Evidence map›Paper›PMID 30153831›Full record

ReviewRetrovirology2018

Nomenclature for endogenous retrovirus (ERV) loci.

Robert J Gifford, Jonas Blomberg, John M Coffin, Hung Fan, Thierry Heidmann, Jens Mayer, Jonathan Stoye, Michael Tristem, Welkin E Johnson

Abstract readReview
In one paragraph

Review in Retrovirology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 96 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
96citing papers in PubMed, 1 pooled it
–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

96 citing papers in PubMed, 1 synthesis or guideline pooled it.

  1. Pooled it
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  17. Microorganisms · 2024
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36 more citing papers are in PubMed but not listed here.

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

9 authors.

Robert J GiffordMRC-University of Glasgow Centre for Virus Research, Glasgow, UK. robert.gifford@glasgow.ac.uk.ORCID 0000-0003-4028-9884
Jonas BlombergDepartment of Medical Sciences, Uppsala University, Uppsala, Sweden.
John M CoffinDepartment of Molecular Biology and Microbiology, Tufts University, Boston, MA, USA.
Hung FanDepartment of Molecular Biology and Biochemistry and Cancer Research Institute, University of California, Irvine, CA, 92697, USA.
Thierry HeidmannDepartment of Molecular Physiology and Pathology of Infectious and Endogenous Retroviruses, CNRS UMR 9196, Institut Gustave Roussy, 94805, Villejuif, France.
Jens MayerDepartment of Human Genetics, Center of Human and Molecular Biology, Medical Faculty, University of Saarland, Homburg, Germany.
Jonathan StoyeThe Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, UK.
Michael TristemImperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire, SL5 7PY, UK.
Welkin E JohnsonBiology Department, Boston College, Chestnut Hill, Massachusetts, 02467, USA. welkin.johnson@bc.edu.

Funding

Retrovirus Evolution and CancerR35CA200421 · NCI · TUFTS UNIVERSITY BOSTON · PI COFFIN, JOHN M · 2016 to 2022
$6.5M
Medical Research Council MC_U117512710Medical Research Council MC_UU_12014/10Medical Research Council MC_UU_12014/12NCI NIH HHS R35 CA200421
6 · The paper itself

Abstract

Retroviral integration into germline DNA can result in the formation of a vertically inherited proviral sequence called an endogenous retrovirus (ERV). Over the course of their evolution, vertebrate genomes have accumulated many thousands of ERV loci. These sequences provide useful retrospective information about ancient retroviruses, and have also played an important role in shaping the evolution of vertebrate genomes. There is an immediate need for a unified system of nomenclature for ERV loci, not only to assist genome annotation, but also to facilitate research on ERVs and their impact on genome biology and evolution. In this review, we examine how ERV nomenclatures have developed, and consider the possibilities for the implementation of a systematic approach for naming ERV loci. We propose that such a nomenclature should not only provide unique identifiers for individual loci, but also denote orthologous relationships between ERVs in different species. In addition, we propose that-where possible-mnemonic links to previous, well-established names for ERV loci and groups should be retained. We show how this approach can be applied and integrated into existing taxonomic and nomenclature schemes for retroviruses, ERVs and transposable elements.

Indexed as

AnimalsEndogenous RetrovirusesEvolution, MolecularGenetic LociGenetic VariationGenomicsHumansTerminology as TopicVertebratesClassificationEndogenousNomenclatureRetrovirusTaxonomy

Identifiers

PMID30153831
PMCPMC6114882

What OpenQuestion holds

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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.