Blood Collection and Cell-Free DNA Isolation Methods Influence the Sensitivity of Liquid Biopsy Analysis for Colorectal Cancer Detection

2018 ◽  
Vol 25 (3) ◽  
pp. 915-923 ◽  
Author(s):  
Barbara Kinga Barták ◽  
Alexandra Kalmár ◽  
Orsolya Galamb ◽  
Barnabás Wichmann ◽  
Zsófia Brigitta Nagy ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Cancer Detection ◽  
Liquid Biopsy ◽  
Dna Isolation ◽  
Blood Collection ◽  
Cell Free Dna ◽  
Free Dna ◽  
Isolation Methods

scholarly journals A simple silica based DNA isolation method for cell-free DNA analysis from liquid biopsy

2020 ◽  
Vol 0 (0) ◽  
Author(s):  
Burhanettin Yalcinkaya ◽  
Kübra Coşkun ◽  
Muslum Akgoz ◽  
Sadrettin Pence
Keyword(s):  
Liquid Biopsy ◽  
Dna Analysis ◽  
Dna Isolation ◽  
Cancer Diagnostics ◽  
Biopsy Material ◽  
Cell Free Dna ◽  
Extracellular Rna ◽  
Free Dna ◽  
Isolation Methods ◽  
Commercial Kits

AbstractObjectivesCell-free DNA (cfDNA) is a promising biomarker for cancer diagnostics. Blood is used as a liquid biopsy material which transports many types of biological components such as protein, circulating tumor cells, cfDNA, and extracellular RNA molecules. In this study, the yield and purity of extracted DNA were compared of seven different in-house DNA isolation methods and two different commercial kits from human blood samples.MethodsDifferent in-house methods, guanidine thiocyanate (GuSCN) with silica method, phenol-chloroform-isoamylalcohol method-1, phenol-chloroform-isoamylalcohol method-2, phenol-chloroform-isoamylalcohol with ammonium acetate method, sodium N-lauryl sarcosine with glycogen method, sodium acetate method, sodium chloride with silica method and two different commercial kits “Quick-cfDNA serum & plasma kit” and “plasma/serum cell-free circulating DNA purification mini kit” were used. After DNA isolation, methods were compared with real time PCR technique (qPCR) and spectrophotometric methods.ResultsThe results showed that the newly modified GuSCN with silica method gave much higher purity and yield than any other analyzed in-house isolation methods and commercial kits that were used.ConclusionsThe GuSCN with silica method is simple to set up, easy to use, inexpensive and environmentally safe. The method would be an alternative method for cfDNA isolation from liquid biopsy samples.

scholarly journals Comparison of Blood Collection Tubes from Three Different Manufacturers for the Collection of Cell-Free DNA for Liquid Biopsy Mutation Testing

2017 ◽  
Vol 19 (5) ◽  
pp. 801-804 ◽  
Author(s):  
Christina Alidousty ◽  
Danielle Brandes ◽  
Carina Heydt ◽  
Svenja Wagener ◽  
Maike Wittersheim ◽  
...  
Keyword(s):  
Liquid Biopsy ◽  
Mutation Testing ◽  
Blood Collection ◽  
Cell Free Dna ◽  
Free Dna ◽  
Blood Collection Tubes

scholarly journals Rapid response of stage IV colorectal cancer with APC/TP53/KRAS mutations to FOLFIRI and Bevacizumab combination chemotherapy: a case report of use of liquid biopsy

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Alexander Hendricks ◽  
Philip Rosenstiel ◽  
Sebastian Hinz ◽  
Greta Burmeister ◽  
Christoph Röcken ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Treatment Response ◽  
Liquid Biopsy ◽  
Metastatic Cancer ◽  
Stage Iv ◽  
Liquid Biopsies ◽  
Kras Mutations ◽  
Cell Free Dna ◽  
Stage Iv Colorectal Cancer ◽  
Free Dna

Abstract Background Liquid biopsies of blood plasma cell free DNA can be used to monitor treatment response and potentially detect mutations that are present in resistant clones in metastatic cancer patients. Case presentation In our non-interventional liquid biopsy study, a male patient in his fifties diagnosed with stage IV colorectal cancer and polytope liver metastases rapidly progressed after completing chemotherapy and deceased 8 months after diagnosis. Retrospective cell free DNA testing showed that the APC/TP53/KRAS major clone responded quickly after 3 cycles of FOLFIRI + Bevacizumab. Retrospective exome sequencing of pre-chemotherapy and post-chemotherapy tissue samples including metastases confirmed that the APC/TP53/KRAS and other major clonal mutations (GPR50, SLC5A, ZIC3, SF3A1 and others) were present in all samples. After the last chemotherapy cycle, CT imaging, CEA and CA19–9 markers validated the cfDNA findings of treatment response. However, 5 weeks later, the tumour had rapidly progressed. Conclusion As FOLFIRI+Bevacizumab has recently also been associated with sustained complete remission in a APC/TP53/KRAS triple-mutated patient, these driver genes should be tested and monitored in a more in-depth manner in future patients. Patients with metastatic disease should be monitored more closely during and after chemotherapy, ideally using cfDNA.

scholarly journals Liquid biopsy by NGS: differential presence of exons (DPE) in cell-free DNA reveals different patterns in metastatic and nonmetastatic colorectal cancer

2018 ◽  
Vol 7 (5) ◽  
pp. 1706-1716 ◽  
Author(s):  
Susana Olmedillas-López ◽  
Dolores C. García-Olmo ◽  
Mariano García-Arranz ◽  
Ramón Peiró-Pastor ◽  
Begoña Aguado ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Liquid Biopsy ◽  
Cell Free Dna ◽  
Free Dna

scholarly journals Cell-Free DNA Blood Collection Tubes Are Appropriate for Clinical Proteomics: A Demonstration in Colorectal Cancer

2018 ◽  
Vol 12 (3) ◽  
pp. 1700121 ◽  
Author(s):  
Juhura G. Almazi ◽  
Peter Pockney ◽  
Craig Gedye ◽  
Nathan D. Smith ◽  
Hubert Hondermarck ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Clinical Proteomics ◽  
Blood Collection ◽  
Cell Free Dna ◽  
Free Dna ◽  
Blood Collection Tubes

scholarly journals Sensitivity assessment of workflows detecting rare circulating cell-free DNA targets: A study design proposal

PLoS ONE ◽  
2021 ◽  
Vol 16 (7) ◽  
pp. e0253401
Author(s):  
Thorsten Voss ◽  
Andrea Ullius ◽  
Maike Schönborn ◽  
Uwe Oelmüller
Keyword(s):  
Study Design ◽  
Liquid Biopsy ◽  
Limit Of Detection ◽  
Test Procedure ◽  
Blood Collection ◽  
Assay Sensitivity ◽  
Cell Free Dna ◽  
Free Dna ◽  
Sensitivity Assessment ◽  
Circulating Cell Free Dna

The field of liquid biopsy has seen extensive growth in recent decades, making it one of the most promising areas in molecular diagnostics. Circulating cell-free DNA (ccfDNA) especially is used as an analyte in a growing number of diagnostic assays. These assays require specified preanalytical workflows delivering ccfDNA in qualities and quantities that facilitate correct and reliable results. As each step and component used in the preanalytical process has the potential to influence the assay sensitivity and other performance characteristics, it is key to find an unbiased experimental setup to test these factors in diagnostic or research laboratories. We defined one such setup by using blood from healthy subjects and commercially available products for blood collection, spike-in material, ccfDNA isolation, and qPCR assays. As the primary read-out, we calculated the probit model-based LOD95 (limit of detection of the 95th percentile) from the qPCR assay results. In a proof of principle study we tested two different but widely used blood ccfDNA profile stabilization technologies in blood collection tubes, the Cell-Free DNA BCT and the PAXgene Blood ccfDNA Tube. We tested assays for three different EGFR gene mutations and one BRAF gene mutation. The study design revealed differences in performance between the two tested technologies for all four mutations. In conclusion, we successfully established a blueprint for a test procedure capable of verifying and validating a liquid biopsy workflow from blood collection to the analytical result.

scholarly journals Liquid Biopsy Cell-free DNA Biomarkers in Patients With Oligometastatic Colorectal Cancer Treated by Ablative Radiotherapy

2021 ◽  
Vol 41 (2) ◽  
pp. 829-834
Author(s):  
MASAKI NAKAMURA ◽  
SHUN-ICHIRO KAGEYAMA ◽  
MASAHIDE SEKI ◽  
AYAKO SUZUKI ◽  
MASAYUKI OKUMURA ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Liquid Biopsy ◽  
Cell Free Dna ◽  
Free Dna

scholarly journals Analysis of colorectal cancer‐related mutations by liquid biopsy: Utility of circulating cell‐free DNA and circulating tumor cells

2019 ◽  
Vol 110 (11) ◽  
pp. 3497-3509 ◽  
Author(s):  
Kohki Takeda ◽  
Takeshi Yamada ◽  
Goro Takahashi ◽  
Takuma Iwai ◽  
Koji Ueda ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Tumor Cells ◽  
Circulating Tumor Cells ◽  
Liquid Biopsy ◽  
Cell Free Dna ◽  
Free Dna ◽  
Circulating Cell Free Dna
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