Poster Presentation 25th Lorne Cancer Conference 2013

Next-Generation Sequence Analysis of Cancer Xenografts (#335)

Fernando Rossello 1 , Richard Tothill 2 , Kara Britt 3 4 , Kieren Marini 1 , Jeanette Falzon 5 , Jason Li 2 , Samara Bennett 5 , Erwin Tantoso 6 , Tracey Brown 5 , Luciano Martelotto 1 , Neil Watkins 1
  1. Monash Institute of Medical Research, Monash University, Clayton, Vic, Australia
  2. Ian Potter Centre Cancer Genomics and Predictive Medicine, Peter MacCallum Cancer Centre, East Melbourne, Vic, Australia
  3. Department of Anatomy and Development Biology, Monash University, Clayton, Vic, Australia
  4. Peter MacCallum Cancer Centre, East Melbourne, Vic, Australia
  5. Department of Biochemistry and Molecular Biology, Monash University, Clayton, Vic, Australia
  6. Partek SG Pte Ltd, Queenstown, Singapore

Primary xenograft models are useful tools in cancer biology when the amount or quality of the original tumour tissue is insufficient for molecular analysis. Although xenograft lines are maintained in immunodeficient mice, we and others have shown that they retain important characteristics that are irreversibly lost in cell culture. Since the stromal component of xenograft tumors is derived from the host, the presence of mouse DNA and RNA has the potential to limit the use of these models for next-generation sequencing (NGS) analysis. We prospectively addressed this question in an established primary xenograft model of small cell lung cancer (SCLC), a malignancy that is almost always diagnosed using small biopsies or needle aspiration cytology. We first developed an in-silico strategy that separates human and mouse reads with at least 97% accuracy. We then compared NGS data from a series of primary xenograft models with clonally derived, stroma-free cell lines, and with published datasets derived from the same models. Starting with the NCI-H209 cell line as a reference sample, we show that low coverage whole genome analysis demonstrated remarkable concordance between published genome data and internal controls, despite the presence of mouse genomic DNA. NGS analysis of exon-capture DNA revealed that this enrichment procedure was highly species-specific, with less than 4% of reads aligning to the mouse genome. Human-specific expression profiling with RNA-Seq replicated array-based gene signatures, whereas mouse- transcript profiles correlated with published datasets from human cancer stroma. Primary xenograft models may therefore be a useful NGS platform for cancers where tissue samples are limiting.