Literature DB >> 33252176

Verifying nomenclature of DNA variants in submitted manuscripts: Guidance for journals.

Jan Higgins1, Raymond Dalgleish2, Johan T den Dunnen3, Greg Barsh4,5, Peter J Freeman6, David N Cooper7, Sara Cullinan8, Kay E Davies9, Huw Dorkins10,11, Li Gong12, Issei Imoto13, Teri E Klein12, Bruce Korf14, Adya Misra15,16, Mark H Paalman17, Sarah Ratzel8, Juergen K V Reichardt18, Heidi L Rehm19,20,21, Katsushi Tokunaga12,22, Karen E Weck23,24, Garry R Cutting25.   

Abstract

Documenting variation in our genomes is important for research and clinical care. Accuracy in the description of DNA variants is therefore essential. To address this issue, the Human Variome Project convened a committee to evaluate the feasibility of requiring authors to verify that all variants submitted for publication complied with a widely accepted standard for description. After a pilot study of two journals, the committee agreed that requiring authors to verify that variants complied with Human Genome Variation Society nomenclature is a reasonable step toward standardizing the worldwide inventory of human variation.
© 2020 Wiley Periodicals LLC.

Entities:  

Keywords:  ClinVar; DNA variants; Human Genome Variation Society; Leiden Open Variation Database

Mesh:

Substances:

Year:  2020        PMID: 33252176      PMCID: PMC7961887          DOI: 10.1002/humu.24144

Source DB:  PubMed          Journal:  Hum Mutat        ISSN: 1059-7794            Impact factor:   4.878


  9 in total

1.  HGVS Nomenclature in Practice: An Example from the United Kingdom National External Quality Assessment Scheme.

Authors:  Zandra C Deans; Jennifer A Fairley; Johan T den Dunnen; Caroline Clark
Journal:  Hum Mutat       Date:  2016-03-18       Impact factor: 4.878

2.  Efficient variant data preparation for Human Mutation manuscripts: Variants and phenotypes.

Authors:  Johan T den Dunnen
Journal:  Hum Mutat       Date:  2019-08       Impact factor: 4.878

3.  What's in a Name? A Coordinated Approach toward the Correct Use of a Uniform Nomenclature to Improve Patient Reports and Databases.

Authors:  Véronique Tack; Zandra C Deans; Nicola Wolstenholme; Simon Patton; Elisabeth M C Dequeker
Journal:  Hum Mutat       Date:  2016-03-14       Impact factor: 4.878

4.  HGVS Recommendations for the Description of Sequence Variants: 2016 Update.

Authors:  Johan T den Dunnen; Raymond Dalgleish; Donna R Maglott; Reece K Hart; Marc S Greenblatt; Jean McGowan-Jordan; Anne-Francoise Roux; Timothy Smith; Stylianos E Antonarakis; Peter E M Taschner
Journal:  Hum Mutat       Date:  2016-03-25       Impact factor: 4.878

5.  Sequence Variant Descriptions: HGVS Nomenclature and Mutalyzer.

Authors:  Johan T den Dunnen
Journal:  Curr Protoc Hum Genet       Date:  2016-07-01

6.  ClinVar: improvements to accessing data.

Authors:  Melissa J Landrum; Shanmuga Chitipiralla; Garth R Brown; Chao Chen; Baoshan Gu; Jennifer Hart; Douglas Hoffman; Wonhee Jang; Kuljeet Kaur; Chunlei Liu; Vitaly Lyoshin; Zenith Maddipatla; Rama Maiti; Joseph Mitchell; Nuala O'Leary; George R Riley; Wenyao Shi; George Zhou; Valerie Schneider; Donna Maglott; J Bradley Holmes; Brandi L Kattman
Journal:  Nucleic Acids Res       Date:  2020-01-08       Impact factor: 16.971

7.  LOVD v.2.0: the next generation in gene variant databases.

Authors:  Ivo F A C Fokkema; Peter E M Taschner; Gerard C P Schaafsma; J Celli; Jeroen F J Laros; Johan T den Dunnen
Journal:  Hum Mutat       Date:  2011-02-22       Impact factor: 4.878

8.  A variant by any name: quantifying annotation discordance across tools and clinical databases.

Authors:  Jennifer L Yen; Sarah Garcia; Aldrin Montana; Jason Harris; Stephen Chervitz; Massimo Morra; John West; Richard Chen; Deanna M Church
Journal:  Genome Med       Date:  2017-01-26       Impact factor: 11.117

9.  VariantValidator: Accurate validation, mapping, and formatting of sequence variation descriptions.

Authors:  Peter J Freeman; Reece K Hart; Liam J Gretton; Anthony J Brookes; Raymond Dalgleish
Journal:  Hum Mutat       Date:  2017-10-17       Impact factor: 4.878

  9 in total
  3 in total

1.  Standardized nomenclature and open science in Human Genomics.

Authors:  Vasilis Vasiliou; Kirill Veselkov; Elspeth Bruford; Juergen K V Reichardt
Journal:  Hum Genomics       Date:  2021-02-22       Impact factor: 4.639

2.  Structure and Function of the ABCD1 Variant Database: 20 Years, 940 Pathogenic Variants, and 3400 Cases of Adrenoleukodystrophy.

Authors:  Eric J Mallack; Kerry Gao; Marc Engelen; Stephan Kemp
Journal:  Cells       Date:  2022-01-14       Impact factor: 6.600

3.  Discovery of genomic variation across a generation.

Authors:  Brett Trost; Livia O Loureiro; Stephen W Scherer
Journal:  Hum Mol Genet       Date:  2021-10-01       Impact factor: 6.150

  3 in total

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