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Mutation detection in formalin-fixed prostate cancer biopsies taken at the time of diagnosis using next-generation DNA sequencing
  1. David Manson-Bahr1,
  2. Richard Ball2,
  3. Gunes Gundem3,
  4. Krishna Sethia1,
  5. Robert Mills1,
  6. Mark Rochester1,
  7. Victoria Goody3,
  8. Elizabeth Anderson3,
  9. Sarah O'Meara3,
  10. Marcus Flather4,
  11. Matthew Keeling5,
  12. Marcelino Yazbek-Hanna1,
  13. Rachel Hurst4,
  14. Helen Curley4,
  15. Jeremy Clark4,
  16. Daniel S Brewer4,
  17. Ultan McDermott3,
  18. Colin Cooper4
  1. 1Department of Urology, Norfolk and Norwich University Hospitals NHS Foundation Trust, Norwich, UK
  2. 2Department of Histopathology, Norfolk and Norwich University Hospitals NHS Foundation Trust, Norwich, UK
  3. 3Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
  4. 4Norwich Medical School and School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
  5. 5Department of Information Services, Norfolk and Norwich University Hospitals NHS Foundation Trust, Norwich, UK
  1. Correspondence to Professor Colin S Cooper, Norwich Medical School and School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; colin.cooper{at}uea.ac.uk

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 biopsies, 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 (94%) of the samples yielded at least 30 ng of DNA, the minimum amount of DNA considered suitable for NGS analysis. Patients in the D'Amico high-risk group yielded an average of 1033 ng, intermediate-risk patients 401 ng, and low-risk patients 97 ng. NGS of eight samples selected from high-risk 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 patients with prostate cancer for mutations in cancer-related genes in tissue samples opening up its general use in the context of clinical trials or routine diagnosis.

  • GENETICS
  • PROSTATE
  • CANCER
  • CANCER GENETICS
  • MOLECULAR GENETICS

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