Table 2.

Sensitivity and specificity of a 7-gene panel in identifying BRAF-mutant, CIMP-H, and/or MLH1-silenced colon cancers from TCGA

A. Individual genesa
GeneSensitivitySpecificity
ZIC50.6770.887
ZIC20.5480.854
FSCN10.5160.947
SEMG10.4840.960
TRNP10.4840.947
CRYBA20.4190.960
MUC60.2580.987
ANXA100.1940.974
CLDN10.0650.881
B. Seven-gene panelb
Minimum # genes positiveSensitivitySpecificity
10.9350.722
20.8390.874
30.6130.960
40.4190.987
50.2901.000
60.1941.000
70.0971.000
  • NOTE: Normalized RNA-Seq gene expression data (RPKM) for each of the 7-gene panel was downloaded from the cBioPortal for Cancer Genomics using the CGDS-R package http://www.cbioportal.org/cgds_r.jsp. A total of 186 TCGA colon cancers had mRNA expression, BRAF mutation, methylation subtype, and MLH1 methylation data available. Thirty-one of 186 colon cancers (17%) were BRAF mutated, CIMP-H, and/or MLH1 silenced. The majority of these cancers (20/31; 64%) had two or more of these DNA alterations, highly suggestive of colon cancers developing via the serrated pathway.

  • aThe sensitivity and specificity of each of our 7-gene panel, and two previously described SSA/P gene markers (ANXA10, CLDN1), in identifying BRAF-mutant, CIMP-H, and/or MLH1-silenced colon cancers.

  • bThe sensitivity and specificity of one or more genes from our 7-gene panel showing a ≥2-fold increased expression in serrated pathway cancers compared with the average of all colon cancers.