An ultrasensitive method for detecting mutations from short and rare cell-free DNA.
Biosens Bioelectron
; 238: 115548, 2023 Oct 15.
Article
in En
| MEDLINE
| ID: mdl-37542979
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.
Key words
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Biosensing Techniques
/
Cell-Free Nucleic Acids
/
Circulating Tumor DNA
/
Lung Neoplasms
Type of study:
Diagnostic_studies
Limits:
Humans
Language:
En
Journal:
Biosens Bioelectron
Journal subject:
BIOTECNOLOGIA
Year:
2023
Document type:
Article
Affiliation country:
China