A5018532839- Cancer Genomics and Diagnostics
- Renal cell carcinoma treatment
- Genetic factors in colorectal cancer
- Ferroptosis and cancer prognosis
- Nutrition, Genetics, and Disease
- Colorectal Cancer Surgical Treatments
- Colorectal Cancer Treatments and Studies
- Single-cell and spatial transcriptomics
- Renal and related cancers
- Epigenetics and DNA Methylation
- Spine and Intervertebral Disc Pathology
- Medical Imaging and Analysis
- Spinal Fractures and Fixation Techniques
- Cancer Cells and Metastasis
- Colorectal Cancer Screening and Detection
- Cancer Immunotherapy and Biomarkers
- Immunotherapy and Immune Responses
- Radiomics and Machine Learning in Medical Imaging
- Herpesvirus Infections and Treatments
- Parvovirus B19 Infection Studies
- Science, Research, and Medicine
- Evolution and Genetic Dynamics
- Cytomegalovirus and herpesvirus research
The Francis Crick Institute
2018-2025
University of Oxford
2023-2025
Centre for Human Genetics
2023-2024
John Radcliffe Hospital
2024
Genomics (United Kingdom)
2024
Oxford Health NHS Foundation Trust
2024
Royal Free London NHS Foundation Trust
2019
Clear-cell renal cell carcinoma (ccRCC) exhibits a broad range of metastatic phenotypes that have not been systematically studied to date. Here, we analyzed 575 primary and 335 biopsies across 100 patients with ccRCC, including two cases sampledat post-mortem. Metastatic competence was afforded by chromosome complexity, identify 9p loss as highly selected event driving metastasis ccRCC-related mortality (p = 0.0014). Distinct patterns dissemination were observed, rapid progression multiple...
The evolutionary features of clear-cell renal cell carcinoma (ccRCC) have not been systematically studied to date. We analyzed 1,206 primary tumor regions from 101 patients recruited into the multi-center prospective study, TRACERx Renal. observe up 30 driver events per and show that subclonal diversification is associated with known prognostic parameters. By resolving patterns event ordering, co-occurrence, mutual exclusivity at clone level, we deterministic nature clonal evolution. ccRCC...
Accurate annotation of vertebral bodies is crucial for automating the analysis spinal X-ray images. However, manual these structures a laborious and costly process due to their complex nature, including small sizes varying shapes. To address this challenge expedite process, we propose an ensemble pipeline called VertXNet. This currently combines two segmentation mechanisms, semantic using U-Net, instance Mask R-CNN, automatically segment label in lateral cervical lumbar VertXNet enhances its...
BackgroundTumour-infiltrating CD8+ cytotoxic T cells confer favourable prognosis in colorectal cancer. The added prognostic value of other infiltrating immune is unclear and so we sought to investigate their two large clinical trial cohorts.MethodsWe used multiplex immunofluorescent staining tissue microarrays assess the densities CD8+, CD20+, FoxP3+, CD68+ intraepithelial intrastromal compartments from tumour samples patients with stage II–III cancer SCOT (ISRCTN59757862), which examined 3...
Lung cancer is the leading cause of mortality in U.S. and world. Although tobacco use has steadily declined with a corresponding decrease lung incidence, impact smoking on progression to its mechanisms are largely unresolved. This further highlighted by fact that presence oncogenic mutations persists histologically normal tissue for years, even decades. Therefore, we sought understand which exposure alters somatic mutational landscape result oncogenesis. To observe mutations, used...
Reliable vertebrae annotations are key to perform analysis of spinal X-ray images. However, obtaining annotation from those images is usually carried out manually due its complexity (i.e. small structures with varying shape), making it a costly and tedious process. To accelerate this process, we proposed an ensemble pipeline, VertXNet, that combines two state-of-the-art (SOTA) segmentation models (respectively U-Net Mask R-CNN) automatically segment label in Moreover, VertXNet introduces...
Abstract Multiplex immunofluorescence (mIF) imaging can provide comprehensive quantitative and spatial information for multiple immune markers tumour immunoprofiling. However, application at scale to clinical trial samples sourced from institutions is challenging due pre‐analytical heterogeneity. This study reports an analytical approach the largest multi‐parameter immunoprofiling of date. We analysed 12,592 tissue microarray (TMA) spots 3,545 colorectal cancers more than 240 in two trials...
SUMMARY Testing for DNA mismatch repair deficiency (MMRd) is recommended all colorectal cancers (CRC). Automation of this would facilitate precision medicine, particularly if it provided information on likely aetiology. We developed AIMMer, an AI -based method determination MMR protein expression at single cell level in routine pathology samples. applied to over 2,000 (CRC) from the SCOT clinical trial, which compared 3 vs 6 months oxaliplatin-based adjuvant chemotherapy (FOLFOX or CAPOX)....
Abstract Intratumor heterogeneity (ITH) is a substrate for tumor evolution and confers amenability to stressors therapies. Sources of ITH include subclonal mutations, microenvironmental factors, plasticity whereby cell has the ability adopt different states. Clear kidney cancer (ccRCC) well-characterized genetic initiating event - VHL inactivation resulting in activation HIF-1 HIF-2 transcription factors. Although consistently clonal nature, ccRCC nonetheless exhibits extensive morphological...
Abstract Why do we get cancer? is cancer highly associated with old age? Aging the accumulation of more mutations; some which can contribute to phenotypes. However, now understand that carcinogenesis much complex than originally appreciated. In particular, there are tissue environmental forces both impede and promote evolution. Just as organismal evolution known be driven by changes, cellular (somatic) in our bodies similarly changes environments, whether caused normal process aging,...
ABSTRACT Multiplex immunofluorescence (mIF) imaging can provide comprehensive quantitative and spatial information for multiple immune markers tumour immunoprofiling. However, application at scale to clinical trial samples sourced from institutions is challenging due pre-analytical heterogeneity. This study reports an analytical approach the largest multiparameter immunoprofiling of date. We analysed 12,592 tissue microarray (TMA) spots 3,545 colorectal cancers (CRC) more than 240 in two...