Fig. 3

Identification of translocation types and breakpoints in SW480 at single base-pair resolution by MGA-Seq. a Identification of translocation in the SW480 cell line by genomic contact matrix constructed with MGA-Seq and Hi-C datasets. The detected structural variations are indicated by arrows. b Translocation types and breakpoint information identified by MGA-Seq. c Application of integrated chromatin contact matrix, CNVs, and split reads analysis to identify translocation types and breakpoints between chr 2 and chr 12 at single base-pair resolution using MGA-Seq datasets. d Identification of translocation types and breakpoints between chr 2 and chr 12 using Hi-C datasets. e Validation of the T(2;12)(q35;q12) translocation in SW480 cells by DNA FISH. FISH probes for 12q12 and 2q35 were directly labelled with Alexa Fluor 555 (red) and Alexa Fluor 488 (green), respectively. K562 cells without the T(2;12)(q35;q12) translocation were used as a control. 4.0% (2/50) 12q12 loci (red) were colocated with 2q35 loci (green) in K562 cells and 88.0% (44/50) 12q12 loci (red) were colocated with 2q35 loci (green) in SW480 cells. Each experiment was replicated three times