ArticleBMC genomics2018
Computational approach to discriminate human and mouse sequences in patient-derived tumour xenografts.
Article in BMC genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed.
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- NF2 loss malignantly transforms human pancreatic acinar cells and enhances cell fitness under environmental stress.The Journal of clinical investigation · 2026Article
- Cross-species comparison reveals therapeutic vulnerabilities halting glioblastoma progression.Nature communications · 2025Article
- Role of the CTCF binding site in Human T-Cell Leukemia Virus-1 pathogenesis.PLoS pathogens · 2025Article
- Modeling Drug Responses and Evolutionary Dynamics Using Patient-Derived Xenografts Reveals Precision Medicine Strategies for Triple-Negative Breast Cancer.Cancer research · 2025Article
- PRMT5 inhibition has a potent anti-tumor activity against adenoid cystic carcinoma of salivary glands.Journal of experimental & clinical cancer research : CR · 2025Article
- Metabolic changes of human induced pluripotent stem cell-derived cardiomyocytes and teratomas after transplantation.iScience · 2024Article
- Representation of genomic intratumor heterogeneity in multi-region non-small cell lung cancer patient-derived xenograft models.Nature communications · 2024Article
- Patient-Derived Models of Cancer in the NCI PDMC Consortium: Selection, Pitfalls, and Practical Recommendations.Cancers · 2024Review
- Article
- Rewiring of the 3D genome during acquisition of carboplatin resistance in a triple-negative breast cancer patient-derived xenograft.Scientific reports · 2023Article
- An integrative approach for exploring the nature of fibroepithelial neoplasms.British journal of cancer · 2023Article
- RNA-Seq Data Processing in Plant-Pathogen Interaction System: A Case Study.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Whole transcriptome profiling of liquid biopsies from tumour xenografted mouse models enables specific monitoring of tumour-derived extracellular RNA.NAR cancer · 2022Article
- AL101, a gamma-secretase inhibitor, has potent antitumor activity against adenoid cystic carcinoma with activated NOTCH signaling.Cell death & disease · 2022Article
- Identification of two cancer stem cell-like populations in triple-negative breast cancer xenografts.Disease models & mechanisms · 2022Article
- Tumor Purity in Preclinical Mouse Tumor Models.Cancer research communications · 2022Article
Corrections and comments
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Authors and funding
11 authors.
Funding
Abstract
backgroundPatient-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.
resultsIn 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.
conclusionsThe 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.
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