Hiscansq system

High-throughput SNP genotyping was carried out in all available family members (Fig. 1A) by using the HumanOmniExpress Exome arrays v1.3 and HiScanSQ system (Illumina Inc., San Diego, CA, USA). Genotyping data was used to perform homozygosity mapping (HM) as previously described (Fig. 1B).^{3 (link)}

DNA methylation status of PE was determined using the Illumina MethylationEPIC BeadChip 850K microarray (66 (link)). Briefly, 600 ng of DNA of the studied samples (T-cell normal donor samples, T-ALL cell lines and primary malignancies) was used to hybridize to the BeadChip and scanned using HiScan SQ system (Illumina). Raw signal intensity data were initially QC’d and pre-processed from resulting idat files in R statistical environment (v3.6.2) using minfi Bioconductor package (v1.32.0). A number of quality control steps were applied to minimize errors and remove erratic probe signals, such as failed probes (detection p value >0.01), cross-reacting probes and probes that overlapped single nucleotide variants within +/− 1 bp of CpG sites followed by background correction and dye-based normalization using ssNoob algorithm (single-sample normal-exponential out-of-band). DNA methylation scores for each CpG were represented as a β-values ranging between standard 0 and 1 where 1 represents fully methylated CpGs and 0, fully unmethylated. All downstream analyses were performed under R statistical environment (v3.6.1). Unsupervised hierarchical clustering analysis using euclidean distance with complete-linkage clustering and heatmaps of methylation CpG Beta-values in the studied samples were used to represent the DNA methylation data. Raw DNA methylation data is available upon request.