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| Product Name | Magnetic Bead-Based FFPE DNA Extraction Kit |
| Catalog No. | DREK-0008 |
| Description | A magnetic bead-based DNA extraction kit developed for the isolation of genomic DNA from formalin-fixed, paraffin-embedded tissue sections. The kit incorporates a paraffin removal step with xylene-free deparaffinization solution, a heat-mediated reversal of formaldehyde crosslinks at controlled temperature and pH, and an optimized binding buffer that recovers both long and fragmented DNA molecules. The magnetic bead chemistry tolerates residual tissue debris, ensuring consistent DNA recovery from challenging archived specimens. |
| Intended Use | Extraction of genomic DNA from FFPE tissue scrolls, curls, and sections for retrospective molecular pathology studies, oncology biomarker analysis, archival specimen sequencing, and genetic epidemiological research using banked tissue specimens. |
| Principle / Technology | FFPE tissue sections are deparaffinized with a non-toxic solvent, then subjected to proteinase K digestion at elevated temperature (56-90°C) to release DNA and reverse formaldehyde-induced crosslinks. After digestion, the lysate is mixed with a guanidine-based binding buffer and DNA binds to silica-coated magnetic beads. The beads are washed to remove residual tissue debris, hematin pigment, and chemical crosslinking byproducts. Purified DNA is eluted under mildly alkaline conditions. |
| Detection Method | UV spectrophotometry; Qubit fluorometric dsDNA quantitation; Bioanalyzer or TapeStation for fragment size distribution; qPCR with amplicons of varying lengths (100 bp, 200 bp, 400 bp) for amplifiability assessment; targeted NGS panel sequencing for functional quality evaluation |
| Sample Type | Formalin-fixed, paraffin-embedded tissue sections (5-20 µm thickness, 1-10 sections depending on tissue area); FFPE tissue scrolls and curls; compatible with tissues fixed in 10% neutral-buffered formalin; may be used with non-standard fixatives with reduced performance |
| Performance Range / Specifications | Input: 1-10 FFPE sections (5-10 µm); deparaffinization: xylene-free protocol, 10 minutes; DNA yield: variable dependent on tissue type, fixation duration, and specimen age (typically 50 ng-5 µg from 5 sections of 10 µm); A260/A280: 1.6-1.9 (formalin modification may affect ratio); fragment size: 100-500 bp distribution typical; qPCR amplifiability: >50% for 200 bp target |
| Sensitivity / LOD | Detectable DNA from single 5 µm FFPE section; effective recovery from archival blocks up to 20 years old; detectable genomic targets at single-copy level by qPCR when input tissue area exceeds 10 mm² |
| Specificity | Extracted DNA is of human genomic origin as confirmed by species-specific qPCR; no detectable microbial DNA enrichment above background; formalin-induced cytosine deamination artifacts consistent with expected rates for given fixation conditions; no detectable PCR inhibitors in standard reaction conditions |
| Reaction Conditions / Protocol | Place FFPE sections in microcentrifuge tube; add deparaffinization solution; incubate 10 minutes at room temperature with vortexing; centrifuge and remove supernatant; add digestion buffer and proteinase K; incubate at 56°C for 1 hour, then 90°C for 1 hour (crosslink reversal); centrifuge briefly; transfer supernatant; add binding buffer and isopropanol; add magnetic bead suspension; incubate 10 minutes; separate beads; wash once with wash buffer 1 and twice with wash buffer 2; air-dry beads; elute in 30-50 µL elution buffer at 56°C for 5 minutes; total protocol: approximately 3-4 hours |
| Components / Formulation | Deparaffinization solution (non-toxic, xylene-free aliphatic hydrocarbon mixture), digestion buffer (Tris-HCl pH 8.0, EDTA, SDS), proteinase K solution (20 mg/mL), binding buffer (guanidine hydrochloride, Tris-HCl, isopropanol), magnetic silica bead suspension (50 mg/mL), wash buffer 1 concentrate, wash buffer 2 concentrate, elution buffer (10 mM Tris-HCl pH 8.5, 0.1 mM EDTA), magnetic separation rack |
| Storage Conditions | Deparaffinization solution and buffers at room temperature; proteinase K at 2-8°C; magnetic beads at 2-8°C; store all components tightly sealed; keep deparaffinization solution away from open flames |
| Shelf Life | 18 months from date of manufacture; proteinase K stable for 12 months at 2-8°C after opening; deparaffinization solution stable for 18 months in sealed container |
| Package Specifications | 50 preparations and 200 preparations; all reagents and consumables included; magnetic rack sold separately |
| Product Form | Liquid buffers and solutions; silica-coated magnetic bead suspension; proteinase K in glycerol-based buffer; deparaffinization solvent |
| Quality Control | Each lot validated with standardized FFPE tissue sections: DNA yield consistent between lots; qPCR amplifiability for 100 bp, 200 bp, and 400 bp confirmed; NGS library quality score ≥Q30 for >80% bases; no PCR inhibition; species specificity confirmed; lot traceability maintained for all components |
| Key Features | Xylene-free deparaffinization eliminates toxic solvent handling; dual-temperature incubation optimizes protein digestion and crosslink reversal; magnetic bead format tolerates residual tissue debris; consistent performance across tissue types; eluted DNA suitable for targeted and whole-exome sequencing |
| Purity | A260/A280: 1.6-1.9 (variable due to formalin modification); A260/A230: >1.5; qPCR amplifiability verified |
| Concentration | Elution volume 30-50 µL; DNA concentration highly variable (1-100 ng/µL) depending on tissue cellularity, section area, and preservation quality |
| Activity / Unit Definition | Not applicable for extraction kits |
| Molecular Weight | Not applicable; FFPE-derived DNA is fragmented with a typical size range of 100-500 bp |
| Source / Origin | Silica-coated magnetic beads from synthetic process; proteinase K expressed recombinantly; deparaffinization solution is a proprietary blend of aliphatic hydrocarbons; all buffers are chemically synthesized, nuclease-free |
| pH Range / Optimal pH | Digestion buffer pH 7.8-8.2; binding buffer pH 5.0-6.0; wash buffers pH 6.5-7.5; elution buffer pH 8.0-8.5 |
| Shipping Conditions | Ambient temperature for all components; deparaffinization solution classified as non-hazardous for transport; proteinase K shipped with cold packs |
| Expiration Date / Stability | 18 months unopened; performance verified at 0, 6, 12, and 18 months with archived FFPE control sections; proteinase K retains >85% activity for 12 months at 2-8°C after opening |
| Regulatory / Compliance | For research use only; not for diagnostic applications; suitable for retrospective studies using archival pathological specimens; compliance with institutional review board and informed consent requirements is the responsibility of the end user |
| Compatibility | Extracted DNA suitable for qPCR, Sanger sequencing, targeted NGS panels, whole-exome sequencing, and microarray copy number analysis; compatible with major NGS library preparation kits with appropriate DNA fragmentation adjustments; compatible with magnetic particle processors |
| Recommended Buffer System | Tris-SDS proteinase K digestion system; guanidine hydrochloride binding buffer; Tris-EDTA elution optimized for FFPE DNA |
| Application Notes / Precautions | Use sections from areas of high tumor cellularity when possible; avoid overloading with excessive sections (>10 sections of 10 µm) to prevent bead saturation; complete removal of deparaffinization solution is essential; for highly degraded specimens, reduce 90°C incubation to 30 minutes; pre-warm elution buffer for maximum recovery; FFPE DNA may contain uracil from cytosine deamination; uracil-DNA glycosylase treatment may be applied before NGS library preparation |
| Batch-to-Batch Consistency | Between-lot DNA yield CV <20% on standardized FFPE reference material; qPCR Ct shift between lots <1.0 cycle for 200 bp target; deparaffinization efficiency >99% verified per batch; proteinase K specific activity verified per batch |
For research use only, not for clinical use.
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