OmicCircos: A Simple-to-Use R Package for the Circular Visualization of Multidimensional Omics Data

Hu, Ying; Yan, Chunhua; Hsu, Chih-Hao; Chen, Qingrong; Niu, Kelvin; Komatsoulis, George A.; Meerzaman, Daoud

doi:10.4137/cin.s13495

Cited by 162 publications

(115 citation statements)

References 9 publications

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“…Only significantly increased interactions (EdgeR p-value <0.05; logFoldChange > 0) between undamaged and damaged condition were drawn, using the Bioconductor OmicCircos R package 60. Connecting lines are coloured based on the log2 fold change.…”

Section: Methodsmentioning

confidence: 99%

Genome-wide mapping of long-range contacts unveils clustering of DNA double-strand breaks at damaged active genes

Aymard

Aguirrebengoa

Guillou

et al. 2017

Nat Struct Mol Biol

225

272

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The ability of DNA Double Strand Breaks (DSBs) to cluster in mammalian cells has been subjected to intense debate over the past few years. Here we used a high throughput chromosome conformation capture assay (Capture Hi-C) to investigate clustering of DSBs induced at defined loci in the human genome. We unambiguously found that DSBs do cluster but only when induced in transcriptionally active genes. Clustering of damaged genes mainly occurs during the G1 cell cycle phase and coincides with delayed repair. Moreover DSB clustering depends on the MRN complex, as well as the Formin 2 (FMN2) nuclear actin organizer and the LINC (LInker of Nuclear and Cytoplasmic skeleton) complex, suggesting that active mechanisms promote DSB clustering. This work reveals that when damaged, active genes exhibit a very peculiar behavior compared to the rest of the genome, being mostly left unrepaired and clustered in G1 while being repaired by homologous recombination in post-replicative cells.

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Section: Methodsmentioning

confidence: 99%

Genome-wide mapping of long-range contacts unveils clustering of DNA double-strand breaks at damaged active genes

Aymard

Aguirrebengoa

Guillou

et al. 2017

Nat Struct Mol Biol

225

272

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“…We plotted the metaplastic carcinoma component and conventional invasive ductal carcinoma copy number calls across the genome, for each patient, using the OmicCircos R package (36). …”

Section: Methodsmentioning

confidence: 99%

Whole-Exome Sequencing of Metaplastic Breast Carcinoma Indicates Monoclonality with Associated Ductal Carcinoma Component

Avigdor

Beierl

Gocke

et al. 2017

Clinical Cancer Research

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Purpose Although most human cancers display a single histology, there are unusual cases where two or more distinct tissue types present within a primary tumor. One such example is metaplastic breast carcinoma, a rare but aggressive cancer with a heterogenous histology, including squamous, chondroid, and spindle cells. Metaplastic carcinomas often contain an admixed conventional ductal invasive or in situ mammary carcinoma component, and are typically triple-negative for estrogen receptor, progesterone receptor and human epidermal growth factor receptor 2 (HER-2) amplification/overexpression. An unanswered question is the origin of metaplastic breast cancers. While they may arise independently from their ductal components, their close juxtaposition favors a model that postulates a shared origin, either as two derivatives from the same primary cancer, or one histology as an outgrowth of the other. Understanding the mechanism of development of these tumors may inform clinical decisions. Experimental Design We performed exome sequencing for paired metaplastic and adjacent conventional invasive ductal carcinomas in eight patients and created a pipeline to identify somatic variants and predict their functional impact, without having normal tissue. We then determined the genetic relationships between the histologically distinct compartments. Results In each case, the tumor components have nearly identical landscapes of somatic mutation, implying that the differing histologies do not derive from genetic clonal divergence. Conclusions A shared origin for tumors with differing histologies suggests that epigenetic or noncoding changes may mediate the metaplastic phenotype, and that alternative therapeutic approaches, including epigenetic therapies, may be required for metaplastic breast cancers. Translational relevance Metaplastic breast cancers are a rare but treatment refractory subtype of breast cancer. It remains unclear whether these tumors are separate cancers that arise independently from their ductal counterparts, or are genetically related, resulting from dedifferentiation of cells. Knowledge of the origin of metaplastic breast cancers may help to develop therapeutic strategies for this group of recalcitrant cancers. Using whole exome sequencing and new bioinformatics tools, we compared variants between paired breast cancer samples exhibiting invasive ductal carcinoma and metaplastic components. Based on the high degree of shared variants between paired tissue types from eight patients, we conclude that invasive ductal carcinomas with an associated metaplastic component are genetically related, and likely the result of epigenetic changes leading to multiple histologies. These results provide new insights into the origin of metaplastic breast cancers that could have implications for treatment strategies.

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“…The R/OmicCircus package46 was used to plot the relationship between the chromosomal and linkage marker groups formed by the abovementioned genetic map.…”

Section: Methodsmentioning

confidence: 99%

High-throughput and Cost-effective Chicken Genotyping Using Next-Generation Sequencing

Pértille

Guerrero-Bosagna

Silva

et al. 2016

Sci Rep

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Chicken genotyping is becoming common practice in conventional animal breeding improvement. Despite the power of high-throughput methods for genotyping, their high cost limits large scale use in animal breeding and selection. In the present paper we optimized the CornellGBS, an efficient and cost-effective genotyping by sequence approach developed in plants, for its application in chickens. Here we describe the successful genotyping of a large number of chickens (462) using CornellGBS approach. Genomic DNA was cleaved with the PstI enzyme, ligated to adapters with barcodes identifying individual animals, and then sequenced on Illumina platform. After filtering parameters were applied, 134,528 SNPs were identified in our experimental population of chickens. Of these SNPs, 67,096 had a minimum taxon call rate of 90% and were considered ‘unique tags’. Interestingly, 20.7% of these unique tags have not been previously reported in the dbSNP. Moreover, 92.6% of these SNPs were concordant with a previous Whole Chicken-genome re-sequencing dataset used for validation purposes. The application of CornellGBS in chickens showed high performance to infer SNPs, particularly in exonic regions and microchromosomes. This approach represents a cost-effective (~US$50/sample) and powerful alternative to current genotyping methods, which has the potential to improve whole-genome selection (WGS), and genome-wide association studies (GWAS) in chicken production.

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OmicCircos: A Simple-to-Use R Package for the Circular Visualization of Multidimensional Omics Data

Cited by 162 publications

References 9 publications

Genome-wide mapping of long-range contacts unveils clustering of DNA double-strand breaks at damaged active genes

Genome-wide mapping of long-range contacts unveils clustering of DNA double-strand breaks at damaged active genes

Whole-Exome Sequencing of Metaplastic Breast Carcinoma Indicates Monoclonality with Associated Ductal Carcinoma Component

High-throughput and Cost-effective Chicken Genotyping Using Next-Generation Sequencing

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