Ensembl variation resources

Hunt, Sarah; McLaren, William; Gil, Laurent; Thormann, Anja; Schuilenburg, Helen; Sheppard, Daniel; Parton, Andrew; Armean, Irina M.; Trevanion, Stephen J.; Flicek, Paul; Cunningham, Fiona

doi:10.1093/database/bay119

Cited by 405 publications

(334 citation statements)

References 60 publications

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“…In addition, a deletion mutant was generated that lacks aa residues 346-348 (Δ346-348). Information on DPP4 polymorphisms was retrieved from the Ensembl database (https://www.ensembl.org/index.html) [31] and the Single Nucleotide Polymorphism Database (dbSNP) of the National Center for Biotechnology Information (NCBI) (https://www.ncbi.nlm.nih.gov/snp) [32], and is based on data provided by the gnomAD database (Genome Aggregation database, https://gnomad. broadinstitute.org/), TOPMed program (Trans-Omics for Precision Medicine, https://www.nhlbiwgs.org/), ExAC consortium (Exome Aggregation Consortium, http://exac.broadinstitute.org/) [33] and the 1000G project (1,000 genomes project, http://www.…”

Section: Plasmids and Generation Of Dpp4 Mutantsmentioning

confidence: 99%

Polymorphisms in dipeptidyl peptidase 4 reduce host cell entry of Middle East respiratory syndrome coronavirus

Kleine-Weber

Schroeder

Krüger

et al. 2020

Emerging Microbes & Infections

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Middle East respiratory syndrome (MERS) coronavirus (MERS-CoV) causes a severe respiratory disease in humans. The MERS-CoV spike (S) glycoprotein mediates viral entry into target cells. For this, MERS-CoV S engages the host cell protein dipeptidyl peptidase 4 (DPP4, CD26) and the interface between MERS-CoV S and DPP4 has been resolved on the atomic level. Here, we asked whether naturally-occurring polymorphisms in DPP4, that alter amino acid residues required for MERS-CoV S binding, influence cellular entry of MERS-CoV. By screening of public databases, we identified fourteen such polymorphisms. Introduction of the respective mutations into DPP4 revealed that all except one (Δ346-348) were compatible with robust DPP4 expression. Four polymorphisms (K267E, K267N, A291P and Δ346-348) strongly reduced binding of MERS-CoV S to DPP4 and S protein-driven host cell entry, as determined using soluble S protein and S protein bearing rhabdoviral vectors, respectively. Two polymorphisms (K267E and A291P) were analyzed in the context of authentic MERS-CoV and were found to attenuate viral replication. Collectively, we identified naturally-occurring polymorphisms in DPP4 that negatively impact cellular entry of MERS-CoV and might thus modulate MERS development in infected patients.

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Section: Plasmids and Generation Of Dpp4 Mutantsmentioning

confidence: 99%

Polymorphisms in dipeptidyl peptidase 4 reduce host cell entry of Middle East respiratory syndrome coronavirus

Kleine-Weber

Schroeder

Krüger

et al. 2020

Emerging Microbes & Infections

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“…The Ensembl genome browser (release version 93) was used to designate wild-type and variant alleles for the investigated SNPs. 25…”

Section: Genotypingmentioning

confidence: 99%

Cytokine rs361525, rs1800750, rs1800629, rs1800896, rs1800872, rs1800795, rs1800470, and rs2430561 SNPs in relation with prognostic factors in acute myeloid leukemia

et al. 2019

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Background Cytokines were correlated with survival and disease progression in acute myeloid leukemia (AML). We aimed to evaluate the multivariate effect of TNF‐α rs361525, rs1800750, rs1800629, IL‐10 rs1800896, rs1800872, IL‐6 rs1800795, TGF‐β1 rs1800470, IFN‐γ rs2430561 single nucleotide polymorphisms (SNPs) on AML risk, the multivariate effect of SNPs on overall survival (OS) in AML and the association between the investigated SNPs and prognostic factors in AML. Methods All SNPs were genotyped in 226 adult AML cases and 406 healthy individuals. AML patients were investigated for FLT3 (ITD, D835), DNMT3A (R882), and NPM1 type A mutations. Results Univariate analysis revealed that age above 65 years had a negative influence on survival (P < .001). The presence of the rs1800750 variant genotype (P = .005) or FLT3‐ITD mutation (P = .009) in a cytogenetic high‐risk group (P = .003) negatively influenced OS. A negative association was observed between Eastern Cooperative Oncologic Group Scale status > 2, lactate dehydrogenase (LDH) level, platelet (PLT) count <40 000 cells/mm3, and OS. Multivariate Cox regression analysis showed that the presence of the rs1800750 variant genotype was a risk factor for death (P = .007), and that blast percentage, LDH level (≥600 IU/L), and cytogenetic high‐risk were independent significant predictors for death in AML (P = .04, corrected HR = 1.20; P = .022, corrected HR = 1.24; P = .021, corrected HR = 1.34, respectively). Conclusions Age above 65 years, PLT count, TNF‐α rs1800750 variant genotype, blast percentage, LDH level, and cytogenetic high‐risk may be used as independent risk factors to assess AML mortality.

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“…1) variation-info : this tool relies on the Ensembl genetic variation information [18] annotated and installed on the corresponding server for each particular genome ( i.e.…”

Section: Var-tools: From Variants To Identification Of Regulatory Effmentioning

confidence: 99%

RSAT Var-tools: an accessible and flexible framework to predict the impact of regulatory variants on transcription factor binding

Santana-Garcia

Rocha-Acevedo

Ramirez-Navarro

et al. 2019

Preprint

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Gene regulatory regions contain short and degenerated DNA sites recognized by transcription factors (TFs). When such regions harbor SNPs, the DNA motifs where TFs bind may be affected, thereby altering the transcriptional regulation of the target genes. Such regulatory SNPs have been implicated as causal variants in GWAS studies. In this study, we describe the application of the programs Var-tools designed to predict regulatory variants, and present four case studies to illustrate their usage and applications. In brief, Var-toolsfacilitate i) obtaining variation information, ii) interconversion of variation file formats, iii) retrieval of sequences surrounding variants, and iv) calculating the change on predicted TF affinity scores between alleles, using motif scanning approaches. Notably, the tools support the analysis of haplotypes. The tools are included within the well-maintained suite Regulatory Sequence Analysis Tools (RSAT, http://rsat.eu ), and accessible through a web interface that currently enables analysis of five metazoa and ten plant genomes.Vart-tools can also be used in command-line with any locally-installed Ensembl genome.Users can input personal collections of variants and motifs, providing flexibility in the analysis.

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Ensembl variation resources

Cited by 405 publications

References 60 publications

Polymorphisms in dipeptidyl peptidase 4 reduce host cell entry of Middle East respiratory syndrome coronavirus

Polymorphisms in dipeptidyl peptidase 4 reduce host cell entry of Middle East respiratory syndrome coronavirus

Cytokine rs361525, rs1800750, rs1800629, rs1800896, rs1800872, rs1800795, rs1800470, and rs2430561 SNPs in relation with prognostic factors in acute myeloid leukemia

RSAT Var-tools: an accessible and flexible framework to predict the impact of regulatory variants on transcription factor binding

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