Recurrent chromosomal rearrangements in PTCL predicted by mate-pair sequencing
| Breakpoint 1 . | Breakpoint 2 . | Rearrangement . | Samples with abnormality (of 21) . | Notations . | ||||
|---|---|---|---|---|---|---|---|---|
| Locus . | Gene . | Locus . | Gene . | Primary samples . | Cell lines . | n . | ||
| Xp22.31 | STS, HDHD1A | Xp22.31 | STS, HDHD1A | Deletion | TCL9 | FE-PD, SU-DHL-1, MAC1/2A* | 4 | Steroid sulfatase; pseudouridine-5′-monophosphatase |
| 2p23.2 | ALK | 5q35.1 | NPM1 | Translocation | TCL3 | SU-DHL-1, Karpas 299, SR-786 | 4 | Anaplastic lymphoma kinase; nucleophosmin |
| 3q26.32 | TBL1XR1 | 3q28 | TP63 | Inversion | TCL5, TCL29 | — | 2 | Transducin (beta)–like 1 X-linked receptor 1, tumor protein p63 |
| 4p15.1 | None | M† | Unknown | Unknown | TCL5, TCL8, TCL3, TCL56 | — | 4 | — |
| 6p25.3 | DUSP22 | 7q32.3 | FLJ43663 | Translocation | TCL1, TCL8, TCL11 | FE-PD | 4 | Dual-specificity phosphatase 22; near FRAH7 fragile site on 7q32.37 |
| 6q27 | None | 8q22.1 | Unknown | Unknown | TCL56 | Karpas 299 | 2 | — |
| 7q31.31 | None | 7q31.31 | None | Deletion | TCL13, TCL65 | — | 2 | No intervening known genes |
| 8q24.21 | Unknown | 8q24.21 | None | Unknown | TCL15 | MAC1/2A | 2 | — |
| 9p21.3 | MTAP | 9p21.3 | MTAP, CDKN2BAS | Deletion | TCL15, TCL29, TCL32 | — | 3 | Deleted region contains CDKN2A encoding p16INK4A and p19ARF (stabilizes p53)14 |
| 10q21.3 | CTNNA3 | 10q21.3 | CTNNA3 | Deletion | TCL6, TCL56 | — | 2 | Catenin alpha-3 |
| 16q23.1 | WWOX | 16q23.1 | WWOX | Deletion | TCL6, TCL29 | SU-DHL-1, Karpas 299, MAC1/2a̱* | 5 | WW domain-containing oxidoreductase (stabilizes p53)15 |
| 16q24.3 | ANKRD11 | 16q24.3 | SPG7 | Deletion | TCL1, TCL2, TCL9, TCL29 | FE-PD, MAC1/2A* | 6 | Ankyrin repeat domain-containing protein 11 (p53 co-activator)16 ; spastic paraplegia 7 |
| 17p13.1 | TMEM95, POLR2A | 17p13.1 | DNAH2, WRAP53 | Deletion | TCL3 | SR-786 | 2 | Deleted region contains TP53 |
| Breakpoint 1 . | Breakpoint 2 . | Rearrangement . | Samples with abnormality (of 21) . | Notations . | ||||
|---|---|---|---|---|---|---|---|---|
| Locus . | Gene . | Locus . | Gene . | Primary samples . | Cell lines . | n . | ||
| Xp22.31 | STS, HDHD1A | Xp22.31 | STS, HDHD1A | Deletion | TCL9 | FE-PD, SU-DHL-1, MAC1/2A* | 4 | Steroid sulfatase; pseudouridine-5′-monophosphatase |
| 2p23.2 | ALK | 5q35.1 | NPM1 | Translocation | TCL3 | SU-DHL-1, Karpas 299, SR-786 | 4 | Anaplastic lymphoma kinase; nucleophosmin |
| 3q26.32 | TBL1XR1 | 3q28 | TP63 | Inversion | TCL5, TCL29 | — | 2 | Transducin (beta)–like 1 X-linked receptor 1, tumor protein p63 |
| 4p15.1 | None | M† | Unknown | Unknown | TCL5, TCL8, TCL3, TCL56 | — | 4 | — |
| 6p25.3 | DUSP22 | 7q32.3 | FLJ43663 | Translocation | TCL1, TCL8, TCL11 | FE-PD | 4 | Dual-specificity phosphatase 22; near FRAH7 fragile site on 7q32.37 |
| 6q27 | None | 8q22.1 | Unknown | Unknown | TCL56 | Karpas 299 | 2 | — |
| 7q31.31 | None | 7q31.31 | None | Deletion | TCL13, TCL65 | — | 2 | No intervening known genes |
| 8q24.21 | Unknown | 8q24.21 | None | Unknown | TCL15 | MAC1/2A | 2 | — |
| 9p21.3 | MTAP | 9p21.3 | MTAP, CDKN2BAS | Deletion | TCL15, TCL29, TCL32 | — | 3 | Deleted region contains CDKN2A encoding p16INK4A and p19ARF (stabilizes p53)14 |
| 10q21.3 | CTNNA3 | 10q21.3 | CTNNA3 | Deletion | TCL6, TCL56 | — | 2 | Catenin alpha-3 |
| 16q23.1 | WWOX | 16q23.1 | WWOX | Deletion | TCL6, TCL29 | SU-DHL-1, Karpas 299, MAC1/2a̱* | 5 | WW domain-containing oxidoreductase (stabilizes p53)15 |
| 16q24.3 | ANKRD11 | 16q24.3 | SPG7 | Deletion | TCL1, TCL2, TCL9, TCL29 | FE-PD, MAC1/2A* | 6 | Ankyrin repeat domain-containing protein 11 (p53 co-activator)16 ; spastic paraplegia 7 |
| 17p13.1 | TMEM95, POLR2A | 17p13.1 | DNAH2, WRAP53 | Deletion | TCL3 | SR-786 | 2 | Deleted region contains TP53 |
Values shown in bold indicate rearrangement validated by PCR and breakpoint identified by Sanger sequencing.
PTCL indicates peripheral T-cell lymphoma; and –, no data.
Present in either cell line from a single patient.
M indicates mitochondrial genome; the mate pairs for breakpoint 2 may map to PCBD2 on 5q31.1, but homology to that locus did not meet alignment criteria.