Different primers for diagnosing circulating cell-free DNA of colorectal cancer

Abstract

Background Cell-free DNA (cfDNA) primers have been designed to screen for cancer diagnosis, but the results have been inconsistent. The study aimed to compare different primers for diagnosing cfDNA of colorectal cancer (CRC). Methods Peripheral blood specimens were collected from 71 patients with CRC and 20 patients with proliferative intestinal polyps. Quantitative polymerase chain reaction (q-PCR) was used to detect the concentration of cfDNA of these primers, including ALU elements (ALU), Beta-actin (ACTB), and glyceraldehyde-3-phosphate dehydrogenase (GAPDH). The receiver operator characteristic curve (ROC) was performed to analyze the diagnostic value. Results The concentration of cfDNA in plasma of the CRC group determined by primers ALU and GAPDH was significantly higher than that of the intestinal polyp group (P<0.05). There was no significant difference in cfDNA level determined by primer ACTB between the CRC group and the intestinal polyp group (P>0.05). The area under curves (AUCs) of ALU, GAPDH, and ACTB were 0.734, 0.800, and 0.503, respectively. Conclusions The GAPDH and ALU in plasma are expected to be sensitive indicators for the diagnosis of CRC.

The level and integrity of plasma circulating cell-free DNA in patients with primary multiple myeloma

“…The level of cfDNA in different studies varies, which may be explained by the fact that there are no unified standards for specimen type, specimen collection process, detection method, and accuracy of test equipment. Generally, when quantitatively detecting cfDNA, each laboratory will choose different reference genes, such as β-actin, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and long interspersed element-1 (LINE-1) ( 10 , 11 ), etc., whose common feature is that they can exist and express stably. However, due to their different copy numbers, it is possible for the test results to vary.…”

The impact of preanalytical variables on the analysis of cell-free DNA from blood and urine samples

“…By detecting housekeeping genes ( Aucamp et al, 2016 ) or noncoding repetitive sequences ( Hussein et al, 2019 ) in cfDNA and fitting the standard curve with a reference substance ( Tang et al, 2020 ), absolute cfDNA concentrations can be quantified using PCR-based methods. Frequently used reference genes include TERT ( Akuta et al, 2020 ), GAPDH ( Salinas-Sanchez et al, 2021 ), EGFR ( Sugimoto et al, 2023 ), KRAS ( Berchuck et al, 2022 ), and ALU ( Shi et al, 2020 ). However, the lack of unified reference genes results in significant variations in the quantitative results of PCR-based methods, hindering efficient comparisons across different studies ( Devonshire et al, 2014 ).…”

Pathogenesis and biomarkers of colorectal cancer by epigenetic alteration

“…A recent case-control study identified 3 novel lncRNAs, XLOC_006844, LOC152578, and XLOC_000303, using highthroughput lncRNA microarray. These were found to be upregulated in CRC patients when compared to HCs, with AUCs of 0.919 and 0.975 in the training and validation sets respectively, hinting at their potential as a biomarker panel for CRC detection [ 160 ]. Gharib et al [ 161 ] examined the levels of a panel of 10 significantly dysregulated lncRNAs (CCAT1, CCAT2, H19, HOTAIR, HULC, MALAT1, PCAT1, MEG3, PTENP1, and TUSC7) identified in stool samples from 150 CRC patients.…”