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Variant classification changes over time in the clinical molecular diagnostic laboratory setting.

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Genetic variant reclassification is common, with most variants downgraded to a more benign classification. Periodic reassessment ensures accurate genetic testing results for patient care.

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Area of Science:

  • Clinical Genetics
  • Genomic Medicine
  • Medical Diagnostics

Background:

  • Germline genetic testing requires accurate variant classification for patient care.
  • Variant classifications include pathogenic, likely pathogenic, uncertain significance, likely benign, and benign.
  • Ongoing literature review and evidence accumulation necessitate variant reclassification.

Purpose of the Study:

  • To characterize variant reclassifications in Ontario.
  • To assess the frequency and nature of variant reclassifications in germline genetic testing.

Main Methods:

  • Analysis of DNA samples from hereditary cancer clinics in Ontario (2012-2022).
  • Inclusion of patients meeting provincial eligibility criteria for hereditary cancer syndromes or polycystic kidney disease testing.
  • Categorization of reclassification events as within or outside the broader category of significance.

Main Results:

  • 23.7% of 8075 unique variants were reassessed, with 7.2% reclassified.
  • 60.7% of reclassified variants changed outside their broader significance category.
  • Most reclassified variants (58.1%) had a significantly different final classification, with a majority downgraded to a more benign status.

Conclusions:

  • Variant reclassification is a frequent event.
  • A significant proportion of reclassifications represent substantial shifts in variant significance.
  • Regular variant reassessment is crucial for maintaining accurate patient care in genetic testing.