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

David Manson-Bahr, Richard Ball, Gunes Gundem, Robert Mills, Mark Rochester, Victoria Goody, Sarah O'Meara, Marcus Flather, Matthew Keeling, Marcelino Yazbek Hanna, Rachel Hurst, Helen Curley, Jeremy Clark, Daniel Brewer, Ultan Mcdermott, Colin Cooper

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16 Citations (Scopus)

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.
Original languageEnglish
Pages (from-to)212-217
Number of pages6
JournalJournal of Clinical Pathology
Volume68
Early online date13 Jan 2015
DOIs
Publication statusPublished - 2015

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