A scoping review of DNA methylation biomarkers for non-invasive detection of colorectal cancer at the CpG site level.

Colorectal cancer screening programs are well-established worldwide, but most applied methods are invasive, have insufficient accuracy, or have a low uptake rate. Several studies have reported DNA methylation biomarkers as promising alternatives to the established diagnostic tools. However, the current reviews on the topic lack information on the exact location of the CpG sites in the analyzed biomarker. As adjacent CpG sites may exert distinct clinical effects, precise identification of the specific CpG sites analyzed is essential for establishing clinical relevance and achieving consensus across studies. This scoping review aimed to uncover the accessibility of CpG site information in the scientific literature, map the CpG sites of the markers, and summarize the accuracy data from studies reporting on the same group of CpG sites. We systematically searched MEDLINE®, EMBASE, and Scopus, and the last search was conducted on the 13th of March 2025. A total of 6180 identified records were screened in Covidence, resulting in the inclusion of 149 articles. Four (2.7%) papers held precise CpG information. Locations of the CpG sites were obtained for additionally 109 (73.2%) papers by running a BLAST search using oligonucleotide sequences from the papers. For the remaining 36 (24.1%) papers without any information to locate the CpG sites, 26 used commercial kits. The three most frequently studied genes were SEPTIN9, SDC2, and SFRP2. We mapped the CpG sites of these to identify recurring sites across the studies. Sixteen of 22 papers analyzing SEPTIN9 had three CpG sites in common, seven of 19 papers analyzing SDC2 had consensus on a single CpG site, while seven of 13 studies reporting on SFRP2 had analyzed eight identical CpG sites. Lastly, we grouped all studies based on whether they targeted the same group of CpG sites within each gene. For genes examined in at least two papers, we summarized the reported accuracy measurements by presenting the average, minimum, and maximum values for each CpG group. This scoping review identifies a profound lack in the reporting of the CpG sites analyzed for non-invasive detection of CRC, which poses a challenge for the comparison of findings across studies.