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Related Experiment Video

Updated: Mar 15, 2026

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
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Actionable Genes, Core Databases, and Locus-Specific Databases.

Amélie Pinard1, Morgane Miltgen1, Arnaud Blanchard1

  • 1Aix Marseille Univ, INSERM, GMGF, Marseille, France.

Human Mutation
|September 8, 2016
PubMed
Summary
This summary is machine-generated.

Secondary variants (SVs) in actionable genes are often underestimated. Locus-specific databases (LSDBs) significantly improve the identification and annotation of these clinically relevant variants compared to general databases.

Keywords:
LSDBNGSactionable genesdatabasessecondary variant

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Area of Science:

  • Genomics
  • Clinical Diagnostics
  • Bioinformatics

Background:

  • Next-generation sequencing (NGS) in diagnostics generates secondary variants (SVs) requiring careful interpretation.
  • Accurate identification and reporting of SVs in actionable genes are crucial for patient care.
  • Current methods may underestimate SVs and their clinical significance.

Purpose of the Study:

  • To investigate the identification and reporting of secondary variants (SVs) in actionable genes.
  • To evaluate the utility of Locus-Specific Databases (LSDBs) in variant annotation.
  • To compare the performance of LSDBs against the Human Gene Mutation Database (HGMD) Professional.

Main Methods:

  • Analysis of 318 SVs in 23 cancer susceptibility genes from 572 participants with atherosclerosis phenotypes.
  • Comparison of variant reporting rates between LSDBs and HGMD Professional.
  • Assessment of reported pathogenicity of variants in both databases.

Main Results:

  • LSDBs reported 71.4% of identified SVs, compared to 43.4% in HGMD Professional.
  • A lower percentage of pathogenic variants were reported in LSDBs (4.8%) versus HGMD Professional (23.9%).
  • LSDBs offer superior annotation and reduce overinterpretation of mutations.

Conclusions:

  • LSDBs are essential resources for accurate SV annotation in clinical genomics.
  • Utilizing LSDBs enhances the detection and correct classification of actionable variants.
  • Improved variant interpretation through LSDBs minimizes misdiagnosis and overinterpretation of pathogenicity.