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An ultrasensitive method for detecting mutations from short and rare cell-free DNA.
- Source :
-
Biosensors & Bioelectronics . Oct2023, Vol. 238, pN.PAG-N.PAG. 1p. - Publication Year :
- 2023
-
Abstract
- Circulating tumor DNA (ctDNA) was short and rare, making the detection performance of the current targeted sequencing methods unsatisfying. We developed the One-PrimER Amplification (OPERA) system and examined its performance in detecting mutations of low variant allelic frequency (VAF) in various samples with short-sized DNA fragments. In cell line-derived samples containing sonication-sheared DNA fragments with 50-150 bp, OPERA was capable of detecting mutations as low as 0.0025% VAF, while CAPP-Seq only detected mutations of >0.03% VAF. Both single nucleotide variant and insertion/deletion can be detected by OPERA. In synthetic fragments as short as 80 bp with low VAF (0.03%-0.1%), the detection sensitivity of OPERA was significantly higher compared to that of droplet digital polymerase chain reaction. The error rate was 5.9×10-5 errors per base after de-duplication in plasma samples collected from healthy volunteers. By suppressing "single-strand errors", the error rate can be further lowered by >5 folds in EGFR T790M hotspot. In plasma samples collected from lung cancer patients, OPERA detected mutations in 57.1% stage I patients with 100% specificity and achieved a sensitivity of 30.0% in patients with tumor volume of less than 1 cm3. OPERA can effectively detect mutations in rare and highly-fragmented DNA. [ABSTRACT FROM AUTHOR]
Details
- Language :
- English
- ISSN :
- 09565663
- Volume :
- 238
- Database :
- Academic Search Index
- Journal :
- Biosensors & Bioelectronics
- Publication Type :
- Academic Journal
- Accession number :
- 170084935
- Full Text :
- https://doi.org/10.1016/j.bios.2023.115548