Influence of storage conditions and extraction methods on the quantity and quality of circulating cell-free DNA (ccfDNA): The SPIDIA-DNAplas External Quality Assessment experience

Francesca Malentacchi, Sara Pizzamiglio, Paolo Verderio, Mario Pazzagli, Claudio Orlando, Chiara Maura Ciniselli, Kalle Günther, Stefania Gelmini

Research output: Contribution to journalArticlepeer-review

Abstract

Background: Circulating cell-free DNA (ccfDNA) has been confirmed as a useful biomarker in cancer and pre-natal clinical practice. One of the main critical points in using ccfDNA is a lack of standardisation for sample processing methods, storage conditions, procedures for extraction, and quantification that can affect ccfDNA quality and quantity. We report the results obtained from the SPIDIA-DNAplas, one of the EU SPIDIA (Standardisation and improvement of generic pre-analytical tools and procedures for in vitro diagnostics) subprojects based on the implementation of an External Quality Assessment scheme for the evaluation of the influence of the pre-analytical phase on ccfDNA. This is the first reported quality control scheme targeting ccfDNA for pre-analytical phase studies. Methods: Fifty-six laboratories throughout Europe were recruited. The participating laboratories received the same plasma sample and extracted ccfDNA by using their own procedures, at defined plasma storage conditions, and sent the isolated ccfDNA to the SPIDIA facility for analyses. Laboratory performance was evaluated by using specific quality parameters such as ccfDNA integrity (by multiplex PCR) and yield (by qPCR). Results: The analysis of the ccfDNA extracted by the laboratories showed that most of them (53 of 56) were able to recover ccfDNA but only 12.5% recovered non-fragmented ccfDNA. Extraction methods specifically designed for ccfDNA preserved the integrity profile. Conclusions: The evidence-based results of the SPIDIA-DNAplas EQA have been proposed as a basis for the development of a Technical Specification by the European Committee for standardisation (CEN).

Original languageEnglish
Pages (from-to)1935-1942
Number of pages8
JournalClinical Chemistry and Laboratory Medicine
Volume53
Issue number12
DOIs
Publication statusPublished - Nov 1 2015

Keywords

  • circulating cell-free DNA
  • External Quality Assessment
  • pre-analytical phase

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Biochemistry, medical

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