Cytogenetic and MECOM-associated alterations in atypical 3q26 AML
| PT # . | Karyotype Chr.3*† . | FISH EVI1‡ . | SNP Chr.3‡ . | EVI1§ . | MDS1-EVI1§ . | Breakpoint . | Gene partner|| . |
|---|---|---|---|---|---|---|---|
| SO-03 | add(3)(q2?6) | Rearranged | Chr.3q26 balanced | + | − | Breakpoint not found | |
| SO-06 | ?der(3)(q2?) | Rearranged | Chr.3q26 CNL 5′ MECOM | + | − | inv(3;3)(p23q26), complex | TGFBR2 |
| SO-11 | der(3)add(3)(p1?2)add(3)(q2?6) | Rearranged | Chr.3q26 CNL 3′ and 5′ MECOM | + | − | t(3;7)(q26;q11.23/q21.12), complex | DMTF1 |
| SO-20 | add(3)(q26) | Rearranged | Chr.3q26 balanced | + | − | t(3;7)(q26;p22.2), complex | TNRC18/FBXL18 |
| SO-23 | add(3)(q2?5) | Rearranged | Chr.3q26 balanced | + | + | t(3;6)(q26;q25) | ARID1B |
| SO-45 | del(3)(q2?3q2?6) | Rearranged | Chr.3q26 balanced | + | − | t(3;3)(q21;q26)+t(3;16)(q26;q22.1), complex | GATA2 |
| SO-47 | add(3)(q2?6) | Rearranged | Chr.3q26 balanced | + | − | t(2;3)(p21;q26) | THADA |
| BB-01 | no 3q aberrations | Rearranged | Chr.3q26 CNL MDS1 | + | − | Breakpoint not found | |
| TG-01 | t(3;11)(q26;q2?4) | Rearranged | Not done | + | + | t(3;11)(q26;q24) | HSPA8-MECOM¶ |
| TG-02 | t(3;18)(q26;q1?) | Rearranged | Not done | + | − | t(3;18)(q26;q21) | MECOM-TCF4¶ |
| TG-03 | no 3q aberrations | Rearranged | Chr.3q26 balanced | + | − | inv(3)(q21q26) | GATA2 |
| TG-04 | ins(3;3)(q26;q21q26) | Unclear | Chr.3q26 balanced | + | + | Breakpoint not found | |
| TG-05 | ?add(3)(q25) | Loss | Chr.3q26 CNL MDS1, CNG EVI1 | + | − | del(3)(q25.3-q26.2) | IL12A-AS1 |
| TG-06 | add(3)(q26) | Normal | Chr.3q26 balanced | + | − | Breakpoint not found | |
| TG-08 | −3[3],del(3)(q2?4)[7] | Loss | Chr.3q21 CNL GATA2 | + | + | Breakpoint not found | |
| TG-10 | −3 | Rearranged | Chr.3q21 CNL GATA2 | + | − | t(3;6)(q26;p22) | TDP2/JARID2 |
| HF-01 | der(7)t(3;7)(q26;q11.2) | Rearranged | Not done | + | − | t(3;7)(q26;q21) | CDK6 |
| HF-02 | der(7)t(3;7)(q26;q22) | Rearranged | Not done | + | − | Breakpoint not found | |
| HF-03 | der(7)t(3;7)(q26;q21) | Rearranged | Not done | + | − | t(3;7)(q26;q21) | CDK6 |
| HF-04 | der(7)t(3;7)(q26;p11)t(3;7)(q26;q21), −3 | Rearranged | Not done | + | − | Breakpoint not found | |
| HF-13 | der(3)t(3;14)(q21;q?) | Amplified | Chr.3q26 CNG, MECOM balanced | + | − | Breakpoint not found | |
| HF-14 | der(3)(::3p12->3q13::3q26->3q26::) | Amplified | Chr.3q26 CNG MECOM | + | − | Breakpoint not found | TRA2B-MECOM¶ |
| HF-15 | r(3)(p11q26)del(3)(q14q26) | Amplified | Chr.3q26 CNG EVI1/CNL MDS1, Chr.3q21 CNL GATA2 | + | − | inv(3)(q13.33q26.2) | GTF2E1/STXBP5L |
| HF-16 | der(2)ins(2;3)(q31;q22q26) | Amplified | Chr.q26 CNG 5′ and 3′ EVI1/CNL MDS1, Chr.3q21 CNL GATA2 | + | − | Breakpoint not found | |
| HF-17 | t(5;8)(p13;p21) | Rearranged | Chr.3q26 balanced | + | − | t(3;8)(q26;q24.1) | MYC |
| HF-18 | t(2;3;6)(p15;q26;q26) | Rearranged | Chr.3q26 balanced | + | − | t(2;3)(p21;q26) +t(3;5)(q26;q34) + t(3;6)(q26;q27) | THADA |
| HF-19 | t(3;4)(q26;p15) | Rearranged | Chr.3q26 balanced | + | − | t(3;4)(q26;p15) | PROM1, CD38 |
| HF-20 | t(3;8)(q26;p23) | Rearranged | Chr.3q26 CNL MDS1 | + | − | t(3;8)(q26;p23) | TNKS/MSRA |
| HF-21 | der(8)t(3;8)(q26;p23) | Rearranged | Chr.3q26 CNL MDS1, Chr.3q21 CNL GATA2 | − | − | t(3;8)(q26;p24), complex | FAM135B |
| HF-22 | der(3)t(2;3)(p14;q26) | Rearranged | Chr.3q26 balanced | + | − | t(2;3)(p21;q26) | THADA |
| HF-23 | ins(6;3)(q21;q21q26) | Rearranged | Chr.3q26 balanced | + | − | ins(6;3)(q21;q21q26) | CD164 |
| HF-24 | der(3)del(3)(p12p26)inv(3)(p26q26) | Rearranged | Chr.3q26 balanced | − | − | Breakpoint not found | |
| HF-25 | t(3;10)(q26;q21) | Rearranged | Chr.3q26 balanced | − | − | t(3;10)(q26;q21) | ARID5B |
| PT # . | Karyotype Chr.3*† . | FISH EVI1‡ . | SNP Chr.3‡ . | EVI1§ . | MDS1-EVI1§ . | Breakpoint . | Gene partner|| . |
|---|---|---|---|---|---|---|---|
| SO-03 | add(3)(q2?6) | Rearranged | Chr.3q26 balanced | + | − | Breakpoint not found | |
| SO-06 | ?der(3)(q2?) | Rearranged | Chr.3q26 CNL 5′ MECOM | + | − | inv(3;3)(p23q26), complex | TGFBR2 |
| SO-11 | der(3)add(3)(p1?2)add(3)(q2?6) | Rearranged | Chr.3q26 CNL 3′ and 5′ MECOM | + | − | t(3;7)(q26;q11.23/q21.12), complex | DMTF1 |
| SO-20 | add(3)(q26) | Rearranged | Chr.3q26 balanced | + | − | t(3;7)(q26;p22.2), complex | TNRC18/FBXL18 |
| SO-23 | add(3)(q2?5) | Rearranged | Chr.3q26 balanced | + | + | t(3;6)(q26;q25) | ARID1B |
| SO-45 | del(3)(q2?3q2?6) | Rearranged | Chr.3q26 balanced | + | − | t(3;3)(q21;q26)+t(3;16)(q26;q22.1), complex | GATA2 |
| SO-47 | add(3)(q2?6) | Rearranged | Chr.3q26 balanced | + | − | t(2;3)(p21;q26) | THADA |
| BB-01 | no 3q aberrations | Rearranged | Chr.3q26 CNL MDS1 | + | − | Breakpoint not found | |
| TG-01 | t(3;11)(q26;q2?4) | Rearranged | Not done | + | + | t(3;11)(q26;q24) | HSPA8-MECOM¶ |
| TG-02 | t(3;18)(q26;q1?) | Rearranged | Not done | + | − | t(3;18)(q26;q21) | MECOM-TCF4¶ |
| TG-03 | no 3q aberrations | Rearranged | Chr.3q26 balanced | + | − | inv(3)(q21q26) | GATA2 |
| TG-04 | ins(3;3)(q26;q21q26) | Unclear | Chr.3q26 balanced | + | + | Breakpoint not found | |
| TG-05 | ?add(3)(q25) | Loss | Chr.3q26 CNL MDS1, CNG EVI1 | + | − | del(3)(q25.3-q26.2) | IL12A-AS1 |
| TG-06 | add(3)(q26) | Normal | Chr.3q26 balanced | + | − | Breakpoint not found | |
| TG-08 | −3[3],del(3)(q2?4)[7] | Loss | Chr.3q21 CNL GATA2 | + | + | Breakpoint not found | |
| TG-10 | −3 | Rearranged | Chr.3q21 CNL GATA2 | + | − | t(3;6)(q26;p22) | TDP2/JARID2 |
| HF-01 | der(7)t(3;7)(q26;q11.2) | Rearranged | Not done | + | − | t(3;7)(q26;q21) | CDK6 |
| HF-02 | der(7)t(3;7)(q26;q22) | Rearranged | Not done | + | − | Breakpoint not found | |
| HF-03 | der(7)t(3;7)(q26;q21) | Rearranged | Not done | + | − | t(3;7)(q26;q21) | CDK6 |
| HF-04 | der(7)t(3;7)(q26;p11)t(3;7)(q26;q21), −3 | Rearranged | Not done | + | − | Breakpoint not found | |
| HF-13 | der(3)t(3;14)(q21;q?) | Amplified | Chr.3q26 CNG, MECOM balanced | + | − | Breakpoint not found | |
| HF-14 | der(3)(::3p12->3q13::3q26->3q26::) | Amplified | Chr.3q26 CNG MECOM | + | − | Breakpoint not found | TRA2B-MECOM¶ |
| HF-15 | r(3)(p11q26)del(3)(q14q26) | Amplified | Chr.3q26 CNG EVI1/CNL MDS1, Chr.3q21 CNL GATA2 | + | − | inv(3)(q13.33q26.2) | GTF2E1/STXBP5L |
| HF-16 | der(2)ins(2;3)(q31;q22q26) | Amplified | Chr.q26 CNG 5′ and 3′ EVI1/CNL MDS1, Chr.3q21 CNL GATA2 | + | − | Breakpoint not found | |
| HF-17 | t(5;8)(p13;p21) | Rearranged | Chr.3q26 balanced | + | − | t(3;8)(q26;q24.1) | MYC |
| HF-18 | t(2;3;6)(p15;q26;q26) | Rearranged | Chr.3q26 balanced | + | − | t(2;3)(p21;q26) +t(3;5)(q26;q34) + t(3;6)(q26;q27) | THADA |
| HF-19 | t(3;4)(q26;p15) | Rearranged | Chr.3q26 balanced | + | − | t(3;4)(q26;p15) | PROM1, CD38 |
| HF-20 | t(3;8)(q26;p23) | Rearranged | Chr.3q26 CNL MDS1 | + | − | t(3;8)(q26;p23) | TNKS/MSRA |
| HF-21 | der(8)t(3;8)(q26;p23) | Rearranged | Chr.3q26 CNL MDS1, Chr.3q21 CNL GATA2 | − | − | t(3;8)(q26;p24), complex | FAM135B |
| HF-22 | der(3)t(2;3)(p14;q26) | Rearranged | Chr.3q26 balanced | + | − | t(2;3)(p21;q26) | THADA |
| HF-23 | ins(6;3)(q21;q21q26) | Rearranged | Chr.3q26 balanced | + | − | ins(6;3)(q21;q21q26) | CD164 |
| HF-24 | der(3)del(3)(p12p26)inv(3)(p26q26) | Rearranged | Chr.3q26 balanced | − | − | Breakpoint not found | |
| HF-25 | t(3;10)(q26;q21) | Rearranged | Chr.3q26 balanced | − | − | t(3;10)(q26;q21) | ARID5B |
Chr., chromosome; CNG, copy-number gain; CNL, copy-number loss; PT, patient.
Cytogenetic aberrations with a specific focus on 3q26. Complete karyotype is provided in supplemental Table 1.
Patients #BB-01, #TG-03, #TG-10 and #HF-17 did not show a 3q26 rearrangement by karyotyping but were identified as rearranged by routine MECOM FISH.
FISH was carried out as outlined in “Methods” and scored as normal, loss, amplified, or rearranged. In sample TG-04, the FISH results were unclear.
EVI1+ and MDS1-EVI1+ were determined as previously reported.2-4
Partner gene. The genes, expressed in CD34+ cells, located in closest vicinity to the breakpoint are indicated.
Fusion transcript.