Please use this identifier to cite or link to this item: https://ahro.austin.org.au/austinjspui/handle/1/11993
Title: Targeted-capture massively-parallel sequencing enables robust detection of clinically informative mutations from formalin-fixed tumours.
Austin Authors: Wong, Stephen Q;Li, Jason;Sheppard, Karen E;Do, Hongdo;Tothill, Richard W;McArthur, Grant A;Dobrovic, Alexander 
Affiliation: Molecular Pathology Research and Development Laboratory, Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne, Victoria, 3002, Australia
Bioinformatics Core, Research Division, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
Molecular Pathology Research and Development Laboratory, Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne, Victoria, 3002, Australia
Bioinformatics Core, Research Division, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia
Translational Genomics and Epigenomics Laboratory, Ludwig Institute for Cancer Research, The Olivia Newton-John Cancer and Wellness Centre, Heidelberg, Victoria, 3084, Australia
Division of Cancer Research, Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, Victoria, 3002, Australia
Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia
Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, 3010, Australia
Department of Pathology, The University of Melbourne, Parkville, Victoria, 3010, Australia
Issue Date: 13-Dec-2013
Publication information: Scientific Reports 2013; 3(): 3494
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-fixed for reported COSMIC variants including BRAF V600E. mutations in genes not conventionally screened including ERBB4, ATM, STK11 and CDKN2A were readily detected. All regions were adequately covered with independent reads regardless of GC content. This study indicates that hybridisation capture is a robust approach for massively parallel sequencing of FFPE samples.
Gov't Doc #: 24336498
URI: http://ahro.austin.org.au/austinjspui/handle/1/11993
DOI: 10.1038/srep03494
URL: https://pubmed.ncbi.nlm.nih.gov/24336498
Type: Journal Article
Appears in Collections:Journal articles

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