Journal article

Targeted-capture massively-parallel sequencing enables robust detection of clinically informative mutations from formalin-fixed tumours

Stephen Q Wong, Jason Li, Renato Salemi, Karen E Sheppard, Hongdo Do, Richard W Tothill, Grant A McArthur, Alexander Dobrovic

SCIENTIFIC REPORTS | NATURE PUBLISHING GROUP | Published : 2013

Abstract

Massively parallel sequencing offers the ability to interrogate a tumour biopsy for multiple mutational changes. For clinical samples, methodologies must enable maximal extraction of available sequence information from formalin-fixed and paraffin-embedded (FFPE) material. We assessed the use of targeted capture for mutation detection in FFPE DNA. The capture probes targeted the coding region of all known kinase genes and selected oncogenes and tumour suppressor genes. Seven melanoma cell lines and matching FFPE xenograft DNAs were sequenced. An informatics pipeline was developed to identify variants and contaminating mouse reads. Concordance of 100% was observed between unfixed and formalin-..

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Grants

Funding Acknowledgements

This project was enabled by the Peter MacCallum Pfizer Translational Oncology Research Collaborative Hub (TORCH) funded by Pfizer Australia, and the Melbourne Melanoma Project funded by the Victorian Cancer Agency Translational research program and established through support of the Victor Smorgon Charitable Fund. We thank Carleen Cullinane for preparing the xenograft blocks and Jia-Min Pang for review of slides for contaminating normal mouse tissue in xenografted formalin-fixed sections. We also thank Andrew Fellowes, Anthony Bell, and Stephen Fox for the TruSeq reagent and access to the MiSeq instrument.