PAX5-ITM characterization by CMA and OGM. (A) A screenshot from the Chromosome Analysis Suite (ChAS) CMA analysis software showing copy number gains in the 5′ portion of the PAX5 gene in the 6 PAX5-ITM⁺ cases (dark blue bars on the Copy Number Segments plots). OGM characterization of PAX5-ITM: case 1, showing 4 extra copies of the affected region in direct orientation, each ∼21 kb in size (B); case 4, showing 5 extra copies of the multiplied region in direct orientation, each ∼26 kb in size (C); and case 6, showing 4 extra copies of the affected region in direct orientation, each ∼21 kb in size (D). Arrows indicate copies of the multiplied region in the Bionano long-molecule assembly for the mutant allele, as compared with the chromosome 9 map (green) and the assembly from reference samples (top, light blue bar). Additional copies of the affected region are also visible in individual long molecules (yellow lines).