Mutation detection in formalin-fixed prostate cancer biopsies taken at the time of diagnosis using next generation DNA sequencing

Manson-Bahr, David, Ball, Richard, Gundem, Gunes, Mills, Robert, Rochester, Mark, Goody, Victoria, O'Meara, Sarah, Flather, Marcus, Keeling, Matthew, Yazbek Hanna, Marcelino, Hurst, Rachel, Curley, Helen, Clark, Jeremy, Brewer, Daniel, Mcdermott, Ultan and Cooper, Colin (2015) Mutation detection in formalin-fixed prostate cancer biopsies taken at the time of diagnosis using next generation DNA sequencing. Journal of Clinical Pathology, 68. pp. 212-217. ISSN 0021-9746

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Abstract

Aims: Assessing whether Next Generation DNA Sequencing (NGS) can be used to screen prostate cancer for multiple gene alterations in men routinely diagnosed with this disease and/or who are entered into clinical trials. Previous studies are limited and have reported only low success rates. Methods: We marked areas of cancer on H&E stained sections from formalin fixed-needle biopsys, and used these as templates to dissect cancer rich tissue from adjacent unstained sections. DNA was prepared using a Qiagen protocol modified to maximise DNA yield. The DNA was screened simultaneously for mutations in 365 cancer-related genes using an Illumina HiSeq 2000 NGS platform. Results: From 63 prostate cancers examined (59/63, 94%) of the samples yielded at least 30ng of DNA, the minimum amount of DNA considered suitable for NGS analysis. Patients in the D’Amico high-risk group yielded an average of 1033ng; intermediate-risk patients 401ng; and low risk patients 97ng. NGS of 8 samples selected from high and intermediate risk groups gave a median exon read depth of 962 and detected TMPRRS2-ERG fusions, as well as a variety of mutations including those in the SPOP, TP53, ATM, MEN1, NBPF10, NCOR2, PIK3CB, and MAP2K5 (MEK5) genes. Conclusions: Using the methods presented here NGS technologies can be used to screen a high proportion of prostate cancer patients for mutations in cancer-related genes in tissue samples opening up its general use in the context of clinical trials or routine diagnosis.

Item Type: Article
Uncontrolled Keywords: cancer research ,/dk/atira/pure/subjectarea/asjc/1300/1306
Faculty \ School: Faculty of Medicine and Health Sciences > Norwich Medical School
Faculty of Science > School of Biological Sciences
Depositing User: Pure Connector
Date Deposited: 09 Mar 2015 07:24
Last Modified: 21 Apr 2020 23:43
URI: https://ueaeprints.uea.ac.uk/id/eprint/52469
DOI: 10.1136/jclinpath-2014-202754

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