GenVisR: Genomic Visualizations in R

Skidmore, Zachary L.; Wagner, Alex H.; Lesurf, Robert; Campbell, Katie M.; Kunisaki, Jason; Griffith, Obi L.

doi:10.1093/bioinformatics/btw325

Cited by 271 publications

(198 citation statements)

References 20 publications

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“…Visualization created using GenVisR. 41 (Inset) Histogram depicts the distribution of expected total histone gene mutation co-occurrences from 10 000 randomly permutated datasets with respect to the observed total co-occurrence in this cohort indicated by a red line (estimated P value , .0001). Although some patients had more than 1 mutation per histone gene, as indicated at the top, genes were considered mutated or not mutated for co-occurrence analysis.…”

Section: Discussionmentioning

confidence: 99%

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Recurrent somatic mutations affecting B-cell receptor signaling pathway genes in follicular lymphoma

Krysiak

Gomez

White

et al. 2017

Blood

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156

131

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• FLs harbor more recurrent mutations in the BCR signaling pathway, SWI/SNF complex, and histone genes than previously known.• Novel recurrent mutations affecting BTK, SYK, and HVCN1 may have therapeutic and prognostic implications for FL.Follicular lymphoma (FL) is the most common form of indolent non-Hodgkin lymphoma, yet it remains only partially characterized at the genomic level. To improve our understanding of the genetic underpinnings of this incurable and clinically heterogeneous disease, whole-exome sequencing was performed on tumor/normal pairs from a discovery cohort of 24 patients with FL. Using these data and mutations identified in other B-cell malignancies, 1716 genes were sequenced in 113 FL tumor samples from 105 primarily treatment-naive individuals. We identified 39 genes that were mutated significantly above background mutation rates. CREBBP mutations were associated with inferior PFS. In contrast, mutations in previously unreported HVCN1, a voltage-gated proton channel-encoding gene and B-cell receptor signaling modulator, were associated with improved PFS. In total, 47 (44.8%) patients harbor mutations in the interconnected B-cell receptor (BCR) and CXCR4 signaling pathways. Histone gene mutations were more frequent than previously reported (identified in 43.8% of patients) and often co-occurred (17.1% of patients). A novel, recurrent hotspot was identified at a posttranslationally modified residue in the histone H2B family. This study expands the number of mutated genes described in several known signaling pathways and complexes involved in lymphoma pathogenesis (BCR, Notch, SWitch/sucrose nonfermentable (SWI/SNF), vacuolar ATPases) and identified novel recurrent mutations (EGR1/2, POU2AF1, BTK, ZNF608, HVCN1) that require further investigation in the context of FL biology, prognosis, and treatment. (Blood. 2017;129(4):473-483)

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Section: Discussionmentioning

confidence: 99%

“…For individuals with multiple samples, the union of mutations in all samples for that individual was used. The mutation waterfall plot was created using the "GenVisR" package in R. 41 …”

Section: /2mentioning

confidence: 99%

Recurrent somatic mutations affecting B-cell receptor signaling pathway genes in follicular lymphoma

Krysiak

Gomez

White

et al. 2017

Blood

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156

131

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“…The SNP and RGA density/distribution plots were generated using karyoploteR v1.4.2 (Gel and Serra, ). Waterfall plots were drawn using Variant Effect Predictor v88.13 (McLaren et al ., ), GenVisR v1.11.3 (Skidmore et al ., ), vcftools v0.1.15 (Danecek et al ., ) and R 3.4.4 (R Core Team, ).…”

Section: Methodsmentioning

confidence: 99%

Characterization of disease resistance genes in the Brassica napus pangenome reveals significant structural variation

Dolatabadian

Bayer

Tirnaz

et al. 2019

Plant Biotechnology Journal

101

104

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Summary Methods based on single nucleotide polymorphism (SNP), copy number variation (CNV) and presence/absence variation (PAV) discovery provide a valuable resource to study gene structure and evolution. However, as a result of these structural variations, a single reference genome is unable to cover the entire gene content of a species. Therefore, pangenomics analysis is needed to ensure that the genomic diversity within a species is fully represented. Brassica napus is one of the most important oilseed crops in the world and exhibits variability in its resistance genes across different cultivars. Here, we characterized resistance gene distribution across 50 B. napus lines. We identified a total of 1749 resistance gene analogs (RGAs), of which 996 are core and 753 are variable, 368 of which are not present in the reference genome (cv. Darmor‐bzh). In addition, a total of 15 318 SNPs were predicted within 1030 of the RGAs. The results showed that core R‐genes harbour more SNPs than variable genes. More nucleotide binding site‐leucine‐rich repeat (NBS‐LRR) genes were located in clusters than as singletons, with variable genes more likely to be found in clusters. We identified 106 RGA candidates linked to blackleg resistance quantitative trait locus (QTL). This study provides a better understanding of resistance genes to target for genomics‐based improvement and improved disease resistance.

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“…Allele frequencies for a set of 24 ‘identity’ SNPs were analyzed to verify that no sample studied was significantly contaminated by DNA from an unrelated sample, (47) and were plotted using the GenVisR package (http://biorxiv.org/content/early/2016/03/25/043604) (Figure 4B). (48) Pairwise comparisons were each performed twice, by swapping the control and variable sample, resulting in a total of 20 comparisons (Supplementary Appendix, Figure 3A). …”

Section: Iii) Materials and Methodsmentioning

confidence: 99%

Melorheostosis: Exome sequencing of an associated dermatosis implicates postzygotic mosaicism of mutated KRAS

Whyte

Griffith

Trani

et al. 2017

Bone

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Melorheostosis (MEL) is the rare sporadic dysostosis characterized by monostotic or polyostotic osteosclerosis and hyperostosis often distributed in a sclerotomal pattern. The prevailing hypothesis for MEL invokes postzygotic mosaicism. Sometimes scleroderma-like skin changes, considered a representation of the pathogenetic process of MEL, overlie the bony changes, and sometimes MEL becomes malignant. Osteopoikilosis (OPK) is the autosomal dominant skeletal dysplasia that features symmetrically distributed punctate osteosclerosis due to heterozygous loss-of-function mutation within LEMD3. Rarely, radiographic findings of MEL occur in OPK. However, germline mutation of LEMD3 does not explain sporadic MEL. To explore if mosaicism underlies MEL, we studied a boy with polyostotic MEL and characteristic overlying scleroderma-like skin, a few bony lesions consistent with OPK, and a large epidermal nevus known to usually harbor a HRAS, FGFR3, or PIK3 gene mutation. Exome sequencing was performed to ~100× average read depth for his two dermatoses, two areas of normal skin, and peripheral blood leukocytes. As expected for non-malignant tissues, the patient’s mutation burden in his normal skin and leukocytes was low. He, his mother, and his maternal grandfather carried a heterozygous, germline, in-frame, 24-base-pair deletion in LEMD3. Radiographs of him and his mother revealed bony foci consistent with OPK, but she showed no MEL. For the patient, somatic variant analysis, using five algorithms to compare all 20 possible pairwise combinations of his five DNA samples, identified only one high-confidence mutation, heterozygous KRAS Q61H (NM_033360.3:c.183A>C, NP_203524.1:p.Gln61His), in both his dermatoses but absent in his normal skin and blood. Thus, sparing our patient biopsy of his MEL bone, we identified a heterozygous somatic KRAS mutation in his scleroderma-like dermatosis considered a surrogate for MEL. This implicates postzygotic mosaicism of mutated KRAS, perhaps facilitated by germline LEMD3 haploinsufficiency, causing his MEL.

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GenVisR: Genomic Visualizations in R

Cited by 271 publications

References 20 publications

Recurrent somatic mutations affecting B-cell receptor signaling pathway genes in follicular lymphoma

Recurrent somatic mutations affecting B-cell receptor signaling pathway genes in follicular lymphoma

Characterization of disease resistance genes in the Brassica napus pangenome reveals significant structural variation

Melorheostosis: Exome sequencing of an associated dermatosis implicates postzygotic mosaicism of mutated KRAS

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