ggbio: an R package for extending the grammar of graphics for genomic data

Yin, Tao; Cook, Dianne; Lawrence, Michael C.

doi:10.1186/gb-2012-13-8-r77

Cited by 296 publications

(236 citation statements)

References 28 publications

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“…Gene list enrichment analysis was performed with ToppGene Suite 69 . The ideograms, coverage plots and the gene models of the fusion partner genes were drawn with the R package ggbio 70 .…”

Section: Article Nature Communications | Doi: 101038/ncomms6135mentioning

confidence: 99%

Variation in genomic landscape of clear cell renal cell carcinoma across Europe

Scélo¹,

Riazalhosseini²,

Greger³

et al. 2014

Nat Commun

180

166

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The incidence of renal cell carcinoma (RCC) is increasing worldwide, and its prevalence is particularly high in some parts of Central Europe. Here we undertake whole-genome and transcriptome sequencing of clear cell RCC (ccRCC), the most common form of the disease, in patients from four different European countries with contrasting disease incidence to explore the underlying genomic architecture of RCC. Our findings support previous reports on frequent aberrations in the epigenetic machinery and PI3K/mTOR signalling, and uncover novel pathways and genes affected by recurrent mutations and abnormal transcriptome patterns including focal adhesion, components of extracellular matrix (ECM) and genes encoding FAT cadherins. Furthermore, a large majority of patients from Romania have an unexpected high frequency of A:T4T:A transversions, consistent with exposure to aristolochic acid (AA). These results show that the processes underlying ccRCC tumorigenesis may vary in different populations and suggest that AA may be an important ccRCC carcinogen in Romania, a finding with major public health implications.

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“…Gene list enrichment analysis was performed with ToppGene Suite 69 . The ideograms, coverage plots and the gene models of the fusion partner genes were drawn with the R package ggbio 70 .…”

Section: Article Nature Communications | Doi: 101038/ncomms6135mentioning

confidence: 99%

Variation in genomic landscape of clear cell renal cell carcinoma across Europe

Scélo¹,

Riazalhosseini²,

Greger³

et al. 2014

Nat Commun

180

166

View full text Add to dashboard Cite

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“…To our knowledge, AKT1 mutation has not The mutation is present at exon9 in most transcripts of the AKT1 gene. The figure was generated using ggbio [17] in R. Effect of AKT1 mutation on the protein structure. (A) Superimposed structures of AKT1 protein structure template (PDB ID = 3O96) and homology model of AKT1 protein with point mutation (from JMML patient) (the AKT1 protein sequence in template structure is shifted by 62 residues in the template sequence).…”

Section: Discussionmentioning

confidence: 99%

Whole‐exome sequencing and microRNA profiling reveal PI3K/AKT pathway’s involvement in juvenile myelomonocytic leukemia

et al. 2018

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Background: Clinical studies and genetic analyses have revealed that juvenile myelomonocytic leukemia (JMML) is caused by somatic and/or germline mutations of genes involved in the RAS/MAPK signalling pathway. Given the vastly different clinical prognosis among individual patients that have had this disease, mutations in genes of other pathways may be involved. Methods: In this study, we conducted whole-exome and cancer-panel sequencing analyses on a bone marrow sample from a 2-year old juvenile myelomonocytic leukemia patient. We also measured the microRNA profile of the same patient's bone marrow sample and the results were compared with the normal mature monocytic cells from the pooled peripheral blood. Results: We identified additional novel mutations in the PI3K/AKT pathway and verified with a cancer panel targeted sequencing. We have confirmed the previously tested PTPN11 gene mutation (exon 3 181G > T) in the same sample and identified new nonsynonymous mutations in NTRK1, HMGA2, MLH3, MYH9 and AKT1 genes. Many of the microRNAs found to be differentially expressed are known to act as oncogenic MicroRNAs (onco-MicroRNAs or oncomiRs), whose target genes are enriched in the PI3K/AKT signalling pathway. Conclusions: Our study suggests an alternative mechanism for JMML pathogenesis in addition to RAS/MAPK pathway. This discovery may provide new genetic markers for diagnosis and new therapeutic targets for JMML patients in the future.Keywords: single-cell; RNA-Seq; differential expression Author summary: We conducted whole-exome sequencing and microRNA profiling to analyze a patient of juvenile myelomonocytic leukemia. Our sequencing data and computational studies identified novel mutations in NTRK1, HMGA2, MLH3, MYH9, and AKT1 genes, which can potentially be used as diagnostic biomarkers and therapeutic targets. We suggest an alternative mechanism for JMML pathogenesis in addition to the RAS/MAPK pathway. We also identified a number of differentially expressed microRNAs that are known to act as oncogenic MicroRNAs in the patient sample. Our work provides an example of precision medicine to characterize the rare disease using a single-patient data.

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“…[10][11][12] were reported by the same research group [28], and contained two complicated inversions. One was nested between 3 and 7 o'clock direction and between 4 and 6 o'clock direction.…”

Section: Three Types Of Genome Rearrangements In H Pylorimentioning

confidence: 99%

“…Several visualizers have been proposed to date [10][11][12][13], but our approach is unique in that we do not presuppose binary comparison between genomes. Comparison against a single reference implicitly assumes the perfection of the reference data.…”

Section: Introductionmentioning

confidence: 99%

Visualization of consensus genome structure without using a reference genome

2017

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Background: Standard graphical tools for whole genome comparison require a reference genome. However, any reference is also subject to annotation biases and rearrangements, and may not serve as the standard except for those of extensively studied model species. To fully exploit the rapidly accumulating sequence data from the recent sequencing technologies, genome comparison without any reference has been anticipated.

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ggbio: an R package for extending the grammar of graphics for genomic data

Cited by 296 publications

References 28 publications

Variation in genomic landscape of clear cell renal cell carcinoma across Europe

Variation in genomic landscape of clear cell renal cell carcinoma across Europe

Whole‐exome sequencing and microRNA profiling reveal PI3K/AKT pathway’s involvement in juvenile myelomonocytic leukemia

Visualization of consensus genome structure without using a reference genome

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