Optimization of circulating cell-free DNA recovery for KRAS mutation and HPV detection in plasma

Mazurek, Agnieszka; Fiszer-Kierzkowska, Anna; Rutkowski, T.; Składowski, Krzysztof; Pierzyna, M; Ścieglińska, Dorota; Woźniak, Grzegorz; Głowacki, Grzegorz; Kawczyński, Rafał; Małusecka, Ewa

doi:10.3233/cbm-130371

Cited by 20 publications

(18 citation statements)

References 28 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…10 To measure the circulating cell-free DNA (cfDNA) concentration in blood plasma, amplification of human telomerase reverse transcriptase (TERT) was performed. DNA was extracted from plasma (1 mL) as described previously.…”

Section: Quantification Of Dna Vls In Plasma (Chpv16 Dna Vls)mentioning

confidence: 99%

“…DNA was extracted from plasma (1 mL) as described previously. 10 To measure the circulating cell-free DNA (cfDNA) concentration in blood plasma, amplification of human telomerase reverse transcriptase (TERT) was performed. 10 Each measurement consisted of a standard curve, a negative control, and the experimental sample.…”

Section: Quantification Of Dna Vls In Plasma (Chpv16 Dna Vls)mentioning

confidence: 99%

“…10 To measure the circulating cell-free DNA (cfDNA) concentration in blood plasma, amplification of human telomerase reverse transcriptase (TERT) was performed. 10 Each measurement consisted of a standard curve, a negative control, and the experimental sample. PCR was performed in a final volume of 30 μL, which was composed of: TaqMan Genotyping Master Mix (Applied Biosystems, Foster City, California), TERT probe (0.2 μM), each primer (0.9 μM), cfDNA (2 μL), and serial dilutions of the control DNA (2 μL; for preparing the standard curve).…”

Section: Quantification Of Dna Vls In Plasma (Chpv16 Dna Vls)mentioning

confidence: 99%

See 2 more Smart Citations

Detection of circulating HPV16 DNA as a biomarker in the blood of patients with human papillomavirus‐positive oropharyngeal squamous cell carcinoma

et al. 2018

Self Cite

View full text Add to dashboard Cite

Background Development of biomarker analysis using the circulating cell‐free DNA (cfDNA) methodology is a challenge for noninvasive cancer diagnosis. In this study, a comparison between the plasma and tumor tissue HPV16 DNA viral loads (VLs) has been presented. Methods Real‐time polymerase chain reaction was performed for quantitating of HPV16 DNA in the plasma and tumor samples of patients with oropharyngeal cancer. Results Among the tissues, HPV16‐positive patients with oropharyngeal squamous cell carcinoma, nonsmoking patients, displayed significantly higher HPV16 DNA VLs in their tissue. No smoking and advanced N disease were the most important predictors for cHPV16 DNA (circulating HPV16 DNA) detection. The cHPV16‐positive women displayed significantly higher VLs in their tumor tissues compared to the men, although without notable impact on the blood detection. Conclusions Many factors were responsible for human papillomavirus DNA circulation in blood. As a result of the small size of the analyzed group, some observed discrepancies need to be proven on a larger cohort.

show abstract

Section: Quantification Of Dna Vls In Plasma (Chpv16 Dna Vls)mentioning

confidence: 99%

Section: Quantification Of Dna Vls In Plasma (Chpv16 Dna Vls)mentioning

confidence: 99%

Section: Quantification Of Dna Vls In Plasma (Chpv16 Dna Vls)mentioning

confidence: 99%

See 1 more Smart Citation

Detection of circulating HPV16 DNA as a biomarker in the blood of patients with human papillomavirus‐positive oropharyngeal squamous cell carcinoma

et al. 2018

Self Cite

View full text Add to dashboard Cite

show abstract

“…Recent progress in the analysis of blood samples for circulating tumor cells or cell-free circulating tumor DNA (ctDNA) has shown that liquid biopsies may have potential applications in the detection and monitoring of cancer [9][10][11]. Similarly, in a study on cervical cancer, ctDNA has become a major focus, providing a strong basis for early diagnosis and 4 prognosis in cervical cancer [10,12,13]. Cervical cancer is typically caused by high-risk HPVs (hrHPVs), primarily genotypes 16 and 18 [4].…”

Section: Introductionmentioning

confidence: 99%

Diagnostic value of circulating tumor DNA as an effective biomarker in cervical cancer: a meta-analysis

C²,

Qiu

et al. 2019

Preprint

View full text Add to dashboard Cite

The applications of liquid biopsy have attracted much attention in biomedical research in recent years. Circulating cell-free DNA (cfDNA) in the serum may serve as a unique tumor marker in various types of cancer. Circulating tumor DNA (ctDNA) is a type of serum cfDNA found in patients with cancer and contains abundant information regarding tumor characteristics, highlighting its potential diagnostic value in the clinical setting. However, the diagnostic value of cfDNA as a biomarker in cervical cancer remains unclear. Here, we performed a metaanalysis to evaluate the applications of ctDNA as a biomarker in cervical cancer. A systematic literature search was performed using PubMed, Embase, and WANFANG MED ONLINE databases up to March 18, 2019. All literature was analyzed using Meta Disc 1.4 and STATA 14.0 software. Diagnostic measures of accuracy of ctDNA in cervical cancer were pooled and 2investigated. Fifteen studies comprising 1109 patients with cervical cancer met our inclusion criteria and were subjected to analysis. The pooled sensitivity and specificity were 0.52 (95% confidence interval [CI], 0.33-0.71) and 0.97 (95% CI, 0.91-0.99), respectively. The pooled positive likelihood ratio and negative likelihood ratio were 16.0 (95% CI, 5.5-46.4) and 0.50 (95% CI, 0.33-0.75), respectively. The diagnostic odds ratio was 32 (95% CI, 10-108), and the area under the summary receiver operating characteristic curve was 0.92 (95% CI, 0.90-0.94). There was no significant publication bias observed. In the included studies, ctDNA showed clear diagnostic value for diagnosing and monitoring cervical cancer. Our metaanalysis suggested that detection of human papilloma virus ctDNA in patients with cervical cancer could be used as a noninvasive early dynamic biomarker of tumors, with high specificity and moderate sensitivity. Further large-scale prospective studies are required to validate the factors that may influence the accuracy of cervical cancer diagnosis and monitoring.

show abstract

“…Numerous studies have identified a correlation between fcDNA and cancer, including ovarian, uterine, colorectal, breast, lung and prostate cancer, cervical and malignant gastrointestinal tumors, glioma, hepatocellular carcinoma, metastatic melanoma, leukemia and lymphoma (8–13). The characteristics of fcDNA may also make this type of DNA a promising tool for the diagnosis of early-stage EOC.…”

Section: Introductionmentioning

confidence: 99%

Detection of OPCML methylation, a possible epigenetic marker, from free serum circulating DNA to improve the diagnosis of early-stage ovarian epithelial cancer

Luo

et al. 2017

Oncology Letters

View full text Add to dashboard Cite

The aim of the present study was to identify the appropriate DNA sequence and design high-quality primers for methylation-specific polymerase chain reaction (MSP). These primers may be used to examine and identify patients with early-stage epithelial ovarian carcinoma (EOC). Opioid binding protein/cell adhesion molecule like (OPCML), Runt-related transcription factor 3 and tissue factor pathway inhibitor 2 were selected as possible molecular markers. MSP primer sets were designed to monitor the methylation of the three markers. Free circulating DNA (fcDNA) from 194 patients with epithelial ovarian carcinoma and healthy donors were templates in the nested MSP. OPCML MSP was effective with respect to screening methylated fcDNA. One-way ANOVA P-values indicated that the difference in cancer antigen 125 (CA125), a biomarker for EOC diagnosis, level between early EOC and healthy donors was not significant. The methylation of OPCML was significantly altered in early-stage EOC compared with healthy donors (P<0.0001), and this supported the hypothesis that specific fcDNA methylation was able to distinguish patients with early-stage EOC from healthy donors. With respect to detecting early EOC, compared with the results of the CA125 test, MSP increased the κ coefficient from 0.140 to 0.757. Therefore, OPCML combined with fcDNA may be used to establish an improved clinical assay compared with the current CA125 test.

show abstract

Optimization of circulating cell-free DNA recovery for KRAS mutation and HPV detection in plasma

Abstract: Data presented in this study facilitate detection of tumour-specific cfDNA and improve standards needed for the implementation of cfDNA technology into routine clinical practice.

Cited by 20 publications

References 28 publications

Detection of circulating HPV16 DNA as a biomarker in the blood of patients with human papillomavirus‐positive oropharyngeal squamous cell carcinoma

Detection of circulating HPV16 DNA as a biomarker in the blood of patients with human papillomavirus‐positive oropharyngeal squamous cell carcinoma

Diagnostic value of circulating tumor DNA as an effective biomarker in cervical cancer: a meta-analysis

Detection of OPCML methylation, a possible epigenetic marker, from free serum circulating DNA to improve the diagnosis of early-stage ovarian epithelial cancer

Contact Info

Product

Resources

About