Ian Vermes
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View article: SPARKI: a tool for the statistical analysis of pathogen identification results
SPARKI: a tool for the statistical analysis of pathogen identification results Open
Motivation Many pathogen identification and microbiome analysis tools have been developed in recent years, with Kraken 2 being one of the most popular. While tools downstream of Kraken 2 can assist in the interpretation of its outputs, a s…
View article: Modelling Acral Melanoma in Admixed Brazilians Uncovers Genomic Drivers and Targetable Pathways
Modelling Acral Melanoma in Admixed Brazilians Uncovers Genomic Drivers and Targetable Pathways Open
Acral melanoma (AM) is an aggressive melanoma subtype with limited therapeutic options and poor outcomes. In non-European descent and admixed populations, like those residing in Latin America, AM accounts for a significant proportion of cu…
View article: Oncogenomic profiling of cutaneous pericytic tumours reveals distinct drivers and shared biological processes
Oncogenomic profiling of cutaneous pericytic tumours reveals distinct drivers and shared biological processes Open
To-date the genomic landscape of cutaneous pericytic tumours (PTs), which represent a morphological continuum, have not been comprehensively explored. In order to identify the driver events of PTs from across their histological spectrum, a…
View article: Wnt/β-catenin activation by mutually exclusive FBXW11 and CTNNB1 hotspot mutations drives salivary basal cell adenoma
Wnt/β-catenin activation by mutually exclusive FBXW11 and CTNNB1 hotspot mutations drives salivary basal cell adenoma Open
View article: Comprehensive profiling of the mutational landscape of hidradenoma papilliferum validates key role of alterations in the PI3K/AKT pathway alterations
Comprehensive profiling of the mutational landscape of hidradenoma papilliferum validates key role of alterations in the PI3K/AKT pathway alterations Open
Background Hidradenoma papilliferum (HP) is a rare, benign epithelial tumour arising from the anogenital mammary-like glands, that occurs almost exclusively in the anogenital region of middle-aged women. To-date, genetic characterisation o…
View article: Exploration of the mutational landscape of cutaneous leiomyoma confirms <i>FH</i> as a driver gene and identifies targeting purine metabolism as a potential therapeutic strategy
Exploration of the mutational landscape of cutaneous leiomyoma confirms <i>FH</i> as a driver gene and identifies targeting purine metabolism as a potential therapeutic strategy Open
To comprehensively explore the mutational landscape of cutaneous leiomyoma (cLM) and identify candidate driver events, we performed a retrospective, multi-institutional, whole-exome sequencing and RNA sequencing study. We confirmed that a …
View article: Activation of Wnt/β-catenin signalling by mutually exclusive<i>FBXW11</i>and<i>CTNNB1</i>hotspot mutations drives salivary gland basal cell adenoma
Activation of Wnt/β-catenin signalling by mutually exclusive<i>FBXW11</i>and<i>CTNNB1</i>hotspot mutations drives salivary gland basal cell adenoma Open
Wnt signalling must be ‘just right’ to promote tumour growth. Basal cell adenoma (BCA) and basal cell adenocarcinoma (BCAC) of the salivary gland are rare tumours that can be difficult to distinguish from each other and other salivary glan…
View article: Comprehensive mutational profiling identifies new driver events in cutaneous leiomyosarcoma
Comprehensive mutational profiling identifies new driver events in cutaneous leiomyosarcoma Open
Background Cutaneous leiomyosarcoma (cLMS) is a rare soft-tissue neoplasm, showing smooth muscle differentiation, that arises from the mesenchymal cells of the dermis. To date, genetic investigation of these tumours has involved studies wi…
View article: Assigning mutational signatures to individual samples and individual somatic mutations with SigProfilerAssignment
Assigning mutational signatures to individual samples and individual somatic mutations with SigProfilerAssignment Open
Motivation Analysis of mutational signatures is a powerful approach for understanding the mutagenic processes that have shaped the evolution of a cancer genome. To evaluate the mutational signatures operative in a cancer genome, one first …
View article: Topography of mutational signatures in human cancer
Topography of mutational signatures in human cancer Open
The somatic mutations found in a cancer genome are imprinted by different mutational processes. Each process exhibits a characteristic mutational signature, which can be affected by the genome architecture. However, the interplay between m…
View article: Assigning mutational signatures to individual samples and individual somatic mutations with SigProfilerAssignment
Assigning mutational signatures to individual samples and individual somatic mutations with SigProfilerAssignment Open
Analysis of mutational signatures is a powerful approach for understanding the mutagenic processes that have shaped the evolution of a cancer genome. Here we present SigProfilerAssignment, a desktop and an online computational framework fo…
View article: Topography of mutational signatures in human cancer
Topography of mutational signatures in human cancer Open
SUMMARY The somatic mutations found in a cancer genome are imprinted by different mutational processes. Each process exhibits a characteristic mutational signature, which can be affected by the genome architecture. However, the interplay b…