Molecular genetic proficiency testing of extracted DNA from archived biobank tissue

January 11, 2018 2:53 pm

The Molecular Genetics discipline at the Royal College of Pathologists of Australasia Quality Assurance Programs (RCPAQAP) have devised a novel strategy that now offers external quality assurance (EQA) to tissue biobanks for proficiency testing of their archived DNA. This new initiative allows for multiple tissues from either recent and/or archived tissue to be quality tested at the same time. Importantly, there are no limitations on the tissue type to be examined. For example, proficiency testing can be performed on DNA extracted from whole blood, from serum (i.e., circulating free DNA), and from formalin-fixed paraffin-embedded (FFPE) organ or tumour tissue.

Current EQA providers offering DNA extraction programs are required to ship whole blood samples to participating laboratories with a request for genomic DNA to be extracted. However, this current EQA strategy is financially prohibitive to laboratories operating on different continents (to that of the EQA provider) as the cost of continental shipping of whole blood is too expensive. More importantly, the shipping of whole blood for DNA extraction EQA assessment is of no use to tissue biobanks who predominantly require proficiency testing of different archived tissue types. This led the RCPAQAP to therefore develop a novel amenable approach that would be applicable for the testing of archived material stored in tissue biobanks. The primary difference between the RCPAQAP and other EQA providers for DNA extraction proficiency testing is that the shipping of whole blood (by the EQA provider) is not required. Instead, the RCPAQAP proficiency test consists of two key developments. Firstly, the RCPAQAP will request that each biobank isolate DNA from tissue of specific interest and forward this to the RCPAQAP. Secondly, validation assays involving spectrophotometric, fluorometric, DNA TapeStation, multiplex PCR, gel electrophoresis, and digital PCR DNA copy number analyses will be performed by the RCPAQAP to determine the quality of each DNA extract. This EQA multi-platform analysis approach allows for a full interrogation of the DNA extract so that the suitability of the DNA for use in downstream genetic diagnostic testing applications can be determined.

For any further information or discussions on this contact martin.horan@rcpatemp.localhost