Proficiency testing and pre-diagnostic characterization of extracted dna for external quality assurance

Background: Current external quality assurance (EQA) programs for DNA extraction require participating laboratories to perform DNA extraction on an EQA provided fresh blood sample or specific tissue type. However, this strategy is too restrictive for laboratories who regularly perform DNA extraction on other tissue types or for biobanks who have vast stores of archived specimens that are unrelated to the EQA material. To address this, a pilot EQA program was developed by the Royal College of Pathologists of Australasia Quality Assurance Programs (RCPAQAP) where laboratories were requested to directly submit to the RCPAQAP five DNA extracts that were of specific interest to them. Methods: Three complementary measuring strategies were used for quality assessing all received DNA extracts. Total DNA integrity was analysed using a DNA TapeStation 4200 (Agilent Technologies) and pre-diagnostic validation was performed using multiplex-PCR and real-time PCR. Results: A total of 89 DNA extracts isolated from 16 different tissue types were submitted for quality assessment between 2016 and 2017. 97% (86/89) of DNA extracts were concordant for DNA integrity with three samples (3%) being discordant. Two of the three discordant samples were however concordant for multiplex and real-time PCR. Only one DNA extract failed all three measuring platforms. Conclusion: The data from this study indicate that DNA extracted from multiple tissue types using an array of extraction platforms can be quality assessed and diagnostically pre-validated at the same time. The RCPAQAP are the first EQA provider to offer this type of proficiency testing program and are developing similar strategies for future fixed-formalin paraffin-embedded and circulating free DNA testing.