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Table 1 Selected examples of genes altered by structural variation in cancers

From: Chromosome structural variation in tumorigenesis: mechanisms of formation and carcinogenesis

Malignancy Structural variation type Affected gene Alteration in TADs Effect References
T-ALL Deletion TAL1, LMO2, etc. Deletion of a loop boundary CTCF site Key oncogenic drivers TAL1 and LMO2 expression from the silent state [130]
Lung squamous carcinoma Deletion IRS4 Deletion of TAD boundary or insulator IRS4 overexpression caused by new enhancer–promoter interactions [129]
Prostate cancer Deletion (17p13.1) TP53 Bifurcation of a single TAD into two distinct smaller TADs Dysregulation of several genes [124]
Colorectal cancer Tandem duplications IGF2 Formation of neo-TAD De novo formation of a 3D contact domain comprising IGF2 and a lineage-specific super-enhancer [129]
Lung adenocarcinoma Inv (2)(p21;p23) EML4-ALK [107]
AML Inv(3)(q21;q26.2) RPN1-EVI1 Fusion of two TADs EVI oncogene expression caused by new enhancer–promoter interactions [132]
Rhabdomyosarcoma t(2;13)(q35;q14) PAX3-FOXO1 Formation of neo-TAD   [133]
AML t(8;21) RUNX1-ETO [78]
  1. AML acute myeloid leukemia, CTCF CCCTC-binding factor, TAD topologically associated domains, T-ALL T-cell acute lymphoblastic leukemia