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Increased detection of circulating tumor DNA by short fragment enrichment
- Source :
- Transl Lung Cancer Res
- Publication Year :
- 2021
- Publisher :
- AME Publishing Company, 2021.
-
Abstract
- Background Circulating cell-free DNA (cfDNA) detection for non-invasive diagnosis requires higher sensitivity and accuracy due to the low circulating tumor DNA (ctDNA) content. Many methods have been developed to improve detection of ctDNA, including ultra-deep sequencing or enrichment of shorter cfDNA fragments, such as those in the range of 90-150 bp. Methods Here, we developed a method for single-stranded DNA (ssDNA) library preparation with a large proportion of magnetic beads to enrich the shorter cfDNA fragments. We aimed to determine if this could increase the ctDNA content and thus improve the sensitivity of ctDNA detection by testing the method in blood samples from patients with advanced cancers (non-small cell lung cancers, esophageal squamous cell carcinoma, cholangiocarcinoma, colorectal cancer and liver cancer). Results This method was able to obtain shorter cfDNA both in commercial cfDNA references and real world clinical cfDNA samples. Plasmid simulation experiments showed that using a large proportion of magnetic beads to construct the library could obtain more ctDNA derived from shorter-fragment plasmids, which could significantly improve the detection of ctDNA especially in the low-variant allele frequency sample. In real-world clinical samples, this method may be able to increase the opportunity to obtain alteration reads from short fragments, which was important to low frequency detection. Conclusions The ssDNA library preparation with large proportion of magnetic beads could increase the opportunity to obtain alteration reads from short fragments, which is crucial for low variant allele frequency detection.
- Subjects :
- 0301 basic medicine
business.industry
Colorectal cancer
Cell-free DNA (cfDNA)
Circulating tumor DNA enrichment (ctDNA enrichment)
CtDNA detection
Single-strand DNA library preparation (ssDNA library preparation)
Variant allele
medicine.disease
Molecular biology
03 medical and health sciences
chemistry.chemical_compound
030104 developmental biology
0302 clinical medicine
Plasmid
Oncology
chemistry
Circulating tumor DNA
030220 oncology & carcinogenesis
medicine
Original Article
Liver cancer
business
Lung cancer
Allele frequency
DNA
Subjects
Details
- Language :
- English
- Database :
- OpenAIRE
- Journal :
- Transl Lung Cancer Res
- Accession number :
- edsair.doi.dedup.....9174c8c0bd7baebfa737ae753ee00504