Centre for Tumour Biology: Recent submissions
Now showing items 221-240 of 380
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Quantification of subclonal selection in cancer from bulk sequencing data
(2016-12-22)Recent studies have identified prevalent subclonal architectures within many cancer types. However, the temporal evolutionary dynamics that produce these subclonal architectures remain unknown. Here we measure evolutionary ... -
Insights Into the Pathophysiology of Esophageal Adenocarcinoma.
(2018-01)Although researchers have identified genetic alterations that contribute to development of esophageal adenocarcinoma, we know little about features of patients or environmental factors that mediate progression of chronic ... -
Tumour associated macrophage recruitment in SCC
(2017-10) -
Inhibition of fatty acid desaturation is detrimental to cancer cell survival in metabolically compromised environments.
(2016)BACKGROUND: Enhanced macromolecule biosynthesis is integral to growth and proliferation of cancer cells. Lipid biosynthesis has been predicted to be an essential process in cancer cells. However, it is unclear which enzymes ... -
Evolutionary dynamics of neoantigens in growing tumours
(2019-01-31)ABSTRACT Cancer evolution is driven by the acquisition of somatic mutations that provide cells with a beneficial phenotype in a changing microenvironment. However, mutations that give rise to neoantigens, novel cancer–specific ... -
Resolving genetic heterogeneity in cancer
(2019-07) -
Spatially constrained tumour growth affects the patterns of clonal selection and neutral drift in cancer genomic data
(2019)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 ... -
NeoPredPipe: high-throughput neoantigen prediction and recognition potential pipeline.
(2019-05-22)BACKGROUND: Next generation sequencing has yielded an unparalleled means of quickly determining the molecular make-up of patient tumors. In conjunction with emerging, effective immunotherapeutics for a number of cancers, ... -
Niche engineering drives early passage through an immune bottleneck in progression to colorectal cancer
(2019-05-03)Colorectal cancer develops from its precursor lesion, the adenoma. The immune system is hypothesized to be key in modulating progression, but tumor-immune eco-evolutionary dynamics remain uncharacterized. Here, we demonstrate ... -
Measuring Clonal Evolution in Cancer with Genomics.
(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 ... -
Measuring the distribution of fitness effects in somatic evolution by combining clonal dynamics with dN/dS ratios
(2019-06-05)Abstract The distribution of fitness effects (DFE) defines how new mutations spread through an evolving population. The ratio of non-synonymous to synonymous mutations (dN/dS) has become a popular method to detect selection ... -
Model-based tumor subclonal reconstruction
(2019)The vast majority of cancer next-generation sequencing data consist of bulk samples composed of mixtures of cancer and normal cells. To study tumor evolution, subclonal reconstruction approaches based on machine learning ... -
Measuring single cell divisions in human cancers from multi-region sequencing data
(2019-02-25)Abstract Cancer is driven by complex evolutionary dynamics involving billions of cells. Increasing effort has been dedicated to sequence single tumour cells, but obtaining robust measurements remains challenging. Here we ...