Journal Article

Computational approach to discriminate human and mouse sequences in patient-derived tumour xenografts

Batra, Ankita Sati, Sammut, Stephen-John, Clifford, Harry, Rueda, Oscar M., Greenwood, Wendy, Chin, Suet-Feung, Batra, Rajbir Nath, Hercus, Colin, Callari, Maurizio, Bruna, Alejandra, Caldas, Carlos

2018

Overview

Background Patient-Derived Tumour Xenografts (PDTXs) have emerged as the pre-clinical models that best represent clinical tumour diversity and intra-tumour heterogeneity. The molecular characterization of PDTXs using High-Throughput Sequencing (HTS) is essential; however, the presence of mouse stroma is challenging for HTS data analysis. Indeed, the high homology between the two genomes results in a proportion of mouse reads being mapped as human. Results In this study we generated Whole Exome Sequencing (WES), Reduced Representation Bisulfite Sequencing (RRBS) and RNA sequencing (RNA-seq) data from samples with known mixtures of mouse and human DNA or RNA and from a cohort of human breast cancers and their derived PDTXs. We show that using an In silico Combined human-mouse Reference Genome (ICRG) for alignment discriminates between human and mouse reads with up to 99.9% accuracy and decreases the number of false positive somatic mutations caused by misalignment by >99.9%. We also derived a model to estimate the human DNA content in independent PDTX samples. For RNA-seq and RRBS data analysis, the use of the ICRG allows dissecting computationally the transcriptome and methylome of human tumour cells and mouse stroma. In a direct comparison with previously reported approaches, our method showed similar or higher accuracy while requiring significantly less computing time. Conclusions The computational pipeline we describe here is a valuable tool for the molecular analysis of PDTXs as well as any other mixture of DNA or RNA species.

• Publisher: BioMed Central,BioMed Central Ltd,BMC
• Subject: Alignment / Animal Genetics and Genomics / Animals / Biomedical and Life Sciences / Breast Neoplasms - genetics / Breast Neoplasms - metabolism / DNA sequencing / Gene expression / Gene Expression Profiling / Genetic aspects / Genomics - methods / High throughput sequencing / High-Throughput Nucleotide Sequencing - methods / House mouse / Human and rodent genomics / Humans / ICRG / In silico combined human-mouse reference genome / Life Sciences / Methodology / Methodology Article / Mice / Microarrays / Microbial Genetics and Genomics / Mouse stroma / Mutation / Plant Genetics and Genomics / Proteomics / Sequence Alignment / Sequence Analysis, DNA / Sequence Analysis, RNA / Short-reads / Tumors / Xenograft Model Antitumor Assays / Xenotransplantation