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

Journal of Clinical Pathology

Volumn 68, Issue 3, 2015, Pages 212-217

  Manson Bahr, David ^a   Ball, Richard ^a   Gundem, Gunes ^b   Sethia, Krishna ^a   Mills, Robert ^a   Rochester, Mark ^a   Goody, Victoria ^b   Anderson, Elizabeth ^b   O'Meara, Sarah ^b   Flather, Marcus ^c   Keeling, Matthew ^a   Yazbek Hanna, Marcelino ^a   Hurst, Rachel ^c   Curley, Helen ^c   Clark, Jeremy ^c   Brewer, Daniel S ^c   McDermott, Ultan ^b   Cooper, Colin ^c  

^a NORFOLK AND NORWICH UNIVERSITY HOSPITAL   (United Kingdom)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^c UNIVERSITY OF EAST ANGLIA   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ATM PROTEIN; DNA; EOSIN; FORMALDEHYDE; HEMATOXYLIN; MITOGEN ACTIVATED PROTEIN KINASE KINASE 5; MULTIPLE ENDOCRINE NEOPLASIA TYPE 1 PROTEIN; NBPF10 PROTEIN; NCOR2 PROTEIN; PHOSPHATIDYLINOSITOL 4,5 BISPHOSPHATE 3 KINASE; PHOSPHATIDYLINOSITOL 4,5 BISPHOSPHATE 3 KINASE BETA; PROTEIN; PROTEIN P53; SPOP PROTEIN; TMPRRS2 PROTEIN; TRANSCRIPTION FACTOR ERG; UNCLASSIFIED DRUG; FIXATIVE; KALLIKREIN; KALLIKREIN-RELATED PEPTIDASE 3, HUMAN; PROSTATE SPECIFIC ANTIGEN; TUMOR MARKER;

ADULT; AGED; ARTICLE; CANCER DIAGNOSIS; CANCER SCREENING; CANCER TISSUE; CONTROLLED STUDY; DNA SEQUENCE; EXON; GENE FUSION; GENE MUTATION; HIGH RISK POPULATION; HUMAN; INTERMEDIATE RISK PATIENT; LOW RISK PATIENT; MAJOR CLINICAL STUDY; MALE; MIDDLE AGED; NEEDLE BIOPSY; NEXT GENERATION SEQUENCING; PRIORITY JOURNAL; PROSTATE BIOPSY; PROSTATE CANCER; TISSUE SECTION; TUMOR BIOPSY; BLOOD; CANCER GRADING; CANCER STAGING; EVALUATION STUDY; FINE NEEDLE ASPIRATION BIOPSY; GENETIC PREDISPOSITION; GENETIC SCREENING; GENETICS; HIGH THROUGHPUT SEQUENCING; MUTATION; NUCLEOTIDE SEQUENCE; PATHOLOGY; PHENOTYPE; PREDICTIVE VALUE; PROCEDURES; PROSTATE TUMOR; RISK ASSESSMENT; RISK FACTOR; TISSUE FIXATION;

AGED; BIOPSY, FINE-NEEDLE; DNA MUTATIONAL ANALYSIS; FIXATIVES; FORMALDEHYDE; GENETIC PREDISPOSITION TO DISEASE; GENETIC TESTING; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; KALLIKREINS; MALE; MIDDLE AGED; MUTATION; NEOPLASM GRADING; NEOPLASM STAGING; PHENOTYPE; PREDICTIVE VALUE OF TESTS; PROSTATE-SPECIFIC ANTIGEN; PROSTATIC NEOPLASMS; RISK ASSESSMENT; RISK FACTORS; TISSUE FIXATION; TUMOR MARKERS, BIOLOGICAL;

EID: 84923327053     PISSN: 00219746     EISSN: 14724146     Source Type: Journal    
DOI: 10.1136/jclinpath-2014-202754     Document Type: Article

References (32)

1. Siegel R, Ma J, Zou Z, et al. Cancer statistics, 2014. CA Cancer J Clin 2014;64:9-29.
2. Barbieri CE, Bangma CH, Bjartell A, et al. The mutational landscape of prostate cancer. Eur Urol 2013;64:567-76.
3. Huang J, Wang JK, Sun Y. Molecular pathology of prostate cancer revealed by next-generation sequencing: opportunities for genome-based personalized therapy. Curr Opin Urol 2013;23:189-93.
4. Grasso CS, Wu Y-M, Robinson DR, et al. The mutational landscape of lethal castration-resistant prostate cancer. Nature 2012;487:239-43.
5. Bismar TA, Yoshimoto M, Duan Q, et al. Interactions and relationships of PTEN, ERG, SPINK1 and AR in castration-resistant prostate cancer. Histopathology 2012;60:645-52.
6. Tomlins SA, Rhodes DR, Perner S, et al. Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science 2005;310:644-8.
7. Attard G, Clark J, Ambroisine L, et al. Duplication of the fusion of TMPRSS2 to ERG sequences identifies fatal human prostate cancer. Oncogene 2008;27:253-63.
8. Reid AHM, Attard G, Ambroisine L, et al. Molecular characterisation of ERG, ETV1 and PTEN gene loci identifies patients at low and high risk of death from prostate cancer. Br J Cancer 2010;102:678-84.
9. Barbieri CE, Baca SC, Lawrence MS, et al. Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer. Nat Genet 2012;44:685-9.
10. Mosquera JM, Beltran H, Park K, et al. Concurrent AURKA and MYCN gene amplifications are harbingers of lethal treatment-related neuroendocrine prostate cancer. Neoplasia 2013;15:1-10.
11. He W, Zhang M-G, Wang X-J, et al. AURKA suppression induces DU145 apoptosis and sensitizes DU145 to docetaxel treatment. Am J Transl Res 2013;5:359-67.
12. Cheok CF, Verma CS, Baselga J, et al. Translating p53 into the clinic. Nat Rev Clin Oncol 2011;8:25-37.
13. Fong PC, Boss DS, Yap TA, et al. Inhibition of poly(ADP-ribose) polymerase in tumors from BRCA mutation carriers. N Engl J Med 2009;361:123-34.
14. Attard G, Cooper CS, de Bono JS. Steroid hormone receptors in prostate cancer: a hard habit to break? Cancer Cell 2009;16:458-62.
15. Beltran H, Yelensky R, Frampton GM, et al. Targeted next-generation sequencing of advanced prostate cancer identifies potential therapeutic targets and disease heterogeneity. Eur Urol 2013;63:920-6.
16. Jhavar S, Corbishley CM, Dearnaley D, et al. Construction of tissue microarrays from prostate needle biopsy specimens. Br J Cancer 2005;93:478-82.
17. McCarthy F, Fletcher A, Dennis N, et al. An improved method for constructing tissue microarrays from prostate needle biopsy specimens. J Clin Pathol 2009;62:694-8.
18. McCarthy F, Dennis N, Flohr P, et al. High-density tissue microarrays from prostate needle biopsies. J Clin Pathol 2011;64:88-90.
19. Gonzalez-Perez A, Deu-Pons J, Lopez-Bigas N. Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation. Genome Med 2012;4:89.
20. Hudson TJ, Anderson W, Artez A, et al; International Cancer Genome Consortium. International network of cancer genome projects. Nature 2010 464: 993-8.
21. Forbes SA, Tang G, Bindal N, et al. COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer. Nucleic Acids Res 2010;38:D652-7.
22. Haque KA, Pfeiffer RM, Beerman MB, et al. Performance of high-throughput DNA quantification methods. BMC Biotechnol 2003;3:20.
23. Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 2010;26:589-95.
24. Nik-Zainal S, Alexandrov LB, Wedge DC, et al. Mutational processes molding the genomes of 21 breast cancers. Cell 2012;149:979-93.
25. Ye K, Schulz MH, Long Q, et al. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 2009;25:2865-71.
26. Tennessen JA, Bigham AW, O'Connor TD, et al. Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science 2012;337:64-9.
27. Abecasis GR, Altshuler D, Auton A, et al; 1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature 2010;467:1061-73.
28. D'Amico AV, Whittington R, Malkowicz SB, et al. Biochemical outcome after radical prostatectomy, external beam radiation therapy, or interstitial radiation therapy for clinically localized prostate cancer. JAMA 1998;280:969-74.
29. Liao G, Chen L-Y, Zhang A, et al. Regulation of androgen receptor activity by the nuclear receptor corepressor SMRT. J Biol Chem 2003;278:5052-61.
30. McCracken SRC, Ramsay A, Heer R, et al. Aberrant expression of extracellular signal-regulated kinase 5 in human prostate cancer. Oncogene 2008;27:2978-88.
31. Nakamura K, Uhlik MT, Johnson NL, et al. PB1 domain-dependent signaling complex is required for extracellular signal-regulated kinase 5 activation. Mol Cell Biol 2006;26:2065-79.
32. Liu J-J, Lichtensztajn DY, Gomez SL, et al. Nationwide prevalence of lymph node metastases in Gleason score 3+3=6 prostate cancer. Pathology 2014;46:306-10.