A novel method for extracting circulating cell‐free DNA from whole blood samples and its utility in the non‐invasive prenatal test. (5th August 2022)

• Record Type: Journal Article
• Authors: Zhong, Hongbin; Zeng, Liuhong; Tao, Mengyuan; Ye, Yuchen; Wang, Yanqi; Hou, Lei; Wu, Miaofeng; Liu, Hui; Zhang, Hongyun; Tang, Meifang
• Is Part Of: Prenatal diagnosis. Volume 42:Number 9(2022)
• Page Start: 1173
• Page End: 1181
• Publication Date: 2022-08-05
• Subjects: Prenatal diagnosis -- Periodicals; Fetus -- Diseases -- Diagnosis -- Periodicals; Electronic journals; 618.32075
• DOI: 10.1002/pd.6212
• Languages: English
• ISSNs: 0197-3851

Abstract

Abstract: Objective: We verified a magnetic bead‐based, simple, and fast method for circulating cell‐free DNA (cfDNA) extraction from whole blood samples(CEWB) and characterised its utility in non‐invasive prenatal testing (NIPT). Method: We extracted cfDNA from both plasma and whole blood of the patients using CEWB and compared it to that extracted using a Qiagen extraction kit; droplet digital polymerase chain reaction test was used to calculate the fragment size bias. In all, 304 samples were used for NIPT. Results: The CEWB group (mean ± standard deviation [SD]: 4.34 ± 0.41 ng/ml plasma) reported less DNA weight yield than the Qiagen group (4.90 ± 0.50 ng/ml plasma). There was no significant difference between the CEWB group and the Qiagen group in the gene fragments (136 bp: p = 0.064 and 420 bp: p = 0.534). In a parallel cohort study to characterise the utility of the CEWB method in NIPT, the treatment group extracted by CEWB showed a sensitivity of 100%, a specificity of 99.65%, and a positive predictive value of 95%. Conclusions: This study demonstrated that CEWB achieves an acceptable yield of DNA without contamination from genomic DNA. Subsequent clinical experiments in a parallel cohort indicated its utility for NIPT. Key points: What's already known about this topic? Extraction of cell‐free DNA (cfDNA) from blood or plasma for non‐invasive prenatal testing is currently the standard method in use, but the centrifugation and transfer of supernatant required by this method is cumbersome, difficult, time‐consuming, and costly. What does this study add? In our method, the cfDNA is directly extracted from blood, simply by adding the blood to magnetic beads for cfDNA extraction. Performance validation of the method was done to determine method reliability.