MLPA and SNP6.0 profiles of patients with PAX5^AMP. (A) Example of MLPA results using the P335 IKZF1 MLPA kit. The plot shows the probe ratio for each target contained in the kit (EBF1, 4 probes; IKZF1, 8 probes; CDKN2A/B, 3 probes; PAX5, 6 probes; ETV6, 6 probes; BTG1, 4 probes; RB1, 5 probes; and the PAR1 region, CRLF2, CSF2RA, and IL3RA, 1 probe each). Probe ratio values between 0.75 and 1.3 were considered to be within the normal range, equivalent to the normal copy number of 2. Values <0.75 or >1.3 indicated loss or gain, respectively, and a value <0.25 indicated biallelic loss. These values correspond to copy numbers of 1, 3 and 4, and 0, respectively. A value ≥2.0 corresponds to a copy number of ≥4 and was interpreted as amplification. Approximate copy numbers of amplified exons ranged from 4 to 22 (median, 5.86). Ratio values of 1 representative patient (patient 64) showing amplification of PAX5 encompassing exons 2 and 5, gain of EBF1 consistent with trisomy 5 in this patient, monoallelic loss of IKZF1, and biallelic loss of CDKN2A/B. (B) Copy number profiles (log2ratio) of the PAX5 locus of 8 patients with PAX5^AMP processed on the SNP6.0 array. *In patient 79, PAX5 amplification was identified at relapse with no material available from diagnosis. **Patient 60 shows amplification of exon 5 only and gain of exons 1 to 4. (C) Exon and protein structure of PAX5; the amplified region encodes the DNA-binding paired domain and the octapeptid motif. PD, paired DNA-binding domain (amino acids 16-142); O, octapeptide (aa 179-186); H, homeodomain (aa 228-254); TA, transactivation domain (aa 304-391); I, inhibitory domain (aa 359-391).