Certainty in uncertainty: Determining the rate and reasons for reclassification of variants of uncertain significance in haematological malignancies

Anoop K Enjeti; Natasha Walker; Oliver Fahey; Elizabeth Johnston; Hannah Legge-Wilkinson; Nateika Ramsurrun; Jonathan Sillar; Lisa F Lincz; Andrew Ziolkowski; David Mossman

doi:10.1002/jha2.1002

Certainty in uncertainty: Determining the rate and reasons for reclassification of variants of uncertain significance in haematological malignancies

EJHaem. 2024 Sep 12;5(5):957-963. doi: 10.1002/jha2.1002. eCollection 2024 Oct.

Authors

Anoop K Enjeti^{1

2

3

4

5}, Natasha Walker³, Oliver Fahey³, Elizabeth Johnston³, Hannah Legge-Wilkinson³, Nateika Ramsurrun³, Jonathan Sillar^{2

3

4

5}, Lisa F Lincz^{2

4}, Andrew Ziolkowski¹, David Mossman¹

Affiliations

¹ Department of Molecular Medicine NSW Health Pathology, John Hunter Hospital Waratah Australia.
² Department of Haematology Calvary Mater Newcastle Waratah Australia.
³ Precision Medicine Research Program, University of Newcastle Waratah Australia.
⁴ School of Medicine and Public Health University of Newcastle Waratah Australia.
⁵ Hunter Medical Research Institute Waratah Australia.

Abstract

Introduction: Variants of uncertain significance (VUS) are commonly reported in cancer with the widespread adoption of diagnostic massive parallel sequencing. The rate of reclassification of VUS in patients with haematological malignancy is not known and we evaluated this retrospectively. We also investigated whether re-evaluating VUS in 12-24 months or greater than 24 months post-initial classification was significant.

Method: A retrospective audit of patients with haematological malignancies referred to the Molecular Medicine Department at the John Hunter Hospital in Newcastle, Australia between September 2018 and December 2021. Data was analysed for VUS, which was then re-analysed in standard software using current somatic variant guidelines. Proportions of VUS at baseline were compared to post-re-analysis.

Results: The most common diagnoses in the patient cohort (n = 944) were acute myelogenous leukaemia (41%), myelodysplastic syndrome (31%), and chronic myelomonocytic leukaemia (7%). A total of 210 VUS were re-analysed. The most common VUS were in the TET2 (20%), RUNX1 (10%) and DNMT3A (9%) genes. A total of 103 were re-analysed at 24-39 months post-initial classification and 107 variants were re-analysed between 12 and 24 months post-initial classification. Of these, 33 (16%) of VUS were re-classified at 24-39 months and 12 (11%) were re-classified at 12-24 months post-initial classification. The most common variants that were re-classified in both groups were CSF3R (32%), TET2 (29%), ASXL1 (11%) and ZRSR2 (11%).

Conclusion: This study on reclassification of VUS in blood cancers demonstrated that one in seven VUS were re-classified 12 months post initial classification. This can inform practice guidelines and potentially impact the prognosis, diagnosis and treatment of haematological malignancies.

Keywords: haematological malignancy; leukaemia; massive parallel sequencing; reclassification; variants of uncertain significance.