A5021741207- Cancer Genomics and Diagnostics
- Genetic factors in colorectal cancer
- DNA and Nucleic Acid Chemistry
- RNA and protein synthesis mechanisms
- Genomics and Rare Diseases
- Thyroid Cancer Diagnosis and Treatment
- RNA Research and Splicing
- CRISPR and Genetic Engineering
- Nanopore and Nanochannel Transport Studies
- RNA modifications and cancer
- Renal and related cancers
- Pluripotent Stem Cells Research
- Neonatal Respiratory Health Research
- Molecular Biology Techniques and Applications
- Cystic Fibrosis Research Advances
- Protein Structure and Dynamics
- Lymphoma Diagnosis and Treatment
- Gene expression and cancer classification
- DNA Repair Mechanisms
- RNA Interference and Gene Delivery
- Genomics and Phylogenetic Studies
- Adenosine and Purinergic Signaling
- T-cell and Retrovirus Studies
- Cutaneous lymphoproliferative disorders research
- Breast Cancer Treatment Studies
University of Cambridge
2018-2022
Hutchison/MRC Research Centre
2020-2022
Cancer Research UK Cambridge Center
2022
MRC Cancer Unit
2020-2021
Wellcome Sanger Institute
2018-2020
Addenbrooke's Hospital
2020
Universidade Federal de Minas Gerais
2014-2016
Whole-genome sequencing (WGS) permits comprehensive cancer genome analyses, revealing mutational signatures, imprints of DNA damage and repair processes that have arisen in each patient's cancer. We performed signature analyses on 12,222 WGS tumor-normal matched pairs, from patients recruited via the UK National Health Service. contrasted our results to two independent datasets, International Cancer Genome Consortium (ICGC) Hartwig Foundation, involving 18,640 cancers total. Our add 40...
Abstract We explored human induced pluripotent stem cells (hiPSCs) derived from different tissues to gain insights into genomic integrity at single-nucleotide resolution. used genome sequencing data two large hiPSC repositories involving 696 hiPSCs and daughter subclones. find ultraviolet light (UV)-related damage in ~72% of skin fibroblast-derived (F-hiPSCs), occasionally resulting substantial mutagenesis (up 15 mutations per megabase). demonstrate remarkable heterogeneity between...
DNA base pairs are known to open more easily at the helix terminal, a process usually called end fraying, details of which still poorly understood. Here, we present mesoscopic model calculation based on available experimental data where consider separately terminal duplex. Our results show an important reduction hydrogen bond strength for cytosine-guanine (CG) is uniform over whole range salt concentrations, while AT pairs, obtain nearly 1/3 but only low concentrations. At higher...
Guanine-Uracil (GU) mismatches are crucial to the stability of RNA double helix and need be considered in folding algorithms for numerous biotechnological applications. Yet despite its importance, many aspects GU base pairs still poorly understood. There is also a lack parametrization which prevents it mesoscopic models. Here, we adapted Peyrard-Bishop model deal with context-dependent hydrogen bonds calculated parameters related bonding stacking from available experimental melting...
Background The RET S836S variant has been associated with early onset and increased risk for metastatic disease in medullary thyroid carcinoma (MTC). However, the mechanism by which this modulates MTC pathogenesis is still open to discuss. Of interest, strong linkage disequilibrium (LD) between 3'UTR variants reported Hirschsprung's patients. Objective To evaluate frequency of (rs76759170 rs3026785) patients determine whether these are LD polymorphism. Methods Our sample comprised 152...
The Peyrard-Bishop model is a mesoscopic approximation to DNA and RNA molecules. Several variants of this exists, from 3D Hamiltonians, including torsional angles, simpler 2D versions. Currently, we are able parametrize the which allows us extract important information about molecule. For example, with technique were recently obtain hydrogen bonds melting temperatures, previously obtainable only NMR measurements. Here, take Hamiltonian set angles zero. Curiously, in doing do not recover...
Summary Human Induced Pluripotent Stem Cells (hiPSC) are an established patient-specific model system where opportunities emerging for cell-based therapies. We contrast hiPSCs derived from different tissues, skin and blood, in the same individual. show extensive single-nucleotide mutagenesis all hiPSC lines, although fibroblast-derived (F-hiPSCs) particularly heavily mutagenized by ultraviolet(UV)-related damage. utilize genome sequencing data on 454 F-hiPSCs 44 blood-derived (B-hiPSCs) to...
Mesoscopic models can be used for the description of thermodynamic properties RNA duplexes. With use experimental melting temperatures, its parametrization provide important insights into hydrogen bonds and stacking interactions as has been done high sodium concentrations. However, lower salt concentrations is still missing due to limited amount published temperature data. While Peyrard-Bishop (PB) was found largely independent strand concentrations, it requires that all temperatures are...
Introduction With the advent of next generation sequencing whole exomes and genomes, we can now obtain a comprehensive view somatic mutations that are present in tumours. Using latent variable discovery approaches such as non-negative matrix factorisation (NMF), recurrent mutational patterns, called signatures, have been identified, some which attributed to processes, sunlight exposure or homologous recombination deficiency. As more cancer genomes available, identification new signatures...
Mesoscopic models can be used for the description of thermodynamic properties RNA duplexes. With use experimental melting temperatures, its parametrization provide important insights into hydrogen bonds and stacking interactions as has been done high sodium concentrations. However, lower salt concentrations is still missing due to limited amount published temperature data. While Peyrard-Bishop (PB) was found largely independent strand concentrations, it requires that all temperatures are...