MutationalPatterns: the one stop shop for the analysis of mutational processes

F Manders, AM Brandsma, J de Kanter, M Verheul… - BMC genomics, 2022 - Springer
Background The collective of somatic mutations in a genome represents a record of
mutational processes that have been operative in a cell. These processes can be …

The co-evolution of the genome and epigenome in colorectal cancer

T Heide, J Househam, GD Cresswell, I Spiteri, C Lynn… - Nature, 2022 - nature.com
Colorectal malignancies are a leading cause of cancer-related death and have undergone
extensive genomic study,. However, DNA mutations alone do not fully explain malignant …

The mutational signature profile of known and suspected human carcinogens in mice

L Riva, AR Pandiri, YR Li, A Droop, J Hewinson… - Nature …, 2020 - nature.com
Epidemiological studies have identified many environmental agents that appear to
significantly increase cancer risk in human populations. By analyzing tumor genomes from …

Computational tools to detect signatures of mutational processes in DNA from tumours: a review and empirical comparison of performance

H Omichessan, G Severi, V Perduca - PloS one, 2019 - journals.plos.org
Mutational signatures refer to patterns in the occurrence of somatic mutations that might be
uniquely ascribed to particular mutational process. Tumour mutation catalogues can reveal …

Mutational signatures: From methods to mechanisms

YA Kim, MDM Leiserson, P Moorjani… - Annual Review of …, 2021 - annualreviews.org
Mutations are the driving force of evolution, yet they underlie many diseases, in particular,
cancer. They are thought to arise from a combination of stochastic errors in DNA processing …

Contribution of pks+E. coli mutations to colorectal carcinogenesis

B Chen, D Ramazzotti, T Heide, I Spiteri… - Nature …, 2023 - nature.com
The dominant mutational signature in colorectal cancer genomes is C> T deamination
(COSMIC Signature 1) and, in a small subgroup, mismatch repair signature (COSMIC …

Mutational signatures and heterogeneous host response revealed via large-scale characterization of SARS-CoV-2 genomic diversity

A Graudenzi, D Maspero, F Angaroni, R Piazza… - Iscience, 2021 - cell.com
To dissect the mechanisms underlying the inflation of variants in the Severe Acute
Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) genome, we present a large-scale …

Spectrum of DNA mismatch repair failures viewed through the lens of cancer genomics and implications for therapy

D Mas-Ponte, M McCullough, F Supek - Clinical Science, 2022 - portlandpress.com
Genome sequencing can be used to detect DNA repair failures in tumors and learn about
underlying mechanisms. Here, we synthesize findings from genomic studies that examined …

Cutting-edge ai technologies meet precision medicine to improve cancer care

PC Lin, YS Tsai, YM Yeh, MR Shen - Biomolecules, 2022 - mdpi.com
To provide precision medicine for better cancer care, researchers must work on clinical
patient data, such as electronic medical records, physiological measurements, biochemistry …

Comprehensive genomic characterization of breast tumors with BRCA1 and BRCA2 mutations

A Lal, D Ramazzotti, Z Weng, K Liu, JM Ford… - BMC Medical …, 2019 - Springer
Background Germline mutations in the BRCA1 and BRCA2 genes predispose carriers to
breast and ovarian cancer, and there remains a need to identify the specific genomic …