier framework for DM detection (DMFinder), thus improving its sensitivity and robustness to noisy sequence data. Experiments on simulated genomic data show that augmenting DMFinder with AmpliconFinder significantly increased the sensitivity of DMFinder on these data. Moreover, DMFinder with AmpliconFinder found all previously reported DMs in three pediatric medulloblastoma datasets, whereas the original DMFinder framework found none.