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Cell fate determination and transformation is intimately related to chromatin interaction and 3D genome structure.Many 1D cancer or other developmental regulatory disease markers,such as GWAS SNPs/CNVs,heritable or somatic cancer mutations,gene fusions,viral insertion hotspots,epi-mutations,etc.,are often linked to dis-regulation of enhancers to their target genes through altered 3D DNA loops.I will introduce some new biochemical (BL-Hi-C),biophysical (Super-resolution imaging) and Bioinformatics (MICC,3CPET)technology developments that may be used for studying 3D cancer genomes and disease markers in the near future.