Cell-free DNA/RNA

What are Cell-Free DNA/RNA Co-Extraction Kits?

Cell-free DNA/RNA co-extraction kits simultaneously isolate circulating cell-free DNA (cfDNA -- ctDNA fragments of 130-250 bp, apoptotic DNA) and cell-free RNA (cfRNA -- microRNAs, lncRNAs, exosomal RNA, circulating mRNA fragments) from the same plasma, serum, or urine sample without phenol-chloroform or protein precipitation, delivering both analytes for parallel liquid biopsy genomic and transcriptomic analysis from a single 1-4 ml blood draw. Unlike dedicated cfDNA kits that miss circulating RNA species, or cfRNA kits that under-recover short cfDNA fragments, co-extraction kits are formulated to bind both nucleic acid classes - including protein-bound RNA, exosomal RNA, and miRNA - from cell-free matrices where total nucleic acid concentration is 1-100 ng/ml. Use a cfDNA/cfRNA co-extraction kit when your liquid biopsy workflow requires both somatic mutation analysis (ctDNA sequencing) and RNA expression profiling (circulating miRNA or cfRNA-seq) from the same blood draw, or when sample volume is limited and splitting between separate DNA and RNA kits would leave insufficient input for either.

What you will find:

• Quick-cfDNA/cfRNA™ Serum & Plasma Kit: An efficient spin-column setup tailored for sample volumes up to 3 ml, providing reduced sequence bias and recovering as much as 515 times more microRNA.

• High-Purity Elution Technology: Nuclease-free methods enabling the separate or co-elution of nucleic acids, ensuring transfection-grade purity for delicate bioinformatics and RT-qPCR uses.

How to Choose a cfDNA/cfRNA Co-Extraction Kit

Input Volume and Assay Sensitivity

cfDNA concentration in cancer patient plasma ranges from 1-1,000 ng/ml depending on tumor stage and type; circulating miRNA concentration is typically 1-100 pg/ml. For low-MAF ctDNA detection (<0.1%), 2-4 ml plasma input is required to obtain sufficient copies for ddPCR or ultra-deep sequencing. For cfRNA profiling only, 200 μL-1 mL is sufficient for miRNA RT-qPCR panels. The Zymo Quick-cfDNA/cfRNA Kit scales linearly up to 3 ml input.

Co-Elution vs. Separate Fractions

The Zymo Quick-cfDNA/cfRNA Serum & Plasma Kit offers the option to co-elute DNA and RNA into a single fraction or to collect separate fractions. Co-elution maximizes nucleic acid recovery in the smallest volume -- optimal for low-abundance targets; separate fractions are needed when DNA-specific (bisulfite sequencing, whole-exome) and RNA-specific (rRNA depletion, miRNA-seq library) downstream protocols cannot use the same input.

miRNA Recovery

Circulating miRNAs (18-22 nt) are small, low-abundance, and easily lost during standard DNA extraction. Confirm the co-extraction kit explicitly recovers small RNAs <200 nt from plasma. The Zymo Quick-cfDNA/cfRNA Kit recovers up to 515x more microRNA than conventional phase-separation methods -- a validated difference confirmed in the Zymo product datasheet.

Phenol-Free Chemistry

For high-throughput liquid biopsy programs, phenol-free kits eliminate fume-hood requirements and toxic waste handling. The QIAGEN ccfDNA/RNA Kit and Zymo Quick-cfDNA/cfRNA Kit are both phenol-free; automated protocols using these kits can process large cohort batches without hazardous chemical handling steps.

Pre-Analytical Standardization

cfDNA/cfRNA concentrations vary with blood collection tube type, time-to-processing, and centrifugation protocol. Standardize on EDTA tubes + two-spin plasma preparation (300xg then 16,000xg) and process within 6 hours of collection or store at -80 degrees C. For samples requiring extended transport, Streck Cell-Free DNA BCT or cfRNA preservation tubes stabilize both analytes at room temperature for up to 7 days before extraction.

Specifications Context

The Zymo Quick-cfDNA/cfRNA Serum & Plasma Kit enables simple spin-column isolation of all circulating cell-free DNA and RNA from serum, plasma, and biological fluids, recovering protein-bound, exosomal, miRNA, and other small RNA in addition to cfDNA. Cell-free nucleic acids scale linearly with input volume up to 3 ml. A 2022 digital PCR comparative study (PMC9805675) evaluated multiple cfDNA/cfRNA co-purification kits across plasma input volumes of 0.06-4 ml, finding that combined cfDNA/cfRNA quantification produces higher total nucleic acid concentrations than parallel separate quantification. cfDNA/cfRNA multi-omic liquid biopsy is an active area of clinical translational research for non-invasive cancer diagnosis and treatment monitoring, with studies underway at MD Anderson Cancer Center and Vanderbilt University using co-extraction formats to maximize information per blood draw.

Close the gap between liquid biopsy and groundbreaking discovery—reach out to MBP Inc. now to obtain a quote for your next-generation sequencing requirements.