Comparison of cell stabilizing blood collection tubes for circulating plasma tumor DNA.
Author(s): Toro PV, Erlanger B, Beaver JA, Cochran RL, VanDenBerg DA, Yakim E, Cravero K, Chu D, Zabransky DJ, Wong HY, Croessmann S, Parsons H, Hurley PJ, Lauring J, Park BH
Publication: Clin Biochem, 2015, Vol. 48, Page 993-8
PubMed ID: 26234639 PubMed Review Paper? No
Purpose of Paper
The purpose of this paper was to compare cell-free DNA levels in plasma among blood specimens collected in different tube types and subjected to a pre-processing delay of 7 days at room temperature.
Conclusion of Paper
Generally, the number of copies of cell-free DNA in plasma were higher when blood was stored for 7 days at room temperature in EDTA or PAXgene tubes, but remained comparable to immediately processed specimens when blood was stored in Streck blood collection tubes (BCT). However, one of the phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha (PIK3CA) hotspot mutations as well as fetal DNA levels were not affected by the pre-processing delay, regardless of tube type.
Studies
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Study Purpose
The purpose of this study was to compare the stabilities of fetal and total cell-free DNA in plasma collected from pregnant women. Blood from a pregnant volunteer was collected into EDTA and BCT tubes and was processed by double centrifugation within 2 h or after 7 days at room temperature. Additional blood from another pregnant volunteer was collected into EDTA, BCT and PAXgene tubes. EDTA specimens were processed by double centrifugation within 2 h while PAXgene and BCT specimens were processed after 7 days at room temperature. Cell-free DNA was extracted from the plasma specimens using the QIAamp Circulating Nucleic Acid kit. Fetal DNA was quantified by digital PCR amplification of E1F1AY region of the Y chromosome and total DNA was quantified by amplification of wild-type PIK3CA exon 9.
Summary of Findings:
Compared to controls processed within 2 h, the number of copies of total cell-free DNA in plasma was unaffected by a pre-processing delay of 7 days at room temperature when specimens were collected and stored in BCT tubes, but the number of copies increased by >10- and >5-fold when blood was collected and stored in EDTA or PAXgene tubes, respectively. Plasma levels of fetal cell-free DNA were not affected by a pre-processing delay of 7 days at room temperature for any of the tube types examined (EDTA, BCT or PAXgene tubes).
Biospecimens
Preservative Types
- PAXgene
- None (Fresh)
- Streck/BCT
Diagnoses:
- Pregnant
Platform:
Analyte Technology Platform DNA Digital PCR Pre-analytical Factors:
Classification Pre-analytical Factor Value(s) Biospecimen Preservation Type of fixation/preservation PAXgene
Blood collection tube additive
None (fresh)
Digital PCR Specific Targeted nucleic acid E1F1AY
PIK3CA exon 9
Storage Time at room temperature <2 h
7 days
Biospecimen Acquisition Type of collection container/solution PAXgene tube
BCT tube
EDTA tube
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Study Purpose
The purpose of this study was to compare wild-type and mutant PIK3CA cell-free DNA levels in plasma among blood specimens collected in different tube types and subjected to a pre-processing delay of 7 days at room temperature. Blood was collected from 9 women with estrogen receptor positive metastatic breast cancer into EDTA, PAXgene and BCT tubes and were processed by double centrifugation within 2 h or after 7 days (PAXgene and BCT tubes only) at room temperature. Cell-free DNA was extracted from plasma specimens using the QIAamp Circulating Nucleic Acid kit.
Summary of Findings:
When blood collected in PAXgene tubes was subjected to a room temperature pre-processing delay of 7 days, DNA levels in plasma increased by an average of 37.14-fold (range: 0.87-191.60 fold, p<0.0059), but when blood was collected and stored for 7 days in BCT tubes levels only increased by an average of 1.17-fold (range 0.46-2.59 fold, p=0.32). Interestingly, for the 2 patients with an E545K mutation the number of E545K copies in plasma when blood was stored for 7 days was comparable to controls processed within 2 h, regardless of tube type. Conversely, copies of the 1047R mutation in plasma increased 22.79- and 33.22-fold when blood was collected and stored in PAXgene tubes for 7 days.
Biospecimens
Preservative Types
- None (Fresh)
- PAXgene
- Streck/BCT
Diagnoses:
- Neoplastic - Carcinoma
Platform:
Analyte Technology Platform DNA Digital PCR Pre-analytical Factors:
Classification Pre-analytical Factor Value(s) Biospecimen Acquisition Type of collection container/solution PAXgene tube
BCT tube
EDTA tube
Digital PCR Specific Targeted nucleic acid PIK3CA E545K
PIK3CA 1047R
PIK3CA wild-type
Storage Time at room temperature <2 h
7 days
Biospecimen Preservation Type of fixation/preservation PAXgene
None (fresh)
Blood collection tube additive