Introduction
Materials and methods
Materials and DNA isolation
DNA labeling and array CGH)
Multiplex ligation-dependent probe amplification
Multiplex ligation-dependent probe amplification data analysis
Statistical analysis
Results
Array CGH analysis and correlation with lymph node status and histological type
Chromosome | Status | All cases | Lymph node status |
P value | Histological type |
P value | |||
---|---|---|---|---|---|---|---|---|---|
LN0 | LN1 | Intestinal | Diffuse | Mixed | |||||
n = 63 |
n = 22 |
n = 41 |
n = 38 |
n = 17 |
n = 8 | ||||
8q | Gain | 49 (77.8%) | 18 (81.8%) | 31 (75.6%) | 0.57 | 29 (76.3%) | 13 (76.5%) | 7 (87.5%) | 0.78 |
No gain | 14 (22.2%) | 4 (18.2%) | 10 (24.4%) | 9 (23.7%) | 4 (23.5%) | 1 (12.5%) | |||
13q | Gain | 25 (39.7%) | 10 (45.5%) | 15 (36.6%) | 0.49 | 19 (50.0%) | 4 (23.5%) | 2 (25.0%) | 0.12 |
No gain | 38 (60.3%) | 12 (54.5%) | 26 (63.4%) | 19 (50.0%) | 13 (76.5%) | 6 (75.0%) | |||
20q | Gain | 49 (77.8%) | 14 (63.6%) | 35 (85.4%) |
0.048
| 33 (86.8%) | 9 (52.9%) | 7 (87.5%) |
0.016
|
No gain | 14 (22.2%) | 8 (36.4%) | 6 (14.6%) | 5 (13.2%) | 8 (47.1%) | 1 (12.5%) | |||
8q + 13q + 20q | Gain | 17 (27.0%) | 6 (27.2%) | 11 (26.8%) | 0.97 | 13 (34.2%) | 2 (11.8%) | 2 (25.0%) | 0.22 |
No gain | 46 (73.0%) | 16 (72.7%) | 30 (73.2) | 25 (65.8%) | 15 (88.2%) | 6 (75.0%) | |||
8q + 13q | Gain | 4 (6.3%) | 3 (13.6%) | 1 (2.4%) | 0.082 | 2 (5.3%) | 2 (11.8%) | 0 (0.0%) | 0.48 |
No gain | 59 (93.7%) | 19 (86.4%) | 40 (97.6%) | 36 (94.7%) | 15 (88.2%) | 8 (100.0%) | |||
8q + 20q | Gain | 24 (38.1%) | 8 (36.4%) | 16 (39.0%) | 0.84 | 14 (36.8%) | 6 (35.3%) | 4 (50.0%) | 0.76 |
No gain | 39 (61.9%) | 14 (63.6%) | 25 (61.0%) | 24 (63.2%) | 11 (64.7%) | 4 (50.0%) | |||
13q + 20q | Gain | 3 (4.8%) | 0 (0.0%) | 3 (7.3%) | 0.19 | 3 (7.9%) | 0 (0.0%) | 0 (0.0%) | 0.36 |
No gain | 60 (95.2%) | 22 (100.0%) | 38 (92.7%) | 35 (92.1%) | 17 (100.0%) | 8 (100.0%) |
Tumor ID | Gender | Age | Histological type | T status | N status | Tumor ID | Gender | Age | Histological type | T status | N status |
---|---|---|---|---|---|---|---|---|---|---|---|
1 | Female | 78 | Intestinal | T3 | N1 | 33 | Male | 75 | Intestinal | T2 | N3 |
2 | Female | 81 | Diffuse | T3 | N1 | 34 | Male | 61 | Intestinal | T3 | N3 |
3 | Female | 54 | Intestinal | T2 | N0 | 35 | Female | 82 | Diffuse | T3 | N1 |
4 | Male | 73 | Intestinal | T3 | N1 | 36 | Male | 74 | Mixed | T2 | N1 |
5 | Male | 81 | Mixed | T2 | N2 | 37 | Female | 87 | Diffuse | T3 | N2 |
6 | Male | 58 | Intestinal | T2 | N1 | 38 | Female | 78 | Intestinal | T1 | N0 |
7 | Female | 72 | Intestinal | T2 | N0 | 39 | Male | 78 | Diffuse | T2 | N0 |
8 | Male | 86 | Intestinal | T2 | N2 | 40 | Female | 84 | Intestinal | T2 | N0 |
9 | male | 71 | Intestinal | T3 | N0 | 41 | Male | 85 | Diffuse | T3 | N2 |
10 | Female | 75 | Intestinal | T4 | N1 | 42 | Male | 62 | Diffuse | T3 | N3 |
11 | Female | 75 | Intestinal | T3 | N2 | 43 | Male | 68 | Intestinal | T3 | N1 |
12 | Male | 64 | Mixed | T3 | N1 | 44 | Male | 58 | Intestinal | T4 | N1 |
13 | Male | 81 | Intestinal | T2 | N2 | 45 | Male | 61 | Diffuse | T3 | N1 |
14 | Male | 63 | Intestinal | T2 | N0 | 46 | Female | 58 | Intestinal | T3 | N1 |
15 | Male | 63 | Intestinal | T3 | N1 | 47 | Male | 81 | Intestinal | T3 | N1 |
16 | Male | 68 | Mixed | T2 | N0 | 48 | Female | 65 | Intestinal | T2 | N1 |
17 | Female | 72 | Intestinal | T2 | N1 | 49 | Female | 65 | Intestinal | T2 | N1 |
18 | Male | 73 | Intestinal | T2 | N2 | 50 | Male | 82 | Intestinal | T1 | N0 |
19 | Male | 71 | Intestinal | T3 | N2 | 51 | Female | 74 | Mixed | T1 | N0 |
20 | Female | 67 | Intestinal | T2 | N0 | 52 | Male | 72 | Diffuse | T3 | N2 |
21 | Male | 67 | Diffuse | T3 | N1 | 53 | Female | 60 | Diffuse | T3 | N0 |
22 | Female | 64 | Intestinal | T3 | N2 | 54 | Male | 47 | Diffuse | T2 | N0 |
23 | Female | 72 | Diffuse | T3 | N2 | 55 | Female | 74 | Diffuse | T2 | N0 |
24 | Male | 74 | Intestinal | T2 | N1 | 56 | Male | 65 | Mixed | T2 | N2 |
25 | Male | 58 | Intestinal | T3 | N3 | 57 | Female | 49 | Intestinal | T1 | N0 |
26 | Male | 71 | Intestinal | T1 | N0 | 58 | Male | 74 | Intestinal | T1 | N0 |
27 | Female | 68 | Mixed | T3 | N1 | 59 | Male | 58 | Intestinal | T1 | N0 |
28 | Male | 74 | Intestinal | T2 | N0 | 60 | Male | 53 | Diffuse | T2 | N0 |
29 | Male | 57 | Mixed | T3 | N1 | 61 | Male | 61 | Diffuse | T2 | N1 |
30 | Male | 69 | Diffuse | T3 | N1 | 62 | Male | 69 | Diffuse | T2 | N1 |
31 | Male | 67 | Intestinal | T2 | N0 | 63 | Male | 56 | Intestinal | T2 | N0 |
32 | Female | 71 | Intestinal | T2 | N1 |
Multiplex ligation-dependent probe amplification analysis of DNA copy-number aberrations and correlation with lymph node status and histological type
Gene | Location | Gains | LN-negative | LN-positive |
p value | Intestinal | Diffuse | Mixed |
p value |
---|---|---|---|---|---|---|---|---|---|
FBXO25
| 8p23.3 | 1.6% | 1.04 (0.68–1.46) | 0.97 (0.48–1.26) | NS | 0.98 (0.48–1.46) | 1.08 (0.81–1.26) | 0.87 (0.63–1.29) | 0.01 |
MOS
| 8q11 | 39.7% | 1.20 (0.78–2.02) | 1.31 (0.73–1.96) | NS | 1.34 (0.92–2.02) | 1.15 (0.77–1.71) | 1.23 (0.73–1.96) | NS |
EYA1
| 8q13.3 | 9.5% | 1.08 (0.55–2.07) | 0.96 (0.65–1.35) | NS | 1.01 (0.66–2.07) | 1.05 (0.75–1.64) | 0.86 (0.55–1.25) | NS |
TPD52
| 8q21 | 25.4% | 1.26 (0.67–1.98) | 1.15 (0.68–1.59) | NS | 1.20 (0.90–1.98) | 1.22 (0.96–1.74) | 1.04 (0.67–1.59) | NS |
RAD54B
| 8q21.3 | 34.9% | 1.33 (0.88–2.29) | 1.22 (0.90–2.06) | NS | 1.30 (0.90–2.29) | 1.20 (0.88–2.06) | 1.19 (0.90–1.59) | NS |
EIF3S6
| 8q22 | 28.6% | 1.27 (0.85–1.82) | 1.12 (0.64–1.74) | 0.04 | 1.19 (0.74–2.82) | 1.13 (0.64–1.70) | 1.18 (0.76–1.59) | NS |
MYC
| 8q24.12 | 73.0% | 1.75 (0.95–3.22) | 1.76 (0.90–5.81) | NS | 1.74 (0.94–3.22) | 1.74 (0.90–5.81) | 1.84 (1.03–2.74) | NS |
WISP1
| 8q24 | 36.5% | 1.26 (0.79–1.68) | 1.26 (0.51–2.08) | NS | 1.28 (0.51–1.88) | 1.20 (0.79–1.64) | 1.27 (0.79–2.08) | NS |
KCNK9
| 8q24.3 | 34.9% | 1.16 (0.59–2.92) | 1.24 (0.58–1.90) | NS | 1.22 (0.77–1.90 | 1.11 (0.59–1.87) | 1.37 (0.58–2.92) | NS |
PTK2
| 8q24 | 47.6% | 1.40 (0.96–3.47) | 1.29 (0.83–1.97) | NS | 1.33 (0.83–1.86) | 1.25 (0.91–1.97) | 1.51 (0.63–5.02) | NS |
PTP4A3
| 8q24.3 | 33.3% | 1.37 (0.62–5.02) | 1.23 (0.63–2.24) | NS | 1.27 (0.86–2.20) | 1.18 (0.62–2.24) | 1.55 (0.63–5.02) | NS |
PSPC1
| 13q11 | 22.2% | 1.12 (0.65–1.48) | 1.18 (0.71–1.75) | NS | 1.20 (0.89–1.75) | 1.15 (0.82–1.48) | 1.01 (0.65–1.51) | NS |
ZNF198
| 13q11 | 20.6% | 1.05 (0.38–2.17) | 1.08 (0.55–2.04) | NS | 1.08 (0.55–2.04) | 1.15 (0.74–2.17) | 0.88 (0.38–1.41) | NS |
RASL11A
| 13q12.2 | 11.1% | 1.09 (0.87–1.35) | 1.10 (0.61–1.66) | NS | 1.15 (0.84–1.66) | 1.08 (0.75–1.52) | 0.93 (0.61–1.15) | 0.03 |
CDX2
| 13q12 | 22.2% | 1.09 (0.70–2.11) | 1.19 (0.67–2.09) | NS | 1.21 (0.76–2.11) | 1.14 (0.70–1.73) | 0.91 (0.67–1.30) | 0.03 |
FLT3
| 13q12 | 12.7% | 1.04 (0.56–2.23) | 1.05 (0.65–1.70) | NS | 1.08 (0.69–2.23) | 1.05 (0.71–1.55) | 0.87 (0.56–1.51) | NS |
FLT1
| 13q12.2 | 20.6% | 1.10 (0.85–1.42) | 1.13 (0.67–1.85) | NS | 1.17 (0.77–1.85) | 1.09 (0.82–1.48) | 0.98 (0.67–1.34) | NS |
BRCA2
| 13q12.3 | 22.2% | 1.15 (0.53–1.85) | 1.22 (0.91–2.62) | NS | 1.23 (0.83–2.62) | 1.17 (0.93–1.85) | 1.08 (0.53–1.31) | NS |
FOXO1A
| 13q14.1 | 28.6% | 1.18 (0.80–1.58) | 1.19 (0.79–1.59) | NS | 1.20 (0.79–1.59) | 1.15 (0.80–1.45) | 1.18 (0.89–1.46) | NS |
EPSTI1
| 13q14.11 | 17.5% | 1.51 (1.02–6.32) | 1.21 (0.62–2.20) | NS | 1.30 (0.94–2.20) | 1.17 (0.62–1.68) | 1.70 (0.90–6.32) | NS |
RB1
| 13q14.2 | 14.3% | 1.12 (0.72–1.87) | 1.04 (0.60–1.97) | NS | 1.06 (0.69–1.89) | 1.13 (0.60–1.97 | 1.01 (0.72–1.55) | NS |
ATP7B
| 13q14.2 | 28.6% | 1.15 (0.77–1.45) | 1.21 (0.90–1.99) | NS | 1.24 (0.91–1.99) | 1.14 (0.86–1.53) | 1.05 (0.77–1.42) | NS |
DACH
| 13q21.32 | 20.6% | 1.13 (0.82–1.42) | 1.13 (0.62–1.72) | NS | 1.15 (0.62–1.72) | 1.15 (0.88–1.42) | 1.05 (0.71–1.36) | NS |
ZCCHC3
| 20p13–p12.2 | 38.1% | 1.19 (0.81–1.82) | 1.28 (0.94–2.29) | NS | 1.26 (0.81–2.29) | 1.21 (0.91–1.92) | 1.27 (0.94–1.96) | NS |
PCNA
| 20pter–p12 | 17.5% | 1.09 (0.48–1.65) | 1.01 (0.45–1.61) | NS | 1.02 (0.45–1.65) | 1.06 (0.64–1.50) | 1.06 (0.48–1.61) | NS |
JAG1
| 20p12.1–p11.23 | 42.9% | 1.24 (0.69–2.05) | 1.29 (0.85–2.13) | NS | 1.31 (0.69–2.13) | 1.17 (0.85–1.68) | 1.31 (0.97–2.05) | NS |
THBD
| 20p12–cen | 31.7% | 1.04 (0.48–1.79) | 1.26 (0.71–3.81) | NS | 1.25 (0.48–3.81) | 1.07 (0.60–1.66) | 1.10 (0.74–1.34) | NS |
KIAA0980
| 20p11.22–p11.1 | 42.9% | 1.17 (0.70–1.76) | 1.31 (0.84–2.73) | NS | 1.32 (0.70–2.73) | 1.12 (0.77–1.55) | 1.29 (0.92–1.76) | NS |
REM1
| 20q11.21 | 34.9% | 1.19 (0.42–2.43) | 1.24 (0.75–2.21) | NS | 1.29 (0.42–2.43) | 1.08 (0.60–1.51) | 1.24 (0.75–1.79) | NS |
BCL2L1
| 20q11.21 | 73.0% | 1.44 (0.97–1.98) | 1.45 (1.04–2.44) | NS | 1.50 (1.10–2.44) | 1.31 (0.97–1.76) | 1.51 (1.19–1.98) | NS |
ID1
| 20q11 | 29.2% | 1.29 (0.66–2.25) | 1.41 (0.80–3.33) | NS | 1.48 (0.77–3.33) | 1.15 (0.66–1.62) | 1.32 (1.00–1.73) | NS |
TPX2
| 20q11.2 | 27.0% | 1.26 (0.58–2.22) | 1.21 (0.71–2.35) | NS | 1.28 (0.58–2.35) | 1.13 (0.80–1.57) | 1.21 (0.97–1.75) | NS |
HCK
| 20q11–q12 | 46.0% | 1.23 (0.71–2.27) | 1.37 (0.90–3.12) | NS | 1.40 (0.71–3.12) | 1.16 (0.73–1.58) | 1.28 (0.93–1.69) | NS |
DNMT3B
| 20q11.2 | 54.0% | 1.29 (0.43–2.26) | 1.42 (0.72–2.60) | NS | 1.42 (0.43–2.55) | 1.20 (0.54–1.74) | 1.51 (0.94–2.60) | NS |
MAPRE1
| 20q11.21 | 20.6% | 1.16 (0.84–1.78) | 1.14 (0.70–1.78) | NS | 1.15 (0.70–1.78) | 1.12 (0.84–1.53) | 1.17 (0.83–1.54) | NS |
E2F1
| 20q11.2 | 44.4% | 1.35 (0.80–2.31) | 1.33 (0.93–2.26) | NS | 1.37 (0.82–2.26) | 1.21 (0.80–1.72) | 1.47 (0.95–2.31) | NS |
SRC
| 20q12–q13 | 57.1% | 1.38 (0.71–2.12) | 1.45 (0.77–2.70) | NS | 1.51 (0.88–2.70) | 1.22 (0.71–1.67) | 1.48 (1.02–2.12) | NS |
NNAT
| 20q11.2–q12 | 52.4% | 1.30 (0.47–2.50) | 1.30 (0.55–2.65) | NS | 1.36 (0.47–2.65) | 1.16 (0.69–1.78) | 1.27 (0.91–1.91) | NS |
TOP1
| 20q12–q13.1 | 63.5% | 1.57 (0.85–2.78) | 1.47 (0.88–2.40) | NS | 1.57 (1.00–2.78) | 1.29 (0.85–1.72) | 1.67 (0.94–2.69) | NS |
MYBL2
| 20q13.1 | 73.0% | 1.49 (0.58–2.79) | 1.73 (0.70–3.83) | NS | 1.79 (0.58–3.83) | 1.34 (0.58–2.51) | 1.62 (0.95–2.65) | NS |
ADA
| 20q12–q13.11 | 41.3% | 1.17 (0.42–1.80) | 1.28 (0.67–2.24) | NS | 1.32 (0.42–2.24) | 1.08 (0.53–1.74) | 1.22 (0.74–1.80) | NS |
WISP2
| 20q12–q13.1 | 52.4% | 1.31 (0.78–2.03) | 1.33 (0.78–2.62) | NS | 1.37 (0.82–2.62) | 1.18 (0.78–1.69) | 1.40 (0.95–2.03) | NS |
MMP9
| 20q11.2–q13.1 | 47.6% | 1.26 (0.76–2.06) | 1.33 (0.87–2.37) | NS | 1.38 (0.81–2.37) | 1.18 (0.76–1.72) | 1.27 (0.87–1.81) | NS |
CSE1L
| 20q13 | 49.2% | 1.40 (0.85–2.65) | 1.31 (0.88–2.54) | NS | 1.37 (0.85–2.65) | 1.25 (0.94–1.60) | 1.43 (1.11–1.82) | NS |
PTPN1
| 20q13.1–q13.2 | 65.1% | 1.46 (0.85–2.76) | 1.51 (0.87–2.62) | NS | 1.55 (0.85–2.76) | 1.32 (0.96–1.82) | 1.57 (1.04–2.54) | NS |
NFATC2
| 20q13.2–q13.3 | 55.6% | 1.31 (0.63–2.34) | 1.60 (0.77–5.60) | NS | 1.61 (0.63–5.60) | 1.27 (0.65–2.09) | 1.45 (0.83–2.50) | NS |
ZNF217
| 20q13.2 | 57.1% | 1.74 (0.99–6.65) | 1.79 (0.96–10.09) | NS | 2.06 (1.05–10.09) | 1.27 (0.96–1.82) | 1.50 (1.15–2.09) | 0.02 |
BCAS1
| 20q13.2–q13.3 | 58.7% | 1.42 (0.80–2.77) | 1.94 (0.95–12.17) | NS | 2.03 (0.80–12.17) | 1.29 (0.85–1.88) | 1.47 (1.05–2.19) | NS |
CYP24A1
| 20q13 | 60.3% | 1.47 (0.85–3.43) | 1.81 (0.80–9.16) | NS | 1.92 (0.85–9.16) | 1.26 (0.80–1.91) | 1.52 (0.96–2.27) | NS |
STX16
| 20q13.32 | 77.8% | 1.78 (0.91–5.05) | 1.81 (0.95–3.95) | NS | 1.90 (1.11–3.95) | 1.47 (0.91–2.62) | 2.03 (1.09–5.05) | 0.03 |
GNAS
| 20q13.3 | 76.2% | 2.00 (0.94–7.97) | 1.82 (0.87–4.68) | NS | 2.02 (0.94–7.97) | 1.48 (0.87–2.26) | 2.12 (1.16–4.99) | NS |
EEF1A2
| 20q13.3 | 47.6% | 1.20 (0.41–2.52) | 1.41 (0.63–2.20) | NS | 1.39 (0.41–2.52) | 1.21 (0.42–2.18) | 1.40 (0.83–2.09) | NS |
TNFRSF6B
| 20q13.3 | 49.2% | 1.20 (0.58–2.51) | 1.45 (0.82–3.21) | 0.02 | 1.41 (0.67–3.21) | 1.25 (0.58–2.01) | 1.36 (0.82–2.13) | NS |
KCNQ2
| 20q13.3 | 38.1% | 1.18 (0.49–2.59) | 1.30 (0.43–2.08) | NS | 1.27 (0.43–2.08) | 1.13 (0.52–1.85) | 1.48 (0.55–2.59) | NS |
GATA5
| 20q13.33 | 60.3% | 1.44 (0.60–4.15) | 1.58 (0.62–4.12) | NS | 1.54 (0.63–4.12) | 1.38 (0.60–2.46) | 1.82 (0.62–4.15) | NS |
FLJ20517
| 20q13.33 | 41.3% | 1.28 (0.65–3.54) | 1.34 (0.80–2.38) | NS | 1.30 (0.80–2.38) | 1.24 (0.65–1.74) | 1.60 (0.95–3.54) | NS |
UCKL1
| 20q13.33 | 39.7% | 1.13 (0.56–2.03) | 1.30 (0.67–2.86) | NS | 1.29 (0.56–2.86) | 1.13 (0.67–1.87) | 1.24 (0.85–1.65) | NS |
OPRL1
| 20q13.33 | 28.6% | 1.15 (0.49–2.70) | 1.19 (0.62–2.28) | NS | 1.18 (0.49–2.28) | 1.08 (0.51–1.57) | 1.38 (0.67–2.70) | NS |