Rapid and Reproducible Karyotyping with Long Read Sequencing in AML Patients

Low-coverage long-read WGS (lcWGS, Oxford Nanopore) as a rapid, scalable alternative to conventional metaphase karyotyping for AML cytogenetic profiling

This study proposes low-coverage long-read WGS (lcWGS, Oxford Nanopore) as a rapid alternative to conventional metaphase karyotyping for cytogenetic profiling of acute myeloid leukemia (AML). On 100 diagnostic samples (50 retrospective with known adverse cytogenetics, 50 prospective de novo), lcWGS achieves 93% sensitivity, specificity, and accuracy, with an AUC of 0.971 for complex karyotypes. Reproducibility is validated across two independent laboratories (R=0.99), and identified complex karyotypes correlate with shorter survival. Median turnaround is approximately 34 hours, enabling an actionable result within 72 hours.

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Conventional karyotyping turnaround is a critical bottleneck for treatment initiation in AML; a 34-hour turnaround with cross-laboratory reproducibility (R=0.99) meets a genuine clinical need. The correlation of complex karyotypes with survival anchors the approach's prognostic value. This is a mature long-read application, directly transposable into the hematology diagnostic workflow.