Patient cytogenetic, FISH, and NGS results
| Patient . | SNV and indels, protein level (VAF, %) . | Karyotype and FISH . | t(4;12) fusions (reads) . |
|---|---|---|---|
| 1 | BCOR p.Ser1189Ter (25.9) BCORL1 p.Val866LeufsTer60 (16.2) DNMT3A p.Arg736His (18.2) DNMT3A p.Leu859Ter (20.2) IDH1 p.Arg132Cys (28.6) NRAS p.Ala59Asp (20.6) | 46,XX,t(4;12)(q12;p13)[19]/46,XX[1] .ish t(4;12)(q12;p13) (SCFD2+;PDGFRA+)[5] | ETV6 exon 1-SCFD2 exon 5 (26)* ETV6 exon 2-SCFD2 exon 5 (346) GSX2 exon 2-ETV6 exon 3 (64) GSX2 exon 1-ETV6 exon 3 (21) |
| 2 | TP53 p.Lys120Glu (87.6) | 45,XY,add(3)(p12),del(5)(q22q32),-9[4]/ 45,idem,t(4;12)(q12;p13)[cp16] .ish t(4;12)(SCFD2+,LNX-,5′ ETV6 dim;PDGFRA+,5′ ETV6 dim,3′ETV6+)[5] | ETV6 exon 1-SCFD2 exon 5 (220)* ETV6 5′ UTR-SCFD2 exon 5 (18) |
| 3 | NA | 46,XX,t(4;12)(q12;p13)[cp3]/46,XX[18] nuc ish (PDGFRAx1),(SCFD2,LNX)x2[4/100] nuc ish(ETV6x3)(5′ETV6 x1)[7/100] | ETV6 exon 1-CHIC2 exon 4 (5)* |
| 4 | ASXL1 p.Gly642fsTer (52.2) EZH2 p.Asp664Glu (97.1) KRAS p.Gly12Arg (41.6) NRAS p.Gly12Asp (4.2) RUNX1 p.Ser322fsTer160 (47.2) TET2 p.Gln740Ter (48.0) | 46,XY,t(4;12)(q12;p13)[18]/46,XY[2] nuc ish(ETV6x2)(3′ETV6 sep 5′ETV6x1)[176/200] nuc ish(SCFD2,LNX,3′PDGFRA/ KIT)x2(SCFD2,LNX sep 3′ PDGFRA/ KITx1)[84/100]† | ETV6 exon 1-CHIC2 exon 2 (73) GSX2 exon 2-ETV6 exon 3 (64) |
| 5 | ASXL1 p.G646WfsTer12 (45.3) PPM1D p.L546PfsTer6 (54.1) SF3B1 p.E592K (25.3) SMC3 c.430-1G>A (27.6) | 46,XX,t(4;12)(q11-12;p13)[20] | GSX2 exon 2-ETV6 exon 2 (77) GSX2 introns 1 and 2-ETV6 exon 2 (12) |
| Patient . | SNV and indels, protein level (VAF, %) . | Karyotype and FISH . | t(4;12) fusions (reads) . |
|---|---|---|---|
| 1 | BCOR p.Ser1189Ter (25.9) BCORL1 p.Val866LeufsTer60 (16.2) DNMT3A p.Arg736His (18.2) DNMT3A p.Leu859Ter (20.2) IDH1 p.Arg132Cys (28.6) NRAS p.Ala59Asp (20.6) | 46,XX,t(4;12)(q12;p13)[19]/46,XX[1] .ish t(4;12)(q12;p13) (SCFD2+;PDGFRA+)[5] | ETV6 exon 1-SCFD2 exon 5 (26)* ETV6 exon 2-SCFD2 exon 5 (346) GSX2 exon 2-ETV6 exon 3 (64) GSX2 exon 1-ETV6 exon 3 (21) |
| 2 | TP53 p.Lys120Glu (87.6) | 45,XY,add(3)(p12),del(5)(q22q32),-9[4]/ 45,idem,t(4;12)(q12;p13)[cp16] .ish t(4;12)(SCFD2+,LNX-,5′ ETV6 dim;PDGFRA+,5′ ETV6 dim,3′ETV6+)[5] | ETV6 exon 1-SCFD2 exon 5 (220)* ETV6 5′ UTR-SCFD2 exon 5 (18) |
| 3 | NA | 46,XX,t(4;12)(q12;p13)[cp3]/46,XX[18] nuc ish (PDGFRAx1),(SCFD2,LNX)x2[4/100] nuc ish(ETV6x3)(5′ETV6 x1)[7/100] | ETV6 exon 1-CHIC2 exon 4 (5)* |
| 4 | ASXL1 p.Gly642fsTer (52.2) EZH2 p.Asp664Glu (97.1) KRAS p.Gly12Arg (41.6) NRAS p.Gly12Asp (4.2) RUNX1 p.Ser322fsTer160 (47.2) TET2 p.Gln740Ter (48.0) | 46,XY,t(4;12)(q12;p13)[18]/46,XY[2] nuc ish(ETV6x2)(3′ETV6 sep 5′ETV6x1)[176/200] nuc ish(SCFD2,LNX,3′PDGFRA/ KIT)x2(SCFD2,LNX sep 3′ PDGFRA/ KITx1)[84/100]† | ETV6 exon 1-CHIC2 exon 2 (73) GSX2 exon 2-ETV6 exon 3 (64) |
| 5 | ASXL1 p.G646WfsTer12 (45.3) PPM1D p.L546PfsTer6 (54.1) SF3B1 p.E592K (25.3) SMC3 c.430-1G>A (27.6) | 46,XX,t(4;12)(q11-12;p13)[20] | GSX2 exon 2-ETV6 exon 2 (77) GSX2 introns 1 and 2-ETV6 exon 2 (12) |
Genes are listed in the 5′ to 3′ direction of the forward strand. Sequences with <5 reads are not reported. Case 3 had poor RNA quality (specimen from 2008). Case 5 SMC3 splice site variant in italics; no protein level change predicted.
NA, data not available; SNV, single nucleotide variants; UTR, untranslated region; VAF, variant allele frequency.
In-frame fusion transcript.
Performed at an outside hospital.