Please use this identifier to cite or link to this item: http://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.
Authors: Wong, Stephen Q;Li, Jason;Sheppard, Karen E;Do, Hongdo;Tothill, Richard W;McArthur, Grant A;Dobrovic, Alexander
Affiliation: 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.
1] Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, 3010, Australia [2] Division of Cancer Research, Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, Victoria, 3002, Australia [3] Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia.
1] Molecular Pathology Research and Development Laboratory, Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne, Victoria, 3002, Australia [2] Translational Genomics and Epigenomics Laboratory, Ludwig Institute for Cancer Research, The Olivia Newton-John Cancer and Wellness Centre, Heidelberg, Victoria, 3084, Australia.
1] Bioinformatics Core, Research Division, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, Australia [2] Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, 3010, Australia [3] Division of Cancer Research, Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, Victoria, 3002, Australia.
1] Department of Pathology, The University of Melbourne, Parkville, Victoria, 3010, Australia [2] Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, 3010, Australia [3] Division of Cancer Research, Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, Victoria, 3002, Australia.
1] Molecular Pathology Research and Development Laboratory, Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne, Victoria, 3002, Australia [2] Department of Pathology, The University of Melbourne, Parkville, Victoria, 3010, Australia [3] Translational Genomics and Epigenomics Laboratory, Ludwig Institute for Cancer Research, The Olivia Newton-John Cancer and Wellness Centre, Heidelberg, Victoria, 3084, Australia.
Issue Date: 13-Dec-2013
Citation: 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.
Internal ID Number: 24336498
URI: http://ahro.austin.org.au/austinjspui/handle/1/11993
DOI: 10.1038/srep03494
URL: http://www.ncbi.nlm.nih.gov/pubmed/24336498
Type: Journal Article
Appears in Collections:Journal articles

Files in This Item:
There are no files associated with this item.


Items in AHRO are protected by copyright, with all rights reserved, unless otherwise indicated.