Table 1.

Somatic alteration rate comparison between AppKY and TCGA of Lung SQCC

Hugo symbolaAppKY (%)TCGA (%)Pbq-valuec
IDH1Embedded Image11.80%1.10%0.0020.039
PCMTD1Embedded Image17.60%3.90%0.0020.045
DEK5.90%0.00%0.0110.200
NFE2L2Embedded Image3.90%15.20%0.0320.584
CDKN2AEmbedded Image3.90%14.60%0.0500.830
HOXA113.90%0.00%0.0490.830
TP53Embedded Image68.60%80.90%0.0821.000
PTENEmbedded Image5.90%7.90%0.7701.000
PIK3CAEmbedded Image11.80%15.70%0.6551.000
KEAP1Embedded Image9.80%12.40%0.8061.000
KMT2DEmbedded Image9.80%19.70%0.1421.000
HLA-AEmbedded Image7.80%3.40%0.2361.000
NOTCH1Embedded Image11.80%8.40%0.4241.000
RB1Embedded Image2.00%6.70%0.3071.000
RNF435.90%1.70%0.1261.000
MLLT107.80%3.90%0.2691.000
STK113.90%1.70%0.3091.000
POT15.90%2.20%0.1861.000
ATP2B33.90%2.20%0.6171.000
HRAS5.90%2.80%0.3811.000
HOXA133.90%0.60%0.1251.000
  • NOTE: The comparison focuses on genes that were identified as significantly mutated based on the MutSigCV analysis in at least one of the two cohorts.

  • aEmbedded Image: significantly mutated in AppKY only; Embedded Image: significantly mutated in TCGA only; Embedded Image: significantly mutated in both cohorts.

  • bThe P value was based on the Fisher exact test to compare percentages of samples that had somatic alterations (somatic mutations or SCNAs) in the two cohorts.

  • cThe q-value was based on the Benjamini–Hochberg procedure. Genes with significant differences (FDR<0.2) in the alteration rate are shown in bold.