This does not alter the authors' adherence to all the PLOS ONE policies on sharing data and materials. Erwin Tantoso is employed by Partek SG Pte. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Ĭompeting interests: Mr. Funding for open access charge: Victorian Cancer Agency. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.įunding: Funding for this work was provided by the National Health and Medical Research Council of Australia (Project Grant 546204), the Victorian Government Operational Infrastructure Support Program, and the Victorian Cancer Agency. Received: ApAccepted: AugPublished: September 26, 2013Ĭopyright: © 2013 Rossello et al. Coleman, University of North Carolina School of Medicine, United States of America (2013) Next-Generation Sequence Analysis of Cancer Xenograft Models. We conclude that primary xenografts represent a useful platform for complex NGS analysis in cancer research for tumours with limited sample resources, or those with prominent stromal cell populations.Ĭitation: Rossello FJ, Tothill RW, Britt K, Marini KD, Falzon J, Thomas DM, et al. Human-specific expression profiling with RNA-Seq replicated array-based gene expression experiments, whereas mouse-specific transcript profiles correlated with published datasets from human cancer stroma. Exome capture sequencing revealed that this enrichment procedure was highly species-specific, with less than 4% of reads aligning to the mouse genome. We show here that low-coverage whole-genome analysis demonstrated remarkable concordance between published genome data and internal controls, despite the presence of mouse genomic DNA. Using an in silico strategy that assign reads according to species-of-origin, we prospectively compared NGS data from primary xenograft models with matched cell lines and with published datasets. We examined this problem in an established primary xenograft model of small cell lung cancer (SCLC), a malignancy often diagnosed from small biopsy or needle aspirate samples. However, the presence of mouse-derived stromal cells represents a technical challenge to their use in NGS studies. In this situation, primary xenografts have proven useful preclinical models. ![]() Next-generation sequencing (NGS) studies in cancer are limited by the amount, quality and purity of tissue samples.
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