Essential for NGS data annotation


QIAGEN Digital Insights

Essential for NGS data annotation

Now with more than 200,000 Mutation Reports, and improvements to help assess pathogenicity, HGMD is confirmed as the essential tool for NGS Data Annotation.

The Human Gene Mutation Database (HGMD) was recently covered in a peer-reviewed paper in Human Genetics entitled “The Human Gene Mutation Database: Towards a Comprehensive Repository of Inherited Mutation Data for Medical Research, Genetic Diagnosis and Next-generation Sequencing Studies”.

Written by the team of researchers from Cardiff University’s School of Medicine at the Institute of Medical Genetics that also develops HGMD, the report sheds light on several areas that they find set HGMD apart.

First, they state that HGMD provides “mutation data based on the cogency and credibility of the associated literature, with a curation policy that opts to minimize false negatives by being broadly inclusive.” They contrast this with the ACMG consortium’s system for variant classifications, the primary purpose of which they say “appears to be to minimize false positives in a clinical setting.” The report warns that the two systems should not be used interchangeably, as this could risk reaching misleading or inaccurate conclusions. To aid NGS researchers in assessing mutations in a clinical context, the paper announces the introduction of a novel variant scoring system to HGMD.

Second, they mentioned that HGMD now features a significant number of mutations with multiple references in the literature as contextual information. These references include functional studies, additional case reports, additional phenotypes and population case-control studies. Such references can play a vital role in confirming the pathogenicity of a variant.

Third, the report states that “HGMD curators have adopted a policy of continual reassessment of the curated content within the database. If and when newly published information relevant to a specific mutation entry becomes available […], the mutation entry may be revised or re-classified”. The value of this approach was confirmed by another paper (Abouelhoda M, et al. (2016) Revisiting the morbid genome of Mendelian disorders. Genome Biol 17:235), which found that a higher proportion of variants in ClinVar required re-classification compared to HGMD Professional.

We at QIAGEN Bioinformatics are passionate about providing the most comprehensive and up-to-date coverage of published human inherited disease mutations. If you’ve used HGMD to unlock valuable insights about variants, or if you’re interested in learning more about how it can help further your science, we would love to hear from you.

To explore HGMD in more depth, visit our resources page.