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 ORCID: https://orcid.org/0000-0003-4753-9794, Mcdermott, Ultan and Cooper, Colin ORCID: https://orcid.org/0000-0003-2013-8042 (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,sdg 3 - good health and well-being ,/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
UEA Research Groups:	Faculty of Medicine and Health Sciences > Research Groups > Cancer Studies Faculty of Medicine and Health Sciences > Research Groups > Cardiovascular and Metabolic Health Faculty of Medicine and Health Sciences > Research Groups > Norwich Clinical Trials Unit Faculty of Medicine and Health Sciences > Research Groups > Public Health and Health Services Research (former - to 2023) Faculty of Medicine and Health Sciences > Research Centres > Metabolic Health
Depositing User:	Pure Connector
Date Deposited:	09 Mar 2015 07:24
Last Modified:	19 Oct 2023 01:25
URI:	https://ueaeprints.uea.ac.uk/id/eprint/52469
DOI:	10.1136/jclinpath-2014-202754

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