Results 41 to 50 of about 77,245 (318)

Deep learning model accurately classifies metastatic tumors from primary tumors based on mutational signatures

Scientific Reports, 2023
Metastatic propagation is the leading cause of death for most cancers. Prediction and elucidation of metastatic process is crucial for the treatment of cancer.
Weisheng Zheng, Mengchen Pu, Xiaorong Li, Zhaolan Du, Sutong Jin, Xingshuai Li, Jielong Zhou, Yingsheng Zhang   +7 more
doaj   +1 more source

Mutational signatures of DNA mismatch repair deficiency in C. elegans and human cancers [PDF]

, 2018
Throughout their lifetime, cells are subject to extrinsic and intrinsic mutational processes leaving behind characteristic signatures in the genome.
Campbell, Peter J., Gartner, Anton, Gerstung, Moritz, Hong, Ye, Meier, Bettina, Schofield, Pieta, Volkova, Nadezda V.   +6 more
core   +3 more sources

An extended APOBEC3A mutation signature in cancer [PDF]

Nature Communications, 2021
AbstractAPOBEC mutagenesis, a major driver of cancer evolution, is known for targeting TpC sites in DNA. Recently, we showed that APOBEC3A (A3A) targets DNA hairpin loops. Here, we show that DNA secondary structure is in fact an orthogonal influence on A3A substrate optimality and, surprisingly, can override the TpC sequence preference.
Adam Langenbucher, Danae Bowen, Ramin Sakhtemani, Elodie Bournique, Jillian F. Wise, Lee Zou, Ashok S. Bhagwat, Rémi Buisson, Michael S. Lawrence   +8 more
openaire   +6 more sources

Mutational processes in cancer preferentially affect binding of particular transcription factors

Scientific Reports, 2021
Protein binding microarrays provide comprehensive information about the DNA binding specificities of transcription factors (TFs), and can be used to quantitatively predict the effects of DNA sequence variation on TF binding.
Mo Liu, Arnoud Boot, Alvin W. T. Ng, Raluca Gordân, Steven G. Rozen   +4 more
doaj   +1 more source

Diffsig: Associating Risk Factors with Mutational Signatures. [PDF]

Cancer Epidemiol Biomarkers Prev, 2023
Abstract Background: Somatic mutational signatures elucidate molecular vulnerabilities to therapy, and therefore detecting signatures and classifying tumors with respect to signatures has clinical value.
Park JE, Smith MA, Van Alsten SC, Walens A, Wu D, Hoadley KA, Troester MA, Love MI.   +7 more
europepmc   +4 more sources

Genomic catastrophes frequently arise in esophageal adenocarcinoma and drive tumorigenesis [PDF]

, 2014
Oesophageal adenocarcinoma (EAC) incidence is rapidly increasing in Western countries. A better understanding of EAC underpins efforts to improve early detection and treatment outcomes.
Anderson, M, Bailey, P, Barbour, A, Bruxner, T, Campbell, P, Christ, A, Fink, J, Gotley, D, Grimmond, S, Harliwong, I, Hayward, N, Holmes, O, Hussey, D, Idrisoglu, S, Kazakoff, S, Krause, L, Lampe, G, Leonard, C, Loffler, K, Lord, R, Manning, S, Miller, D, Nancarrow, D, Newell, F, Nones, K, Nourbakhsh, E, Nourse, C, Patch, A, Pearson, J, Phillips, W, Quek, K, Quinn, M, Reid, L, Simpson, P, Smithers, B, Tang, Y, Waddell, N, Waddell, N, Watson, D, Wayte, N, Whiteman, D, Wilson, P, Wood, S, Xu, Q   +43 more
core   +4 more sources

Pan-cancer mutational signature surveys correlated mutational signature with geospatial environmental exposures and viral infections

Computational and Structural Biotechnology Journal, 2023
Cancer has been disproportionally affecting minorities. Genomic-based cancer disparity analyses have been less common than conventional epidemiological studies. In the past decade, mutational signatures have been established as characteristic footprints of endogenous or exogenous carcinogens.Integrating datasets of diverse cancer types from The Cancer ...
Judy Bai, Katherine Ma, Shangyang Xia, Richard Geng, Claire Shen, Limin Jiang, Xi Gong, Hui Yu, Shuguang Leng, Yan Guo   +9 more
openaire   +3 more sources

The Mutational Signature Comprehensive Analysis Toolkit (musicatk) for the Discovery, Prediction, and Exploration of Mutational Signatures [PDF]

Cancer Research, 2020
Abstract Mutational signatures are patterns of somatic alterations in the genome caused by carcinogenic exposures or aberrant cellular processes. To provide a comprehensive workflow for preprocessing, analysis, and visualization of mutational signatures, we created the Mutational Signature ...
Aaron Chevalier, Shiyi Yang, Zainab Khurshid, Nathan Sahelijo, Tong Tong, Jonathan H. Huggins, Masanao Yajima, Joshua D. Campbell   +7 more
openaire   +3 more sources

SUITOR: Selecting the number of mutational signatures through cross-validation.

PLoS Computational Biology, 2022
For de novo mutational signature analysis, the critical first step is to decide how many signatures should be expected in a cancer genomics study. An incorrect number could mislead downstream analyses.
Donghyuk Lee, Difei Wang, Xiaohong R Yang, Jianxin Shi, Maria Teresa Landi, Bin Zhu   +5 more
doaj   +1 more source

Two subtypes of cutaneous melanoma with distinct mutational signatures and clinico-genomic characteristics

Frontiers in Genetics, 2022
Background: To decipher mutational signatures and their associations with biological implications in cutaneous melanomas (CMs), including those with a low ultraviolet (UV) signature.Materials and Methods: We applied non-negative matrix factorization (NMF)
Yoon-Seob Kim, Yoon-Seob Kim, Yoon-Seob Kim, Minho Lee, Yeun-Jun Chung, Yeun-Jun Chung, Yeun-Jun Chung, Yeun-Jun Chung   +7 more
doaj   +1 more source