ArticleBriefings in bioinformatics2015
Rich annotation of DNA sequencing variants by leveraging the Ensembl Variant Effect Predictor with plugins.
Article in Briefings in bioinformatics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
29 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Common Genetic Polymorphisms Influence Blood Biomarker Measurements in COPD.PLoS genetics · 2016Pooled it
- MuSA: a Nextflow pipeline for deep, reproducible annotation and clinical ranking of genomic variants.BMC bioinformatics · 2026Article
- OpenVariant: a toolkit to parse and operate multiple input file formats.Bioinformatics (Oxford, England) · 2024Article
- Large-scale exome array summary statistics resources for glycemic traits to aid effector gene prioritization.Wellcome open research · 2023Article
- Three chromosome-level duck genome assemblies provide insights into genomic variation during domestication.Nature communications · 2021Article
- PBX-WNT-P63-IRF6 pathway in nonsyndromic cleft lip and palate.Birth defects research · 2020Article
- Hadoop and PySpark for reproducibility and scalability of genomic sequencing studies.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2020Article
- Genome-wide discovery of somatic regulatory variants in diffuse large B-cell lymphoma.Nature communications · 2018Article
- Functional annotation of genomic variants in studies of late-onset Alzheimer's disease.Bioinformatics (Oxford, England) · 2018Article
- Mutations in DYNC2H1, the cytoplasmic dynein 2, heavy chain 1 motor protein gene, cause short-rib polydactyly type I, Saldino-Noonan type.Clinical genetics · 2017Article
- Knowledge Discovery in Biological Databases for Revealing Candidate Genes Linked to Complex Phenotypes.Journal of integrative bioinformatics · 2017Review
- Phenotypic spectrum of POLR3B mutations: isolated hypogonadotropic hypogonadism without neurological or dental anomalies.Journal of medical genetics · 2017Article
- Rare genetic variants in the endocannabinoid system genes CNR1 and DAGLA are associated with neurological phenotypes in humans.PloS one · 2017Article
- An inactivating mutation in intestinal cell kinase, ICK, impairs hedgehog signalling and causes short rib-polydactyly syndrome.Human molecular genetics · 2016Article
- Truncating mutations in APP cause a distinct neurological phenotype.Annals of neurology · 2016Article
- A Genome-Wide Association Study for Regulators of Micronucleus Formation in Mice.G3 (Bethesda, Md.) · 2016Article
- The Ensembl Variant Effect Predictor.Genome biology · 2016Article
- Article
- A novel follicle-stimulating hormone receptor mutation causing primary ovarian failure: a fertility application of whole exome sequencing.Human reproduction (Oxford, England) · 2016Article
- Exome Sequencing Identified a Splice Site Mutation in FHL1 that Causes Uruguay Syndrome, an X-Linked Disorder With Skeletal Muscle Hypertrophy and Premature Cardiac Death.Circulation. Cardiovascular genetics · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
High-throughput DNA sequencing has become a mainstay for the discovery of genomic variants that may cause disease or affect phenotype. A next-generation sequencing pipeline typically identifies thousands of variants in each sample. A particular challenge is the annotation of each variant in a way that is useful to downstream consumers of the data, such as clinical sequencing centers or researchers. These users may require that all data storage and analysis remain on secure local servers to protect patient confidentiality or intellectual property, may have unique and changing needs to draw on a variety of annotation data sets and may prefer not to rely on closed-source applications beyond their control. Here we describe scalable methods for using the plugin capability of the Ensembl Variant Effect Predictor to enrich its basic set of variant annotations with additional data on genes, function, conservation, expression, diseases, pathways and protein structure, and describe an extensible framework for easily adding additional custom data sets.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.