Timing chromosomal amplification events using patterns of somatic mutations in high hyperdiploid acute lymphoblastic leukemia

All samples were subjected to whole genome sequencing by the Illumina HiSeqX platform. Paired-end sequencing (2x150bp) was done to ~60x coverage for diagnostic samples and ~30x coverage for remission.

The paired-end reads were aligned to the human reference genome GRCh37 (ncbi.nlm.nih.gov/assembly/GCF_000001405.25/) by the Burrows-Wheeler Aligner tool (version 0.7.17). Duplicate reads marking and local realignment were performed by GATK (version 4.0.11.0). Somatic variants were identified by the GDC DNA-Seq analysis pipeline (Zhang et al.,2021).