A Discriminant DNA Marker Panel for Detection of Colorectal Adenomas

Abstract

Purpose: On well characterized tissue, to compare adenoma detection rates by a set of DNA markers used in previous clinical studies (Version 1) with a novel panel of markers (Version 2). Methods: Assays were performed in blinded fashion on Qiagen-extracted DNA from colonoscopy-obtained tissue comprising 50 paraffin-fixed adenomas ≥ 1.0 cm and control mucosal biopsies from eleven healthy subjects without pathology. Median age was 63 (range 50–80) for patients and 67 (51–72) for controls; patients and controls comprised 60% and 55% men, respectively. Median adenoma size was 1.1cm (range 1.0–5.0), 22 were proximal to splenic flexure, and 49 had low grade dysplasia only. Version 1 (V1) is made up of a panel of the 22 markers including selected sequence specific mutations within APC, Kras, p53, and Bat-26 genes (N Engl J Med 2004: 351:2704). Version 2 (V2) assays a panel of 7 markers including the detection of de novo mutations within APC-Mutator Cluster Region (APC-MCR), P1K3CA-Exons 9 and 20 (P1K9, P1K20), and B-catenin; point mutation on BRAF; and hypermethylation on vimentin 29 (Vi29) and HLTF. Results: At specificity cut-offs of 100% for all component markers, sensitivity for adenomas by V1 was 62% and by V2 was 94% (p = 0.0003). For V1, component marker yields were APC (38%), Kras (38%), p53 (4%), Bat-26 (4%). For V2, component yields were APC-MCR (74%), Vi29 (50%), HLTF (38%), P1K 9 (14%), P1K 20 (4%), BRAF (4%), and B-catenin (4%). Combinations of markers are compared against V1 in Table.Table: Marker CombinationsConclusions: Wit a panel of just a few candidate DNA markers, high tissue sensitivity for adenomas can be achieved with high specificity. APC-MCR is a particularly informative single marker for adenomas. The improved yield over V1 with substantially fewer markers could influence simplicity and cost of an applied screening assay.