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Subclonal reconstruction of tumors by using machine learning and population genetics.
(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 ...
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 ...
Germline MBD4 deficiency causes a multi-tumor predisposition syndrome.
(CELL PRESS, 2022-05-05)
We report an autosomal recessive, multi-organ tumor predisposition syndrome, caused by bi-allelic loss-of-function germline variants in the base excision repair (BER) gene MBD4. We identified five individuals with bi-allelic ...
Cell Competition in Carcinogenesis.
(AMER ASSOC CANCER RESEARCH, 2022-12-16)
The majority of human cancers evolve over time through the stepwise accumulation of somatic mutations followed by clonal selection akin to Darwinian evolution. However, the in-depth mechanisms that govern clonal dynamics ...
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 ...
Clinical trial designs for evaluating and exploiting cancer evolution.
(ELSEVIER SCI LTD, 2023-07-01)
The evolution of drug-resistant cell subpopulations causes cancer treatment failure. Current preclinical evidence shows that it is possible to model herding of clonal evolution and collateral sensitivity where an initial ...
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 ...
Measuring cancer evolution from the genome.
(WILEY-BLACKWELL, 2017-01-01)
The temporal dynamics of cancer evolution remain elusive, because it is impractical to longitudinally observe cancers unperturbed by treatment. Consequently, our knowledge of how cancers grow largely derives from inferences ...
Detecting repeated cancer evolution from multi-region tumor sequencing data.
(NATURE PUBLISHING GROUP, 2018-08-31)
Recurrent successions of genomic changes, both within and between patients, reflect repeated evolutionary processes that are valuable for the anticipation of cancer progression. Multi-region sequencing allows the temporal ...