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Detecting Presence Of Mutational Signatures In Cancer With Confidence [article]

Xiaoqing Huang, Damian Wojtowicz, Teresa M. Przytycka
2017 bioRxiv   pre-print
We proposed two complementary ways of measuring confidence and stability of decomposition results and applied them to analyze mutational signatures in breast cancer genomes.  ...  Decomposition of cancer's mutation catalog into mutations consistent with such signatures can provide valuable information about cancer etiology.  ...  Re-analysis of mutational signatures presence in breast cancers Nik-Zainal et al.  ... 
doi:10.1101/132597 fatcat:fhi6itixsrg5pnf7qtegjn56ki

Detecting presence of mutational signatures in cancer with confidence

Xiaoqing Huang, Damian Wojtowicz, Teresa M Przytycka, Christina Curtis
2017 Bioinformatics  
We proposed two complementary ways of measuring confidence and stability of decomposition results and applied them to analyze mutational signatures in breast cancer genomes.  ...  Decomposition of cancer's mutation catalog into mutations consistent with such signatures can provide valuable information about cancer etiology.  ...  Re-analysis of mutational signatures presence in breast cancers Nik-Zainal et al.  ... 
doi:10.1093/bioinformatics/btx604 pmid:29028923 fatcat:xrorvjv2avbudg7dpvg7bvz4d4

Analysis of Mutational Signatures with YAPSA (Yet Another Package for Signature Analysis)

Daniel Hübschmann, Lea Jopp‐Saile, Carolin Andresen, Stephen Krämer, Zuguang Gu, Christoph E. Heilig, Simon Kreutzfeldt, Veronica Teleanu, Stefan Fröhling, Roland Eils, Matthias Schlesner
2020 Genes, Chromosomes and Cancer  
With this functionality, YAPSA has proved to be a valuable tool for analysis of mutational signatures in molecular tumor boards in a precision oncology context.  ...  Different mutational processes leave characteristic patterns of somatic mutations in the genome that can be identified as mutational signatures.  ...  The presence of this mutational mechanism in this cohort can thus be detected with high confidence in this ovarian cancer cohort.  ... 
doi:10.1002/gcc.22918 pmid:33222322 fatcat:am2622yevfd2djkhqqpyuhuf4q

Somatic mutations reveal asymmetric cellular dynamics in the early human embryo

Young Seok Ju, Inigo Martincorena, Moritz Gerstung, Mia Petljak, Ludmil B. Alexandrov, Raheleh Rahbari, David C. Wedge, Helen R. Davies, Manasa Ramakrishna, Anthony Fullam, Sancha Martin, Christopher Alder (+29 others)
2017 Nature  
Somatic mutations reveal asymmetric cellular dynamics in the early human embryo. Nature, 543(7647), 714-718. https://doi.  ...  Dawson at Wellcome Trust Sanger Institute and Thomas Bleazard at University of Manchester for discussion and assistance with manuscript preparation. This work was supported by the Wellcome Trust.  ...  The mutation is present in the cancer sample with a VAF of 42.1% in targeted amplicon sequencing, consistent with its presence in all cancer cells and a contaminating population of non-neoplastic cells  ... 
doi:10.1038/nature21703 pmid:28329761 fatcat:xi2smu3k65ayndyptvvaiuwjbm

Clock-like mutational processes in human somatic cells

Ludmil B Alexandrov, Philip H Jones, David C Wedge, Julian E Sale, Peter J Campbell, Serena Nik-Zainal, Michael R Stratton
2015 Nature Genetics  
Different mutational processes may contribute to the mutations accumulated in a cell, with each imprinting a mutational signature on the cell's genome.  ...  For one signature, the rate of cell division may influence its mutation rate. This study provides the first survey of clock-like mutational processes operative in human somatic cells.  ...  Mutations associated with signature 1 were correlated with age of diagnosis in 17 of the cancer types, while mutations associated with signature 5 in 12 of the cancer types.  ... 
doi:10.1038/ng.3441 pmid:26551669 pmcid:PMC4783858 fatcat:uk7adilqjvcwjofhfbc4p6b3eq

Ultra-deep targeted sequencing of advanced oral squamous cell carcinoma identifies a mutation-based prognostic gene signature

Shu-Jen Chen, Hsuan Liu, Chun-Ta Liao, Po-Jung Huang, Yi Huang, Ann Hsu, Petrus Tang, Yu-Sun Chang, Hua-Chien Chen, Tzu-Chen Yen
2015 OncoTarget  
Genetic mutations on the hotspot regions of 45 cancer-related genes were detected using an ultra-deep (>1000×) sequencing approach.  ...  Multivariate analysis demonstrated that presence of a mutated gene signature was an independent predictor of poorer DFS (P = 0.005).  ...  ACKNOWLEDGMENTS We appreciate the contribution and the valuable assistance of the Linkou Chang Gung Memorial Hospital Cancer Center databank and the Bioinformatics Core and Genomic Core of the Molecular  ... 
doi:10.18632/oncotarget.3768 pmid:25980437 pmcid:PMC4621868 fatcat:vrtuomh5x5c4zlenfncckxknc4

Somatic POLE exonuclease domain mutations are early events in sporadic endometrial and colorectal carcinogenesis, determining driver mutational landscape, clonal neoantigen burden and immune response

Daniel Temko, Inge C Van Gool, Emily Rayner, Mark Glaire, Seiko Makino, Matthew Brown, Laura Chegwidden, Claire Palles, Jeroen Depreeuw, Andrew Beggs, Chaido Stathopoulou, John Mason (+14 others)
2018 Journal of Pathology  
Tumours with somatic POLE exonuclease domain mutations are notable for their extreme genomic instability (their mutation burden is among the highest in human cancer), distinct mutational signature, lymphocytic  ...  Here, we have shown that pathogenic POLE mutations are detectable in non-malignant precursors of endometrial and colorectal cancer.  ...  Acknowledgments We thank Michelle Osse, Natalja ter Haar, Nienke Solleveld-Westerink and Dina Ruano for help with performing and interpretation of the Ion AmpliSeq Cancer Hotspot Panel.  ... 
doi:10.1002/path.5081 pmid:29604063 pmcid:PMC6032922 fatcat:5ln5tbxhhzbj5dqbkz7fjwn4wi

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

Nicholas McGranahan, Francesco Favero, Elza C. de Bruin, Nicolai Juul Birkbak, Zoltan Szallasi, Charles Swanton
2015 Science Translational Medicine  
The frequent presence of subclonal driver mutations suggests the need to stratify targeted therapy response according to the proportion of tumor cells in which the driver is identified.  ...  Mutations in the RAS-MEK (mitogen-activated protein kinase kinase) signaling axis were less likely to be subclonal than mutations in genes associated with PI3K-AKT-mTOR signaling.  ...  The presence of subclonal mutations may reduce the clinical benefit of cancer therapies.  ... 
doi:10.1126/scitranslmed.aaa1408 pmid:25877892 pmcid:PMC4636056 fatcat:y7gu44pb6zgn5e55hzj2wkpbyi

Telomere Maintenance Associated Mutations in the Genetic Landscape of Gynecological Mucosal Melanoma

Guangwen Yuan, Jinge Song, Ning Li, Qianqian Song, Yifei Li, Yingxi Du, Xiaobing Wang, Yuchen Jiao, Lingying Wu
2020 Frontiers in Oncology  
TERT promoter mutation was not detected in GMs (n = 40), but copy number variations in the TERT region were observed in 20% (7/35) of the samples.  ...  Gynecological melanomas (GMs) are rare tumors with a poor prognosis. Here, we performed exome sequencing to generate the mutational landscape of GMs.  ...  Signature 3 is also associated with germline and somatic BRCA1 and BRCA2 mutations in breast, pancreatic, and ovarian cancers.  ... 
doi:10.3389/fonc.2020.01707 pmid:32984050 pmcid:PMC7492295 fatcat:x7blm6lndfaatcyptwgm3szpzy

Tumor Mutation Burden, Expressed Neoantigens and the Immune Microenvironment in Diffuse Gliomas

Guangyang Yu, Ying Pang, Mythili Merchant, Chimene Kesserwan, Vineela Gangalapudi, Abdalla Abdelmaksoud, Alice Ranjan, Olga Kim, Jun S. Wei, Hsien-Chao Chou, Xinyu Wen, Sivasish Sindiri (+8 others)
2021 Cancers  
A consistent correlation between tumor mutation burden (TMB) and tumor immune microenvironment has not been observed in gliomas as in other cancers.  ...  Methods: Driver germline and somatic mutations, TMB, neoantigen, and immune cell signatures were analyzed using whole exome sequencing (WES) and transcriptome sequencing of tumor and WES of matched germline  ...  Conflicts of Interest: The authors declare no conflict of interest. Cancers 2021, 13, 6092  ... 
doi:10.3390/cancers13236092 pmid:34885201 fatcat:zril73b6tvhtdb7opnedmida4i

Risk factors for a serous cancer precursor ("p53 signature") in women with inherited BRCA mutations

Aasia Saleemuddin, Ann K. Folkins, Leslie Garrett, Judy Garber, Michael G. Muto, Christopher P. Crum, Shelley Tworoger
2008 Gynecologic Oncology  
This study examined the relationship of putative ovarian cancer risk factors with the presence of p53 signatures in women with BRCA mutations (BRCA+).  ...  Recently, a candidate serous cancer precursor (the p53 signature) with p53 mutations and other features in common with serous cancer has been discovered in distal fallopian tube mucosa.  ...  whether variables associated with risk of epithelial ovarian cancer in BRCA+ women also were associated with the presence of p53 signatures.  ... 
doi:10.1016/j.ygyno.2008.07.018 pmid:18718648 pmcid:PMC2613977 fatcat:f4kybj2wvvegvpayehlvohvom4

UV-exposure, endogenous DNA damage, and DNA replication errors shape the spectra of genome changes in human skin

Natalie Saini, Camille K. Giacobone, Leszek J. Klimczak, Brian N. Papas, Adam B. Burkholder, Jian-Liang Li, David C. Fargo, Re Bai, Kevin Gerrish, Cynthia L. Innes, Shepherd H. Schurman, Dmitry A. Gordenin (+1 others)
2021 PLoS Genetics  
In addition, we detect accumulation of mutations due to spontaneous deamination of methylated cytosines as well as insertions and deletions characteristic of DNA replication errors in these cells.  ...  The endogenously induced somatic mutations and indels also demonstrate a linear increase with age, while UV-induced mutation load is age-independent.  ...  In fact, melanoma genomes have the highest burdens of mutations with UV-induced mutation signatures predominating amongst the mutation signatures identified in this cancer type [12, 13] .  ... 
doi:10.1371/journal.pgen.1009302 pmid:33444353 fatcat:t2iixvoiobawlh2yxx3sxwmnqm

The effects of mutational processes and selection on driver mutations across cancer types

Daniel Temko, Ian P. M. Tomlinson, Simone Severini, Benjamin Schuster-Böckler, Trevor A. Graham
2018 Nature Communications  
First, we detect associations between a range of mutational processes, including those linked to smoking, ageing, APOBEC and DNA mismatch repair (MMR) and the presence of key driver mutations across cancer  ...  Here we have used public cancer sequencing data from 11,336 cancers of various types to infer the independent effects of mutation and selection on the set of driver mutations in a cancer type.  ...  For each of these signatures, we tested for a correlation between mutational process activity and presence of the mutation in the cancer type.  ... 
doi:10.1038/s41467-018-04208-6 pmid:29748584 pmcid:PMC5945620 fatcat:mwkit4m3jfbgpe7unsikhn5gqi

Whole genome deep sequencing analysis of cell-free DNA in samples with low tumour content

Devika Ganesamoorthy, Alan James Robertson, Wenhan Chen, Michael B. Hall, Minh Duc Cao, Kaltin Ferguson, Sunil R. Lakhani, Katia Nones, Peter T. Simpson, Lachlan J. M. Coin
2022 BMC Cancer  
However, 90% of high confidence somatic cfDNA variants were not detected in matched tumour samples and were found to comprise two background plasma mutational signatures.  ...  Conclusions Deep sequencing analysis of plasma samples revealed higher fraction of unique somatic mutations in plasma samples, which were not detected in matched tumour samples.  ...  We acknowledge the support of Metro North Hospital and Health Services in the collection of the Clinical Subject Data and Clinical Subject Materials.  ... 
doi:10.1186/s12885-021-09160-1 pmid:35057759 pmcid:PMC8772083 fatcat:u2dfl3jkrjc53cxifiuqmiqqiy

Signatures Beyond Oncogenic Mutations in Cell-Free DNA Sequencing for Non-Invasive, Early Detection of Cancer

Subhajyoti De
2021 Frontiers in Genetics  
Early detection of cancer saves lives, but an effective detection strategy in public health settings requires a delicate balance - periodic screening should neither miss rapidly progressing disease nor  ...  Genomic data from cell-free DNA can not only identify oncogenic mutation status, but also additional molecular signatures related to potential tissue of origin, the extent of clonal growth, and malignant  ...  Collectively, the presence of oncogenic mutations, as well as the somatic mutations with distinct mutational signatures and inferred chromatin makeups in cfDNA can help identify potentially malignant clonal  ... 
doi:10.3389/fgene.2021.759832 pmid:34721546 pmcid:PMC8551553 fatcat:xrxm6pni5vfztbh4plgvdk75fi
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