Q40 sequencing reduces costs and enhances detection of low- frequency somatic variants

Abstract Background High quality scores (Q-scores) are critical for sequencing accuracy, yet the impact of Q40-achieving sequencing technologies (99.99% accuracy) on detecting subtle biological variations remains unvalidated. Results Using a comprehensive set of well-established DNA/RNA reference materials (Quartet, NIST-RM8398, SEQC2-HCC1395/BL, MAQC, and ERCC), we benchmarked Q40 sequencing (Element AVITI) against the conventional Q30 standard (Illumina NovaSeq 6000). Q40 reduced required sequencing depth by 33.3% while maintaining accuracy for germline variants (20× vs. 30×) and somatic SNV/InDels (60× vs. 90×). Crucially, Q40 enhanced sensitivity for low-frequency somatic mutations (VAF ≤ 0.2) by 33.3% and 12.6-fold higher CNV detection reproducibility (77.7% vs. 5.7%) with Q40 at 30× depth, directly reducing per-sample costs by 30-50%. In addition, Q40 improved the discriminatory resolution between biological samples with 13.1% SNR enhancement. Conclusions This work establishes Q40 as a cost-effective solution for enhancing rare variant detection in precision oncology applications such as liquid biopsy and minimal residual disease monitoring.