Table 2.
Alterations detected by 400 gene hybrid capture next generation sequencing panel in 9 patients with breast implant associated anaplastic large cell lymphoma.
| Patient | Gene Altered | Reference Sequence | Protein Change | cDNA Change | Location | Type of Alteration | VAF (%) | JAK2 FISH Results | FACETS Results |
|---|---|---|---|---|---|---|---|---|---|
| 1 |
TP53
MGAM PAK7 SMARCB1 |
NM_000546 NM_004668 NM_177990 NM_003073 |
p.A307P p.X1449_splice p.P358R p.Q368* |
c.919G>C c.4345+1G>A c.1073C>G c.1102C>T |
exon 8 exon 36 exon 5 exon 8 |
Missense Splice Missense Nonsense |
6.9 9.9 3.9 8.4 |
JAK2 translocation positive; 70%, large cells, complex patterns | No calls |
| STAT3-JAK2 |
NM_139276 NM_004972 |
t(17;9)(q21.1) | Fusion | ||||||
| 2 |
ATM
JAK1 JARID2 TET3 TET3 |
NM_000051 NM_002227 NM_004973 NM_144993 NM_144993 |
p.M900I p.G1097S p.V1019L p.V595L p.V787I |
c.2700G>C c.3289G>A c.3055G>C c.1783G>T c.2359G>A |
exon 18 exon 24 exon 14 exon 1 exon 4 |
Missense Missense Missense Missense Missense |
5.1 27 8.6 15.8 17.1 |
Gain of extra copies; 3–5 signals, 50–60% | No calls |
| 3 |
TET2
JAK1 STAT5B |
NM_001127208 NM_002227 NM_012448 |
p.Q960* p.G1097D p.I174S |
c.2878C>T c.3290G>A c.521T>G |
exon 3 exon 24 exon 5 |
Nonsense Missense Missense |
2.4 10.1 5.6 |
Normal | No calls |
| 4 |
BCR
JAK1 SMARCB1 |
NM_004327 NM_002227 NM_003073 |
p.R162C p.G1097D p.D101N |
c.484C>T c.3290G>A c.301G>A |
exon 1 exon 24 exon 3 |
Missense Missense Missense |
34.4 41.4 25.5 |
Normal |
Gain:1p32–36, 2p (including ALK, REL), 2q11–35, 6p, 17q11–21, Xq25, Xq26.1, Xq26.2 (including STAG2, BCORL1, and PHF6) CNLOH: SP140 Loss: on 1p (JAK1, BCL10), 12q13 (including ARID2, HDAC7 and KMT2D/MLL2), 16q23 (including PLCG2, IRF8 and FANCA), 20p and 20q12–13, Xq12 (AR) |
| 5 |
ARID4B
BRIP1 DDR2 DDX3X JAK1 MITF WHSC1 |
NM_016374 NM_032043 NM_006182 NM_001356 NM_002227 NM_198159 NM_001042424 |
p.P134A p.G763A p.X189_splice p.G533E p.G1097V p.E303V p.X961_splice |
c.400C>G c.2288G>C c.566–2A>G c.1598G>A c.3290G>T c.908A>T c.2882–28_2895del |
exon 7 exon 16 exon 7 exon 14 exon 24 exon 7 exon 16 |
Missense Missense Splice Missense Missense Missense Splice |
11.6 33 9.7 13.4 36 7 11.3 |
Gain of extra copies; 3–4 signals, 30–40% |
Gain: 8q, 17q |
| 6 | None | N/A | N/A | N/A | N/A | N/A | N/A | Gain of extra copies; 3–5 signals, 60–80% |
No calls |
| 7 |
JARID2
SOCS1 |
NM_004973 NM_003745 |
p.A700V p.S32Ffs*44 |
c.2099C>T c.95_142delins TCCTTCCTCCTCCTCGCCCG |
exon 8 exon 2 |
Missense Frameshift, deletion |
37.9 76.9 |
Gain of extra copies; 3 signals, 10–20% |
Gain: 2p, 2q11–35, 17q11–21, ASXL1 (20q11.21) CNLOH: HDAC4, chr22q Loss: 1p22.3-p12, 20p, 20q12–13 |
| 8 |
AXIN1
GNAS KDM6A RARA |
NM_003502 NM_000516 NM_021140 NM_000964 |
p.Q476* p.R201C p.V1113Sfs*8 p.R272W |
c.1426C>T c.601C>T c.3334_3335dupGT c.814C>T |
exon 6 exon 8 exon 23 exon 7 |
Nonsense Missense Frameshift, insertion Missense |
2.3 2.4 14.2 41.1 |
Gain of extra copies; 3–4 signals, 40–50% |
No calls |
| 9 |
PIK3CA
STAT3 KMT2B KMT2C KMT2C NCOR2 |
NM_006218 NM_139276 NM_014727 NM_170606 NM_170606 NM_006312 |
p.H1047R p.S614R S1739F L596V S593L S1518L |
c.3140A>G c.1842C>G c.5216C>T c.1786C>G c.1778C>T c.4553C>T |
exon 21 exon 20 exon 25 exon 13 exon 13 exon 34 |
Missense Missense Missense Missense Missense Missense |
3.2 7.7 14.3 5.9 6.1 5.2 |
Gain of extra copies; 3–4 signals, 50–60% |
No calls |
VAF, variant allele frequency; Chr, chromosome; CNLOH, copy neutral loss of heterozygosity; FISH, fluorescence in situ hybridization.