Table 2.

MYC rearrangements and associated enhancers in 17 MM cell lines

MMCL	Description of MYC locus structural variation
LP1	FISH analyses have shown that variant IGH translocations involving MYC have 3’ IGH SE (E⍰) and VH telomeric sequences located telomeric to MYC.10, 11 The chr8 breakpoint is ~390 kb downstream of MYC and the chr14 breakpoint is located at the telomeric end of the Ea1 SE, but with chr 14 sequences proceeding in a centromeric direction away from the breakpoint as a result of an inversion within the IGH locus that was detected from mate pair sequences (SF1 and Discussion)
H929	a deletion of 8:126344414-128713154 positions MYC ~100 kb from a SE and other enhancer elements in intron 4 of NSCME2
XG6	has a deletion 8 breakpoint 126324977>|<128737494 but also a second breakpoint downstream of MYC: 128775373>|<126287002. There is a copy number gain by CGH related to these breakpoints, i.e., 126287002-126324977 (~38kb) and 128737494-128775373 (~38kb). These data indicate that MYC is flanked by a SE and other enhancer sequences located in intron 4 of NSMCE2 and vice versa, with several copies of both regions on the rearranged chromosome (see SF1)
INA6	der(1) of a reciprocal t(1;8) translocation has a chr1 breakpoint within or just beyond FAM46C, so that the downstream SE region is near the breakpoint. MYC is predicted to be ~1209 Mb from the chr8 breakpoint, but numerous intrachromosomal rearrangements in the MYC locus suggest that MYC might be much closer to the breakpoint
U266	a 77 Mb inversion on 1p has breakpoints located 7 kb downstream of MYCL and in the 3’ untranslated region of FAM46C; MYCL is repositioned near the SE region downstream of FAM46C
KMS18	an interchromosomal translocation has a chr6 breakpoint ~50kb upstream of TXNDC5 so that SEs associated with TXNDC5 are predicted to be located ~500 kb upstream of MYC
OCIMY1	a complex translocation shows that ~15kb of chr6 sequences that contain a SE region located downstream of TXNDC5 are positioned ~560 kb downstream of MYC; the other end of the chr 6 segment is juxtaposed to chr22, with the breakpoint located ~530 kb centromeric to the 3’ IGL SE
ARP1	this der(8)t(6;8) translocation has a chr 6 breakpoint immediately downstream of PRDM1 so that a pair of flanking SEs are repositioned ~530 kb downstream of MYC. In addition, there is an ~60 kb tandem duplication of the sequences that contain the pair of super enhancers that flank PRDM1
SKMM2	an ~3.1 Mb inversion on chr8 (125.697-128.848) positions stretch enhancers in intron 3 of MTSS1 ~95kb downstream of MYC
FLAM76	an interchromosomal translocation into FAM188A on chr 10 positions a SE ~25 kb from the breakpoint, which is ~30 kb downstream of MYC
L363	a complex translocation indicates that an ~30 kb segment of chr2, which includes an SE flanking the 3’ end of CTLA4, is positioned ~560kb downstream of MYC; the downstream side of the chr 2 fragment is juxtaposed into the 3’ end of ANKRD55, so that a SE within ANKRD55 is located ~32 kb from the chr2 fragment and ~ 610 kb from MYC
VP6	chr14 sequences including a 3’ IGH SE are inserted downstream of MYC between duplicated flanking sequences (8:129.216-129.305)
EJM	a 58 kb fragment from chr11, which contains a stretch enhancer in the ultimate intron of AHNAK, is inserted downstream of MYC between duplicated flanking sequences (8:129.265-129.346)
KP6	an ~90kb tandem duplication ~500 kb downstream of MYC (8:129.239-129.329)
XG2	an ~341 kb tandem duplication ~500 kb downstream of MYC (8:129.072-129.413)
JIM3	an interchromosomal translocation repositions a chr6 “gene dessert” with no apparent enhancers ~45 kb downstream of MYC; mate pair sequences did not detect other rearrangements on the region of chr6 repositioned downstream of MYC
XG7 (not in Fig.3)	chr8 and chr6 segments inserted into chr17 with a chr 6 TXNDC5 SE repositioned ~38 kb upstream of MYC; and chr 17 UBRE2G1 enhancers located ~110 kb downstream of MYC