Enrichment of mutant KRAS alleles in pancreatic juice by subtractive iterative polymerase chain reaction

Abstract

The detection of mutant tumor genes holds great promise for an early diagnosis of primary tumors and residual malignant disease. When few tumor cells are present with an excess of nonmalignant cells of the same lineage, the excess of wild-type alleles over mutant tumor alleles presents an analytical problem. The subtractive iterative PCR (siPCR) assay presents a new approach to solving this problem. To achieve an enrichment of mutant alleles, wild-type alleles are removed by differential hybridization to complementary oligonucleotides spanning the region of the gene in which point mutations are expected. The nonbound fraction is reamplified by PCR. By iterating this process, mutant alleles can be detected in the presence of an excess of wild-type alleles with high sensitivity. To prove the feasibility of siPCR, pancreatic juice samples were analyzed for KRAS mutations. Pancreatic juice obtained from patients with pancreatic carcinoma or chronic pancreatitis during endoscopic retrograde cholangiopancreatography was analyzed for point mutations in codons 12 and 13 of the KRAS gene. In each of six samples from tumor patients, mutations in codon 12 were detected. One of nine samples from patients with chronic pancreatitis scored positive.