Real time analysis 2

Haplotype-phasing of the patient and his father were performed through synthetic long-read whole genome sequencing (Macrogen, Seoul, South Korea). Genomic DNA samples were extracted from leukocytes. Sequencing libraries were prepared using the 10x Genomics Chromium System (10x Genomics, Pleasanton, CA, USA) and loaded on the HiSeqX sequencer (Illumina). Sequence data were obtained as 150-bp paired-end reads. Base calling and quality scoring were performed using Real Time Analysis 2 (Illumina). The base call files were converted to FASTQ files using the Long Ranger 2.1.3 (10x Genomics). Then, Long Ranger 2.1.5 (10x Genomics) was used to align sequence reads and to call single nucleotide variants (SNVs), indels, and structural variants. The output data were visualized on the Loupe 2.1.2 (10x Genomics). We genotyped SNVs of the patient and his father and constructed haplotype-phase blocks. In this analysis, we focused primarily on genomic regions flanking the breakpoints.

Murine genomic DNA was extracted from the whole blood using the DNeasy Blood & Tissue Kit (Qiagen) and sequenced using a HiSeq X with 2 × 150-bp reads (Illumina, San Diego, CA, USA). Base calls and fastq generation were performed using Real-Time Analysis 2 (Illumina) and Bcl2fastq 2.20.0 (Illumina). Read filtering and mapping referenced with C57BL/6J genome assembly (GRCm38.p6) were performed using Trimmomatic 0.36^{56 (link)}, BWA 0.7.17^{57 (link)}, and Picard tools 1.111 (https://broadinstitute.github.io/picard).