Fig. 2: Identification of a translocation on chromosome 6, by using sequence from the CHM13-T2T assembly.

A Overview of the breakpoint region in hg19 and T2T-CHM13 assemblies. Nearby gene MANEA is shown for reference. The breakpoint was previously mapped by FISH to a gap in the hg19 assembly using a BAC probe (RP11-134M2) anchored on the telomeric side of the gap region. The gap region, estimated to 150 kb in hg19, corresponds to a > 360 kb region in T2T-CHM13. Targeting this sequence with adaptive sampling led to the identification of the exact chr6 breakpoint. B Circos plot showing the (t6;22)(q16.1;p13) translocation. C IGV image showing reads spanning the translocation breakpoints, which can be mapped at nucleotide resolution on chr6, while the breakpoint on the short arm of chr22 maps to a region of identical repeats where no exact breakpoint could be established.