Bluefuse multi 4

All cell lines were analyzed using Illumina CytoSNP analysis and the BlueFuse Multi 4.3 software (Illumina, San Diego, United States) according to standard protocols of the manufacturer.

CN calls automatically generated by Bluefuse Multi™ 4.3 (Illumina. Inc, San Diego, CA, USA) or by Ion Reporter™ 5.10 (Thermo Fisher, Waltham, MA, USA) software (company, city, state (for USA), country), then were assessed manually and compared for sample ploidy status, sample karyotype, and chromosome ploidy status.
The results were compared to the karyotype of cells and the concordance was calculated with the use of the classifications true positive (TP; gain or loss call detected), true negative (TN; euploidy status confirmed), false negative (FN; gain or loss call missed), and false positive (FP; additional gain or loss called).

Karyotypes were determined by chromosomal G-banding. The results of the analysis for ETV6::RUNX1 translocation by FISH of the leukemia samples obtained during routine diagnostics were compiled from the patient records for this study (Suppl. Tables S2 and S3). To detect CN alterations and CN neutral loss of heterozygosity (CNN-LOH), all 60 leukemia samples were analyzed using SNP-arrays. For 18 leukemia cases, the CytoScan HD array (Thermo Fisher Scientific, Waltham, MA) was used as described.^{21 (link)} The data were initially aligned to GRCh37 and a lift-over to GRCh38 was performed for downstream analysis. The remaining 42 leukemia cases were analyzed using the Illumina CytoSNP-12 v2.1 array (Illumina, San Diego, CA) according to the manufacturer’s protocol. The array was scanned using the scanner option on the NextSeq550 sequencing platform (Illumina). The raw data were processed and analyzed using the Beeline 2.0.3.3 and the BlueFuse Multi 4.5 software from Illumina. The human reference genome GRCh38 was used. We included SVs encompassing ≥20 probes, ≥50 kb for deletions and duplications, or ≥5 Mb for CNN-LOH. For all samples, B- and T-cell receptor rearrangements were excluded from downstream analysis and SVs overlapping with centromere or reference gap regions. The filtered molecular genetic results are summarized in Suppl. Table S4.