SRs identified by oligonucleotide capture sequencing of primary B-cell lymphoma tissue specimens
| Case . | Path . | Event . | Gene 1 . | Gene 2 . | Break 1 . | Break 2 . | FISH . | Sanger . | Subtype . |
|---|---|---|---|---|---|---|---|---|---|
| CS01 | DLBCL | DEL | CD274 | MLANA | Chr9:5467908 | Chr9:5889215 | CNV | Y | Intrachromosomal |
| CS02 | PMBCL | TRA | CTSL1P2 | PDCD1LG2 | Chr10:48174662 | Chr9:5526439 | BA | Y | Other TRA (5′) |
| CS08 | PMBCL | DUP | CD274 | PDCD1LG2 | Chr9:5447066 | Chr9:5570695 | Normal | Y | Intrachromosomal |
| CS09 | PTL | INV | CD274 | GRHPR | Chr9:5477220 | Chr9:37409812 | BA | Y | Intrachromosomal |
| CS10 | PTL | TRA | PTPN1 | CD274 | Chr20:49127848 | Chr9:5450396 | BA | Y | CBR1 |
| DUP | CD274 | CD274 | Chr9:5451269 | Chr9:5467963 | Y | Intrachromosomal | |||
| INV | CD274 | RIC1 | Chr9:5467981 | Chr9:5627175 | Y | Intrachromosomal | |||
| DEL | CD274 | RIC1 | Chr9:5466595 | Chr9:5775524 | Y | Intrachromosomal | |||
| DEL | CD274 | CD274 | Chr9:5451258 | Chr9:5451585 | Y | Intrachromosomal | |||
| CS11 | PCNSL | TRA | CD44 | CD274 | Chr11:35161226 | Chr9:5452813 | BA | N* | CBR1 |
| DEL | PDCD1LG2 | IL33 | Chr9:5491418 | Chr9:6135848 | N* | Intrachromosomal | |||
| CS12 | PMBCL | TRA | BZRAP1-AS1 | PDCD1LG2 | Chr17:56409009 | Chr9:5518645 | BA | Y | CBR2 |
| TRA | AK309109 | PDCD1LG2 | Chr10:47272696 | Chr9:5518489 | Y | CBR2 | |||
| CS21 | PMBCL | DEL | CD274 | PDCD1LG2 | Chr9:5467992 | Chr9:5508323 | Normal | N# | Intrachromosomal |
| CS25 | PMBCL | TRA | RCC1 | PDCD1LG2 | Chr1:28833535 | Chr9:5518615 | BA | Y | CBR2 |
| CS29 | PMBCL | DUP | PDCD1LG2 | PDCD1LG2 | Chr9:5500059 | Chr9:5570090 | Normal | Y | Intrachromosomal |
| CS33 | PMBCL | TRA | BZRAP1-AS1 | PDCD1LG2 | Chr17:56409576 | Chr9:5517129 | BA | Y | CBR2 |
| CS36 | PMBCL | TRA | IGK | PDCD1LG2 | Chr2:89159416 | Chr9:5510982 | BA | Y | CBR2 |
| CS38 | PMBCL | DEL | CD274 | CD274 | Chr9:5467983 | Chr9:5470588 | BA | Y | Intrachromosomal |
| CS39 | DLBCL | TRA | KIAA0226L | CD274 | Chr13:46946572 | Chr9:5451322 | BA | Y | CBR1 |
| CS42 | DLBCL | TRA | CD274 | MCM3 | Chr9:5466034 | Chr6:52178267 | BA | Y | Other TRA (3′) |
| CS43 | PTL | INV | CD274 | GRHPR | Chr9:5480091 | Chr9:37381934 | BA | Y | Intrachromosomal |
| CS44 | PMBCL | DEL | PDCD1LG2 | KIAA2026 | Chr9:5563053 | Chr9:5984410 | BA | N# | Intrachromosomal |
| CS47 | PMBCL | TRA | IL4R | PDCD1LG2 | Chr16:27326593 | Chr9:5511678 | BA | Y | CBR2 |
| TRA | GET4 | PDCD1LG2 | Chr7:932289 | Chr9:5513369 | Y | CBR2 | |||
| TRA | PDCD1LG2 | MID1 | Chr9:5565388 | ChrX:10651175 | N# | Other TRA (3′) | |||
| CS48 | PMBCL | TRA | OCLN | PDCD1LG2 | Chr5:68784424 | Chr9:5491406 | BA | N# | Other TRA (intergenic) |
| CS49 | PMBCL | TRA | IGLL5 | PDCD1LG2 | Chr22:23231719 | Chr9:5510728 | BA | Y | CBR2 |
| CS51 | PMBCL | TRA | IL4R | PDCD1LG2 | Chr16:27326880 | Chr9:5518313 | BA | Y | CBR2 |
| CS52 | DLBCL | INV | PDCD1LG2 | POLR1E | Chr9:5527098 | Chr9:37498687 | BA | Y | Intrachromosomal |
| CS54 | PMBCL | INV | CD274 | PDCD1LG2 | Chr9:5469428 | Chr9:5561319 | Normal | Y | Intrachromosomal |
| CS63 | DLBCL | TRA | IGK | CD274 | Chr2:89157495 | Chr9:5450316 | BA | N* | CBR1 |
| TRA | RPIA | PDCD1LG2 | Chr2:89051353 | Chr9:5502180 | N* | Other TRA (intergenic) | |||
| DEL | CD274 | UHRF2 | Chr9:5470453 | Chr9:6440816 | N* | Intrachromosomal | |||
| CS65 | PMBCL | DEL | PDCD1LG2 | PDCD1LG2 | Chr9:5518701 | Chr9:5520276 | BA | Y | Intrachromosomal |
| TRA | IGLL5 | PDCD1LG2 | Chr22:23235076 | Chr9:5511361 | Y | CBR2 |
| Case . | Path . | Event . | Gene 1 . | Gene 2 . | Break 1 . | Break 2 . | FISH . | Sanger . | Subtype . |
|---|---|---|---|---|---|---|---|---|---|
| CS01 | DLBCL | DEL | CD274 | MLANA | Chr9:5467908 | Chr9:5889215 | CNV | Y | Intrachromosomal |
| CS02 | PMBCL | TRA | CTSL1P2 | PDCD1LG2 | Chr10:48174662 | Chr9:5526439 | BA | Y | Other TRA (5′) |
| CS08 | PMBCL | DUP | CD274 | PDCD1LG2 | Chr9:5447066 | Chr9:5570695 | Normal | Y | Intrachromosomal |
| CS09 | PTL | INV | CD274 | GRHPR | Chr9:5477220 | Chr9:37409812 | BA | Y | Intrachromosomal |
| CS10 | PTL | TRA | PTPN1 | CD274 | Chr20:49127848 | Chr9:5450396 | BA | Y | CBR1 |
| DUP | CD274 | CD274 | Chr9:5451269 | Chr9:5467963 | Y | Intrachromosomal | |||
| INV | CD274 | RIC1 | Chr9:5467981 | Chr9:5627175 | Y | Intrachromosomal | |||
| DEL | CD274 | RIC1 | Chr9:5466595 | Chr9:5775524 | Y | Intrachromosomal | |||
| DEL | CD274 | CD274 | Chr9:5451258 | Chr9:5451585 | Y | Intrachromosomal | |||
| CS11 | PCNSL | TRA | CD44 | CD274 | Chr11:35161226 | Chr9:5452813 | BA | N* | CBR1 |
| DEL | PDCD1LG2 | IL33 | Chr9:5491418 | Chr9:6135848 | N* | Intrachromosomal | |||
| CS12 | PMBCL | TRA | BZRAP1-AS1 | PDCD1LG2 | Chr17:56409009 | Chr9:5518645 | BA | Y | CBR2 |
| TRA | AK309109 | PDCD1LG2 | Chr10:47272696 | Chr9:5518489 | Y | CBR2 | |||
| CS21 | PMBCL | DEL | CD274 | PDCD1LG2 | Chr9:5467992 | Chr9:5508323 | Normal | N# | Intrachromosomal |
| CS25 | PMBCL | TRA | RCC1 | PDCD1LG2 | Chr1:28833535 | Chr9:5518615 | BA | Y | CBR2 |
| CS29 | PMBCL | DUP | PDCD1LG2 | PDCD1LG2 | Chr9:5500059 | Chr9:5570090 | Normal | Y | Intrachromosomal |
| CS33 | PMBCL | TRA | BZRAP1-AS1 | PDCD1LG2 | Chr17:56409576 | Chr9:5517129 | BA | Y | CBR2 |
| CS36 | PMBCL | TRA | IGK | PDCD1LG2 | Chr2:89159416 | Chr9:5510982 | BA | Y | CBR2 |
| CS38 | PMBCL | DEL | CD274 | CD274 | Chr9:5467983 | Chr9:5470588 | BA | Y | Intrachromosomal |
| CS39 | DLBCL | TRA | KIAA0226L | CD274 | Chr13:46946572 | Chr9:5451322 | BA | Y | CBR1 |
| CS42 | DLBCL | TRA | CD274 | MCM3 | Chr9:5466034 | Chr6:52178267 | BA | Y | Other TRA (3′) |
| CS43 | PTL | INV | CD274 | GRHPR | Chr9:5480091 | Chr9:37381934 | BA | Y | Intrachromosomal |
| CS44 | PMBCL | DEL | PDCD1LG2 | KIAA2026 | Chr9:5563053 | Chr9:5984410 | BA | N# | Intrachromosomal |
| CS47 | PMBCL | TRA | IL4R | PDCD1LG2 | Chr16:27326593 | Chr9:5511678 | BA | Y | CBR2 |
| TRA | GET4 | PDCD1LG2 | Chr7:932289 | Chr9:5513369 | Y | CBR2 | |||
| TRA | PDCD1LG2 | MID1 | Chr9:5565388 | ChrX:10651175 | N# | Other TRA (3′) | |||
| CS48 | PMBCL | TRA | OCLN | PDCD1LG2 | Chr5:68784424 | Chr9:5491406 | BA | N# | Other TRA (intergenic) |
| CS49 | PMBCL | TRA | IGLL5 | PDCD1LG2 | Chr22:23231719 | Chr9:5510728 | BA | Y | CBR2 |
| CS51 | PMBCL | TRA | IL4R | PDCD1LG2 | Chr16:27326880 | Chr9:5518313 | BA | Y | CBR2 |
| CS52 | DLBCL | INV | PDCD1LG2 | POLR1E | Chr9:5527098 | Chr9:37498687 | BA | Y | Intrachromosomal |
| CS54 | PMBCL | INV | CD274 | PDCD1LG2 | Chr9:5469428 | Chr9:5561319 | Normal | Y | Intrachromosomal |
| CS63 | DLBCL | TRA | IGK | CD274 | Chr2:89157495 | Chr9:5450316 | BA | N* | CBR1 |
| TRA | RPIA | PDCD1LG2 | Chr2:89051353 | Chr9:5502180 | N* | Other TRA (intergenic) | |||
| DEL | CD274 | UHRF2 | Chr9:5470453 | Chr9:6440816 | N* | Intrachromosomal | |||
| CS65 | PMBCL | DEL | PDCD1LG2 | PDCD1LG2 | Chr9:5518701 | Chr9:5520276 | BA | Y | Intrachromosomal |
| TRA | IGLL5 | PDCD1LG2 | Chr22:23235076 | Chr9:5511361 | Y | CBR2 |
Rearrangement partner genes listed are those that are either the closest to the breakpoint or most biologically plausible based on chromosomal strand orientation. Coordinates are based on the GRCh37 genome build.
BA, break-apart positive; DEL, deletion; DUP, duplication/eversion; INV, inversion; N*, not validated due to tissue unavailability; N#, PCR but not Sanger sequencing validated; Path, pathology; TRA, translocation; Y, yes.