Appreciation of spatial genome organization has improved our understanding of the genetic basis of disease. Large structural variations (SVs), a class of mutations encompassing deletions, inversions, duplications, or translocations of hundreds of kb to megabase in size, underlie a wide range of congenital diseases [1] and a hallmark of aggressive cancer 2, 3•. Identifying SVs with standard short-read sequencing (see Box 1) remains challenging. And even when identified, interpreting disease-associated SVs is complicated due to their large size, sometimes encompassing hundreds of genes. Moreover, a large proportion of disease-related SVs affect noncoding regions, and the disease pathomechanism of these SVs has remained elusive 2, 4, 5•.

Development of chromatin-conformation capture techniques [6] transformed our ability to explore the pathomechanisms of these SVs, in particular high-resolution Hi-C 7, 8, which revealed how large SVs change 3D genome architecture causing gene misexpression and disease (reviewed in [9]). These findings motivated a deeper investigation of how SVs modulate gene regulation and allowed the development of a framework to identify the genetic cause underlying previously unsolved cases of both congenital malformations and cancer 10, 11, 12. Although genetic diseases, be it congenital malformations and cancer are often subsumed as one entity, disease, they represent classes with distinct etiologies and pathophysiologies. These have implications for the genetic variants that can be observed and their genomic effects.

Here, we first give an overview of recent insights into germline and somatic SVs affecting 3D chromatin structure. We then discuss how the pathophysiologies of rare congenital disease and cancer influence the type of SVs observed and their genetic consequences, and how understanding these can feed back into our understanding of 3D genome architecture. Finally, we propose guiding principles for interpreting disease-associated SVs, derived from a deep understanding of 3D chromatin architecture and the gene-regulatory and physiological mechanisms disrupted in ‘disease’ (Figures 1 and 2).