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

Tack, Véronique; Deans, Zandra C.; Wolstenholme, Nicola; Patton, S.; Dequeker, Elisabeth

doi:10.1002/humu.22975

Cited by 25 publications

(30 citation statements)

References 21 publications

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“…The Human Genome Variation Society (HGVS) nomenclature is currently the standard worldwide and is recommended for variant reporting 71 . Unambiguous naming of the variants is critical for the patient's medical records as well as for the pre-symptomatic genetic testing that could be offered to the patient's relatives.…”

Section: Nomenclaturementioning

confidence: 99%

Consensus Statement on next-generation-sequencing-based diagnostic testing of hereditary phaeochromocytomas and paragangliomas

et al. 2016

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Phaeochromocytomas and paragangliomas (PPGLs) are neural-crest-derived tumours of the sympathetic or parasympathetic nervous system that are often inherited and are genetically heterogeneous. Genetic testing is recommended for patients with these tumours and for family members of patients with hereditary forms of PPGLs. Due to the large number of susceptibility genes implicated in the diagnosis of inherited PPGLs, next-generation sequencing (NGS) technology is ideally suited for carrying out genetic screening of these individuals. This Consensus Statement, formulated by a study group comprised of experts in the field, proposes specific recommendations for the use of diagnostic NGS in hereditary PPGLs. In brief, the study group recommends target gene panels for screening of germ line DNA, technical adaptations to address different modes of disease transmission, orthogonal validation of NGS findings, standardized classification of variant pathogenicity and uniform reporting of the findings. The use of supplementary assays, to aid in the interpretation of the results, and sequencing of tumour DNA, for identification of somatic mutations, is encouraged. In addition, the study group launches an initiative to develop a gene-centric curated database of PPGL variants, with annual re-evaluation of variants of unknown significance by an expert group for purposes of reclassification and clinical guidance.

Funding Agencies|Cancer Prevention and Research Institute of Texas (CPRIT) [RP101202, RP57154]; Department of Defense [CDMRP W81XWH-12-1-0508]; Voelcker Fund; National Institutes of Health (NIH)s National Center for Research Resources; National Center for Advancing Translational Sciences [8UL1TR000149]; INSERM; French National Cancer Institute (INCA); Direction Generale de lOffre de Soins (DGOS); INCA [INCA-DGOS_8663]; European Union [633983]; Brazilian National Council for Scientific and Technological Development (CNPq); Cancer Research for PErsonalized Medicine (CARPEM); ERC Advanced Researcher Award

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Section: Nomenclaturementioning

confidence: 99%

Consensus Statement on next-generation-sequencing-based diagnostic testing of hereditary phaeochromocytomas and paragangliomas

et al. 2016

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“…This is discussed in more depth in Tack et al. (). Finally, submission to variant databases, with an inherent variant description check, might also help to get uniform and correct variant descriptions.…”

Section: Overview Of All Variants Reportedmentioning

confidence: 95%

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

et al. 2016

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ABSTRACT:The recommendations for the description of sequence variants from the Human Genome Variation Society (HGVS) were published in 2000. Over the years, the recommendations became widely adopted, especially in human clinical genetics and DNA laboratory reporting. As part of a testing scheme performed by the United Kingdom National External Quality Assessment Scheme (UK NEQAS) for Molecular Genetics, we assessed the current variability in the use and interpretation of the guidelines by diagnostic laboratories based across the globe. Twenty-six participating laboratories gave 21 different descriptions. Six laboratories gave fully compliant HGVS descriptions, 12 laboratories reported the correct variant, although not using the recommended format, whilst eight laboratory reports (31%) were not correct. The results indicate that available tools to check variant descriptions were not used. We conclude that education appears to be the way forward to eliminate the observed variability in data reporting. Hum Mutat 37:576-578, 2016. C 2016 Wiley Periodicals, Inc.

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“…The Human Genome Variation Society (HGVS) nomenclature for the description of human sequence variants (den Dunnen et al., ) is widely adopted by scientific journals and variant databases and is endorsed by professional organizations (Deans, Fairley, den Dunnen, & Clark, ; Richards et al., ; Tack, Deans, Wolstenhome, Patton, & Dequeker, ). As high‐throughput sequencing has become more common, HGVS recommendations have evolved to communicate a plethora of new variants to the scientific and healthcare communities (Taschner & den Dunnen, ).…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2017

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The Human Genome Variation Society (HGVS) variant nomenclature is widely used to describe sequence variants in scientific publications, clinical reports, and databases. However, the HGVS recommendations are complex and this often results in inaccurate variant descriptions being reported. The open‐source hgvs Python package (https://github.com/biocommons/hgvs) provides a programmatic interface for parsing, manipulating, formatting, and validating of variants according to the HGVS recommendations, but does not provide a user‐friendly Web interface. We have developed a Web‐based variant validation tool, VariantValidator (https://variantvalidator.org/), which utilizes the hgvs Python package and provides additional functionality to assist users who wish to accurately describe and report sequence‐level variations that are compliant with the HGVS recommendations. VariantValidator was designed to ensure that users are guided through the intricacies of the HGVS nomenclature, for example, if the user makes a mistake, VariantValidator automatically corrects the mistake if it can, or provides helpful guidance if it cannot. In addition, VariantValidator has the facility to interconvert genomic variant descriptions in HGVS and Variant Call Format with a degree of accuracy that surpasses most competing solutions.

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

Cited by 25 publications

References 21 publications

Consensus Statement on next-generation-sequencing-based diagnostic testing of hereditary phaeochromocytomas and paragangliomas

Consensus Statement on next-generation-sequencing-based diagnostic testing of hereditary phaeochromocytomas and paragangliomas

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

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

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