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

Manson-Bahr, David; Ball, Richard Y.; Gundem, Gunes; Sethia, Krishna; Mills, Robert; Rochester, Mark; Goody, Victoria; Anderson, Elizabeth; O’Meara, Sarah; Flather, Marcus; Keeling, M. M.; Yazbek-Hanna, Marcelino; Hurst, Rachel; Curley, Helen; Clark, Jeremy; Brewer, Daniel; McDermott, Ultan; Cooper, Christopher S.

doi:10.1136/jclinpath-2014-202754

Cited by 22 publications

(14 citation statements)

References 31 publications

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“…Manson-Bahr et al showed that DNA from cancer material dissected from transrectal ultrasound needle-core biopsy specimens can be analyzed 15. The authors observed a pattern of mutation consistent with those previously observed in PC surgical tissues, including TMPRSS2 – ERG fusion and mutations in SPOP , TP53 , ATM , and MEN1 , while nonsense mutations were observed in the MAP2K5 and the NCOR2 genes.…”

Section: Ngs Analysis For Solid Cancer Diagnosissupporting

confidence: 57%

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Next-generation sequencing: advances and applications in cancer diagnosis

Serratì¹,

Summa²,

Pilato³

et al. 2016

OTT

168

113

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Technological advances have led to the introduction of next-generation sequencing (NGS) platforms in cancer investigation. NGS allows massive parallel sequencing that affords maximal tumor genomic assessment. NGS approaches are different, and concern DNA and RNA analysis. DNA sequencing includes whole-genome, whole-exome, and targeted sequencing, which focuses on a selection of genes of interest for a specific disease. RNA sequencing facilitates the detection of alternative gene-spliced transcripts, posttranscriptional modifications, gene fusion, mutations/single-nucleotide polymorphisms, small and long noncoding RNAs, and changes in gene expression. Most applications are in the cancer research field, but lately NGS technology has been revolutionizing cancer molecular diagnostics, due to the many advantages it offers compared to traditional methods. There is greater knowledge on solid cancer diagnostics, and recent interest has been shown also in the field of hematologic cancer. In this review, we report the latest data on NGS diagnostic/predictive clinical applications in solid and hematologic cancers. Moreover, since the amount of NGS data produced is very large and their interpretation is very complex, we briefly discuss two bioinformatic aspects, variant-calling accuracy and copy-number variation detection, which are gaining a lot of importance in cancer-diagnostic assessment.

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Section: Ngs Analysis For Solid Cancer Diagnosissupporting

confidence: 57%

“…Two studies have evidenced the possibility for huge screening of PC patients in routine diagnosis 15,16. Manson-Bahr et al showed that DNA from cancer material dissected from transrectal ultrasound needle-core biopsy specimens can be analyzed 15.…”

Section: Ngs Analysis For Solid Cancer Diagnosismentioning

confidence: 99%

Next-generation sequencing: advances and applications in cancer diagnosis

Serratì¹,

Summa²,

Pilato³

et al. 2016

OTT

168

113

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“…Intra-individual metastases, however, might undergo a monoclonal selection process attributable to aggressive treatments, which would account for the inconsistency between this and other reports documenting a multiclonal seeding process resulting in intra-individual molecular heterogeneity either in primary prostate tumours 114 or metastases 126 . Despite these challenges, new developments in applied techniques (such as genomic and/or transcriptional profiling of AR signatures) and lineage markers might enable the advancement of clinical characterization of lineage crises because they can be used in clinical settings to evaluate treatment-induced lineage crises in formalin-fixed, paraffin-embedded primary or metastatic tumour samples 74,127 and even in urine samples 27 . Increasingly sensitive assays can also be used to screen for the presence of neuroendocrine or EMT-like cells in patient blood samples 28 , thereby enabling more frequent sampling than many other sampling techniques.…”

Section: Treatment-induced Prostate Lineagesmentioning

confidence: 99%

Strategies to avoid treatment-induced lineage crisis in advanced prostate cancer

Roubaud

Liaw

et al. 2016

Nat Rev Clin Oncol

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The increasing potency of therapies that target the androgen receptor (AR) signalling axis has correlated with a rise in the proportion of patients with prostate cancer harbouring an adaptive phenotype, termed treatment-induced lineage crisis. This phenotype is characterized by features that include soft-tissue metastasis and/or resistance to standard anticancer therapies. Potent anticancer treatments might force cancer cells to evolve and develop alternative cell lineages that are resistant to primary therapies, a mechanism similar to the generation of multidrug-resistant microorganisms after continued antibiotic use. Herein, we assess the hypothesis that treatmentadapted phenotypes harbour reduced AR expression and/or activity, and acquire compensatory strategies for cell survival. We highlight the striking similarities between castration-resistant prostate cancer and triple-negative breast cancer, another poorly differentiated endocrine malignancy. Alternative treatment paradigms are needed to avoid therapy-induced resistance. Herein, we present a new clinical trial strategy designed to evaluate the potential of rapid drug cycling as an approach to delay the onset of resistance and treatment-induced lineage crisis in patients with metastatic castration-resistant prostate cancer.Potent clinical suppression of androgen receptor (AR) signalling has been achieved with the pharmacological inhibitors abiraterone acetate 1,2 and enzalutamide 3,4 (drugs that were approved by the FDA in 2011 and 2014, respectively), resulting in significant survival benefits for men with metastatic castration-resistant prostate cancer (mCRPC). Emerging evidence suggests, however, that the prolonged therapeutic use of abiraterone and enzalutamide induces adaptive clinical phenotypes -including histological dedifferentiation and lineage alterations, such as treatment-induced neuroendocrine prostate cancer (t-NEPC) 5 and treatment-induced epithelial-to-mesenchymal transition 6,7 (t-EMT) (BOX 1). Such resistant phenotypes, in turn, might cause aggressive visceral metastases, a trend that has been reported with increasing prevalence in patients with prostate cancer who have received long-term androgen deprivation therapy (ADT) 5,[8][9][10][11][12] . While the mechanisms Correspondence to D.J.M. david.mulholland@mssm.edu. Author contributions: G.R. and D.J.M researched data and wrote the manuscript. All authors discussed the article's contents, revised and edited the manuscript before submission. B.C.L. and W.K.O. designed the PRINT clinical protocol. Competing interests statement:The authors declare no competing interests. Increased research emphasis should be placed on the development of preclinical models, in which the effects of treatment-induced resistance can be tested directly, as well as on the development of alternative treatment strategies that could be used to prolong the survival of men with advanced-stage prostate cancer by delaying the onset of resistance and minimizing toxicities. We suggest a new treatment approach, ...

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“…However, tissue from small diagnostic samples have demonstrated their utility for providing MPS starting material. Ninety‐four per cent of prostate core biopsies (FFPE) yielded sufficient DNA for MPS analysis of 365 cancer‐related genes, and FNA smears and cellblocks have also been used to provide sufficient DNA yield . FNA samples [e.g.…”

Section: Clinical Genomics In Pathology Practicementioning

confidence: 99%

Massive parallel sequencing of solid tumours – challenges and opportunities for pathologists

et al. 2016

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The role of pathologists is to provide diagnostic, prognostic and predictive data to enable clinical colleagues to manage patients optimally. Current histo/anatomical pathology is predominantly morphology-based, with the addition of biomarkers, applied largely through immunohistochemistry, fluorescence in-situ hybridization (FISH) and a limited range of polymerase chain reaction (PCR)-based molecular tests. The desire to apply genomics to the clinical care of patients has been facilitated by the human genome project and subsequently by high-throughput technologies known collectively as massive parallel sequencing (MPS, also referred to as next-generation sequencing, NGS). The use of MPS to identify mutations/variants and tissue RNA expression profiles for diagnosis, prognostication and targeted therapy stratification is now a reality in many clinical specialities. If histopathologists are considered experts in solid tumour pathology, MPS potentially falls within their scope; however, it challenges our predominant morphology-based paradigm. This review summarizes and comments on the current and future state of play of MPS for the practising histopathologist. It will focus on somatic mutations in solid tumours and will challenge histopathologists to take further leadership roles in this area.

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

Abstract: 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.

Cited by 22 publications

References 31 publications

Next-generation sequencing: advances and applications in cancer diagnosis

Next-generation sequencing: advances and applications in cancer diagnosis

Strategies to avoid treatment-induced lineage crisis in advanced prostate cancer

Massive parallel sequencing of solid tumours – challenges and opportunities for pathologists

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