Plasma cfDNA extraction: Which liquid biopsy kit provides more consistent recovery rates?

If the lead time is within one week, imported brands can basically be ruled out. Specialized liquid biopsy products such as QIAamp and MagMAX are not very suitable in terms of turnaround time and price. Among domestic options, you can ask local distributors whether they have stock or trial samples. Tiangen, Vazyme, Beaver, and Kangwei Century all have cfDNA extraction product lines, but be careful to distinguish "trace DNA extraction" from "circulating nucleic acid specific." The latter is more suitable for decontamination and small fragment recovery. You can also ask suppliers to provide concentration and fragment distribution data from three extractions of the same batch as a reference for stability. At around one hundred yuan, it is advisable to negotiate a small-package trial purchase rather than buying large packaging right away.

We ran a round of comparison. Stability cannot be judged by a single concentration measurement alone. I suggest you aliquot the same pooled plasma into 5 tubes, extract each separately, and measure twice with Qubit HS, focusing on CV and fragment distribution. For a budget in the hundreds of RMB and 2 mL plasma, among domestic column-based extraction methods, you can focus on products from Vazyme, Tiangen, and TransGen that have dedicated cfDNA lines; imported liquid biopsy kits generally exceed the budget and have non-short lead times. Ask clearly whether carrier RNA is included and whether the elution volume can be reduced to 30-50 μL. Qubit itself fluctuates greatly with low-concentration samples, so it is recommended to also run 2100/TapeStation to check the proportion of the 170 bp main peak.

For low-abundance mutation detection, the greater concern is fluctuating recovery rates and fragment bias. It is advisable not to focus solely on Qubit concentration; instead, spike a synthetic short DNA internal standard into the plasma, and after extraction, use qPCR or dPCR to back-calculate recovery. This better reflects true cfDNA behavior. In addition, elution volume, extraction column membrane binding capacity, centrifugation speed, and drying time all affect batch-to-batch variability; operationally, having the same person perform extraction on the same day improves comparability. Extracting from 2 mL plasma is not a large volume to begin with, so prioritize kits with small elution volumes and fewer steps. You may first request trial samples and perform 3 replicate batches before deciding, rather than purchasing in bulk directly.

We have used Q and T. Q gives stable recovery but is expensive, while T occasionally fluctuates. Domestic alternatives are worth trying, but quality control is required.

It is recommended to add an internal reference for quantification in each batch; otherwise, relying solely on Nanodrop is not accurate.