Extended Data Fig. 4: Examples of complex SVs assembled by NeoLoopFinder using Hi-C data.
All these complex SVs were also reported in our previous work, where the structure of each assembly was manually reconstructed by combining optical mapping, Hi-C and WGS. a–c, Assembly of a complex SV in K562 cells. a, The abnormal signals on the original Hi-C map indicate the complex SV structures between chromosome 13 and chromosome 9 in K562 cells. b, The correct lengths and orders of the rearranged regions B2 (chr13: 92.3M-92.66M), B3 (chr13: 93.2M-93.37M), C (chr13: 107.84M-108M) and D (chr9: 130.72M-131.28M) can be automatically identified and assembled by NeoLoopFinder solely based on Hi-C data. c, Linear regression of the global distance averaged contact frequencies and local distance averaged contact frequencies within the indicated contact regions, for example, ‘D-C’ represents the contacts between region D and region C in b. d–f, Assembly of another complex SV in K562 cells. g–i, Reconstruction of a complex SV in T47D cells.
