TY - JOUR
T1 - Observed frequency and challenges of variant reclassification in a hereditary cancer clinic
AU - Macklin, Sarah
AU - Durand, Nisha
AU - Atwal, Paldeep
AU - Hines, Stephanie
N1 - Publisher Copyright:
© 2018 American College of Medical Genetics and Genomics.
PY - 2018/3/1
Y1 - 2018/3/1
N2 - Purpose: Efforts have been made by the American College of Medical Genetics and Genomics and the Association for Molecular Pathology to make variant classification more uniform, but many limitations remain. Reclassification of a variant of uncertain significance (VUS) is expected, but other more certain calls, like pathogenic or benign, can also be reclassified once additional information is gathered. Variant reclassification can create difficult circumstances for both patients and clinicians. Methods: Retrospective review of all variant reclassifications in genes associated with hereditary cancer syndromes at one clinic between September 2013 and February 2017 was completed. All variant reclassifications were completed and reported by the original testing laboratory. Results: A total of 1,103 hereditary cancer tests were ordered. Fewer than 5% (40/1,103) of the initial reports were updated during that time period. Most reclassifications (29/40) were downgrades of VUS to likely benign. Only three reclassifications could potentially alter medical management. Conclusion: The majority of variant reclassifications do not impact medical management. Upgrading a variant call to pathogenic could be important for a patient's care and shows the importance of open communication between laboratories and clinicians. A variant downgrade from pathogenic can be a significant reclassification as well, especially if prophylactic surgery has been completed.
AB - Purpose: Efforts have been made by the American College of Medical Genetics and Genomics and the Association for Molecular Pathology to make variant classification more uniform, but many limitations remain. Reclassification of a variant of uncertain significance (VUS) is expected, but other more certain calls, like pathogenic or benign, can also be reclassified once additional information is gathered. Variant reclassification can create difficult circumstances for both patients and clinicians. Methods: Retrospective review of all variant reclassifications in genes associated with hereditary cancer syndromes at one clinic between September 2013 and February 2017 was completed. All variant reclassifications were completed and reported by the original testing laboratory. Results: A total of 1,103 hereditary cancer tests were ordered. Fewer than 5% (40/1,103) of the initial reports were updated during that time period. Most reclassifications (29/40) were downgrades of VUS to likely benign. Only three reclassifications could potentially alter medical management. Conclusion: The majority of variant reclassifications do not impact medical management. Upgrading a variant call to pathogenic could be important for a patient's care and shows the importance of open communication between laboratories and clinicians. A variant downgrade from pathogenic can be a significant reclassification as well, especially if prophylactic surgery has been completed.
KW - hereditary cancer clinic
KW - hereditary cancer syndrome
KW - variant classification
KW - variant of uncertain significance
KW - variant reclassification
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U2 - 10.1038/gim.2017.207
DO - 10.1038/gim.2017.207
M3 - Article
AN - SCOPUS:85044618205
SN - 1098-3600
VL - 20
SP - 346
EP - 350
JO - Genetics in Medicine
JF - Genetics in Medicine
IS - 3
ER -