scholarly journals Egfr Testing from Circulating Cell-Free Dna: Ready for Routine Practice

2014 ◽  
Vol 25 ◽  
pp. iv83
Author(s):  
M.G. Denis ◽  
A. Vallee ◽  
C. El Kouri ◽  
H. Lacroix ◽  
M. Marcq ◽  
...  
Keyword(s):  
Routine Practice ◽  
Cell Free Dna ◽  
Free Dna ◽  
Circulating Cell Free Dna

scholarly journals Multicenter Evaluation of Circulating Cell-Free DNA Extraction and Downstream Analyses for the Development of Standardized (Pre)analytical Work Flows

2019 ◽  
Vol 66 (1) ◽  
pp. 149-160 ◽  
Author(s):  
Rita Lampignano ◽  
Martin H.D Neumann ◽  
Sabrina Weber ◽  
Vera Kloten ◽  
Andrei Herdean ◽  
...  
Keyword(s):  
Clinical Decision Making ◽  
Clinical Decision ◽  
Digital Pcr ◽  
Blood Collection ◽  
Routine Practice ◽  
Acid Extraction ◽  
Cell Free Dna ◽  
Free Dna ◽  
Analytical Work ◽  
Circulating Cell Free Dna

Abstract BACKGROUND In cancer patients, circulating cell-free DNA (ccfDNA) can contain tumor-derived DNA (ctDNA), which enables noninvasive diagnosis, real-time monitoring, and treatment susceptibility testing. However, ctDNA fractions are highly variable, which challenges downstream applications. Therefore, established preanalytical work flows in combination with cost-efficient and reproducible reference materials for ccfDNA analyses are crucial for analytical validity and subsequently for clinical decision-making. METHODS We describe the efforts of the Innovative Medicines Initiative consortium CANCER-ID (http://www.cancer-id.eu) for comparing different technologies for ccfDNA purification, quantification, and characterization in a multicenter setting. To this end, in-house generated mononucleosomal DNA (mnDNA) from lung cancer cell lines carrying known TP53 mutations was spiked in pools of plasma from healthy donors generated from 2 different blood collection tubes (BCTs). ccfDNA extraction was performed at 15 partner sites according to their respective routine practice. Downstream analysis of ccfDNA with respect to recovery, integrity, and mutation analysis was performed centralized at 4 different sites. RESULTS We demonstrate suitability of mnDNA as a surrogate for ccfDNA as a process quality control from nucleic acid extraction to mutation detection. Although automated extraction protocols and quantitative PCR-based quantification methods yielded the most consistent and precise results, some kits preferentially recovered spiked mnDNA over endogenous ccfDNA. Mutated TP53 fragments derived from mnDNA were consistently detected using both next-generation sequencing-based deep sequencing and droplet digital PCR independently of BCT. CONCLUSIONS This comprehensive multicenter comparison of ccfDNA preanalytical and analytical work flows is an important contribution to establishing evidence-based guidelines for clinically feasible (pre)analytical work flows.

scholarly journals Comparison of Circulating Cell-Free DNA Extraction Methods for Downstream Analysis in Cancer Patients

Cancers ◽  
2020 ◽  
Vol 12 (5) ◽  
pp. 1222 ◽  
Author(s):  
Paul van der Leest ◽  
Pieter A. Boonstra ◽  
Arja ter Elst ◽  
Léon C. van Kempen ◽  
Marco Tibbesma ◽  
...  
Keyword(s):  
Cancer Patients ◽  
Predictive Testing ◽  
High Volume ◽  
Extraction Methods ◽  
Response Monitoring ◽  
Routine Practice ◽  
Plasma Samples ◽  
Cell Free Dna ◽  
Free Dna ◽  
Circulating Cell Free Dna

Circulating cell-free DNA (ccfDNA) may contain DNA originating from the tumor in plasma of cancer patients (ctDNA) and enables noninvasive cancer diagnosis, treatment predictive testing, and response monitoring. A recent multicenter evaluation of workflows by the CANCER-ID consortium using artificial spiked-in plasma showed significant differences and consequently the importance of carefully selecting ccfDNA extraction methods. Here, the quantity and integrity of extracted ccfDNA from the plasma of cancer patients were assessed. Twenty-one cancer patient-derived cell-free plasma samples were selected to compare the Qiagen CNA, Maxwell RSC ccfDNA plasma, and Zymo manual quick ccfDNA kit. High-volume citrate plasma samples collected by diagnostic leukapheresis from six cancer patients were used to compare the Qiagen CNA (2 mL) and QIAamp MinElute ccfDNA kit (8 mL). This study revealed similar integrity and similar levels of amplified short-sized fragments and tumor-specific mutants comparing the CNA and RSC kits. However, the CNA kit consistently showed the highest yield of ccfDNA and short-sized fragments, while the RSC and ME kits showed higher variant allelic frequencies (VAFs). Our study pinpoints the importance of standardizing preanalytical conditions as well as consensus on defining the input of ccfDNA to accurately detect ctDNA and be able to compare results in a clinical routine practice, within and between clinical studies.

304-OR: 5-Hydroxymethylcytosines in Circulating Cell-Free DNA Reveal Diabetic Nephropathy

Diabetes ◽  
2020 ◽  
Vol 69 (Supplement 1) ◽  
pp. 304-OR
Author(s):  
CHANG ZENG ◽  
YING YANG ◽  
ZHOU ZHANG ◽  
CHUAN HE ◽  
WEI ZHANG ◽  
...  
Keyword(s):  
Diabetic Nephropathy ◽  
Cell Free Dna ◽  
Free Dna ◽  
Circulating Cell Free Dna

scholarly journals Cell-free DNA Testing in Routine Practice: Characterisation of a Cohort with Positive Results for Trisomies, Sex Chromosome Anomalies and Microdeletions

2020 ◽  
Author(s):  
Ismail Tekesin
Keyword(s):  
Sex Chromosome ◽  
Screening Method ◽  
First Trimester ◽  
Routine Practice ◽  
Cell Free Dna ◽  
Patient Counselling ◽  
Chromosome Anomalies ◽  
Free Dna ◽  
Autosomal Aneuploidy ◽  
Current Guidelines

Abstract Introduction Cell-free DNA (cfDNA) testing is increasingly used as a screening method not only for trisomy (T) 21 but also for T18 and T13, sex chromosome anomalies (SCA) and microdeletions. Based on cases with a positive cfDNA result in our specialised prenatal practice, this study aims to characterise the usage of cfDNA testing and to estimate the positive predictive value (PPV) in routine practice in Germany. Patients and Methods In this retrospective study we analysed the data of all pregnant women with a positive cfDNA result seen between 09/2013 and 12/2019. Women were either referred due to the positive result or the test was initiated in our practice. The primary parameter of interest was the concordance of cfDNA tests with confirmatory genetic testing. Results We encountered 81 cases with a positive cfDNA test (T21: 49.4%; T18: 9.9%; T13: 8.6%; SCA: 22.2%; 22q12del: 8.6%). The PPV was 95.0% for T21, but considerably lower for T18 (55.6%) and T13 (28.6%). For SCAs it was 23.1% and no case with DiGeorge syndrome was confirmed. 63% of the patients had not received a fetal anomaly scan before cfDNA testing. In first-trimester fetuses with a cfDNA test predicting an autosomal aneuploidy, fetal anomalies were detected in 90.3% of the cases. No false positive case had an abnormal US result. Conclusions Despite the excellent specificity of cfDNA tests, the PPV for aneuploidies other than T21 is low in routine practice. In discordance with the current guidelines, cfDNA test is often used without a previous detailed anomaly scan. Our data provide valuable information to assist patient counselling and shared decision making.

scholarly journals Circulating Cell-Free DNA in Breast Cancer: Searching for Hidden Information towards Precision Medicine

Cancers ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 728
Author(s):  
Maria Panagopoulou ◽  
Manel Esteller ◽  
Ekaterini Chatzaki
Keyword(s):  
Breast Cancer ◽  
Treatment Options ◽  
Treatment Monitoring ◽  
Circulating Biomarkers ◽  
Hidden Information ◽  
Cell Free Dna ◽  
Free Dna ◽  
Current Review ◽  
Circulating Cell Free Dna

Breast cancer (BC) is a leading cause of death between women. Mortality is significantly raised due to drug resistance and metastasis, while personalized treatment options are obstructed by the limitations of conventional biopsy follow-up. Lately, research is focusing on circulating biomarkers as minimally invasive choices for diagnosis, prognosis and treatment monitoring. Circulating cell-free DNA (ccfDNA) is a promising liquid biopsy biomaterial of great potential as it is thought to mirror the tumor’s lifespan; however, its clinical exploitation is burdened mainly by gaps in knowledge of its biology and specific characteristics. The current review aims to gather latest findings about the nature of ccfDNA and its multiple molecular and biological characteristics in breast cancer, covering basic and translational research and giving insights about its validity in a clinical setting.

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