Introduction
Formalin-fixed paraffin-embedded (FFPE) tissues represent an important source of archival clinical material for molecular analysis. However, nucleic acids recovered from FFPE samples are often fragmented and contain a high proportion of short DNA fragments generated during fixation and long-term storage.
The MagPure FFPE DNA Kit (D6323B) is designed for magnetic bead-based purification of genomic DNA from FFPE tissue sections. The binding chemistry enables efficient recovery of DNA fragments suitable for downstream molecular workflows while allowing selective removal of very short degraded fragments generated during FFPE processing.
This characteristic can be beneficial in workflows where excessive small DNA fragments may interfere with downstream sequencing or library preparation steps. Purified DNA can be directly used for PCR amplification, mutation analysis, or sequencing-based applications.
For laboratories requiring a column-based workflow for FFPE DNA extraction, the HiPure FFPE DNA Kit (D3126) provides a membrane purification system within the Magen FFPE product line.
For applications requiring simultaneous recovery of both DNA and RNA from the same FFPE sample, the MagPure FFPE DNA/RNA Kit (R6327) provides a magnetic bead-based co-extraction workflow.
When higher DNA purity is required for inhibitor-sensitive downstream assays, the MagPure FFPE DNA Kit (High Pure) (D6323D) offers an alternative purification chemistry optimized for removal of pigments and contaminants.
Details
Specifications
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Features
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Specifications
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Main Functions
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Isolation total DNA from FFPE using high bind beads
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Applications
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RT-PCR, northern blot, poly A purification, nucleic acid protection and in vitro translation, etc.
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Purification technology
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Magnetic beads technology
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Process method
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Manual or automatic
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Sample type
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Large quantities of solids
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Sample amount
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Appropriate
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Elution volume
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≥50μl
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Time per run
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30 - 120 minutes
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Extraction Principle
Samples are first deparaffinized and digested with Proteinase K to release nucleic acids from crosslinked tissue matrices. Heat treatment partially reverses formaldehyde-induced crosslinking, improving DNA accessibility.
Following lysis, DNA molecules bind to magnetic particles under chaotropic salt conditions. By adjusting the amount of binding buffer during the adsorption step, fragmented DNA molecules within the range of approximately 100–300 bp can be selectively removed from the lysate. This selective binding strategy enriches longer DNA fragments that are more suitable for downstream sequencing analysis.
After washing steps to remove contaminants, purified DNA is eluted in a low-salt buffer suitable for molecular biology workflows.
Technical Validation
The MagPure FFPE DNA Kit was evaluated for size-selective DNA recovery using DNA marker fragments and FFPE-derived DNA samples. The validation showed that the recovery profile could be adjusted by changing the Buffer BD volume, allowing selective reduction of short DNA fragments during magnetic bead purification.
In the fragment recovery test, D6323B showed lower recovery of short DNA fragments compared with non-size-selective magnetic bead workflows. By adjusting the Buffer BD volume, the workflow could reduce recovery of fragments below approximately 150–400 bp under the tested conditions, supporting its use in FFPE workflows where excessive short-fragment background may reduce downstream NGS efficiency.
In comparative FFPE extraction testing, D6323B showed higher Qubit-based DNA recovery than a reference column-based FFPE DNA workflow in most tested samples, while maintaining comparable DNA fragment size profiles. These results support the use of D6323B for FFPE DNA extraction where DNA recovery and sequencing-compatible fragment quality are important.
Additional automated extraction testing on MagMix 32 showed no detectable SRY gene cross-contamination between alternating male and female FFPE samples under the tested conditions, supporting the workflow’s compatibility with automated FFPE DNA extraction.
Application Scenario Summary
FFPE DNA extraction workflows are selected according to the downstream assay. For focused PCR-based applications such as MSI-PCR, Sanger sequencing or mutation-specific analysis, the main requirement is amplifiable DNA from FFPE sections. For sequencing-oriented applications such as WES, targeted NGS, methylation profiling, HRD-related analysis, TMB evaluation or matched tissue-reference studies, fragment handling, inhibitor background and library preparation compatibility may become more important.
The selected examples below summarize published research workflows involving Magen FFPE DNA extraction formats, including D3126 / HiPure FFPE DNA Kit, D6323B / MagPure FFPE DNA Kit and D6323D / MagPure FFPE DNA Kit High Pure. These examples are organized to illustrate typical FFPE DNA application contexts rather than to compare kit performance directly.
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Application Scenario
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Related Format
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Sample / cfDNA Source
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Downstream Research Use
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De novo high-grade meningioma TERT promoter mutation analysis for post-radiotherapy progression risk research
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D3126
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FFPE tumor tissue from de novo WHO grade 2–3 high-grade meningioma patients treated with postoperative radiotherapy
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Genomic DNA extraction for PCR amplification and Sanger sequencing of TERT promoter mutations, supporting analysis of tumor progression, PFS and postoperative radiotherapy outcome
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CRC and gastric cancer MSI-PCR panel comparison for optimized molecular pathology testing
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D3126
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FFPE biopsy and surgical specimens from colorectal and gastric cancer patients
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Genomic DNA extraction for PCR-based MSI status detection using NCI, five-mononucleotide and six-mononucleotide panels, supporting comparison of panel performance, MSI-L interpretation and optimal MSI-PCR workflow selection
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Pulmonary nodule malignancy assessment using paired FFPE tissue and plasma methylation profiling
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D6323B
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Malignant and benign FFPE lung tissue samples from patients with CT-detected pulmonary nodules
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Tissue gDNA extraction for DNA methylation sequencing, paired tissue–plasma methylation concordance analysis and validation of an integrative blood-based model for distinguishing malignant lung nodules from benign lesions
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View more application scenarios
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Application Scenario
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Related Format
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Sample / cfDNA Source
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Downstream Research Use
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Pancreatic adenocarcinoma CNV-driven molecular subtyping for prognosis and treatment stratification research
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D6323B
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FFPE tumor samples from pathologically diagnosed pancreatic adenocarcinoma patients in a 608-patient Chinese cohort
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Tumor genomic DNA extraction for 566-gene / 764-gene targeted sequencing, somatic mutation profiling, germline HRR variant analysis, CNV-based molecular subtyping and relapse-risk model construction
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NSCLC postoperative MRD monitoring using tumor-informed personalized ctDNA analysis
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D6323D
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FFPE tumor tissue sections from early-stage NSCLC patients, paired with peripheral blood or buffy coat normal DNA
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Tumor gDNA and matched normal gDNA extraction for WES, patient-specific PROPHET panel design, postoperative plasma ctDNA MRD monitoring, recurrence risk prediction and TNMB prognostic classification
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FFPE tumor HRD assessment using genomic scar and allele-specific CNV analysis
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D6323B
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FFPE human tissue samples from ovarian and breast cancer cohorts
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Tumor DNA extraction for capture-based HRD panel sequencing, allele-specific CNV analysis, Genomic Scar Score modeling and PARP inhibitor response prediction
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Early TNBC HRR mutation profiling for immune infiltration and prognosis association research
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D6323B
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Archival FFPE tumor blocks from early triple-negative breast cancer patients
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Tumor genomic DNA extraction for HRR-targeted NGS, mutation spectrum analysis, CD8+ T cell / PD-L1 association study and combined immune-genomic prognosis stratification
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Pediatric hepatoblastoma trans-ancestry mutation landscape research using paired FFPE tumor and noncancerous tissue WES
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D6323B
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FFPE hepatoblastoma tumor samples and corresponding noncancerous liver tissues from pediatric patients
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Tumor and matched noncancerous tissue DNA extraction for WES, somatic mutation detection, copy number alteration analysis, pathway enrichment and trans-ancestry genomic comparison
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Matched FFPE tumor sequencing for distinguishing clonal hematopoiesis interference in liquid biopsy
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D6323B
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FFPE tumor tissue samples from Chinese pan-cancer patients with matched PBL DNA and plasma cfDNA
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Tumor genomic DNA extraction for targeted sequencing, validation of candidate CH mutations, exclusion of tumor-derived variants and improved interpretation of cfDNA liquid biopsy results
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LUAD tumor mutation burden and immune phenotype profiling for EGFR-mutant immunotherapy response research
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D6323B
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FFPE lung adenocarcinoma tissue blocks from treatment-naïve surgical patients
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Tumor DNA extraction for targeted panel sequencing, TMB evaluation, EGFR/KRAS/BRCA2 mutation comparison and association analysis with PD-L1 / CD8-based immune phenotypes
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Note: The selected examples are provided to illustrate application fit for FFPE DNA workflows, including PCR-based molecular pathology, Sanger sequencing, targeted sequencing, WES, methylation profiling, HRD-related analysis and tissue-reference studies. They do not represent a complete publication list or direct comparative kit-performance evaluation. Product selection should consider whether the downstream assay mainly requires routine amplifiable DNA, sequencing-compatible DNA, or high-purity DNA for inhibitor-sensitive applications.
Kit Contents
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Contents
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D632301B
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D632302B
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Purification Times
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48 Preps
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96 Preps
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MagBind Particles
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1.1 ml
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2 x 1.1 ml
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RNase A
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10 mg
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20 mg
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Proteinase K
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24 mg
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48 mg
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Protease Dissolve Buffer
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3 ml
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6 ml
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Buffer DPS
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60 ml
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100 ml
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Buffer ATL
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15 ml
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30 ml
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Buffer AL
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15 ml
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30 ml
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Buffer BD*
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6 ml
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15 ml
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Buffer BXW1*
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13 ml
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44 ml
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Elution Buffer
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15 ml
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30 ml
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Storage and Stability
RNase A, Proteinase K and MagBind Particles should be stored at 2-8°C upon arrival. However, short-term storage (up to 12 weeks) at room temperature (15-25°C) does not affect their performance. The remaining kit components can be stored at room temperature (15-25°C) and are stable for at least 18 months under these conditions.
Experiment Data
Purchase Guide
For guidance on selecting the most appropriate FFPE nucleic acid extraction system based on target analyte, workflow format and downstream application requirements:
👉 FFPE Nucleic Acid Extraction Purchase Guide
For a broader technical overview of FFPE DNA, RNA and DNA/RNA co-extraction workflow routes, processing logic and application-oriented route design:
👉 FFPE Nucleic Acid Extraction Workflows Explained
For detailed workflow structure, estimated processing time and route-specific handling logic across representative FFPE workflows:
