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The MOBSTER R package for tumour subclonal deconvolution from bulk DNA whole-genome sequencing data.
(BMC, 2020-11-17)
BACKGROUND: The large-scale availability of whole-genome sequencing profiles from bulk DNA sequencing of cancer tissues is fueling the application of evolutionary theory to cancer. From a bulk biopsy, subclonal deconvolution ...
Spatially constrained tumour growth affects the patterns of clonal selection and neutral drift in cancer genomic data.
(PUBLIC LIBRARY SCIENCE, 2019-07-29)
Quantification of the effect of spatial tumour sampling on the patterns of mutations detected in next-generation sequencing data is largely lacking. Here we use a spatial stochastic cellular automaton model of tumour growth ...
Measuring Clonal Evolution in Cancer with Genomics.
(ANNUAL REVIEWS, 2019-08-31)
Cancers originate from somatic cells in the human body that have accumulated genetic alterations. These mutations modify the phenotype of the cells, allowing them to escape the homeostatic regulation that maintains normal ...
Evolutionary dynamics of neoantigens in growing tumors.
(NATURE PORTFOLIO, 2020-10-01)
Cancers accumulate mutations that lead to neoantigens, novel peptides that elicit an immune response, and consequently undergo evolutionary selection. Here we establish how negative selection shapes the clonality of ...
The mutational signatures of formalin fixation on the human genome.
(NATURE PORTFOLIO, 2022-09-06)
Clinical archives of patient material near-exclusively consist of formalin-fixed and paraffin-embedded (FFPE) blocks. The ability to precisely characterise mutational signatures from FFPE-derived DNA has tremendous ...
Immune selection determines tumor antigenicity and influences response to checkpoint inhibitors.
(NATURE PORTFOLIO, 2023-03-01)
In cancer, evolutionary forces select for clones that evade the immune system. Here we analyzed >10,000 primary tumors and 356 immune-checkpoint-treated metastases using immune dN/dS, the ratio of nonsynonymous to synonymous ...
Catch my drift? Making sense of genomic intra-tumour heterogeneity.
(ELSEVIER, 2017-04-01)
The cancer genome is shaped by three components of the evolutionary process: mutation, selection and drift. While many studies have focused on the first two components, the role of drift in cancer evolution has received ...
Between-region genetic divergence reflects the mode and tempo of tumor evolution.
(NATURE PUBLISHING GROUP, 2017-06-05)
Given the implications of tumor dynamics for precision medicine, there is a need to systematically characterize the mode of evolution across diverse solid tumor types. In particular, methods to infer the role of natural ...
Genomic landscape and clonal architecture of mouse oral squamous cell carcinomas dictate tumour ecology.
(NATURE PORTFOLIO, 2020-11-09)
To establish whether 4-nitroquinoline N-oxide-induced carcinogenesis mirrors the heterogeneity of human oral squamous cell carcinoma (OSCC), we have performed genomic analysis of mouse tongue lesions. The mutational ...
First passage time analysis of spatial mutation patterns reveals sub-clonal evolutionary dynamics in colorectal cancer.
(PUBLIC LIBRARY SCIENCE, 2023-03-01)
The signature of early cancer dynamics on the spatial arrangement of tumour cells is poorly understood, and yet could encode information about how sub-clones grew within the expanding tumour. Novel methods of quantifying ...