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We have investigated compliance with guidelines regarding HGVS nomenclature and/or submission of variants to public databases in the author instructions of several genetics and genomics journals. For this, we used a list of genetics and genomics journals created by the Human Variome Project (HVP) office (See http://www.humanvariomeproject.org/resources/genetics-and-genomics-journals.html). The HVP aims to work towards open and free sharing of high quality information on genetic variation and its effect on human health. The HVP Gene and Disease-specific Database Council has created example instructions for authors for genetics and genomic journals containing guidelines regarding HGVS nomenclature and submission of variants to public databases. The HVP office has sent this document to journal editors asking them to include similar requirements in their instructions for authors. The rationale is that better instructions will help improving the quality of variant descriptions in manuscripts and access to variant information in databases.
We have used this list to select journals including both requirements. We have investigated the January 2016 issue of several of them. A group of students has checked the publications first for the basic requirements: mentions of the reference sequence used to describe variants and the presence of the variants in public databases. The next step was to check variant and phenotype descriptions with specific attention for predicted protein effects. Our preliminary results suggest that predicted protein effects in publications cannot be verified in case of altered splice sites without supporting RNA-level evidence or in case of insertions of unspecified nucleotides. Although the underlying variants are likely to have disease-causing effects, lack of supporting evidence disqualifies this information for diagnostic use. In several cases, the RNA-level information was specified in the gene variant database submission, indicating that submission of variants to databases prior to manuscript acceptance might improve the quality of publications. We have observed that authors include statements suggesting variants have been submitted to databases, but the variants were not found. Reviewers and journal editors could help improving manuscript quality by insisting on compliance and enforcing the existing guidelines.Checking the experts: compliance with author instructions regarding HGVS nome...
Checking the experts: compliance with author instructions regarding HGVS nome...Human Variome Project
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We have investigated compliance with guidelines regarding HGVS nomenclature and/or submission of variants to public databases in the author instructions of several genetics and genomics journals. For this, we used a list of genetics and genomics journals created by the Human Variome Project (HVP) office (See http://www.humanvariomeproject.org/resources/genetics-and-genomics-journals.html). The HVP aims to work towards open and free sharing of high quality information on genetic variation and its effect on human health. The HVP Gene and Disease-specific Database Council has created example instructions for authors for genetics and genomic journals containing guidelines regarding HGVS nomenclature and submission of variants to public databases. The HVP office has sent this document to journal editors asking them to include similar requirements in their instructions for authors. The rationale is that better instructions will help improving the quality of variant descriptions in manuscripts and access to variant information in databases.
We have used this list to select journals including both requirements. We have investigated the January 2016 issue of several of them. A group of students has checked the publications first for the basic requirements: mentions of the reference sequence used to describe variants and the presence of the variants in public databases. The next step was to check variant and phenotype descriptions with specific attention for predicted protein effects. Our preliminary results suggest that predicted protein effects in publications cannot be verified in case of altered splice sites without supporting RNA-level evidence or in case of insertions of unspecified nucleotides. Although the underlying variants are likely to have disease-causing effects, lack of supporting evidence disqualifies this information for diagnostic use. In several cases, the RNA-level information was specified in the gene variant database submission, indicating that submission of variants to databases prior to manuscript acceptance might improve the quality of publications. We have observed that authors include statements suggesting variants have been submitted to databases, but the variants were not found. Reviewers and journal editors could help improving manuscript quality by insisting on compliance and enforcing the existing guidelines.Checking the experts: compliance with author instructions regarding HGVS nome...
Checking the experts: compliance with author instructions regarding HGVS nome...Human Variome Project
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