We observed significant DNA hypermethylation in AIS compared to AAH for seven loci: 2C35, EYA4, HOXA1, HOXA11, NEUROD1, NEUROD2 and TEMFF2. 2C35 was identified through restriction landmark genomic scanning to be hypermethylated in lung cancer [43] as well as in primitive neuroectodermal tumors, gliomas and colon cancer, and these observations were the basis for the design of MethyLight probe/primer set and our examination of this locus in lung cancer. Here, HOXA1 is linked to lung cancer.