Results 21 to 30 of about 84,630 (272)

Switching APOBEC mutation signatures [PDF]

Nature Reviews Genetics, 2019
Two studies report substantial temporal and spatial variability in mutagenic signatures caused by APOBEC cytidine deaminases in cancer.
openaire   +2 more sources

iMutSig: a web application to identify the most similar mutational signature using shiny [version 2; peer review: 2 approved]

F1000Research, 2020
There are two frameworks for characterizing mutational signatures which are commonly used to describe the nucleotide patterns that arise from mutational processes.
Zhi Yang, Priyatama Pandey, Paul Marjoram, Kimberly D. Siegmund   +3 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

The genomic landscape of cutaneous SCC reveals drivers and a novel azathioprine associated mutational signature [PDF]

, 2018
Cutaneous squamous cell carcinoma (cSCC) has a high tumour mutational burden (50 mutations per megabase DNA pair). Here, we combine whole-exome analyses from 40 primary cSCC tumours, comprising 20 well-differentiated and 20 moderately/poorly ...
A Gonzalez-Perez, A Gonzalez-Perez, A Sekulic, AH Ramos, AP South, AZ Dayem Ullah, CA Harwood, CA Harwood, CA Harwood, CA Miller, CH An, CH Mermel, CR Pickering, CS Lee, CS Nowell, D Roy, D Tamborero, DA Landau, DC Koboldt, EM Briso, F Vandin, G Petrof, GF Hofbauer, GL Garrett, GP Dotto, GP Guy Jr, H Mitsui, I Martincorena, I Nindl, J Drost, J Okosun, J Okosun, JA Oyer, JW Peacock, K Tawana, KJ Purdie, KJ Purdie, L Hameetman, LB Alexandrov, LB Alexandrov, LB Alexandrov, LB Alexandrov, LB Alexandrov, M Duff Le, M Herman, M Hollstein, M Ibarrola-Villava, M Ming, M Petljak, MC Hollander, ME Ritchie, ML Slattery, MS Lawrence, MS Stark, N Andor, N Andor, N McCarroll, P Bailey, P Cammareri, P Du, P Karran, P Loo Van, P O’Donovan, PS Karia, R Salgado, RJ Cutts, S Alsafadi, S Fawdar, S Popp, S Schubbert, SL Stroschein, SP O’Hara, SR Lambert, V Chitsazzadeh, W Chen, X Xue, YY Li, Z Zhu   +77 more
core   +6 more sources

Diffsig: Associating Risk Factors with Mutational Signatures

Cancer Epidemiology, Biomarkers & Prevention, 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.
Ji-Eun Park, Markia A. Smith, Sarah C. Van Alsten, Andrea Walens, Di Wu, Katherine A. Hoadley, Melissa A. Troester, Michael I. Love   +7 more
openaire   +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

Integrative genomic analyses of APOBEC-mutational signature, expression and germline deletion of APOBEC3 genes, and immunogenicity in multiple cancer types

BMC Medical Genomics, 2019
Background Although APOBEC-mutational signature is found in tumor tissues of multiple cancers, how a common germline APOBEC3A/B deletion affects the mutational signature remains unclear.
Zhishan Chen, Wanqing Wen, Jiandong Bao, Krystle L. Kuhs, Qiuyin Cai, Jirong Long, Xiao-ou Shu, Wei Zheng, Xingyi Guo   +8 more
doaj   +1 more source

A practical framework RNMF for exploring the association between mutational signatures and genes using gene cumulative contribution abundance

Cancer Medicine, 2022
Background Mutational signatures are somatic mutation patterns enriching operational mutational processes, which can provide abundant information about the mechanism of cancer.
Zhenzhang Li, Haihua Liang, Shaoan Zhang, Wen Luo   +3 more
doaj   +1 more source

Somatic mutation load of estrogen receptor-positive breast tumors predicts overall survival: an analysis of genome sequence data. [PDF]

, 2014
Breast cancer is one of the most commonly diagnosed cancers in women. While there are several effective therapies for breast cancer and important single gene prognostic/predictive markers, more than 40,000 women die from this disease every year.
Bainbridge, Matthew N, Brown, Powel H, Haricharan, Svasti, Scheet, Paul   +3 more
core   +1 more source

Mutational Signatures in Salivary Gland Carcinomas

Cancer Diagnosis & Prognosis, 2023
Salivary gland carcinomas belong to the head and neck carcinoma super category of malignancies. They are characterized by histopathological diversity and comprise a variety of entities and subtypes. Mucoepidermoid, adenoid cystic and salivary duct carcinomas represent the most prominent malignancies. Concerning their corresponding genetic background, a
Chrysovergis, Aristeidis, Papanikolaou, Vasileios, Spyropoulou, Despoina, Roukas, Dimitrios, Asimakopoulos, Asimakis D., Papanastasiou, George, Mastronikoli, Sofianiki, Falidas, Evangelos, Papouliakos, Sotirios, Tsiambas, Evangelos, Pantos, Pavlos, Ragos, Vasileios, Peschos, Dimitrios, Mastronikolis, Nicholas, Kyrodimos, Efthymios   +14 more
openaire   +3 more sources