Optical Genome Mapping Identifies Novel Recurrent Structural Alterations in Childhood and High Hyperdiploid Acute Lymphoblastic Leukemia.

The mutational landscape of B-cell precursor acute lymphoblastic leukemia (BCP-ALL), the most common pediatric cancer, is not fully described partially because commonly applied short-read next generation sequencing has a limited ability to identify structural variations. By combining comprehensive analysis of structural variants (SVs), single-nucleotide variants (SNVs), and small insertions-deletions, new subtype-defining and therapeutic targets may be detected. We analyzed the landscape of somatic alterations in 60 pediatric patients diagnosed with the most common BCP-ALL subtypes, + and classical hyperdiploid (HD), using conventional cytogenetics, single nucleotide polymorphism (SNP) array, whole exome sequencing (WES), and the novel optical genome mapping (OGM) technique. Ninety-five percent of SVs detected by cytogenetics and SNP-array were verified by OGM. OGM detected an additional 677 SVs not identified using the conventional methods, including (subclonal) deletions. Based on OGM, + BCP-ALL harbored 2.7 times more SVs than HD BCP-ALL, mainly focal deletions. Besides SVs in known leukemia development genes (, , ), we identified 19 novel recurrently altered regions (in n ≥ 3) including 9p21.3 (), 8p11.21 (), 1p34.3 (), 4q24 (), 8p23.1 (), and 10p14 (), as well as subtype-specific SVs (12p13.1 (), 12q24.21 (), 18q11.2 (), 20q11.22 ()). We detected 3 novel fusion genes ( and ), for which the sequence and expression were validated by long-read and whole transcriptome sequencing, respectively. OGM and WES identified double hits of SVs and SNVs (, , , , , ) in the same patient demonstrating the power of the combined approach to define the landscape of genomic alterations in BCP-ALL.