High-Resolution Proximity-Guided Cytogenomics Improves Patient Stratification and Uncovers New Variants in Acute Myeloid Leukemia

Cytogenetic methods are a cornerstone of the modern diagnostic workflow for acute myeloid leukemia and related disorders. The goal of these methods is to identify structural genomic aberrations that drive the cancer or otherwise act as an indicator of patient risk. Despite their success, any one cytogenetic test is limited either in resolution, ability to provide unbiased survey of the genome, or ability to detect balanced aberrations. To address these limitations, we have applied proximity ligation sequencing (PLS) to characterize structural variants (SV) in AML genomes. PLS captures ultra-long-range sequence information without high-molecular-weight DNA and requires a modest (5-7x) sequence coverage of the genome. Applying this method to AML diagnostic specimens, we find that PLS identifies cytogenetically defined translocations (reciprocal and non-reciprocal) and inversions with specificity and sensitivity >0.95. The high resolution of PLS (<10kb) detected non-canonical variants missed by standard methods as well as structural variants below limits of detection by karyotyping, identifying variants in over half the patients previously determined to have a normal karyotype (Table 1). This included previously described variants of clinical significance as well as a recurrent inversion not previously described in AML. These observations highlight the effectiveness of PLS to provide high-resolution insights into known clinically relevant variants and discover variants missed by traditional methodologies.