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Table 1 Association of clinicopathological parameters with PITX3 methylation in HNSCC patients of the training cohort (n = 326) and the validation cohort (n = 528)

From: PITX3 DNA methylation is an independent predictor of overall survival in patients with head and neck squamous cell carcinoma

  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)   
  1. 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/
  2. NA data not available
  3. asignificance