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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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Lampignano_2019.pdf (Verlagsversion), 3MB
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© 2019 American Association for Clinical Chemistry
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 Urheber:
Lampignano , Rita , Autor
Neumann, Martin H.D. , Autor
Weber, Sabrina, Autor
Kloten, Vera, Autor
Herdean, Andrei , Autor
Voss, Thorsten, Autor
Groelz, Daniel , Autor
Babayan, Anna, Autor
Tibbesma, Marco , Autor
Schlumpberger, Martin, Autor
Chemi, Francesca , Autor
Rothwell, Dominic G. , Autor
Wikman, Harriet, Autor
Galizzi, Jean-Pierre , Autor
Bergheim, Inger Riise , Autor
Russnes, Hege, Autor
Mussolin, Benedetta , Autor
Bonin, Serena, Autor
Voigt, Christine , Autor
Musa, Hanny, Autor
Pinzani, Pamela , AutorLianidou, Evi, AutorBrady, Ged, AutorSpeicher, Michael R., AutorPantel, Klaus, AutorBetsou, Fay, AutorSchuuring, Ed, AutorKubista, Mikael , AutorAmmerlaan, Wim, AutorSprenger-Haussels, Markus , AutorSchlange, Thomas, AutorHeitzer, Ellen , AutorLehrach, Hans1, 2, 3, Autor           Yaspo, Marie-Laure3, 4, Autor            mehr..
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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 Zusammenfassung: 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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Sprache(n): eng - English
 Datum: 2019-08-052019-12-302020-01
 Publikationsstatus: Erschienen
 Seiten: -
 Ort, Verlag, Ausgabe: -
 Inhaltsverzeichnis: -
 Art der Begutachtung: -
 Identifikatoren: DOI: 10.1373/clinchem.2019.306837
 Art des Abschluß: -

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Titel: Clinical Chemistry : International Journal of Molecular Diagnostics and Laboratory Medicine
  Andere : Clin Chem
Genre der Quelle: Zeitschrift
 Urheber:
Affiliations:
Ort, Verlag, Ausgabe: Washington, DC : American Association for Clinical Chemistry
Seiten: 12 Band / Heft: 66 (1) Artikelnummer: - Start- / Endseite: 149 - 160 Identifikator: ISSN: 0009-9147 (print)
ISSN: 1530-8561 (electronic)
CoNE: https://pure.mpg.de/cone/journals/resource/954925263191