QIAamp MinElute ccfDNA Kits

For isolation of free-circulating DNA from human plasma or serum

Features

  • Efficient recovery of fragmented DNA
  • High yield ensuring detection of low frequency biomarkers
  • Low elution volume in water (20 µl) for high concentration of nucleic acids
  • Scalable sample input volume of 1–10 ml
  • Removal of contaminants and inhibitors
QIAamp MinElute ccfDNA Midi Kit (50)

Cat. No. / ID: 55284

For 50 preps (4 or 5 ml sample input volume each): QIAamp UCP MinElute Columns, QIAGEN Proteinase K, Magnetic Bead Suspension, Buffers, Bead Elution Tubes, and Collection Tubes (1.5 ml and 2 ml)
KitAccessories
QIAamp MinElute ccfDNA Kit
Accessories
Volume
5–10 ml
1–4 ml
QIAamp MinElute ccfDNA Kits are intended for molecular biology applications. These products are not intended for the diagnosis, prevention, or treatment of a disease.

Product Details

QIAamp MinElute ccfDNA Kits greatly simplify concentration and purification of free-circulating DNA from plasma or serum. The procedure can be partially automated on the QIAcube Connect.

Performance

The quantity of free-circulating DNA in plasma, serum and other body fluids is usually low, and isolation is a challenge. QIAamp MinElute ccfDNA Kits provide excellent results with efficient purification of high-quality ccfDNA from serum and plasma samples, even when small amounts are present. Compared with other commercially available kits, QIAamp MinElute ccfDNA Kits recovered the greatest amount of ccfDNA.
Pre-concentration of ccfDNA on magnetic beads allows flexible and scalable handling of volumes from 1 to 10 ml while the use of a MinElute column allows flexible elution volumes between 20 μl and 80 μl, providing the highest possible concentration of nucleic acid species that are present in low concentrations (typically 1–100 ng/ml circulating DNA in human plasma). ​
The QIAamp MinElute ccfDNA Mini Kit has been optimized for sample volumes from 1 to 4 ml while the QIAamp MinElute ccfDNA Midi Kit has been optimized for sample volumes from 4 to 10 ml. QIAamp MinElute columns can bind fragmented nucleic acids that are as short as 20 bases, but yield depends on the sample volume and the concentration of circulating nucleic acids in the sample.​

Principle

Free-circulating DNA, such as tumor-specific extracellular DNA fragments in the blood or fetal DNA in maternal blood, is present in serum or plasma usually as short fragments of <1000 bp. Because ccfDNA may reflect the entire tumor genome, it has gained attention for its potential clinical utility, enabling use of “liquid biopsies” in the form of blood draws.
QIAamp MinElute ccfDNA Kits enable efficient purification of these circulating DNAs from human plasma or serum. ​The procedure can be partially automated on the QIAcube.

Procedure

The kits use a fast procedure involving pre-concentration of circulating nucleic acids onto magnetic beads and a cleanup of the resulting pre-eluate on QIAamp MinElute columns in a quick and convenient spin procedure. The robust procedure helps to eliminate sample-to-sample cross-contamination and increases user safety when handling potentially infectious samples.
The simple procedure, which is highly suited for simultaneous processing of multiple samples, provides pure nucleic acids in less than 1 hour for 24 samples. Free-circulating DNA is eluted in Ultra-clean Water, ready for use in downstream reactions or storage a –30 to –15°C. Purified nucleic acids are free of proteins, nucleases and other impurities. The procedure can be partially automated on the QIAcube.

Applications

QIAamp MinElute ccfDNA Kits enable efficient purification of circulating DNAs from human plasma or serum.

Supporting data and figures

Resources

Kit Handbooks (3)
for separation of BioMag® particles in 15 ml or 50 ml tubes
PAXgene Blood ccfDNA Tube (RUO) Handbook
Application Notes (2)

IATA-conform transport of whole blood samples in PAXgene Blood ccfDNA Tubes – a simulation and functional test

Demonstrated 3-in-1 workflow for the simultaneous extraction of circulating tumor cell RNA, ccfDNA and leukocyte-derived gDNA from a single blood sample collected and stored in a PAXgene Blood ccfDNA Tube (RUO)

FAQ

Which protocol line should I use to process plasma samples?
The QIAsymphony PAXgene Blood ccfDNA Kit can be sued with 2 protocol lines. The standard protocols (STA) predominantely isolate small ccfDNA fragments. The large fragment protocols (LAF) efficiently co-purify large and small ccfDNA fragments. Both lines include a protocol for 2.4 ml and another for 4.8 ml plasma input.
FAQ ID - 3654
Which elution volumes are available with the QIAsymphony PAXgene Blood ccfDNA Kit?
The elution volume of the standard protocols (STA) is fixed at 60 µl. The large fragment protocols (LAF) enable elution in 3 different volumes: 60, 100 and 150 µl.
FAQ ID - 3655
What is the shelf life of the QIAsymphony PAXgene Blood ccfDNA Kit?
The expiration date is printed on the kit label and encoded in the bar code of the reagent cartridges.
FAQ ID - 3651
What is the Globally Harmonized System of Classification and Labelling of Chemicals (GHS) and what is the impact for me as a customer?
For overview and further information on the Globally Harmonized System of Classification and Labelling of Chemicals (GHS) please visit www.qiagen.com/ghs .
FAQ ID - 3428
Can whole blood in PAXgene Blood ccfDNA Tubes be stored at temperatures above 25°C?
Whole blood drawn into PAXgene Blood ccfDNA Tubes can be stored for at least 24 hours at 35°C. Higher temperatures will lead to lysis of blood cells and release of genomic DNA into plasma.
FAQ ID - 3640
Which downstream applications have been tested with ccfDNA purified from whole blood collected and processed with the PAXgene Blood ccfDNA System?
To date, ccfDNA from blood samples collected and processed using the PAXgene Blood ccfDNA System have been successfully tested in PCR, including multiplex qPCR, and NGS applications.
FAQ ID - 3658
Which tubes are recommended for the QIAsymphony sample rack
The recommended sample input format is the 14 ml Falcon® polystyrene round bottom tube 17 x 100 mm supplied by Corning (formerly supplied by BD).
FAQ ID - 3653
Can whole blood be frozen in PAXgene Blood ccfDNA Tubes?
No. Freezing blood drawn into PAXgene Blood ccfDNA Tubes results in lysis of red and white blood cells and release of genomic DNA.
FAQ ID - 3642
Are PAXgene Blood ccfDNA Tubes sterile?
Yes, the inside of PAXgene Blood ccfDNA Tubes is sterilized during production.
FAQ ID - 3636
What is the shelf life of unused PAXgene Blood ccfDNA Tubes?
The expiration date is printed on the tube label and on the shelf carton. 
FAQ ID - 3633
How long after first use can a reagent cartridge be stored for further use?
When closed properly with the provided strips and stored at room temperature (15–25°C), a reagent cartridge can be used up to 6 weeks after the initial run.
FAQ ID - 3650
Can whole blood in PAXgene Blood ccfDNA Tubes be stored at temperatures below 15°C?
Yes. Whole blood in PAXgene Blood ccfDNA Tubes can be stored at 8–15°C for up to 7 days. Storing blood in PAXgene Blood ccfDNA Tubes below room temperature does not extend stability. 
FAQ ID - 3641
What should I do if cryoprecipitates form while thawing a frozen plasma sample?

If cryoprecipitates cannot be resolved completely by vortexing, the sample should be centrifuged to prevent precipitates from blocking the column. To ensure that no cfDNA is co-precipitated,  centrifugation can be performed at a lower speed (at 6,800xg for 3 minutes at room temperature, as stated in the Protocol Sheet for the QS DSP Circulating DNA Kit). 



FAQ ID - 3646
How long and at which temperature can plasma generated from whole blood in PAXgene Blood ccfDNA Tubes be stored?
Plasma generated from whole blood collected into PAXgene Blood ccfDNA Tubes can be stored at 28°C for up to 14 days. We recommend freezing plasma at 20°C or 80°C for longer storage periods (long-term storage studies are ongoing).
FAQ ID - 3644
What is the expected ccfDNA yield from plasma generated from 10 ml of blood?
The yield of ccfDNA depends on the target ccfDNA. Nevertheless, yields obtained from PAXgene Blood ccfDNA Tubes are comparable to those obtained from the same volume of plasma separated directly after drawing blood into a spray-dried EDTA tube. In the PAXgene Blood ccfDNA Tube, however, this yield remains stable for up to 7 days when the tube is stored at 15–25°C or for up to 24 hours when stored at 35°C. In contrast, genomic DNA is released from lysed and apoptotic cells in the unstabilized contents of the EDTA tube soon after blood draw.


FAQ ID - 3637
Do I need to use a blood collection set with the PAXgene Blood ccfDNA Tube?
Yes. Further information on phlebotomy technique with the PAXgene Blood ccfDNA Tube can be found in the PAXgene Blood ccfDNA Tube Product Circular under the Resources tab.
FAQ ID - 3626
How many extractions can I perform with a QIAsymphony PAXgene Blood ccfDNA Kit, using the 2.4 ml or the 4.8 ml protocols?
The number of extractions that can be performed with a kit is independent of sample volume. A kit contains sufficient reagents for 192 extractions.
FAQ ID - 3649
Can reagent from the PAXgene Blood ccfDNA Tube flow back into the patient’s arm?
If the instructions for use are followed, there is no possibility of backflow during phlebotomy and thus, no possibility of reagent going into the patient’s arm.
FAQ ID - 3629
Can I use plasma from underfilled PAXgene Blood ccfDNA Tubes?
A complete 10 ml blood draw ensures optimal results. However, depending on the downstream application and target ccfDNA fragment size, tubes filled with as little as 6.5 ml whole blood can be used without adversely affecting results.
FAQ ID - 3638
Can I use a different brand blood collection set with the PAXgene Blood ccfDNA Tube?
Yes, as long as the phlebotomy instructions included with the PAXgene Blood ccfDNA Tubes are properly followed.
FAQ ID - 3630
What is the reagent in the PAXgene Blood ccfDNA Tube?
The PAXgene Blood ccfDNA Tube contains a proprietary formulation that prevents blood coagulation and the release of genomic DNA from blood cells into plasma. Contents of the tube may cause irritation to the eyes, respiratory system and skin. Please refer to the PAXgene Blood ccfDNA Tube Product Circular. For additional information, visit www.preanalytix.com or review the Safety Data Sheet under the Resources tab.
FAQ ID - 3632
What is the blood draw volume of the PAXgene Blood ccfDNA Tube
The blood draw volume is 10 ml and the stabilization reagent volume is 1.5 ml. Thus, a filled tube holds a volume of 11.5 ml.
FAQ ID - 3631
For what type of sample material is the QIAsymphony PAXgene Blood ccfDNA Kit intended?
The QIAsymphony PAXgene Blood ccfDNA Kit is designed to be used with plasma generated from whole blood collected into PAXgene Blood ccfDNA Tubes.
FAQ ID - 3652
How should I thaw frozen plasma samples?
Thaw the tubes at room temperature (15–25°C). To minimize the formation of cryoprecipitates, do not thaw at lower temperatures (e.g., 4°C). Alternatively, thaw plasma for 30 minutes at 30°C to completely avoid the formation of cryoprecipitates.
FAQ ID - 3645
Are there special considerations for phlebotomy when using the PAXgene Blood ccfDNA Tube (blood collection set, discard tube, positioning of the tube, issues with short draws, etc.)?

Yes. Following a standard phlebotomy protocol, blood is collected into the evacuated tube using a blood collection set and a standardized needle holder that can accommodate a 16 mm diameter tube. Make sure that blood has stopped flowing into the tube before removing the tube from the holder.

For more information on phlebotomy technique, please refer to the PAXgene Blood ccfDNA Tube Product Circular under the Resources tab.
FAQ ID - 3635
Is double centrifugation required for plasma processing?
No. However, a second centrifugation step helps remove traces of buffy coat that may be accidentally transferred when aspirating plasma after the first centrifugation step.
FAQ ID - 3643
How should eluates produced with the PAXgene Blood ccfDNA System be stored?
Eluates should be stored at 20°C (long-term storage studies are ongoing).
FAQ ID - 3657
Does the QIAsymphony PAXgene Blood ccfDNA Kit also allow eluting ccfDNA in less than 60 µl?
Yes, a customized protocol for elution with 50 µl is available on request.
FAQ ID - 3656
What type of magnet do you recommend for handling the magnetic beads in the Qproteome Plasma Membrane Protein protocol?

Since the Qproteome Plasma Membrane Protein procedure requires 1.5 ml/2.0 ml reaction tubes, we recommend using the follwing magnets for handling the magnetic beads:

Alternatively, comparable tube magnets or a standard clip-board magnet should also work.

FAQ ID -1193
How long can whole blood stabilized in PAXgene Blood ccfDNA Tubes be stored at room temperature?
Whole blood drawn into PAXgene Blood ccfDNA Tubes can be stored at 15–25°C for up to 7 days.
FAQ ID - 3639
Why have the hazard symbols accompanying products changed?
The Globally Harmonized System (GHS) is an initiative by the United Nations aiming to harmonize chemical hazard communication worldwide. Hazards symbols accompanying products are changing to those of the GHS. Information on the adoption of this new system is available on our GHS Hazard Labeling pages.
FAQ ID - 3430
Which plasma volumes can I process with the QIAsymphony PAXgene Blood ccfDNA protocols?
The normal protocols enable processing 2.4 or 4.8 ml plasma. Other volumes can be accommodated using customized protocols. 
FAQ ID - 3648
How should unused PAXgene Blood ccfDNA Tubes be stored?
Store PAXgene Blood ccfDNA Tubes at room temperature (15–25°C) and protect them from direct sunlight.
FAQ ID - 3634
Why is a blood collection set required to collect blood into the PAXgene Blood ccfDNA Tube?
When used in accordance with instructions, the blood collection set eliminates the possibility of patient contact with the reagent in the tube due to backflow of blood.
FAQ ID - 3628