Browsing ICR Divisions by author "Salto-Tellez, Manuel"
Now showing items 21-39 of 39
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NUQA: Estimating Cancer Spatial and Temporal Heterogeneity and Evolution through Alignment-Free Methods.
Roddy, AC; Jurek-Loughrey, A; Souza, J; Gilmore, A; O'Reilly, PG; et al. (OXFORD UNIV PRESS, 2019-12-01)Longitudinal next-generation sequencing of cancer patient samples has enhanced our understanding of the evolution and progression of various cancers. As a result, and due to our increasing knowledge of heterogeneity, such ... -
Orthogonal MET analysis in a population-representative stage II-III colon cancer cohort: prognostic and potential therapeutic implications.
Craig, SG; Mende, S; Humphries, MP; Bingham, V; Viratham Pulsawatdi, A; et al. (WILEY, 2021-12-01)Clinical trials for MET inhibitors have demonstrated limited success for their use in colon cancer (CC). However, clinical efficacy may be obscured by a lack of standardisation in MET assessment for patient stratification. ... -
PD-L1 Multiplex and Quantitative Image Analysis for Molecular Diagnostics.
Abdullahi Sidi, F; Bingham, V; Craig, SG; McQuaid, S; James, J; et al. (MDPI, 2020-12-23)Multiplex immunofluorescence (mIF) and digital image analysis (DIA) have transformed the ability to analyse multiple biomarkers. We aimed to validate a clinical workflow for quantifying PD-L1 in non-small cell lung cancer ... -
Potential quality pitfalls of digitalized whole slide image of breast pathology in routine practice.
Atallah, NM; Toss, MS; Verrill, C; Salto-Tellez, M; Snead, D; et al. (ELSEVIER SCIENCE INC, 2022-07-01)Using digitalized whole slide images (WSI) in routine histopathology practice is a revolutionary technology. This study aims to assess the clinical impacts of WSI quality and representation of the corresponding glass slides. ... -
QuPath: The global impact of an open source digital pathology system.
Humphries, MP; Maxwell, P; Salto-Tellez, M (ELSEVIER, 2021-01-29)QuPath, originally created at the Centre for Cancer Research & Cell Biology at Queen's University Belfast as part of a research programme in digital pathology (DP) funded by Invest Northern Ireland and Cancer Research UK, ... -
Recommendations for determining HPV status in patients with oropharyngeal cancers under TNM8 guidelines: a two-tier approach.
Craig, SG; Anderson, LA; Schache, AG; Moran, M; Graham, L; et al. (SPRINGERNATURE, 2019-04-16)BACKGROUND: TNM8 staging for oropharyngeal squamous cell carcinomas (OPSCC) surrogates p16 immunohistochemistry for HPV testing. Patients with p16+ OPSCC may lack HPV aetiology. Here, we evaluate the suitability of TNM8 ... -
Robustness of differential gene expression analysis of RNA-seq.
Stupnikov, A; McInerney, CE; Savage, KI; McIntosh, SA; Emmert-Streib, F; et al. (ELSEVIER, 2021-01-01)RNA-sequencing (RNA-seq) is a relatively new technology that lacks standardisation. RNA-seq can be used for Differential Gene Expression (DGE) analysis, however, no consensus exists as to which methodology ensures robust ... -
Severity of gastric intestinal metaplasia predicts the risk of gastric cancer: a prospective multicentre cohort study (GCEP).
Lee, JWJ; Zhu, F; Srivastava, S; Tsao, SK; Khor, C; et al. (BMJ PUBLISHING GROUP, 2021-05-11)OBJECTIVE: To investigate the incidence of gastric cancer (GC) attributed to gastric intestinal metaplasia (IM), and validate the Operative Link on Gastric Intestinal Metaplasia (OLGIM) for targeted endoscopic surveillance ... -
Spatial analyses of immune cell infiltration in cancer: current methods and future directions: A report of the International Immuno-Oncology Biomarker Working Group on Breast Cancer.
Page, DB; Broeckx, G; Jahangir, CA; Verbandt, S; Gupta, RR; et al. (WILEY, 2023-08-01)Modern histologic imaging platforms coupled with machine learning methods have provided new opportunities to map the spatial distribution of immune cells in the tumor microenvironment. However, there exists no standardized ... -
Subcellular Epithelial HMGB1 Expression Is Associated with Colorectal Neoplastic Progression, Male Sex, Mismatch Repair Protein Expression, Lymph Node Positivity, and an 'Immune Cold' Phenotype Associated with Poor Survival.
Porter, RJ; Murray, GI; Hapca, S; Hay, A; Craig, SG; et al. (MDPI, 2023-03-20)New treatment targets are needed for colorectal cancer (CRC). We define expression of High Mobility Group Box 1 (HMGB1) protein throughout colorectal neoplastic progression and examine the biological consequences of aberrant ... -
Systematic evaluation of PAXgene® tissue fixation for the histopathological and molecular study of lung cancer.
Southwood, M; Krenz, T; Cant, N; Maurya, M; Gazdova, J; et al. (WILEY, 2019-11-11)Whilst adequate for most existing pathological tests, formalin is generally considered a poor DNA preservative and use of alternative fixatives may prove advantageous for molecular testing of tumour material; an increasingly ... -
Technical note on the exploration of COVID-19 in autopsy material.
Humphries, MP; Bingham, V; Abdullah Sidi, F; Craig, S; Lara, B; et al. (BMJ PUBLISHING GROUP, 2023-01-30)Interrogation of immune response in autopsy material from patients with SARS-CoV-2 is potentially significant. We aim to describe a validated protocol for the exploration of the molecular physiopathology of SARS-CoV-2 ... -
The adaptive immune and immune checkpoint landscape of neoadjuvant treated esophageal adenocarcinoma using digital pathology quantitation.
Humphries, MP; Craig, SG; Kacprzyk, R; Fisher, NC; Bingham, V; et al. (BMC, 2020-06-01)BACKGROUND: Limited studies examine the immune landscape in Esophageal Adenocarcinoma (EAC). We aim to identify novel associations, which may inform immunotherapy treatment stratification. METHODS: Three hundred twenty-nine ... -
The clinical and molecular significance associated with STING signaling in breast cancer.
Parkes, EE; Humphries, MP; Gilmore, E; Sidi, FA; Bingham, V; et al. (NATURE RESEARCH, 2021-06-25)STING signaling in cancer is a crucial component of response to immunotherapy and other anti-cancer treatments. Currently, there is no robust method of measuring STING activation in cancer. Here, we describe an ... -
The use of digital pathology and image analysis in clinical trials.
Pell, R; Oien, K; Robinson, M; Pitman, H; Rajpoot, N; et al. (WILEY, 2019-04-01)Digital pathology and image analysis potentially provide greater accuracy, reproducibility and standardisation of pathology-based trial entry criteria and endpoints, alongside extracting new insights from both existing and ... -
Training and accreditation standards for pathologists undertaking clinical trial work.
Rees, G; Salto-Tellez, M; Lee, JL; Oien, K; Verrill, C; et al. (WILEY, 2019-04-01)Clinical trials rely on multidisciplinary teams for successful delivery. Pathologists should be involved in clinical trial design from the outset to ensure that protocols are optimised to deliver maximum data collection ... -
Transcriptional Profiling of a Patient-Matched Cohort of Glioblastoma (IDH-Wildtype) for Therapeutic Target and Repurposing Drug Identification.
Roddy, AC; McInerney, CE; Flannery, T; Healy, EG; Stewart, JP; et al. (MDPI, 2023-04-19)Glioblastoma (GBM) is the most prevalent and aggressive adult brain tumor. Despite multi-modal therapies, GBM recurs, and patients have poor survival (~14 months). Resistance to therapy may originate from a subpopulation ... -
Translation of tissue-based artificial intelligence into clinical practice: from discovery to adoption.
Geaney, A; O'Reilly, P; Maxwell, P; James, JA; McArt, D; et al. (SPRINGERNATURE, 2023-11-24)Digital pathology (DP), or the digitization of pathology images, has transformed oncology research and cancer diagnostics. The application of artificial intelligence (AI) and other forms of machine learning (ML) to these ... -
True-T - Improving T-cell response quantification with holistic artificial intelligence based prediction in immunohistochemistry images.
Makhlouf, Y; Singh, VK; Craig, S; McArdle, A; French, D; et al. (ELSEVIER, 2024-12-01)The immune response associated with oncogenesis and potential oncological ther- apeutic interventions has dominated the field of cancer research over the last decade. T-cell lymphocytes in the tumor microenvironment are a ...