Comparison of different semi-automated cfDNA extraction methods in combination with UMI-based targeted sequencing Article Swipe
Anna Streubel
,
Albrecht Stenzinger
,
Susann Stephan-Falkenau
,
Jens Kollmeier
,
Daniel Misch
,
Torsten Blum
,
Torsten T. Bauer
,
Olfert Landt
,
Alexander Am Ende
,
Peter Schirmacher
,
Thomas Mairinger
,
Volker Endris
·
YOU?
·
· 2019
· Open Access
·
· DOI: https://doi.org/10.18632/oncotarget.27183
YOU?
·
· 2019
· Open Access
·
· DOI: https://doi.org/10.18632/oncotarget.27183
The analysis of circulating cell-free DNA (cfDNA) extracted from peripheral blood can serve as a minimally invasive alternative to tumor tissue biopsies in cases with impaired access to tissue. Its clinical utility has been well demonstrated for EGFR T790M testing in lung cancer patients suffering progress after tyrosine kinase inhibitor treatment. At present, highly sensitive unique molecular identifiers (UMI)-based NGS for liquid biopsy testing is less established compared to single gene assays. However, the critical bottleneck are sufficient cfDNA yields, which are essentially required to obtain meaningful test results. We compared four different cfDNA extraction methods (Qiagen, Promega, Thermo and Stratec) using the same plasma samples in order to evaluate their suitability for further NGS analysis. We managed to draw 60 ml blood from 12 patients each and equally collected 30ml in PAXgene and EDTA tubes at the same time point, sufficient for total of 96 cfDNA extractions. CfDNA concentrations and total amounts were highest for Qiagen and Promega protocols, showing the best read length profiles after sequencing. Known oncogenic driver mutations were identified in 9 out of 12 patients with at least one of the cfDNA extraction methods, again favoring the extraction protocols from Qiagen and Promega. We also uncovered putative sequencing artefacts including known driver genes pointing to a careful consideration for the limit of detection of this methodology. Our study shows that pre-analytical optimization is necessary to achieve the maximum sensitivity of UMI-based sequencing but also highlights the low abundance of tumor-derived cfDNA in lung cancer samples.
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- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.18632/oncotarget.27183
- https://www.oncotarget.com/article/27183/pdf/
- OA Status
- diamond
- Cited By
- 19
- References
- 23
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W2980641810
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W2980641810Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.18632/oncotarget.27183Digital Object Identifier
- Title
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Comparison of different semi-automated cfDNA extraction methods in combination with UMI-based targeted sequencingWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2019Year of publication
- Publication date
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2019-10-01Full publication date if available
- Authors
-
Anna Streubel, Albrecht Stenzinger, Susann Stephan-Falkenau, Jens Kollmeier, Daniel Misch, Torsten Blum, Torsten T. Bauer, Olfert Landt, Alexander Am Ende, Peter Schirmacher, Thomas Mairinger, Volker EndrisList of authors in order
- Landing page
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https://doi.org/10.18632/oncotarget.27183Publisher landing page
- PDF URL
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https://www.oncotarget.com/article/27183/pdf/Direct link to full text PDF
- Open access
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YesWhether a free full text is available
- OA status
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diamondOpen access status per OpenAlex
- OA URL
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https://www.oncotarget.com/article/27183/pdf/Direct OA link when available
- Concepts
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Liquid biopsy, Medicine, T790M, Lung cancer, Biopsy, Oncology, Cancer, Internal medicine, Pathology, Adenocarcinoma, ROS1Top concepts (fields/topics) attached by OpenAlex
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19Total citation count in OpenAlex
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2025: 3, 2023: 4, 2022: 6, 2021: 4, 2020: 2Per-year citation counts (last 5 years)
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23Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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