For lung cancer ctDNA testing, is digital PCR or an NGS panel more cost-effective?

Hospital clinical laboratories must pay special attention to registration certificates and reimbursement codes when launching tests. If digital PCR reagents are billed as PCR items, the explanation and medical insurance coordination are usually easier than for NGS panels. NGS involves price filing, patient informed consent, and genetic counseling processes, resulting in high startup costs. Performance validation can be done first: use known T790M-positive/negative plasma gradient dilutions to confirm the limit of detection and precision, then conduct parallel comparison on 30-50 clinical samples. If cost is a concern, orders can initially be limited to patients with clinical progression or resistance to first-generation EGFR-TKIs to reduce unnecessary testing. The difference between imported and domestic reagents is not as large as imagined; the key is batch-to-batch stability and reproducible standard curves.

Eighty cases per month is not a small volume. When calculating costs, besides reagents, you must include extraction, library preparation/droplet generation, positive and negative controls, replicate wells, failed reruns, bioinformatics analysis, and manual reporting time. Digital PCR provides fast reports for a single locus, has simple quality control, and is easy for the clinical laboratory to scale up; NGS small panels may have a higher reagent unit price, but a single run can cover multiple targets, so the cost per marker is not necessarily high. It is recommended to run a parallel comparison using the same batch of 30 samples and calculate the effective report cost per case yourself, rather than being led by a distributor's per-well or per-run quote. For units with large sample volumes, it is usually more cost-effective to use digital PCR for screening and NGS for supplementation.

T790M is a well-established point mutation. If testing only this single site, dPCR has advantages in sensitivity and absolute quantification, and the per-sample testing cost is not necessarily higher than NGS; the advantage of a small NGS panel lies in simultaneously covering other EGFR mutations and bypass resistance genes. In clinical resistance monitoring, the greatest concern is focusing only on T790M, as patients may develop C797S, MET amplification, etc. after progression. We suggest that you first consider the clinical pathway: after first-line resistance, use dPCR to rapidly screen for T790M, and for those who are negative but highly suspected of having complex resistance mechanisms, follow up with a small NGS panel. In this way, the total cost is more controllable.

Known sites are cheaper and faster with dPCR, but discovering new mutations still requires NGS.

Hospital billing depends on the clinical scenario: multi-gene panels are cost-effective for initial screening, while dPCR is more practical for drug resistance monitoring.