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Systematic errors in annotations of truncations, loss-of-function and synonymous variants

Vihinen, Mauno LU orcid (2023) In Frontiers in Genetics 14.
Abstract

Description of genetic phenomena and variations requires exact language and concepts. Vast amounts of variation data are produced with next-generation sequencing pipelines. The obtained variations are automatically annotated, e.g., for their functional consequences. These tools and pipelines, along with systematic nomenclature, mainly work well, but there are still some problems in nomenclature, organization of some databases, misuse of concepts and certain practices. Therefore, systematic errors prevent correct annotation and often preclude further analysis of certain variation types. Problems and solutions are described for presumed protein truncations, variants that are claimed to be of loss-of-function based on the type of... (More)

Description of genetic phenomena and variations requires exact language and concepts. Vast amounts of variation data are produced with next-generation sequencing pipelines. The obtained variations are automatically annotated, e.g., for their functional consequences. These tools and pipelines, along with systematic nomenclature, mainly work well, but there are still some problems in nomenclature, organization of some databases, misuse of concepts and certain practices. Therefore, systematic errors prevent correct annotation and often preclude further analysis of certain variation types. Problems and solutions are described for presumed protein truncations, variants that are claimed to be of loss-of-function based on the type of variation, and synonymous variants that are not synonymous and lead to sequence changes or to missing protein.

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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
frameshift variation, loss-of-function variation, mutation, protein truncation, synonymous variation, variation annotation errors
in
Frontiers in Genetics
volume
14
article number
1015017
publisher
Frontiers Media S. A.
external identifiers
  • scopus:85146996138
  • pmid:36713076
ISSN
1664-8021
DOI
10.3389/fgene.2023.1015017
language
English
LU publication?
yes
id
228251f5-f869-47e6-8f3c-7d6e2700100a
date added to LUP
2023-02-13 08:47:06
date last changed
2025-07-14 01:05:20
@article{228251f5-f869-47e6-8f3c-7d6e2700100a,
  abstract     = {{<p>Description of genetic phenomena and variations requires exact language and concepts. Vast amounts of variation data are produced with next-generation sequencing pipelines. The obtained variations are automatically annotated, e.g., for their functional consequences. These tools and pipelines, along with systematic nomenclature, mainly work well, but there are still some problems in nomenclature, organization of some databases, misuse of concepts and certain practices. Therefore, systematic errors prevent correct annotation and often preclude further analysis of certain variation types. Problems and solutions are described for presumed protein truncations, variants that are claimed to be of loss-of-function based on the type of variation, and synonymous variants that are not synonymous and lead to sequence changes or to missing protein.</p>}},
  author       = {{Vihinen, Mauno}},
  issn         = {{1664-8021}},
  keywords     = {{frameshift variation; loss-of-function variation; mutation; protein truncation; synonymous variation; variation annotation errors}},
  language     = {{eng}},
  publisher    = {{Frontiers Media S. A.}},
  series       = {{Frontiers in Genetics}},
  title        = {{Systematic errors in annotations of truncations, loss-of-function and synonymous variants}},
  url          = {{http://dx.doi.org/10.3389/fgene.2023.1015017}},
  doi          = {{10.3389/fgene.2023.1015017}},
  volume       = {{14}},
  year         = {{2023}},
}