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

Lampignano, R., Neumann, M. H., Weber, S., Kloten, V., Herdean, A., Voss, T., et al. (2020). Multicenter Evaluation of Circulating Cell-Free DNA Extraction and Downstream Analyses for the Development of Standardized (Pre)analytical Work Flows. Clinical Chemistry: International Journal of Molecular Diagnostics and Laboratory Medicine, 66(1), 149-160. doi:10.1373/clinchem.2019.306837.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0006-3AC3-D Version Permalink: http://hdl.handle.net/21.11116/0000-0006-3AC4-C
Genre: Journal Article

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© 2019 American Association for Clinical Chemistry
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Lampignano , Rita , Author
Neumann, Martin H.D. , Author
Weber, Sabrina, Author
Kloten, Vera, Author
Herdean, Andrei , Author
Voss, Thorsten, Author
Groelz, Daniel , Author
Babayan, Anna, Author
Tibbesma, Marco , Author
Schlumpberger, Martin, Author
Chemi, Francesca , Author
Rothwell, Dominic G. , Author
Wikman, Harriet, Author
Galizzi, Jean-Pierre , Author
Bergheim, Inger Riise , Author
Russnes, Hege, Author
Mussolin, Benedetta , Author
Bonin, Serena, Author
Voigt, Christine , Author
Musa, Hanny, Author
Pinzani, Pamela , AuthorLianidou, Evi, AuthorBrady, Ged, AuthorSpeicher, Michael R., AuthorPantel, Klaus, AuthorBetsou, Fay, AuthorSchuuring, Ed, AuthorKubista, Mikael , AuthorAmmerlaan, Wim, AuthorSprenger-Haussels, Markus , AuthorSchlange, Thomas, AuthorHeitzer, Ellen , AuthorLehrach, Hans1, 2, 3, Author              Yaspo, Marie-Laure3, 4, Author               more..
Affiliations:
1Emeritus Group of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_2385697              
2Alacris Theranostics GmbH, Berlin, Germany, ou_persistent22              
3CANCER-ID Consortium (Innovative Medicines Initiative), ou_persistent22              
4Gene Regulation and Systems Biology of Cancer (Marie-Laure Yaspo), Independent Junior Research Groups (OWL), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_2117287              

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 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.

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Language(s): eng - English
 Dates: 2019-08-052019-12-302020-01
 Publication Status: Published in print
 Pages: -
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 Table of Contents: -
 Rev. Method: -
 Identifiers: DOI: 10.1373/clinchem.2019.306837
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Title: Clinical Chemistry : International Journal of Molecular Diagnostics and Laboratory Medicine
  Other : Clin Chem
Source Genre: Journal
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Publ. Info: Washington, DC : American Association for Clinical Chemistry
Pages: 12 Volume / Issue: 66 (1) Sequence Number: - Start / End Page: 149 - 160 Identifier: ISSN: 0009-9147 (print)
ISSN: 1530-8561 (electronic)
CoNE: https://pure.mpg.de/cone/journals/resource/954925263191