A5077121856- Cancer Genomics and Diagnostics
- Genomics and Rare Diseases
- Genomic variations and chromosomal abnormalities
- Lung Cancer Treatments and Mutations
- SARS-CoV-2 and COVID-19 Research
- Genetic factors in colorectal cancer
- COVID-19 epidemiological studies
- Research on Leishmaniasis Studies
- Cancer Immunotherapy and Biomarkers
- SARS-CoV-2 detection and testing
- Trypanosoma species research and implications
- Parasites and Host Interactions
Genomics England
2024
European Bioinformatics Institute
2024
University College London
2024
Royal National Orthopaedic Hospital
2024
Boston Children's Hospital
2024
University of Sheffield
2019-2020
University of Cambridge
2015
A SARS-CoV-2 variant carrying the Spike protein amino acid change D614G has become most prevalent form in global pandemic. Dynamic tracking of frequencies revealed a recurrent pattern G614 increase at multiple geographic levels: national, regional, and municipal. The shift occurred even local epidemics where original D614 was well established prior to introduction variant. consistency this highly statistically significant, suggesting that may have fitness advantage. We found grows higher...
Summary In this study, we followed the genomic, lipidomic and metabolomic changes associated with selection of miltefosine (MIL) resistance in two clinically derived Leishmania donovani strains different inherent to antimonial drugs (antimony sensitive strain Sb‐S; antimony resistant Sb‐R). MIL‐R was easily induced both using promastigote‐stage, but a significant increase intracellular amastigote compared corresponding wild‐type did not occur until promastigotes had adapted 12.2 μM MIL. A...
Accurate detection of somatic structural variants (SVs) and copy number aberrations (SCNAs) is critical to inform the diagnosis treatment human cancers. Here, we describe SAVANA, a computationally efficient algorithm designed for joint analysis SVs, SCNAs, tumour purity ploidy using long-read sequencing data. SAVANA relies on machine learning distinguish true SVs from artefacts provide prediction errors individual SVs. Using high-depth Illumina nanopore whole-genome data 99 tumours matched...
<title>Abstract</title> Accurate detection of somatic structural variants (SVs) and copy number aberrations (SCNAs) is critical to inform the diagnosis treatment human cancers. Here, we describe SAVANA, a computationally efficient algorithm designed for joint analysis SVs, SCNAs, tumour purity ploidy using long-read sequencing data. SAVANA relies on machine learning distinguish true SVs from artefacts provide prediction errors individual SVs. Using high-depth Illumina nanopore whole-genome...
Accurate massively parallel sequencing (MPS) of genetic variants is key to many areas science and medicine, such as cataloging population variation diagnosing diseases. Certain genomic positions can be prone higher rates systematic alignment bias that limit accuracy, resulting in false positive variant calls. Current standard practices differentiate between loci cannot sequenced with high confidence utilize consensus different methods a proxy for confidence. These have significant...
The burden of somatic mutations and neoantigens has been associated with improved survival in cancer treated immunotherapies, especially non-small cell lung (NSCLC). However, there is uncertainty about their effect on outcome early-stage untreated cases. We posited that the a specific set genes may also contribute to prognosis early NSCLC patients. From small cohort 36 cases, we were able identify copy number alterations 865 contributed patient overall survival. Simply, altered (NAG) among...
Abstract Accurate massively parallel sequencing (MPS) of genetic variants is key to many areas science and medicine, such as cataloguing population variation diagnosing diseases. Certain genomic positions can be prone higher rates systematic alignment bias that limit accuracy, resulting in false positive variant calls. Current standard practices differentiate between loci cannot sequenced with high confidence utilise consensus different methods a proxy for confidence. These have significant...
ABSTRACT Background Genomic profiling of patient tumors has linked somatic driver mutations to survival outcomes non-small cell lung cancer (NSCLC) patients, especially for those receiving targeted therapies. However, it remains unclear whether specific non-driver have any prognostic utility. Methods Whole exomes and transcriptomes were measured from NSCLC xenograft models patients with diverse clinical outcomes. Penalised regression analysis was performed identify a set 865 genes associated...