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Pan-cancer integrative analysis of whole-genome De novo somatic point mutations reveals 17 cancer types

Amin Ghareyazi, Amirreza Kazemi, Kimia Hamidieh, Hamed Dashti, Maedeh Sadat Tahaei, Hamid R Rabiee, Hamid Alinejad-Rokny, Iman Dehzangi
We apply our pipeline to 12,270 samples collected from the international cancer genome consortium, covering 19 cancer types. As a result, we identify 17 different cancer subtypes.  ...  The source codes for our proposed clustering pipeline and analysis are publicly available at: .  ...  Analysis was made possible with the Telethon Kids Bioinformatics Server's computational resources with funding from the Australian Government and the Government of Western Australia.  ... 
doi:10.1186/s12859-022-04840-6 pmid:35879674 pmcid:PMC9316662 fatcat:ohyr66zugrdd5hnjwo2oxcde3q

Pan-cancer analysis of whole genomes [article]

Peter J. Campbell, Gad Getz, Joshua M. Stuart, Jan O. Korbel, Lincoln D. Stein
2017 bioRxiv   pre-print
We report the integrative analysis of more than 2,600 whole cancer genomes and their matching normal tissues across 39 distinct tumour types.  ...  NOTE TO READERS: This is an incomplete draft of the marker paper for the Pan-Cancer Analysis of Whole Genomes Project, and is intended to provide the background information for a series of in-depth papers  ...  The Pan-Cancer Analysis of Whole Genomes Collaboration The early studies from ICGC and TCGA revealed both commonalities and differences of somatic genomic architecture across tumour types.  ... 
doi:10.1101/162784 fatcat:5kyv666yxzfv5cfvpsrbmbyxea

Uncovering novel mutational signatures by de novo extraction with SigProfilerExtractor [article]

S M Ashiqul Islam, Yang Wu, Marcos Diaz-Gay, Erik N Bergstrom, Yudou He, Mark Barnes, Mike Vella, Jingwei Wang, Jon W Teague, Peter Clapham, Sarah Moody, Sergey Senkin (+23 others)
2020 bioRxiv   pre-print
Here we present SigProfilerExtractor, an automated tool for accurate de novo extraction of mutational signatures for all types of somatic mutations.  ...  Applying SigProfilerExtractor to 2,778 whole-genome sequenced cancers reveals three previously missed mutational signatures.  ...  ACKNOWLEDGEMENTS The authors would like to thank Allan Balmain (UC San Francisco) for the many useful discussions as well as Ville Mustonen (University of Helsinki) and Israel Tojal Da Silva (A.C.  ... 
doi:10.1101/2020.12.13.422570 fatcat:rulhlqhserbahl4horyxyhzqka

Genetic immune escape landscape in primary and metastatic cancer [article]

Francisco Martínez-Jiménez, Peter Priestley, Charles Shale, Jonathan Baber, Erik Rozemuller, Edwin Cuppen
2022 bioRxiv   pre-print
Here, we performed a pan-cancer characterization of GIE prevalence across six immune escape pathways in 6,457 uniformly processed Whole Genome Sequencing (WGS) tumor samples including 58 cancer types from  ...  Positive selection analysis revealed that GIE alterations are frequently selected for in tumor evolution and that focal LOH of HLA-I, unlike non-focal LOH of HLA-I, tends to lose the HLA allele that presents  ...  Acknowledgements This publication and the underlying study have been made possible partly on the basis of the data that Hartwig Medical Foundation and the Center of Personalised Cancer Treatment (CPCT)  ... 
doi:10.1101/2022.02.23.481444 fatcat:ywab7fzptzegvcr55uhkajnxxa

Cancer whole-genome sequencing: present and future

H Nakagawa, C P Wardell, M Furuta, H Taniguchi, A Fujimoto
2015 Oncogene  
WGS approaches can detect these unexplored mutations, as well as coding mutations and somatic copy number alterations, and help us to better understand the whole landscape of cancer genomes and elucidate  ...  To explore cancer genomic alterations and their diversity comprehensively, global and local cancer genome-sequencing projects, including ICGC and TCGA, have been analyzing many types of cancer genomes  ...  efforts to cancer genome sequencing in ICGC project.  ... 
doi:10.1038/onc.2015.90 pmid:25823020 fatcat:b2mot3e2tzbkjl5g4twehj6ude

Modeling cancer rearrangement landscapes

John Maciejowski, Marcin Imielinski
2017 Current Opinion in Systems Biology  
Cancer genome sequences contain footprints of somatic mutational processes, whose analysis in large tumor sequencing datasets has revealed novel mutational signatures, correlative features of variant topography  ...  Conversely, analytic studies evaluating quantitative footprints of specific genome integrity hypotheses will be critical in fitting naturally occurring mutational patterns to the predictions of a particular  ...  Similar analyses have not been, to our knowledge, applied to pan-cancer whole genome sequencing data.  ... 
doi:10.1016/j.coisb.2016.12.005 pmid:29177203 pmcid:PMC5699513 fatcat:qp7mp6nz2zatpip4hfif3upmpm

Acute myeloid leukemia ontogeny is defined by distinct somatic mutations

R. C. Lindsley, B. G. Mar, E. Mazzola, P. V. Grauman, S. Shareef, S. L. Allen, A. Pigneux, M. Wetzler, R. K. Stuart, H. P. Erba, L. E. Damon, B. L. Powell (+7 others)
2014 Blood  
Analysis of the publicly available exome-and genome-level data from The Cancer Genome Atlas (TCGA) de novo AML cohort was restricted to the same genomic coordinates as our focused analysis of the s-AML  ...  A systematic evaluation of MDS cases with secondary-type vs TP53 vs de novo/pan-AML mutations that integrates genetics with clinicopathologic data, disease latency, and kinetics would inform interpretation  ... 
doi:10.1182/blood-2014-11-610543 pmid:25550361 pmcid:PMC4342352 fatcat:u32t7lz6crd7rijqxn4mh5rjqy


2013 Biocomputing 2014  
, SNP array, DNA methylation array, and de novo genome assembly.  ...  We conducted an integrative analysis of both cell lines to distinguish between potential driver and passenger alterations.  ...  Acknowledgments We thank Jens Reeder and Gregoire Pau for development of the transcriptome sequencing analysis pipeline, Allison Bruce for help with the design of figure graphics, and Gerard Manning for  ... 
doi:10.1142/9789814583220_0008 fatcat:i6fgz4xspfep7ibkock2xnlbuu

Integrative analysis of two cell lines derived from a non-small-lung cancer patient--a panomics approach

Oleg Mayba, Florian Gnad, Michael Peyton, Fan Zhang, Kimberly Walter, Pan Du, Melanie A Huntley, Zhaoshi Jiang, Jinfeng Liu, Peter M Haverty, Robert C Gentleman, Ruiqiang Li (+4 others)
2014 Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing  
, SNP array, DNA methylation array, and de novo genome assembly.  ...  We conducted an integrative analysis of both cell lines to distinguish between potential driver and passenger alterations.  ...  Acknowledgments We thank Jens Reeder and Gregoire Pau for development of the transcriptome sequencing analysis pipeline, Allison Bruce for help with the design of figure graphics, and Gerard Manning for  ... 
pmid:24297535 pmcid:PMC3940063 fatcat:niprdfflmnetfbv3vgqewofz4i

Maftools: efficient and comprehensive analysis of somatic variants in cancer

Anand Mayakonda, De-Chen Lin, Yassen Assenov, Christoph Plass, H. Phillip Koeffler
2018 Genome Research  
Numerous large-scale genomic studies of matched tumor-normal samples have established the somatic landscapes of most cancer types.  ...  However, the downstream analysis of data from somatic mutations entails a number of computational and statistical approaches, requiring usage of independent software and numerous tools.  ...  This research is also supported by the RNA Biology Center at the Cancer Science Institute of Singapore, NUS, as part of funding under the Singapore Ministry of Education's Tier 3 grants, grant number MOE2014  ... 
doi:10.1101/gr.239244.118 fatcat:wdwhjuddsze25c5zfkoeq4xcru

Germline determinants of the somatic mutation landscape in 2,642 cancer genomes [article]

Sebastian M. Waszak, Grace Tiao, Bin Zhu, Tobias Rausch, Francesc Muyas, Bernardo Rodriguez-Martin, Raquel Rabionet, Sergei Yakneen, Georgia Escaramis, Yilong Li, Natalie Saini, Steven A. Roberts (+79 others)
2017 bioRxiv   pre-print
resource to study genetic determinants of somatic mutagenesis across 39 cancer types.  ...  Genome-wide association analysis implicated common genetic variation at the APOBEC3 gene cluster with reduced basal levels of somatic mutagenesis attributable to APOBEC cytidine deaminases across cancer  ...  Acknowledgements This project received funding by the European Commission (EC) through an ERC Starting Grant to JOK, the EurocanPlatform project of the EC (to JOK and AB), the European Open Science Cloud  ... 
doi:10.1101/208330 fatcat:eticqnr63zbc7gmmshncnkvy3e

Transcriptional dysregulation by aberrant enhancer activation and rewiring in cancer

Atsushi Okabe, Atsushi Kaneda
2021 Cancer Science  
Small genomic alterations such as mutations, insertions, and amplifications can form aberrant enhancers.  ...  Dysregulation of these elements and their interactions can lead to loss of cell identity and promote the development of diseases such as cancer.  ...  Analysis of somatic copy-number changes from 3131 cancer patient samples from 26 different tumor types revealed that extensive copy-number changes were observed in 25% of the cancer genome. 20 In addition  ... 
doi:10.1111/cas.14884 pmid:33728716 fatcat:lv3vckrnsvb5fo2paazbej4s7q

A Systematic Pan-Cancer Analysis of Genetic Heterogeneity Reveals Associations with Epigenetic Modifiers

Mafalda de Matos, Ioana Posa, Filipa Carvalho, Vanessa Morais, Ana Grosso, Sérgio de Almeida
2019 Cancers  
Integration of ITH scores and somatic variants detected in each tumor sample revealed that mutations in epigenetic modifier genes are associated with higher ITH levels.  ...  Here, we conducted an exhaustive characterization of ITH across 2807 tumor samples from 16 cancer types.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/cancers11030391 pmid:30897760 pmcid:PMC6468518 fatcat:4qcunxm6e5fdpdtco47juqcyj4

Response to angiotensin blockade with irbesartan in a patient with metastatic colorectal cancer

M. R. Jones, K. A. Schrader, Y. Shen, E. Pleasance, C. Ch'ng, N. Dar, S. Yip, D. J. Renouf, J. E. Schein, A. J. Mungall, Y. Zhao, R. Moore (+7 others)
2016 Annals of Oncology  
Results: Integrative genomic analysis indicated overexpression of the AP-1 transcriptional complex suggesting experimental therapeutic rationales, including blockade of the renin-angiotensin system.  ...  Conclusions: This case highlights the utility of comprehensive integrative genomic profiling and bioinformatics analysis to provide hypothetical rationales for personalized treatment options.  ...  This strategy included integrative genomic analysis of whole-genome tumor and normal DNA sequencing and whole transcriptome sequence of tumor RNA.  ... 
doi:10.1093/annonc/mdw060 pmid:27022066 pmcid:PMC4843189 fatcat:g72aq4jc7jhtncea5w7cmuf5jy

Aberrant integration of Hepatitis B virus DNA promotes major restructuring of human hepatocellular carcinoma genome architecture [article]

Eva G Alvarez, Jonas Demeulemeester, Clemency Jolly, Daniel Garcia-Souto, Paula Otero, Ana Pequeno, Jorge Zamora, Marta Tojo, Javier Temes, Adrian Baez-Ortega, Bernardo Rodriguez-Martin, Yilong Li (+29 others)
2021 bioRxiv   pre-print
There are different mutational mechanisms causing structural variation, some of which are specific to particular cancer types.  ...  Most cancers are characterized by the somatic acquisition 52 of genomic rearrangements during tumour evolution that eventually drive the oncogenesis.  ...  ACKNOWLEDGEMENTS We thank the Supercomputing Centre of Galicia (CESGA) for providing complementary  ... 
doi:10.1101/2021.04.19.440412 fatcat:u5h6fpvw35cwnckp6tcm3mbphe
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