Fig. 1

Experimental procedure, time, and cost of multiple genetic abnormalities sequencing (MGA-Seq). a Flowchart of MGA-Seq. Nuclei were cross-linked with 0.5% formaldehyde and then digested with HindIII. 5′ DNA overhangs of digested chromatin fragments were filled in by DNA polymerase and then proximity ligated by T4 DNA ligase. The proximity ligation products were fragmented and then subjected to high-throughput sequencing library construction. After sequencing, all the reads were used to generate a chromatin contact matrix for genome structural variation calling. In the sequencing library, the reads without ligation junction “AAGCTAGCTT” were used for the detection of CNV, SNP, small indels (< 50 bp), region of focal amplification, and genome breakpoints. By combining all information, the types and breakpoints of structural variation can be decoded. Notably, MGA-Seq can distinguish ecDNA and HSR, predict the structure of simple focal amplification regions, and construct the interaction network of focal amplificated genes. b The main steps, time, and cost of MGA-Seq