Short‐DNA Specific Blocker PCR for Efficient and Simple Enrichment of Cell Free Fetal DNAs with Short Lengths

Abstract

Main observation and conclusionAs an innate characteristic, DNA length has attracted more and more attention. The length of some important biomarkers such as ctDNA (Circulating tumor DNA) and cffDNA (Cell free fetal DNA) is shorter than that of cell‐free DNA. Researchers have utilized the difference in length to increase the abundance of ctDNA or cffDNA in total cell‐free DNA to overcome the difficulties in detection due to their low abundance. They have developed short‐stranded DNA enrichment technology, which complemented the blind spots of the application range of typical enrichment technology based on DNA sequence differences. However, the existing short‐stranded DNA enrichment technology cannot possess high efficiency and simplicity simultaneously. Herein, we developed the SSB‐PCR (Short‐DNA Specific Blocker PCR) technology to enrich the short‐stranded DNA in an efficient and simple way. Through theoretical and experimental verification, it was proved that this method could increase the abundance of short‐stranded DNA by more than 10 times. Based on this, we have found an application scenario for this method in cffDNA enrichment. Further, a procedure was established to perform a reliable diagnosis of the genotype of cffDNA samples. We believe that this method has great potential to achieve accurate, fast, and cost‐effective non‐invasive prenatal testing.