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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)