Evidence map›Paper›PMID 31765830›Full record

ArticleGenomics, proteomics & bioinformatics2019

VPOT: A Customizable Variant Prioritization Ordering Tool for Annotated Variants.

Eddie Ip, Gavin Chapman, David Winlaw, Sally L Dunwoodie, Eleni Giannoulatou

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genomics, proteomics & bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.

0numbers the graph read from it
0cells of the map it votes in
13citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from 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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

13 citing papers in PubMed.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

5 authors.

Eddie IpVictor Chang Cardiac Research Institute, Sydney 2010, Australia; St Vincent's Clinical School, University of New South Wales, Sydney 2052, Australia.
Gavin ChapmanVictor Chang Cardiac Research Institute, Sydney 2010, Australia; St Vincent's Clinical School, University of New South Wales, Sydney 2052, Australia.
David WinlawHeart Centre for Children, The Children's Hospital at Westmead, Sydney 2145, Australia; Sydney Medical School, University of Sydney, Sydney 2050, Australia.
Sally L DunwoodieVictor Chang Cardiac Research Institute, Sydney 2010, Australia; St Vincent's Clinical School, University of New South Wales, Sydney 2052, Australia; School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney 2033, Australia.
Eleni GiannoulatouVictor Chang Cardiac Research Institute, Sydney 2010, Australia; St Vincent's Clinical School, University of New South Wales, Sydney 2052, Australia. Electronic address: e.giannoulatou@victorchang.edu.au.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Next-generation sequencing (NGS) technologies generate thousands to millions of genetic variants per sample. Identification of potential disease-causal variants is labor intensive as it relies on filtering using various annotation metrics and consideration of multiple pathogenicity prediction scores. We have developed VPOT (variant prioritization ordering tool), a python-based command line tool that allows researchers to create a single fully customizable pathogenicity ranking score from any number of annotation values, each with a user-defined weighting. The use of VPOT can be informative when analyzing entire cohorts, as variants in a cohort can be prioritized. VPOT also provides additional functions to allow variant filtering based on a candidate gene list or by affected status in a family pedigree. VPOT outperforms similar tools in terms of efficacy, flexibility, scalability, and computational performance. VPOT is freely available for public use at GitHub (https://github.com/VCCRI/VPOT/). Documentation for installation along with a user tutorial, a default parameter file, and test data are provided.

Indexed as

User-Computer Interface3-Hydroxyanthranilate 3,4-DioxygenaseAlgorithmsDatabases, GeneticExome SequencingHeart DiseasesHumansPolymorphism, Genetic3-Hydroxyanthranilate 3,4-DioxygenaseCustomizable rankingGenomic annotationNext-generation sequencingPathogenicity predictionsVariant prioritization

Identifiers

PMID31765830
PMCPMC7056850

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

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.