Building a ‘Repository of Science’: The importance of integrating biobanks within molecular pathology programmes

Lewis, Claire E.; McQuaid, Stephen; Hamilton, Peter; Salto-Tellez, Manuel; McArt, Darragh G.; James, Jacqueline

doi:10.1016/j.ejca.2016.08.009

Cited by 33 publications

(19 citation statements)

References 35 publications

(41 reference statements)

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“…However, the quality of FFPE samples retrieved from storage archives following routine pathology management pathways which may have relatively wide variations in fixation times compared to prospectively targeted biobank collections has not been fully established. Indeed there are contradictory opinions about the quality and quantity of nucleic acids that can be extracted from such FFPE collections and their potential use in downstream analysis [ 4 ].…”

Section: Introductionmentioning

confidence: 99%

RNAscope in situ hybridization confirms mRNA integrity in formalin-fixed, paraffin-embedded cancer tissue samples

et al. 2017

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Immunohistochemistry remains the overwhelming technique of choice for test biomarker evaluation in both clinical or research settings when using formalin-fixed, paraffin embedded tissue sections. However, validations can be complex with significant issues about specificity, sensitivity and reproducibility. The vast array of commercially available antibodies from many vendors may also lead to non-standard approaches which are difficult to cross-reference. In contrast mRNA detection, by in situ hybridization (ISH) with sequence specific probes, offers a realistic alternative, with less validation steps and more stringent and reproducible assessment criteria. In the present study mRNA ISH was evaluated in prospectively and retrospectively collected FFPE samples within a cancer biobank setting. Three positive control probes, POLR2A, PPIB and UBC were applied to FFPE sections from a range of tumour types in FFPE whole-face (prospective collection) or TMA (retrospective collection) formats and evaluated semi-quantitatively and by image analysis. Results indicate that mRNA can be robustly evaluated by ISH in prospectively and retrospectively collected tissue samples. Furthermore, for 2 important test biomarkers, PD-L1 and c-MET, we show that mRNA ISH is a technology that can be applied with confidence in the majority of tissue samples because there are quantifiable levels of control probes indicating overall mRNA integrity.

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Section: Introductionmentioning

confidence: 99%

RNAscope in situ hybridization confirms mRNA integrity in formalin-fixed, paraffin-embedded cancer tissue samples

et al. 2017

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“…This biobank contains tissue samples obtained from regional Health Trust pathology departments for use in research. 19 It has ethical approval from the Office for Research Ethics Committees Northern Ireland (ORECNI; reference 16/ NI/0030) to obtain, store and distribute samples for research purposes. The Northern Ireland Biobank granted approval for this study (study number NIB15-0176).…”

Section: A T a S O U R C E Smentioning

confidence: 99%

High PTGS2 expression in post‐neoadjuvant chemotherapy‐treated oesophageal adenocarcinoma is associated with improved survival: a population‐based cohort study

et al. 2019

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Aims High prostaglandin endoperoxide synthase‐2 (PTGS2) enzyme expression in oesophageal adenocarcinoma has been shown to independently predict poor prognosis; however, the evidence is inconsistent. The aim of this study was to investigated the association between PTGS2 expression and prognosis in patients with oesophageal adenocarcinoma. Methods and results A cohort of 135 patients with oesophageal adenocarcinoma who received neoadjuvant chemotherapy and surgery from 2004 to 2012 was identified in the Northern Ireland Cancer Centre. Tissue microarrays were created in the Northern Ireland Biobank, with triplicate cores being sampled from each tumour. Immunohistochemical PTGS2 expression was scored by two independent assessors, with intensity and proportion of tumour staining being used to calculate H‐scores for each patient. Cox regression models were used to calculate hazard ratios (HRs) and 95% confidence intervals (CIs) for overall and cancer‐specific survival, and recurrence‐free survival by PTGS2 expression, with adjustment for potential confounders. Patients were followed up for a mean of 3.0 years (standard deviation 1.8 years). The PTGS2 expression cut‐off value was determined from the median H‐score of the cohort (270/300). High (n = 79), as compared with low (n = 56), PTGS2 expression was associated with improved cancer‐specific survival (adjusted HR 0.56, 95% CI 0.33–0.94; P = 0.03). PTGS2 expression was not significantly associated with recurrence‐free survival (adjusted HR 0.85, 95% CI 0.52–1.38; P = 0.51). Conclusions High PTGS2 expression in oesophageal adenocarcinoma tissue was associated with improved overall and cancer‐specific survival, in contrast to previous evidence. As this is the first study of its kind to include patients who had undergone neoadjuvant chemotherapy, further studies are needed to clarify these associations.

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“…Digital Pathology allows the digitization of the glass slide, thus adding visual documentation of the specimen stored and avoiding the unnecessary preparation of new HE slides and allowing the archiving and retrieval of images and the potential use of image analysis and artificial intelligence to enhance and automate this process. [ 1 2 ]…”

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confidence: 99%

Digital and Computational Pathology: Bring the Future into Focus

Sylvia¹,

Pantanowitz²,

Parwani³

et al. 2019

Journal of Pathology Informatics

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Building a ‘Repository of Science’: The importance of integrating biobanks within molecular pathology programmes

Cited by 33 publications

References 35 publications

RNAscope in situ hybridization confirms mRNA integrity in formalin-fixed, paraffin-embedded cancer tissue samples

RNAscope in situ hybridization confirms mRNA integrity in formalin-fixed, paraffin-embedded cancer tissue samples

High PTGS2 expression in post‐neoadjuvant chemotherapy‐treated oesophageal adenocarcinoma is associated with improved survival: a population‐based cohort study

Digital and Computational Pathology: Bring the Future into Focus

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