scholarly journals Correction: Versatile hybrid acoustic micromixer with demonstration of circulating cell-free DNA extraction from sub-ml plasma samples

Lab on a Chip ◽  
2021 ◽  
Author(s):  
Alvaro J. Conde ◽  
Ieva Keraite ◽  
Alfredo E. Ongaro ◽  
Maïwenn Kersaudy-Kerhoas
Keyword(s):  
Dna Extraction ◽  
Plasma Samples ◽  
Cell Free Dna ◽  
Free Dna ◽  
Circulating Cell Free Dna

Correction for ‘Versatile hybrid acoustic micromixer with demonstration of circulating cell-free DNA extraction from sub-ml plasma samples’ by Alvaro J. Conde et al., Lab Chip, 2020, 20, 741–748, DOI: 10.1039/C9LC01130G.

scholarly journals Versatile hybrid acoustic micromixer with demonstration of circulating cell-free DNA extraction from sub-ml plasma samples

Lab on a Chip ◽  
2020 ◽  
Vol 20 (4) ◽  
pp. 741-748 ◽  
Author(s):  
Alvaro J. Conde ◽  
Ieva Keraite ◽  
Alfredo E. Ongaro ◽  
Maïwenn Kersaudy-Kerhoas
Keyword(s):  
Dna Extraction ◽  
Low Cost ◽  
Plasma Samples ◽  
Cell Free Dna ◽  
Free Dna ◽  
Circulating Cell Free Dna

A low-cost and easy to implement acoustic micromixer compatible with multiple fabrication technologies that can provide efficient and vigorous mixing.

scholarly journals Detection of Colorectal Cancer in Circulating Cell-Free DNA by Methylated CpG Tandem Amplification and Sequencing

2019 ◽  
Vol 65 (7) ◽  
pp. 916-926 ◽  
Author(s):  
Jingyi Li ◽  
Xin Zhou ◽  
Xiaomeng Liu ◽  
Jie Ren ◽  
Jilian Wang ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Early Stage ◽  
Plasma Samples ◽  
Dna Hypermethylation ◽  
Cell Free Dna ◽  
Noncancerous Tissue ◽  
Clinical Sensitivity ◽  
Free Dna ◽  
A Genome ◽  
Circulating Cell Free Dna

Abstract BACKGROUND Aberrant DNA hypermethylation of CpG islands occurs frequently throughout the genome in human colorectal cancer (CRC). A genome-wide DNA hypermethylation analysis technique using circulating cell-free DNA (cfDNA) is attractive for the noninvasive early detection of CRC and discrimination between CRC and other cancer types. METHODS We applied the methylated CpG tandem amplification and sequencing (MCTA-Seq) method, with a fully methylated molecules algorithm, to plasma samples from patients with CRC (n = 147) and controls (n = 136), as well as cancer and adjacent noncancerous tissue samples (n = 66). We also comparatively analyzed plasma samples from patients with hepatocellular carcinoma (HCC; n = 36). RESULTS Dozens of DNA hypermethylation markers including known (e.g., SEPT9 and IKZF1) and novel (e.g., EMBP1, KCNQ5, CHST11, APBB1IP, and TJP2) genes were identified for effectively detecting CRC in cfDNA. A panel of 80 markers discriminated early-stage CRC patients and controls with a clinical sensitivity of 74% and clinical specificity of 90%. Patients with early-stage CRC and HCC could be discriminated at clinical sensitivities of approximately 70% by another panel of 128 markers. CONCLUSIONS MCTA-Seq is a promising method for the noninvasive detection of CRC.

313 Development of a one-step isolation platform for exosomal RNA and circulating cell-free DNA from cancer plasma samples

2014 ◽  
Vol 50 ◽  
pp. 102
Author(s):  
D. Enderle ◽  
K. Brinkmann ◽  
T. Koestler ◽  
S. Bentink ◽  
C. Berking ◽  
...  
Keyword(s):  
Plasma Samples ◽  
Cell Free Dna ◽  
Free Dna ◽  
One Step ◽  
Circulating Cell Free Dna

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.

scholarly journals Plasma free DNA

2018 ◽  
Vol 29 (1) ◽  
pp. 153-156 ◽  
Author(s):  
Dietmar Enko ◽  
Gabriele Halwachs-Baumann ◽  
Gernot Kriegshäuser
Keyword(s):  
Blood Collection ◽  
Plasma Samples ◽  
Cell Free Dna ◽  
Free Dna ◽  
Roche Diagnostics Gmbh ◽  
Dna Collection ◽  
Roche Diagnostics ◽  
The Impact ◽  
Time Point ◽  
Circulating Cell Free Dna

Introduction: Standardized pre-analytical blood sample procedures for the analysis of circulating cell-free DNA (ccfDNA) are still not available. Therefore, the present study aimed at evaluating the impact of storage conditions related to different times (24 and 48 h) and temperatures (room temperature (RT) and 4 - 8 °C) on the plasma ccfDNA concentration of blood samples drawn into Cell-Free DNA collection tubes (Roche Diagnostics GmbH, Mannheim, Germany). Materials and methods: Venous blood from 30 healthy individuals was collected into five 8.5 mL Cell-Free DNA Collection Tubes (Roche Diagnostics GmbH) each. Plasma samples were processed at time point of blood collection (tube 1), and after storage under the following conditions: 24 h at RT (tube 2) or 4-8 °C (tube 3), and 48 h at RT (tube 4) or 4 - 8 °C (tube 5). Circulating cell-free DNA concentrations were determined by EvaGreen chemistry-based droplet digital PCR (ddPCR). Results: No statistically significant differences between median (interquartile range) plasma ccfDNA concentrations (ng/mL) at time point of blood collection (3.17 (2.13 – 3.76)) and after storage for 24 h (RT: 3.02 (2.41 – 3.68); 4-8 °C: 3.21 (2.19 – 3.46)) and 48 h (RT: 3.13 (2.10 – 3.76); 4-8 °C: 3.09 (2.19 – 3.50)) were observed (P values from 0.102 – 0.975). Conclusions: No unwanted release of genomic DNA from white blood cells could be detected in plasma samples after tube storage for 24 and 48 h regardless of storage temperature.

5-hydroxymethylation signatures in plasma circulating cell-free DNA as markers for appendiceal and colorectal peritoneal metastasis.

2020 ◽  
Vol 38 (4_suppl) ◽  
pp. 195-195
Author(s):  
Yaniv Berger ◽  
Xiao-Long Cui ◽  
Diana West ◽  
Marco Rivas ◽  
Phillip Hsu ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Peritoneal Metastasis ◽  
Peritoneal Cancer Index ◽  
Tissue Bank ◽  
Low Grade ◽  
Plasma Samples ◽  
Appendiceal Cancer ◽  
Cell Free Dna ◽  
Free Dna ◽  
Circulating Cell Free Dna

195 Background: Noninvasive tests for peritoneal metastasis (PM) detection lack sensitivity. Genome-wide mapping of 5-hydroxymethylcytosine (5hmC) on nanogram quantities of peripheral plasma circulating cell-free DNA (PcfDNA) was previously shown to differentiate non-metastatic colorectal cancer from healthy subjects. We aimed to examine if patients with colorectal cancer (CRC), high grade appendiceal cancer (HGA) or low grade appendiceal cancer (LGA) with PM have distinct signatures of 5hmC in PcfDNA compared to each other and to patients matched for tumors without PM. Methods: We analyzed plasma samples from a prospectively collected tissue bank. To correlate 5hmC signatures with intraoperative findings, only patients who underwent abdominal surgery in proximity to plasma collection were selected. Key steps of PcfDNA processing included extraction from plasma, nano-hmC-Seal chemical labeling and enrichment of 5hmC-modified fragments, next-generation sequencing, and mapping to the reference human genome. DESeq2 R package was finally used to compare relative 5hmC enrichment and detect distinct 5hmC signatures according to disease histology and PM presence. Results: Plasma samples were collected between 11/2016 – 3/2019 from 46 patients with CRC (n = 21), HGA (n = 17) and LGA (n = 8). Of those, 32 (70%) had PM based on intraoperative findings (median peritoneal cancer index score = 15, range 2-39) and 14 did not have PM. Most samples (91%) were collected on the same day as surgery. An average of 24 million paired-end reads were sequenced for each sample. Four samples (8.7%) were excluded from the analysis due to low sequencing coverage or high duplication level. Unique 5hmC enrichment patterns were found to discriminate with p < 0.05 between CRC PM and HGA PM (n = 616 differentially hydroxymethylated genes (DHMGs)), CRC/HGA PM and LGA PM (n = 1074 DHMGs), and CRC/HGA PM and CRC/HGA patients without PM (n = 1576 DHMGs). Conclusions: Distinct signatures of 5hmC in PcfDNA could differentiate patients with CRC/HGA/LGA PM from each other and from patients with similar tumor histologies without PM. Thus 5hmC signatures in PcfDNA might potentially serve as a sensitive marker of occult PM.

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
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