Skip to main content

Table 1 FISH results of 3881 FFPE, FF and cytological patient samples tested with the optimized pretreatment protocol in combination with Vysis, Cytocell and ZytoLight commercial probes

From: One-fits-all pretreatment protocol facilitating Fluorescence In Situ Hybridization on formalin-fixed paraffin-embedded, fresh frozen and cytological slides

Gene of Interest (Chromosomal location)

Probe

Manufacturer

Diagnostic requests (# slides)

Cut off criteria for aberrant signal pattern

# slides with interpretable results (%)

# slides with uninterpretable results (%)

ALK (2p23.2-p23.1)

ALK Breakapart

Cytocell

219

15%

195 (89%)

24 (11%)

BCL2 (18q21.33-q22.1)

BCL2 Breakapart

Cytocell

312

10%

300 (96%)

12 (4%)

BCL6 (3q27.3-q28)

BCL6 Breakapart

Cytocell

269

10%

261 (97%)

8 (3%)

CEP6 (6p11.1-q11)

CEP 6 (D6Z1)

Vysis

30

< 2copies

30 (100%)

–

CHOP (DDIT3) (12q13.3)

CHOP (DDIT3) Breakapart

Cytocell

18

10%

16 (89%)

2 (11%)

DDIT3 (12q13.3-q14.1)

SPEC DDIT3 Dual Color Break Apart Probe

ZytoLight

17

10%

17 (100%)

–

c-MET (MET) (7q31.2)

c-MET (MET) Amplification

Cytocell

94

*

92 (98%)

2 (2%)

cMYC (MYC) (8q24.21)

cMYC (MYC) Breakapart

Cytocell

346

10%

336 (97%)

10 (3%)

IGH (14q32.33) / cMYC (MYC) (8q24.21)

IGH/cMYC (MYC) Translocation, Dual Fusion

Cytocell

315

10%

302 (96%)

13 (4%)

COL1A1 (17q21.33) / PDGFB (22q13.1)

SPEC COL1A1/PDGFB Dual Color Dual Fusion Probe

ZytoLight

12

10%

12 (100%)

–

CCND1 (11q13.3)

CCND1 Breakapart

Cytocell

42

10%

40 (95%)

2 (5%)

CCND1 (11q13.3) / CEP11 (11p11.11-q11)

LSI Cyclin D1 (11q13) Spectrum Orange/ CEP 11 Spectrum Green

Vysis

9

10%

9 (100%)

–

CCND1 (11q13.2-q13.3)

SPEC CCND1 Dual Color Break Apart Probe

ZytoLight

9

10%

9 (100%)

–

ETV6 (12p13.2)

ETV6 Break Apart FISH Probe

Vysis

33

10%

31 (94%)

2 (6%)

EWSR1 (22q12.1-q12.2)

EWSR1 Breakapart

Cytocell

47

10%

42 (89%)

5 (11%)

EWSR1 (22q12.1-q12.2)

SPEC EWSR1 Dual Color Break Apart Probe

ZytoLight

46

10%

43 (93%)

3 (7%)

EWSR1 (22q12.1-q12.2) / FLI1 (11q24.3)

SPEC EWSR1/FLI1 TriCheck Probe

ZytoLight

20

10%

20 (100%)

–

FOXO1 (13q14.1)

FOXO1 Break Apart FISH Probe

Vysis

30

10%

30 (100%)

–

FUS (16p11.2)

FUS Breakapart Probe

Cytocell

24

10%

24 (100%)

–

FUS (16p11.2)

SPEC FUS Dual Color Break Apart Probe

ZytoLight

24

10%

21 (87%)

3 (13%)

HER2 (ERBB2) (17q12)

HER2 (ERBB2) Amplification

Cytocell

150

**

149 (99%)

1 (1%)

MALT1 (18q21.31-q21.32)

MALT1 Breakapart

Cytocell

25

10%

25 (100%)

–

MALT1 (18q21.31-q21.32)

SPEC MALT1 Dual Color Break Apart Probe

ZytoLight

25

10%

25 (100%)

–

MAML2 (11q21)

SPEC MAML2 Dual Color Break Apart Probe

ZytoLight

33

10%

32 (97%)

1 (3%)

MDM2 (12q15)

MDM2 Amplification

Cytocell

27

***

26 (96%)

1 (4%)

IRF4,DUSP22 (6p25.3)

SPEC IRF4,DUSP22 Dual Color Break Apart Probe

ZytoLight

17

10%

17 (100%)

–

MYB (6q23.2-q23.3)

SPEC MYB Dual Color Break Apart Probe

ZytoLight

83

10%

79 (95%)

4 (5%)

N-MYC (2p24.3), LAF4(AFF3) (2q11.2)

N-MYC (MYCN) Amplification

Cytocell

133

****

133 (100%)

–

PLAG1 (8q12.1) / CTNNB1 (3p22.1)

PLAG1/CTNNB1 Fusion

Cytocell

79

10%

75 (95%)

4 (5%)

CEP X (Xp11.1 - q11.1), CEP Y (Yp11.1 - q11.1), CEP 18 (18p11.1 - q11.1)

Prenatal X, Y and 18 Enumeration Probe

Cytocell

39

≥3 copies

39 (100%)

–

13 unique sequence (13q14.2), CEP 18 (18p11.1 - q11.1), 21 unique sequence (21q22.13)

Prenatal 13, 18 and 21 Enumeration Probe

Cytocell

59

≥3 copies

58 (98%)

1 (2%)

RET (10q11.21)

RET Breakapart

Cytocell

575

15%

500 (87%)

75 (13%)

ROS1 (6q22.1)

ROS1 Plus Breakapart

Cytocell

555

15%

461 (83%)

94 (17%)

SYT (SS18) (18q11.2)

SYT (SS18) Breakapart

Cytocell

35

10%

28 (80%)

7 (20%)

SS18 (18q11.2)

SPEC SS18 Dual Color Break Apart Probe

ZytoLight

35

10%

35 (100%)

–

TFE3 (Xp11.23)

SPEC TFE3 Dual Color Break Apart Probe

ZytoLight

15

10%

15 (100%)

–

USP6 (17p13.2)

SPEC USP6 Dual Color Break Apart Probe

ZytoLight

59

10%

55 (94%)

4 (6%)

YWHAE (17p13.3)

SPEC YWHAE Dual Color Break Apart Probe

ZytoLight

21

10%

21 (100%)

–

Total

38 probes

3 manufacturers

3881

 

3603 (93%)

278 (7%)

  1. *c-MET according to Garcia L. University of Colorado defined criteria. Dual-probe MET/CEP7 ratio < 1.8 is not amplified, ratio ≥ 1.8 - ≤2.2 is low level MET amplification, ratio > 2.2 - ≤5.0 is intermediate level MET amplification, ratio ≥ 5.0 is high level MET amplification [7]. ** HER2 according to ASCO–CAP Guidelines. Her2 is amplified when; Single-probe average HER2 copy number ≥ 6.0 signals/cell, Dual-probe HER2/CEP17 ratio ≥ 2.0 with an average HER2 copy number ≥ 4.0 signals/cell, ratio ≥ 2.0 with an average HER2 copy number < 4.0 signals/cell, ratio < 2.0 with an average HER2 copy number ≥ 6.0 signals/cell. Her2 is equivocal when; Single-probe ISH average HER2 copy number ≥ 4.0 and < 6.0 signals/cell, Dual-probe HER2/CEP17 ratio < 2.0 with an average HER2 copy number ≥ 4.0 and < 6.0 signals/cell. Her2 is negative when; Single-probe average HER2 copy number < 4.0 signals/cell, Dual-probe HER2/CEP17 ratio < 2.0 with an average HER2 copy number < 4.0 signals/cell [8]. *** MDM2/CEP12 ratio ≥ 2.0 is considered amplified, < 2.0 not amplified, and cases displaying > 2 signals of both probes and an MDM2 ratio < 2.0 polysomic for chromosome 12 [9]. ****MYCN-Status according to the DCOG NBL 2009 treatment protocol. Dual-probe MYCN/CEP2 ratio 1 is not amplified, MYCN/CEP2 ratio 1.5–4 indicates a gain, MYCN/CEP2 ratio > 4 is amplified (DCOG NBL 2009 Final Version Amendment 1)
Back to article page

Molecular Cytogenetics

ISSN: 1755-8166