Results 111 to 120 of about 18,512,812 (309)

Impact of cancer mutational signatures on transcription factor motifs in the human genome

BMC Medical Genomics, 2019
Background Somatic mutations in cancer genomes occur through a variety of molecular mechanisms, which contribute to different mutational patterns. To summarize these, mutational signatures have been defined using a large number of cancer genomes, and ...
Calvin Wing Yiu Chan, Zuguang Gu, Matthias Bieg, Roland Eils, Carl Herrmann   +4 more
doaj   +1 more source

pyCancerSig: subclassifying human cancer with comprehensive single nucleotide, structural and microsatellite mutational signature deconstruction from whole genome sequencing

BMC Bioinformatics, 2020
Background DNA damage accumulates over the course of cancer development. The often-substantial amount of somatic mutations in cancer poses a challenge to traditional methods to characterize tumors based on driver mutations.
Jessada Thutkawkorapin, Jesper Eisfeldt, Emma Tham, Daniel Nilsson   +3 more
doaj   +1 more source

Surfaceome: a new era in the discovery of immune evasion mechanisms of circulating tumor cells

Molecular Oncology, EarlyView.
In the era of immunotherapies, many patients either do not respond or eventually develop resistance. We propose to pave the way for proteomic analysis of surface‐expressed proteins called surfaceome, of circulating tumor cells. This approach seeks to identify immune evasion mechanisms and discover potential therapeutic targets. Circulating tumor cells (
Doryan Masmoudi, Jérome Vialaret, Christophe Hirtz, Catherine Alix‐Panabières   +3 more
wiley   +1 more source

Clonal status of actionable driver events and the timing of mutational processes in cancer evolution

Science Translational Medicine, 2015
Pan-cancer analysis of tumor subclonal structures uncovers widespread intratumor heterogeneity in actionable driver events and reveals mutational processes fueling their selection. Uncovering a tumor’s family tree In the era of targeted anticancer drugs,
N. Mcgranahan, F. Favero, E. D. de Bruin, Nicolai J. Birkbak, Z. Szallasi, C. Swanton   +5 more
semanticscholar   +1 more source

Mutational signature distribution varies with DNA replication timing and strand asymmetry

Genome Biology, 2018
Background DNA replication plays an important role in mutagenesis, yet little is known about how it interacts with other mutagenic processes. Here, we use somatic mutation signatures—each representing a mutagenic process—derived from 3056 patients ...
Marketa Tomkova, Jakub Tomek, Skirmantas Kriaucionis, Benjamin Schuster-Böckler   +3 more
doaj   +1 more source

Clinical applications of next‐generation sequencing‐based ctDNA analyses in breast cancer: defining treatment targets and dynamic changes during disease progression

Molecular Oncology, EarlyView.
Circulating tumor DNA (ctDNA) offers a possibility for different applications in early and late stage breast cancer management. In early breast cancer tumor informed approaches are increasingly used for detecting molecular residual disease (MRD) and early recurrence. In advanced stage, ctDNA provides a possibility for monitoring disease progression and
Eva Valentina Klocker, Samantha Hasenleithner, Rupert Bartsch, Simon P. Gampenrieder, Daniel Egle, Christian F. Singer, Gabriel Rinnerthaler, Michael Hubalek, Katja Schmitz, Zsuzsanna Bago‐Horvath, Andreas Petzer, Sonja Heibl, Ellen Heitzer, Marija Balic, Michael Gnant   +14 more
wiley   +1 more source

Faster Mutation Analysis via Equivalence Modulo States [PDF]

arXiv, 2017
Mutation analysis has many applications, such as asserting the quality of test suites and localizing faults. One important bottleneck of mutation analysis is scalability. The latest work explores the possibility of reducing the redundant execution via split-stream execution.
arxiv  

A practical guide for mutational signature analysis in hematological malignancies

Nature Communications, 2019
Mutational signature analysis provides important information about the mutational processes underpinning different stages of tumorigenesis. Here, the authors compare publicly available signature extraction tools and suggest a framework for the generation
Francesco Maura, Andrea Degasperi, Ferran Nadeu, Daniel Leongamornlert, Helen Davies, Luiza Moore, Romina Royo, Bachisio Ziccheddu, Xose S. Puente, Herve Avet-Loiseau, Peter J. Campbell, Serena Nik-Zainal, Elias Campo, Nikhil Munshi, Niccolò Bolli   +14 more
doaj   +1 more source

Circulating tumor cells: advancing personalized therapy in small cell lung cancer patients

Molecular Oncology, EarlyView.
Small cell lung cancer (SCLC) is an aggressive form of lung cancer that spreads rapidly to secondary sites such as the brain and liver. Cancer cells circulating in the blood, “circulating tumor cells” (CTCs), have demonstrated prognostic value in SCLC, and evaluating biomarkers on CTCs could guide treatment decisions such as for PARP inhibitors ...
Prajwol Shrestha, Steven Kao, Veronica K. Cheung, Wendy A. Cooper, Nico van Zandwijk, John E. J. Rasko, Dannel Yeo   +6 more
wiley   +1 more source

Fixation probability of a nonmutator in a large population of asexual mutators [PDF]

Journal of Theoretical Biology 433 (2017) 85-93, 2017
In an adapted population of mutators in which most mutations are deleterious, a nonmutator that lowers the mutation rate is under indirect selection and can sweep to fixation. Using a multitype branching process, we calculate the fixation probability of a rare nonmutator in a large population of asexual mutators.
arxiv