Peripheral blood was collected in EDTA Vacutainer tubes (BD) or Streck Cell-Free DNA tubes and processed within 3 hours of collection. Plasma was separated by centrifugation at 1,600g for 10 minutes, transferred to microcentrifuge tubes, and centrifuged at 3,000g at room temperature for 10 minutes. The supernatant was aliquoted and stored at -80°C until the time of DNA extraction. cfDNA was isolated from 1 mL of plasma, using the QIAGEN Circulating Nucleic Acids Kit (QIAGEN), eluted in AE buffer, and stored at -80°C. LPWGS was performed on all cfDNA samples. The ichorCNA R package was used to infer copy-number profiles and cfDNA tumor content from read abundance across bins spanning the genome using default parameters.(39) Per the published limit of detection of ichorCNA, estimated cfDNA tumor content cut-off of greater than or less than 0.03 were used to characterize samples as having detectable or undetectable circulating tumor DNA, respectively.
Cell free dna tubes
Manufactured by Streck
Sourced in United States
Streck Cell-Free DNA tubes are designed for the collection, stabilization, and transport of cell-free DNA samples. These tubes help preserve the integrity of cell-free DNA for downstream analysis.
Automatically generated - may contain errors
Lab products found in correlation
3 protocols using cell free dna tubes
1
Circulating Tumor DNA Profiling
2
Liquid Biopsy for HCC and CRCLM
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Patients diagnosed with HCC and CRCLM from July 2015 to Dec 2019 at Queen Mary Hospital were recruited. All HCC samples were from patients diagnosed with Barcelona Clinic Liver Cancer (BCLC) intermediate stage B. All CRCLM samples were from patients diagnosed with CRC having synchronous liver metastasis. All blood samples were obtained after written informed consent. A total of 133 samples were collected including 22 healthy individuals, 63 CRCLM, and 48 HCC patients. Eight milliliters of peripheral blood samples were collected in the Streck Cell-Free DNA tubes (Streck Inc., USA). The study was approved by the Institutional Review Board of the University of Hong Kong.
3
Plasma and Cell Pellet Isolation
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Blood samples were collected as part of an ancillary study to the main clinical trials. Samples were collected at predetermined time points within each trial. Samples were either collected in 6 or 9 ml EDTA tubes and processed within 2 hours, or in 10ml Streck cell-free DNA tubes (Streck, Omaha, NE) or 10ml PAXgene blood ccfDNA tubes (Qiagen, Hilden, Germany) and processed within 3 days. In case Streck cell-free DNA or PAXgene blood ccfDNA tubes were used, they were first centrifuged at 1900g for 15 minutes at room temperature to separate the plasma. For further plasma purification, the plasma layer was pipetted into a clean 15ml LoBind tube (Eppendorf, Hamburg, Germany) and centrifuged at 1900 g for another 10 minutes. Plasma was then aliquoted into 2-5ml cryotubes and stored at -80°C.
The cell pellet fraction remaining after the first centrifugation step was also aliquoted into 2-5ml cryotubes and stored along with plasma samples at -80°C for use as a germline control.
In case EDTA tubes were used, the same protocol was followed, but the first centrifugation step was performed at 900g for 7 minutes at room temperature and the second centrifugation step was performed at 2500g for 10 minutes at room temperature.
The cell pellet fraction remaining after the first centrifugation step was also aliquoted into 2-5ml cryotubes and stored along with plasma samples at -80°C for use as a germline control.
In case EDTA tubes were used, the same protocol was followed, but the first centrifugation step was performed at 900g for 7 minutes at room temperature and the second centrifugation step was performed at 2500g for 10 minutes at room temperature.
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