Table 1.
Association of clinicopathological parameters with PITX3 methylation in HNSCC patients of the training cohort (n = 326) and the validation cohort (n = 528)
| Training cohort | Validation cohort (TCGA) | |||||
|---|---|---|---|---|---|---|
| Variable | No. (%) of patients | Mean PITX3 methylation (%) | p value | No. (%) of patients | Mean PITX3 methylation (%) | p value |
| All patients | 326 (100) | 69.0 | 528 (100) | 36.5 | ||
| Sex | 0.58 | 0.42 | ||||
| Female | 74 (22.7) | 68.0 | 142 (26.9) | 35.6 | ||
| Male | 252 (77.3) | 69.3 | 386 (73.1) | 36.8 | ||
| Age (years) | 0.16 | 0.32 | ||||
| Mean | 62.2 | 60.9 | ||||
| Median | 62 | 0.55 | 61 | 0.48 | ||
| n < Median | 132 (40.5) | 70.3 | 282 (53.4) | 36.1 | ||
| n > Median | 119 (36.5) | 71.7 | 245 (46.4) | 36.9 | ||
| Unknown | 75 (23.0) | 1 (0.2) | ||||
| Smoking status | 0.91 | 0.92 | ||||
| Non-smoker | 25 (7.7) | 69.8 | 122 (23.1) | 36.7 | ||
| Smoker | 178 (54.6) | 70.2 | 393 (74.4) | 36.6 | ||
| Unknown | 123 (37.7) | 13 (2.5) | ||||
| Pack years | 0.17 | 0.60 | ||||
| <40 | 92 (28.2) | 72.0 | 168 (31.8) | 36.5 | ||
| >40 | 46 (14.1) | 76.0 | 130 (24.6) | 37.3 | ||
| Unknown | 188 (57.7) | 230 (43.6) | ||||
| Alcohol consumption | 0.10 | 0.37 | ||||
| Yes | 81 (24.8) | 74.8 | 352 (66.7) | 37.0 | ||
| No | 47 (14.4) | 69.8 | 165 (31.3) | 35.9 | ||
| Unknown | 198 (60.7) | 11 (2.1) | ||||
| Tumor site | 0.023a | 0.017a | ||||
| Oral cavity | 50 (15.3) | 69.0 | 320 (60.6) | 36.6 | ||
| Oropharynx | 139 (42.6) | 72.0 | 81 (15.3) | 40.2 | ||
| Hypopharynx | 22 (6.7) | 72.8 | 10 (1.9) | 33.6 | ||
| Larynx | 95 (29.1) | 67.0 | 117 (22.2) | 33.9 | ||
| Unknown | 20 (6.1) | |||||
| pT | 0.80 | 0.22 | ||||
| T1/T2 | 160 (49.1) | 69.8 | 190 (36.0) | 34.9 | ||
| T3/T4 | 119 (36.5) | 69.2 | 276 (52.3) | 36.5 | ||
| Unknown | 47 (14.4) | 62 (11.7) | ||||
| pN | 0.006a | <0.001a | ||||
| N0 | 128 (39.3) | 66.3 | 180 (34.1) | 32.8 | ||
| N1/2/3 | 173 (53.1) | 72.0 | 240 (45.5) | 37.7 | ||
| Unknown | 25 (7.7) | 108 (20.5) | ||||
| p16 | 0.013a | 0.015a | ||||
| Negative | 200 (61.3) | 66.2 | 74 (14) | 33.1 | ||
| Positive | 51 (15.6) | 73.7 | 41 (7.8) | 40.0 | ||
| Unknown | 75 (23.0) | 413 (78.2) | ||||
| Grade | 0.40 | 0.33 | ||||
| 1 | 7 (1.8) | 62.3 | 63 (11.9) | 34.7 | ||
| 2 | 199 (49.9) | 70.1 | 311 (58.9) | 36.3 | ||
| 3 | 107 (26.8) | 68.8 | 125 (23.7) | 37.5 | ||
| 4 | 0 (0) | 7 (1.3) | 43.5 | |||
| Unknown | 86 (21.6) | 22 (4.2) | ||||
| Surgical margin | 0.18 | 0.40 | ||||
| Negative | 225 (69.0) | 69.7 | 407 (77.1) | 36.0 | ||
| Positive | 41 (12.6) | 65.6 | 60 (11.4) | 37.6 | ||
| Unknown | 60 (18.4) | 61 (11.6) | ||||
| Second tumor | 0.070 | NA | ||||
| Yes | 38 (11.7) | 72.7 | ||||
| No | 140 (42.9) | 77.9 | ||||
| Unknown | 148 (45.4) | 528 (100) | ||||
| Vascular invasion | 0.083 | 0.072 | ||||
| Yes | 22 (6.7) | 63.0 | 124 (23.5) | 38.4 | ||
| No | 170 (52.1) | 70.1 | 232 (43.9) | 35.6 | ||
| Unknown | 134 (41.1) | 172 (32.6) | ||||
Mann-Whitney U test for sex, age (dichotomized), smoking status, pT, p16, surgical margin, second tumor, lymphovascular invasion, and pack years; One-way ANOVA for alcohol consumption, lymph node, grade, and tumor site; Spearman’s rank correlation for age. Results from the validation cohort are entirely based upon the data generated by the TCGA Research Network: http://cancergenome.nih.gov/
NA data not available
asignificance