Protocol 4A: PANAMAX 48 extraction of plasma cfDNA

What the automated extractor does, what comes out, and why the exact kit configuration matters

Instrument role

PANAMAX 48 is an automated magnetic-bead nucleic-acid extraction platform. Lysis releases nucleic acids, they bind to magnetic particles under kit-specific conditions, programmed washes remove contaminants, and purified material is eluted.

Input	Machine action	Physical output	Recorded data
plasma aliquot	bind–wash–elute magnetic-bead program	purified cfDNA eluate	run ID, kit/lot, positions, volume, flags

The instrument does not produce sequence reads or methylation calls. Those appear only after library preparation, NovaSeq sequencing, alignment, and cytosine extraction.

WarningKit identity must be locked before this becomes an SOP

PANAMAX 48 supports kit-specific programs. The exact plasma-cfDNA kit name, catalogue number, validated input volume, elution volume, software/program version, and intended sample type must be copied from the study laboratory record. A viral DNA/RNA protocol is not automatically a validated cfDNA protocol.

QC gate

Track extraction blanks, positive/process controls where appropriate, eluate volume, fluorometric yield, fragment profile, contamination/hemolysis context, freeze–thaw history, and replicate concordance. Avoid relying on absorbance ratios alone at cfDNA concentrations.

PANAMAX example documentation confirms the platform’s automated kit/program model but does not substitute for this study’s cfDNA kit manual.

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