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Genomic basis for RNA alterations in cancer
2020
Nature
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This compendium of RNA alterations in the genomic context provides a rich resource for identifying genes and mechanisms that are functionally implicated in cancer. ...
Various forms of RNA alterations have been described in cancer, including overexpression2, altered splicing3 and gene fusions4; however, it is difficult to attribute these to underlying genomic changes ...
collation, realignment and harmonized variant calling of the cancer genomes used in this study. ...
doi:10.1038/s41586-020-1970-0
pmid:32025019
pmcid:PMC7054216
fatcat:mlq5hbjn4rd6xp5ej6t42i4mqe
Genomic basis for RNA alterations in cancer
2021
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This compendium of RNA alterations in the genomic context provides a rich resource for identifying genes and mechanisms that are functionally implicated in cancer. ...
Various forms of RNA alterations have been described in cancer, including overexpression2, altered splicing3 and gene fusions4; however, it is difficult to attribute these to underlying genomic changes ...
Identified eQTLs are in https://dcc.icgc.org/releases/PCAWG/transcriptome/eQTL and a binarized table indicating all RNA and DNA alterations for each gene can be found in the subfolder https://dcc.icgc.org ...
doi:10.17863/cam.64275
fatcat:lspoy33h7fdyxnla5w43dksxmy
Comprehensive Genomic Characterization of Long Non-coding RNAs across Human Cancers
2015
Cancer Cell
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RNA (lncRNA) has dramatically altered our understanding of cancer. ...
Graphical Abstract Highlights d lncRNA dysregulation was characterized in 5,037 tumor samples across 13 cancer types d lncRNAs are altered in cancers at transcriptional, genomic, and epigenetic levels ...
This work was supported, in whole or in part, by the Basser Center for BRCA (L.Z.), the Harry Fields Professorship (L.Z.); the NIH (grants R01CA142776 to L.Z., R01CA190415 to L.Z., ...
doi:10.1016/j.ccell.2015.09.006
pmid:26461095
pmcid:PMC4777353
fatcat:reoj3omeqvdgrdo7ruc6hefsm4
Tumour genomic and microenvironmental heterogeneity for integrated prediction of 5-year biochemical recurrence of prostate cancer: a retrospective cohort study
2014
The Lancet Oncology
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We identifi ed four genomic subtypes for prostate cancer, which had diff erent 5-year biochemical relapse-free survival. ...
We aimed to test combined genomic and microenvironmental indices in prostate cancer to improve risk stratifi cation and complement clinical prognostic factors. ...
Acknowledgments We thank study volunteers for their participation, and staff at the Wellcome ...
doi:10.1016/s1470-2045(14)71021-6
pmid:25456371
fatcat:qw6sp5xitfgk7jzr3mcwcezldm
Global analysis of somatic structural genomic alterations and their impact on gene expression in diverse human cancers
2016
Proceedings of the National Academy of Sciences of the United States of America
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of cancer genomes. ...
For somatic SVs to be functional in cancer, they need to have an influence on transcription in some way, by altering mRNA structures or levels. ...
A detailed description of the methods used in the study is provided in SI Methods. ...
doi:10.1073/pnas.1606220113
pmid:27856756
pmcid:PMC5137778
fatcat:htzutidxcjhkdliwjmebmyhi5y
New Views into the Prostate Cancer Genome
2010
Cancer Cell
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Thus, both RNA expression profiling and DNA expression profiling work for breast cancer. So the real question is why doesn't RNA expression profiling work for prostate cancer? ...
This integrated approach paid off in this case, as the authors were able to test two classes of alterations for their ability to predict recurrence, RNA expression profiling, and DNA copy-number profiling ...
doi:10.1016/j.ccr.2010.06.011
pmid:20609345
fatcat:mbcwngm24zettfnwoizpqmewwi
Noncoding RNAs serve as the deadliest regulators for cancer
[article]
2019
arXiv
pre-print
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Strikingly, noncoding RNAs serves as the universal strongest regulators for all cancer types although personal clinic variables such as alcohol and smoking significantly alter cancer genome. ...
Therefore, noncoding RNAs overall serve as the deadliest cancer regulators, which refreshes the basic concept of cancer mechanism and builds a novel basis for cancer research and therapy. ...
We further ranked these 428 regulators in basis of their absolute coefficients (coef), higher coefficient, more important in regulating cancer death. ...
arXiv:1910.03934v1
fatcat:rf4v7fdsbbga7jws7zxwjqtj6q
Non-coding RNAs for Medical Practice in Oncology
2011
The Keio Journal of Medicine
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Alterations in microRNA (miRNA) and other short or long non-coding RNA (ncRNA) are involved in the initiation, progression, and metastasis of human cancer. ...
These discoveries could be exploited for the development of useful markers for diagnosis and prognosis in cancer, as well as for the development of new RNA-based cancer therapies. ...
May Result in Cancer Predisposition Despite extensive research, the molecular basis for most familial cancers is unknown. ...
doi:10.2302/kjm.60.106
pmid:22200634
fatcat:kswhts3vznhp7ofmrv2bl7xbbm
Exploring cancer genomic data from the cancer genome atlas project
2016
BMB Reports
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The Cancer Genome Atlas (TCGA) has compiled genomic, epigenomic, and proteomic data from more than 10,000 samples derived from 33 types of cancer, aiming to improve our understanding of the molecular basis ...
Availability of these genome-wide information provides an unprecedented opportunity for uncovering new key regulators of signaling pathways or new roles of pre-existing members in pathways. ...
The GCCs aim to identify all genomic alterations in the tumors in each cancer type. ...
doi:10.5483/bmbrep.2016.49.11.145
pmid:27530686
pmcid:PMC5346320
fatcat:2g3o7hrzsnft3hsrnfa5gjx6mi
Cis-regulatory mutations associate with transcriptional and post-transcriptional deregulation of the gene regulatory program in cancers
[article]
2020
bioRxiv
pre-print
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Most cancer alterations occur in the noncoding portion of the human genome, which contains important regulatory regions acting as genetic switches to ensure gene expression occurs at correct times and ...
By combining cancer somatic mutations in TFBSs and expression data for protein-coding and miRNA genes, we evaluated the combined effects of transcriptional and post-transcriptional alteration on the dysregulation ...
We thank Jiarui Ding for his help on using xseq for this study; Marcel Smid for providing raw RNA-seq data for the BASIS cohort; Georgios Magklaras and Georgios Marselis for their IT support; Ingrid Kjelsvik ...
doi:10.1101/2020.06.25.170738
fatcat:j6cxqjqdonafvbkntw22jqehku
The Non-Coding Oncogene: A Case of Missing DNA Evidence?
2012
Frontiers in Genetics
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However, in comparison with coding cancer genes, the genomic (DNA-level) evidence is sparse for ncRNAs. ...
Multiple lines of proof show how random somatic genomic alteration of such genes (e.g., mutation, deletion, or amplification), followed by selection and clonal expansion, forms the main molecular basis ...
Anders Jacobsen and Nicholas Gauthier for critical review of the manuscript. ...
doi:10.3389/fgene.2012.00170
pmid:22988449
pmcid:PMC3439828
fatcat:2mkyfpj7tjaxngbtta5z4crtay
Sequencing Technologies and their Importance in the Field of Oncology
2017
Indo global journal of pharmaceutical sciences
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approaches in cancer genomics. ...
It has been at the forefront of medical research with huge leaps in the field of cancer genomics. ...
approaches in cancer genomics. ...
doi:10.35652/igjps.2017.86
fatcat:66hufdg7rjhkbi7wx6rvgjwn7q
Integrated analysis of expression and genome alteration reveals putative amplified target genes in esophageal cancer
2007
Oncology Reports
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Thus, the integration of DNA and RNA profiles provides a highly productive entry point for the discovery of genes involved in the development and progression of esophageal cancer. ...
Microarray and comparative genomic hybridization (CGH) studies have provided a wide range of information about esophageal cancer, but the correlations between gene expression and copy number alteration ...
Many of these genome alterations were observed in all cell lines (Fig. 1 ). ...
doi:10.3892/or.18.2.465
fatcat:ewcghthng5bfpoknplggfegkwy
An expanding universe of the non-coding genome in cancer biology
2014
Carcinogenesis
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A number of non-coding RNAs (ncRNAs) derived from the 'dark matter' of the human genome exhibit cancer-specific differential expression and/or genomic alterations, and it is increasingly clear that ncRNAs ...
Reactivation of retrotransposons in cancer, while capable of causing insertional mutagenesis and genome rearrangements to promote oncogenesis, could also alter host gene expression networks to favor tumor ...
which L1 mobilize to alter cancer genome. ...
doi:10.1093/carcin/bgu099
pmid:24747961
pmcid:PMC4110481
fatcat:2pxpsytdpvgpre6xs6iramtaxi
Prediction of breast cancer proteins involved in immunotherapy, metastasis, and RNA-binding using molecular descriptors and artificial neural networks
2020
Scientific Reports
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Breast cancer (BC) is a heterogeneous disease where genomic alterations, protein expression deregulation, signaling pathway alterations, hormone disruption, ethnicity and environmental determinants are ...
Scripts can be downloaded at https://github.com/muntisa/neural-networks-for-breast-cancer-proteins. ...
Additionally, Fig. 9B shows the most altered RNA-binding proteins per genomic alteration type. ...
doi:10.1038/s41598-020-65584-y
pmid:32444848
fatcat:ee6xzbzlqrgafeug5fu4rsxbd4
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