Comparison of 7 Methods for Extracting Cell-Free DNA from Serum Samples of Colorectal Cancer Patients

Fong, Siew Lee; Zhang, Ji Tuan; Lim, Che Kang; Eu, Kong Weng; Yan-qun, Liu

doi:10.1373/clinchem.2008.110122

Cited by 59 publications

(44 citation statements)

References 3 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In a previous study, QIAamp DNA extraction columns performed satisfactorily in conjunction with 7 different cfDNA isolation methods for 2mL pooled serum samples [17]. QIAamp Midi Blood DNA Kit outperformed four other commercial kits and was surpassed by two in-house methods, Sodium-iodide (NaI) and phenol-chloroform (PC).…”

Section: Methods Units N Min Max Median Mean Sd Sem L95% U95% Pmentioning

confidence: 96%

“…While PerfeCta performed better with whole plasma, it was not observed with purified plasma cfDNA. An alternative approach to removal of PCR inhibitors by bisulfite treatment has been reported although no beneficial effect on qPCR results was found [17].…”

Section: Methods Units N Min Max Median Mean Sd Sem L95% U95% Pmentioning

confidence: 99%

“…While plasma was found to be a more reliable source for cfDNA analysis than serum [9,10], the quality of data varied according to the type of anticoagulant used, and conditions of blood storage and plasma processing applied [11][12][13][14][15][16]. Previous studies comparing efficiency of various plasma cfDNA isolation procedures indicated that in-house procedures were more efficient than the commercial ones though time consuming [17]. Different anticoagulants such as EDTA, citrate and heparin, in combination with varied durations and blood storage temperatures showed different effects on plasma cfDNA levels.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Evaluation of Clinical Laboratory Methods for Plasma Cell-Free DNA Analysis in Suspected Septicaemia

TJJ¹

2013

J Med Diagn Meth

View full text Add to dashboard Cite

Background: The amount and quality of plasma cell free DNA (cfDNA) changes in extreme physiological and pathological conditions. These changes could provide a basis for a novel prognostic biomarker in conditions as diverse as pregnancy, cancer, organ transplantation and septicaemia. Evaluation of current methods for cfDNA analysis is needed to identify the best practical approach to medical diagnostics.

show abstract

Section: Methods Units N Min Max Median Mean Sd Sem L95% U95% Pmentioning

confidence: 96%

Section: Methods Units N Min Max Median Mean Sd Sem L95% U95% Pmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Evaluation of Clinical Laboratory Methods for Plasma Cell-Free DNA Analysis in Suspected Septicaemia

TJJ¹

2013

J Med Diagn Meth

View full text Add to dashboard Cite

show abstract

“…protocols according to Schmidt et al [8], Yuan et al [9], and Hufnagl et al [10], and a THP (triton/heat/phenol) protocol according to Xue et al [11].…”

Section: Extraction With Organic Solvents Eg Phenol-chloroform Sepamentioning

confidence: 99%

Isolation of Cell-Free DNA from Seminal Fluid

Draškovič¹

2017

JPP

View full text Add to dashboard Cite

Cell-free DNA (cfDNA) is small short double stranded molecule that is also found in seminal fluid. It is a product of apoptotic cells in different developmental stages during spermatogenesis. To final concentration of total cfDNA in semen contributes also cfDNA secreted from living cells and cfDNA that is result of different diseases e.g. prostate cancer or infertility. Amended concentration (high or low) can be connected to prostate cancer or male infertility and can represent important non-invasive diagnostic biomarker for detection and prognosis of these pathological conditions. In this paper, I will discuss different approaches for isolation of cfDNA from seminal fluid, which includes selection of the samples, separation, isolation, extraction, purification and analysis. Today's most popular approach for isolation is the use of commercial kits based on selective binding and elution on silica-membrane technology, magnetic-bead technology or extraction with organic solvents and salting out procedure. Furthermore I will present that I tried to isolate cfDNA from semen with QIAamp DNA Mini Kit to confirm the presence of cell-free DNA in our samples. In the end I will describe problems we are facing during cfDNA measurement which are mainly associated with low concentration of cfDNA in samples.

show abstract

“…In 23 individuals (6 male, 17 female) only serum samples were available; DNA from these samples was purified using a previously described sodium iodine extraction method. 10 As the DNA quality from this source is of a poorer quality, we controlled all statistical analyses (later) by omitting this subset. In the NOS3 promoter region the -922A > G (rs 1800779) and the -786T > C (rs2070744) along with the nonsynonymous exon-7 894G > T, Glu298Asp (rs1799983) were determined using TaqMan probes on an Applied Biosystem 7500 Fast Real Time polymerase chain reaction (PCR) device according to the manufacturer's instructions.…”

Section: Purification Of Dna and Genotypingmentioning

confidence: 99%

Association of the NOS3 intron-4 VNTR polymorphism with aneurysmal subarachnoid hemorrhage

Staalsø

Edsen²,

Kotinis³

et al. 2014

JNS

View full text Add to dashboard Cite

Object. The nitric oxide system has been linked to the pathogenesis of aneurysmal subarachnoid hemorrhage (SAH). The authors performed a case-control study to investigate the association between SAH and common genetic variants within the endothelial nitric oxide synthase gene (NOS3).Methods. Three hundred thirty-three Caucasian SAH patients and 498 controls were genotyped for the -922A > G (rs 1800779), -786T > C (rs2070744), and 894G > T (rs1799983) single nucleotide polymorphisms and the intron-4 27-bp variable number of tandem repeats polymorphism (27-bp-VNTR).Results. The b/b (5 repeats) genotype of the 27-bp-VNTR was overrepresented in cases (77%) versus controls (69%) (p = 0.02). In male patients the b/b genotype was found in 85% compared with 67% in male controls, whereas in women, the frequencies were 73% and 72%, respectively. This corresponds to an odds ratio of 2.8 (95% CI 1.5-5.6, p = 0.0005) for SAH in men with the b/b genotype versus men with a/b or a/a. In women, no such association was found (OR 1.1, 95% CI 0.7-1.6, p = 0.76). Stepwise logistic regression including arterial hypertension, smoking, sex, and age with interactions yielded similar effect estimates of the 27-bp-VNTR. Haplotype analysis revealed that no single haplotype containing the b-allele was responsible for the observed genotype effect.Conclusions. The authors' results suggest that the NOS3 27-bp-VNTR b/b genotype independent of other risk factors act in concert with male sex to substantially increase risk of SAH. This effect is not mediated by any single NOS3 haplotype.

show abstract

Comparison of 7 Methods for Extracting Cell-Free DNA from Serum Samples of Colorectal Cancer Patients

Cited by 59 publications

References 3 publications

Evaluation of Clinical Laboratory Methods for Plasma Cell-Free DNA Analysis in Suspected Septicaemia

Evaluation of Clinical Laboratory Methods for Plasma Cell-Free DNA Analysis in Suspected Septicaemia

Isolation of Cell-Free DNA from Seminal Fluid

Association of the NOS3 intron-4 VNTR polymorphism with aneurysmal subarachnoid hemorrhage

Contact Info

Product

Resources

About