Browsing by author "Sottoriva, Andrea"
Now showing items 41-53 of 53
-
Reply to 'Revisiting signatures of neutral tumor evolution in the light of complexity of cancer genomic data'.
Williams, MJ; Werner, B; Heide, T; Barnes, CP; Graham, TA; et al. (2018-12) -
Reply: Is the evolution of tumors Darwinian or non-Darwinian?
Williams, MJ; Werner, B; Barnes, CP; Graham, TA; Sottoriva, A (OXFORD UNIV PRESS, 2018-01-01) -
Reply: Uncertainties in tumor allele frequencies limit power to infer evolutionary pressures.
Williams, MJ; Werner, B; Barnes, CP; Graham, TA; Sottoriva, A (2017-08) -
Resolving genetic heterogeneity in cancer.
Turajlic, S; Sottoriva, A; Graham, T; Swanton, C (NATURE PUBLISHING GROUP, 2019-07-01)To a large extent, cancer conforms to evolutionary rules defined by the rates at which clones mutate, adapt and grow. Next-generation sequencing has provided a snapshot of the genetic landscape of most cancer types, and ... -
Robust RNA-based in situ mutation detection delineates colorectal cancer subclonal evolution.
Baker, A-M; Huang, W; Wang, X-MM; Jansen, M; Ma, X-J; et al. (NATURE PUBLISHING GROUP, 2017-12-08)Intra-tumor heterogeneity (ITH) is a major underlying cause of therapy resistance and disease recurrence, and is a read-out of tumor growth. Current genetic ITH analysis methods do not preserve spatial context and may not ... -
Spatially constrained tumour growth affects the patterns of clonal selection and neutral drift in cancer genomic data.
Chkhaidze, K; Heide, T; Werner, B; Williams, MJ; Huang, W; et al. (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 ... -
Subclonal reconstruction of tumors by using machine learning and population genetics.
Caravagna, G; Heide, T; Williams, MJ; Zapata, L; Nichol, D; et al. (NATURE PUBLISHING GROUP, 2020-09-01)Most cancer genomic data are generated from bulk samples composed of mixtures of cancer subpopulations, as well as normal cells. Subclonal reconstruction methods based on machine learning aim to separate those subpopulations ... -
The co-evolution of the genome and epigenome in colorectal cancer
Sottoriva, A; Heide, T; Cresswell, G; Spiteri, I; Lynn, C; et al. (2021-07-12)Colorectal malignancies are a leading cause of cancer death. Despite large-scale genomic efforts, DNA mutations do not fully explain malignant evolution. Here we study the co-evolution of the genome and epigenome of ... -
The co-evolution of the genome and epigenome in colorectal cancer.
Heide, T; Househam, J; Cresswell, GD; Spiteri, I; Lynn, C; et al. (NATURE PORTFOLIO, 2022-11-24)Colorectal malignancies are a leading cause of cancer-related death1 and have undergone extensive genomic study2,3. However, DNA mutations alone do not fully explain malignant transformation4-7. Here we investigate the ... -
The evolutionary landscape of colorectal tumorigenesis.
Cross, W; Kovac, M; Mustonen, V; Temko, D; Davis, H; et al. (NATURE PORTFOLIO, 2018-10-01)The evolutionary events that cause colorectal adenomas (benign) to progress to carcinomas (malignant) remain largely undetermined. Using multi-region genome and exome sequencing of 24 benign and malignant colorectal tumours, ... -
The MOBSTER R package for tumour subclonal deconvolution from bulk DNA whole-genome sequencing data.
Caravagna, G; Sanguinetti, G; Graham, TA; Sottoriva, A (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 ... -
The Spatiotemporal Evolution of Lymph Node Spread in Early Breast Cancer.
Barry, P; Vatsiou, A; Spiteri, I; Nichol, D; Cresswell, GD; et al. (SPRINGER, 2018-02-01)Purpose: The most significant prognostic factor in early breast cancer is lymph node involvement. This stage between localized and systemic disease is key to understanding breast cancer progression; however, our knowledge ... -
Variation of mutational burden in healthy human tissues suggests non-random strand segregation and allows measuring somatic mutation rates.
Werner, B; Sottoriva, A (PUBLIC LIBRARY SCIENCE, 2018-06-07)The immortal strand hypothesis poses that stem cells could produce differentiated progeny while conserving the original template strand, thus avoiding accumulating somatic mutations. However, quantitating the extent of ...