NEXTFLEX Cell Free DNA-Seq Library Prep Kit 2.0

Low-Input cfDNA Performance

Generate deep-coverage libraries from just 10 ng of plasma- or serum-derived cfDNA, the amount typically recovered from under 3 mL samples. Our chemistry preserves the native cfDNA fragment profile, which presents 5′-phosphate and 3′-hydroxyl ends typical of nuclease cleavage. That means you can profile early-stage cancers or run cell-free fetal DNA tests on these small input samples without resorting to pre-amplification or whole-genome amplification that can skew variant calls.

Figure 1: Electropherograms of cfDNA libraries prepared from 10 ng plasma cfDNA with the NEXTFLEX Cell Free DNA-Seq Kit 2.0 show a clean ~320 bp peak, negligible adapter-dimer, and highly consistent low-input performance.

Accelerated cfDNA Workflow Efficiency

A consolidated, single-tube end-repair/A-tailing step merges multiple enzymatic reactions, while magnetic-bead clean-ups are tuned for fast binding and elution. The result is a roughly 2-hour start-to-finish protocol with minimal hands-on pipetting, short enough to move from sample intake to sequencer load in the same shift. Less bench time frees staff for higher value tasks, reduces pipetting error, and helps labs hit aggressive turnaround targets.

High-Complexity Libraries with Uniform Genome Coverage

Optimized ligation chemistry and precisely calibrated adapter stoichiometry maximize single-insert tagging efficiency, minimizing adapter-dimer formation and PCR duplicates while enriching the pool of unique cfDNA molecules that reach the flow cell. At the same time, a balanced buffer matrix, tuned for salt, PEG, and enzyme concentrations, suppresses sequence-dependent bias, delivering uniform coverage across GC-rich, AT-rich, and repetitive regions from telomere to telomere. Together, the resulting high library complexity and even genome representation drive deeper usable read depth and sharper quantitative resolution, enabling confident detection of low-frequency SNVs, indels, CNVs, and aneuploidies, essential for minimal-residual-disease monitoring, clonal evolution analysis, and other applications that demand analytical sensitivity.

Scalable Multiplexing & Error Correction

Select from 1,536 NEXTFLEX Unique Dual Index (UDI) pairs to pool thousands of samples per flow cell with negligible index crosstalk or deploy the 96-plex NEXTFLEX® UDI-UMI set when single-molecule error correction is needed for ultra-rare variant or MRD applications. Both index formats slot seamlessly into Illumina® and Element Biosciences® workflows, so you can dial in either throughput or precision without altering the core protocol.

Balanced cfDNA pools without extra QC steps

For high-plex cfDNA studies, apply NEXTFLEX NGS Library Normalization Beads post-PCR to equalize library molarity and pool directly, saving time and reducing variability in per-sample reads. On-bead normalization preserves the native cfDNA fragment profile and supports consistent, deep coverage at scale.

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