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Cytogenetics Laboratory

Cytogenetic Testing for Neoplastic Disorders

Chromosome Analyses for Neoplastic Disorders
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FISH studies for Neoplastic Disorders
The following FISH tests/panels are also listed below by corresponding disorder.
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Acute Lymphoblastic Leukemia (ALL) -  B-Cell
Panel includes testing for the following anomalies via the probes listed:
t(4;11)(q21;q23), AFF1(AF4)/MLL
t(9;22), ABL1/BCR
t(12;21), ETV6/RUNX1
t(1;19), PBX1/TCF3
+4, +10, +17, Cen4/10/17
t(11q23;var), MLL
del (9p), CDKN2A/Cen9
t(X;14)(p22.3;q32), CRLF2/IGH
t(Y;14)(p11.3;q32), CRLF2/IGHI
t(9;11), ELL
t(11;19), ELL
 
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Acute Lymphoblastic Leukemia (ALL) – T-Cell
Please indicate that the patient has pre-T cell ALL. 
ABL1/NUP214 co-amplification, ABL1/NUP214/Cen 9
del(9)(p21), CDKN2A/Cen9
t(11;var)(q23;var), MLL
t(9;11), ELL
t(11;19), ELL
17p-, TP53/D17Z1
7q34 rearrangement, TCRβ
1p32 rearrangement, TAL1/STIL(SIL)
t(5;14)(q35;q32), TLX3(HOX11L2)/BCL11B
t(10;11)(p13;q14), MLLT10(AF10)/PICALM
14q11.2 rearrangement, TRAD(TCRαδ)
Reflex for TCRβ anomaly:
t(7;10)(q34;q24), TCRβ/HOX11
t(7;11)(q34;p13), TCRβ/LMO1
t(7;11)(q34;p15), TCRβ/LMO2
t(6;7)(q27;q34), TCRβ/MYB
Reflex for MLL anomaly:
t(4;11)(q21;q23), AFF1(AF4)/MLL
t(6;11)(q27;q23), MLLT4(AF6)/MLL
t(10;11)(p13;q23), MLLT10(AF10)/MLL
t(11;19)(q23;p13.3), MLL/MLLT1(ENL)
Reflex for TCRαδ anomaly:
t(8;14)(q24.1;q11.2), MYC/TRAD(TCRαδ)
t(10;14)(q24.1;q11.2), TLX1(HOX11)/TRAD(TCRαδ)
t(11;14)(p15;q11.2), LMO1/TRAD(TCRαδ)
t(11;14)(p13;q11.2), LMO2/TRAD(TCRαδ)
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Acute Myeloid Leukemia (AML)
Please indicate subtype as well as which anomalies need to be investigated, from the following profile:
t(8;21), [M2], RUNX1T1/RUNX1
t(15;17), [M3], PML/RARA
t(11q23;var), [M0-M7], MLL
inv(16), [M4, Eos], MYH11/CBFbeta
+8, [M0-M7], Cen8/c-MYC
t(6;9), [M2, M4], DEK/NUP214
inv(3), [M1,2,4,6,7], RPN1/MECOM
t(3;5)(q25;q34), MLF1/NPM1I
5q-/monosomy 5, EGR1/D5S630
7q-/monosomy 7, D7Z1/D7S486
13q-/monosomy 13/+13, D13S319/LAMP1
20q-/isodicentric 20, D20S108/20qter
17p-/monosomy 17, TP53(p53)/D17Z1
t(8;16)(p11.2;p13.3), KAT6A(MYST3)/CREBBP
t(9;22)(q34;q11.2), ABL1(ABL)/BCR
Reflex Probes:
t(1;3)(p36.6;q21.3), PRDM16/RPN1
t(3;21)(q26.2;q22), MECOM(EVI1)/RUNX1(AML1)
t(6;11)(q27;q23), MLLT4(AF6)/MLL
t(9;11)(p22;q23), MLLT3(AF9)/MLL
t(10;11)(p13;q23), MLLT10(AF10)/MLL
t(11;16)(q23;p13.3), MLL/CREBBP
t(11;19)(q23;p13.1), MLL/ELL
t(11;19)(q23;p13.3), MLL/MLLT1(ENL)
17q21 rearrangement, RARA
16q22 rearrangement, CBFB
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Chronic Lymphocytic Leukemia (CLL)
 FISH panel is recommended in place of chromosome analysis for this disorder.  Panel includes testing for the following anomalies via the probes listed:
6q-, c-MYB/Cen6
11q-, ATM/Cen11
+12, D12Z3/MDM2
13q-, D13S319/LAMP1
17p-, TP53/Cen17
t(11;14), CCND1/IgH
Reflex for IgH anomaly:
t(14;18), IgH /BCL2
t(14;19), IgH /BCL3  
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Chronic Myeloid Leukemia (CML)
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Chronic Myelomonocytic Leukemia  (CMML)
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Hypereosinophilic Syndrome
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Imatinib Mesylate Responsive Genes
Panel, recommended for pediatric patients, includes testing for the following anomalies via the probes listed:
1q25 anomalies, ABL2
4q12 anomalies, PDGFRA
5q33 anomalies, PDGFRB
9q34 anomalies, ABL1
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Lymphoma
Includes a mini-pathology consult to evaluate appropriate FISH probes and translocations to investigate.  Panel includes testing for the following anomalies via the probes listed:
t(8;14), c-MYC/IGH
t(8q24.1;var), c-MYC
t(8;22)(q24;q11.2), MYC/IGL
t(11;14), CCND1/IGH
t(11;18), BIRC3/MALT1
t(14;18), IGH/MALT1
t(14;18), IGH/BCL2
t(3q27;var), BCL6
t(2;8)(p12;q24.1), IGK/MYC
12p13 rearrangement, CCND2
Includes a mini-pathology consult to evaluate appropriate FISH probes and translocations to investigate.  Panel includes testing for the following anomalies via the probes listed:
t(11;14), CCND1/IGH
t(14;18), IGH/BCL2
t(8q24.1;var), c-MYC
t(8;14), c-MYC/IGH
t(11;18) , BIRC3/MALT1
reflex t(14;18), IGH/MALT1
t(3q27;var), BCL6
22q11.2 rearrangement, IGL
t(2;8)(p12;q24.1), IGK/MYC
12p13 rearrangement, CCND2
Includes a mini-pathology consult to evaluate appropriate FISH probes and translocations to investigate.  Panel includes testing for the following anomalies via the probes listed:
1p32 rearrangement, TAL1/STIL(SIL)
t(5;14)(q35;q32), TLX3(HOX11L2)/BCL11B
7q34 rearrangement, TRB(TCRβ)
9p-/monosomy 9/+9, CDKN2A(p16)/D9Z1
t(9;22)(q34;q11.2), ABL amplification, ABL1(ABL)/BCR
t(10;11)(p13;q14), MLLT10(AF10)/PICALM
11q23 rearrangement, MLL
14q11.2 rearrangement, TRAD(TCRαδ)
Reflex Probes:
t(4;11)(q21;q23), AFF1(AF4)/MLL
t(6;11)(q27;q23), MLLT4(AF6)/MLL
t(9;11)(p22;q23), MLLT3(AF9)/MLL
t(10;11)(p13;q23), MLLT10(AF10)/MLL
t(11;19)(q23;p13.1), MLL/ELL
t(11;19)(q23;p13.3), MLL/MLLT1(ENL)
t(6;7)(q23;q34), MYB/TRB(TCRβ)
t(7;10)(q34;q24), TRB(TCRβ)/TLX1(HOX11)
t(7;11)(q34;p13), TRB(TCRβ)/LMO1
t(7;11)(q34;p13), TRB(TCRβ)/LMO2
t(8;14)(q24.1;q11.2), MYC/TRAD(TCRαδ)
t(10;14)(q24;q11.2), TLX1(HOX11)/TRAD(TCRαδ)
t(11;14)(p15;q11.2), LMO1/TRAD(TCRαδ)
t(11;14)(p13;q11.2), LMO2/TRAD(TCRαδ)
Includes a mini-pathology consult to evaluate appropriate FISH probes and translocations to investigate.  Panel includes testing for the following anomalies via the probes listed:
t(14;var)(q32.1;var)/inv(14)(q32.1;var), TCL1A
7q-/monosomy 7/iso(7q), D7Z1/D7S486
+8, D8Z2/MYC
t(2;var)(p23.2;var)/inv(2) ALK
ABL1(ABL/NUP214(CAN) co-amplication, D9Z1/ABL1(ABL)/NUP214(CAN)
 
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Myelodysplastic Syndrome (MDS)
Chromosome analysis is recommended as first tier testing for this disorder; FISH should be used if chromosomes are not successful.
Panel includes testing for the following anomalies via the probes listed:
5q-/monosomy 5, EGR1/D5S630
7q-/monosomy 7, D7Z1/D7S486
+8, D8Z2/MYC
13q-/monosomy 13/+13, D13S319/LAMP1
11q23 rearrangement, MLL
17p-/monosomy 17, TP53(p53)/D17Z1
Reflex Probes:
t(1;3)(p36.3;q21.3), PRDM16/RPN1
t(3;21)(q26.2;q22), MECOM(EVI1)/RUNX1(AML1)
t(6;11)(q27;q23), MLLT4(AF6)/MLL
t(9;11)(p22;q23), MLLT3(AF9)/MLL
t(10;11)(p13;q23), MLLT10(AF10)/MLL
t(11;16)(q23;p13.3), MLL/CREBBP
t(11;19)(q23;p13.1), MLL/ELL
t(11;19)(q23;p13.3), MLL/MLLT1(ENL)
20q-, 20qter/D20S108
 inv(3), RPN1/MECOM
Please indicate if you would like us to run the entire panel.  This is suggested for patients with a new diagnosis.  If patient is being tracked for known anomalies, please indicate which anomalies need to be investigated.
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Plasma Cell Proliferative Disorder (PCPD)
Testing for Multiple Myeloma, intended for diagnosis only.  Testing can be performed on fresh bone marrow or fixed cell pellet. Panel includes testing for the following anomalies via the probes listed:
13q-/monosomy 13, RB1/LAMP1
t(11;14), CCND1/IGH
14q23 rearrangement, IGH
17p-/monosomy 17/+17, TP53(p53)/D17Z1
+3/+7, D3Z1/D7Z1
+9/+15, D9Z1/D15Z43
1p36.3 loss/1q21 gain, TP73/CKS1B
t(8q24.1;var), c-MYC
Reflex Probes:
t(4;11)(p16.3;q32), FGFR3/IGH
t(6;14)(p21;q32), CCND3/IGH
t(14;16)(q32;q23), IGH/MAF(c-MAF)
t(14;20)(q32;q12), IGH/MAFB
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8p11 Myeloroliferative Disorder (EMS)
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