PTEN genetics of T-ALL patients
| Patient . | PTEN mutation . | PTEN deletion (FISH/ array-CGH) . | PTEN deletion (MLPA) . | Genomic breakpoint PCR . | Aberrant transcript . | PTEN protein . | Cytogenetic aberration . | NOTCH/ FBXW7 mutation . | |
|---|---|---|---|---|---|---|---|---|---|
| Allele A . | Allele B . | ||||||||
| Clonal inactivation of 2 alleles | |||||||||
| 1 | R129G | T231fsX24 | — | — | — | ND | Mutant | LMO3 | — |
| 2 | F144fsX37 | R232fsX23 | Subcl Del | — | — | ND | Absent | LMO2 | PEST |
| 3 | P246fsX11 | — | Het Del | Het Del exons 2-9 | — | ND | Absent | SIL-TAL1 | — |
| 4 | D235fsX9 | P245fsX12 | ND | ND | — | ND | Absent | CALM-AF10 | PEST |
| 5 | R232fsX13 | Q244fsX8 | — | — | — | ND | Absent | Unknown | — |
| 6 | R233fsX10 | P245fsX9 | — | — | — | ND | ND | Unknown | FBXW7 |
| 7 | R232fsX10 | P243fsX18 | — | — | — | ND | ND | TLX1 | — |
| 8 | R232fsX10 | P245fsX14 | — | — | — | ND | Absent | LMO2 | FBXW7 |
| 9 | L180fsX2 | I305fsX7 | — | — | Intron 1-3 Del (type II; Subcl) | ND | Absent | NKX2-5 | HD |
| 10 | C104fsX2 | K236fsX5 | — | — | — | ND | Absent | SIL-TAL1 | — |
| 11 | P245fsX3 | — | ND | Het Del exons 2-3 | Intron 1-3 Del (type II, clonal) | in1/2-ex4 | ND | MYC | — |
| 12 | — | — | Hom Del/FISH negative | Hom Del exons 2-3 | 2 Intron 1-3 Del variants (type I, clonal) | in1/2-ex4 | Absent | SIL-TAL1 | — |
| Clonal inactivation of 1 allele | |||||||||
| 13 | R129fsX4/ P245fsX3 | — | Subcl Del | Het Del exons 1-9 | — | ND | ND | Unknown | — |
| 14 | R232 (STOP) | — | — | — | — | — | ND | SIL-TAL1 | — |
| 15 | C249fsX10 | — | — | — | Intron 1-3 Del (type I; Subcl) | — | Absent | Unknown | — |
| 16 | T231fsX14 | — | — | — | — | — | Absent | NKX2-1 | HD/FBXW7 |
| 17 | T276A | — | — | — | Intron 1-3 Del (type I; Subcl) | — | Absent | Unknown | — |
| 18 | — | — | Het Del | Het Del exons 1-9 | — | WT | Absent | Unknown | PEST |
| 19 | — | — | Het Del | Het Del exons 3-9 | Intron 1-3 Del (type I; Subcl) | Altered | Absent | SIL-TAL1 | — |
| 20 | — | — | — | Het Del exons 4-5 | Intron 3-5 Del (type III, clonal) /Intron 1-3 Del (type I; Subcl) | ex3-ex6 splice | Absent | SIL-TAL1 | — |
| 21 | — | — | ND | Het Del exons 1-3 | Intron 1-3 Del (type I, clonal) | in1/2-ex4 | ND | SIL-TAL1 | HD |
| 22 | — | — | Het Del | Het Del exons 2-9 | — | ND | ND | Unknown | — |
| Subclonal-inactivating event only | |||||||||
| 23 | R232fsX (Subcl) | — | — | — | — | — | ND | SIL-TAL1 | — |
| 24 | — | — | — | — | Intron 1-3 Del (type I; Subcl) | ND | ND | SIL-TAL1 | HD/PEST |
| 25 | — | — | ND | — | Intron 1-3 Del (type I; Subcl) | ND | ND | SIL-TAL1 | — |
| 26 | — | — | — | — | Intron 1-3 Del (type I; Subcl) | ND | ND | Unknown | — |
| Others | |||||||||
| 27 | — | — | — | — | — | — | Absent | TAL2 | FBXW7 |
| 28 | — | — | — | — | — | — | Absent | TAL1 | HD |
| Patient . | PTEN mutation . | PTEN deletion (FISH/ array-CGH) . | PTEN deletion (MLPA) . | Genomic breakpoint PCR . | Aberrant transcript . | PTEN protein . | Cytogenetic aberration . | NOTCH/ FBXW7 mutation . | |
|---|---|---|---|---|---|---|---|---|---|
| Allele A . | Allele B . | ||||||||
| Clonal inactivation of 2 alleles | |||||||||
| 1 | R129G | T231fsX24 | — | — | — | ND | Mutant | LMO3 | — |
| 2 | F144fsX37 | R232fsX23 | Subcl Del | — | — | ND | Absent | LMO2 | PEST |
| 3 | P246fsX11 | — | Het Del | Het Del exons 2-9 | — | ND | Absent | SIL-TAL1 | — |
| 4 | D235fsX9 | P245fsX12 | ND | ND | — | ND | Absent | CALM-AF10 | PEST |
| 5 | R232fsX13 | Q244fsX8 | — | — | — | ND | Absent | Unknown | — |
| 6 | R233fsX10 | P245fsX9 | — | — | — | ND | ND | Unknown | FBXW7 |
| 7 | R232fsX10 | P243fsX18 | — | — | — | ND | ND | TLX1 | — |
| 8 | R232fsX10 | P245fsX14 | — | — | — | ND | Absent | LMO2 | FBXW7 |
| 9 | L180fsX2 | I305fsX7 | — | — | Intron 1-3 Del (type II; Subcl) | ND | Absent | NKX2-5 | HD |
| 10 | C104fsX2 | K236fsX5 | — | — | — | ND | Absent | SIL-TAL1 | — |
| 11 | P245fsX3 | — | ND | Het Del exons 2-3 | Intron 1-3 Del (type II, clonal) | in1/2-ex4 | ND | MYC | — |
| 12 | — | — | Hom Del/FISH negative | Hom Del exons 2-3 | 2 Intron 1-3 Del variants (type I, clonal) | in1/2-ex4 | Absent | SIL-TAL1 | — |
| Clonal inactivation of 1 allele | |||||||||
| 13 | R129fsX4/ P245fsX3 | — | Subcl Del | Het Del exons 1-9 | — | ND | ND | Unknown | — |
| 14 | R232 (STOP) | — | — | — | — | — | ND | SIL-TAL1 | — |
| 15 | C249fsX10 | — | — | — | Intron 1-3 Del (type I; Subcl) | — | Absent | Unknown | — |
| 16 | T231fsX14 | — | — | — | — | — | Absent | NKX2-1 | HD/FBXW7 |
| 17 | T276A | — | — | — | Intron 1-3 Del (type I; Subcl) | — | Absent | Unknown | — |
| 18 | — | — | Het Del | Het Del exons 1-9 | — | WT | Absent | Unknown | PEST |
| 19 | — | — | Het Del | Het Del exons 3-9 | Intron 1-3 Del (type I; Subcl) | Altered | Absent | SIL-TAL1 | — |
| 20 | — | — | — | Het Del exons 4-5 | Intron 3-5 Del (type III, clonal) /Intron 1-3 Del (type I; Subcl) | ex3-ex6 splice | Absent | SIL-TAL1 | — |
| 21 | — | — | ND | Het Del exons 1-3 | Intron 1-3 Del (type I, clonal) | in1/2-ex4 | ND | SIL-TAL1 | HD |
| 22 | — | — | Het Del | Het Del exons 2-9 | — | ND | ND | Unknown | — |
| Subclonal-inactivating event only | |||||||||
| 23 | R232fsX (Subcl) | — | — | — | — | — | ND | SIL-TAL1 | — |
| 24 | — | — | — | — | Intron 1-3 Del (type I; Subcl) | ND | ND | SIL-TAL1 | HD/PEST |
| 25 | — | — | ND | — | Intron 1-3 Del (type I; Subcl) | ND | ND | SIL-TAL1 | — |
| 26 | — | — | — | — | Intron 1-3 Del (type I; Subcl) | ND | ND | Unknown | — |
| Others | |||||||||
| 27 | — | — | — | — | — | — | Absent | TAL2 | FBXW7 |
| 28 | — | — | — | — | — | — | Absent | TAL1 | HD |
PTEN frameshift mutations are indicated with the number of encoded amino acids in the alternative reading frame. PTEN deletion status was determined by FISH, array-CGH, and/or MLPA. Introns harboring the genomic breakpoints of PTEN deletions and/or microdeletions have been indicated. Exons for alternative spliced PTEN transcripts are indicated.
Del, deletion; FS, frameshift; HD, NOTCH1 heterodimerization domain mutation; Het, heterozygous; Hom, homozygous; PEST, NOTCH1 mutation in the proline, glutamine, serine and threonine-rich C-terminal region; Subcl, subclonal; WT, wild-type.