title: Assessing quality and functionality of DNA isolated from FFPE tissues through external quality assessment in tissue banks.
abstract: BACKGROUND
  Biobanks are becoming increasingly important for assessment of disease risk as well as identification and validation of new diagnostic biomarkers and druggable targets. The validity of data obtained from biobanks is critically limited by the biomaterial quality of the biological samples. External quality assessment (EQA) programs suitable to comprehensively measure the biomaterial quality in archived materials are currently lacking. We report on quantitative assay designs for the analysis of both structural and functional integrity of DNAs that were applied in a first pilot EQA within the priority program on tumor tissue biobanking funded by the German Cancer Aid.
  
  
  METHODS
  Participating biobanks isolated DNAs from a standardized set of 10 samples comprising sections of four different formalin-fixed paraffin-embedded tissues using their standard operating procedures. Isolated DNAs and analytical results were returned and analyzed centrally for nucleic acids yield, purity, fragmentation and amplificability at a quantitative level using dedicated assay designs.
  
  
  RESULTS
  The amount of extracted DNA varied in isolates ranging between 1.5 μg and 25.8 μg. Quantification of DNA fragmentation and amplificability allowed to highlight considerable discrepancies in DNA quality. Amplicons yielded from the isolates of these identical EQA samples ranged from 105 to 411 bp suggesting differences between residual inhibitors of downstream enzymatic reactions.
  
  
  CONCLUSIONS
  The quality of extraction of bioanalytes from biomaterial archives is heterogeneous even for stable biomolecules like DNA isolated with highly standardized methods. EQAs are appropriate tools to uncover strengths and weaknesses in biobanks in a systematic fashion. Biomaterial integrity is insufficiently reflected by standard methods, but needs to be assessed to improve biobank interoperability. Finally, our results also point towards the problem of measuring the quality of more delicate biomolecules like proteins or metabolites.
authors.forename: Parviz
authors.initials: P
authors.lastname: Ahmad-Nejad
authors.forename: Angelika
authors.initials: A
authors.lastname: Duda
authors.forename: Antje
authors.initials: A
authors.lastname: Sucker
authors.forename: Martin
authors.initials: M
authors.lastname: Werner
authors.forename: Peter
authors.initials: P
authors.lastname: Bronsert
authors.forename: Elmar
authors.initials: E
authors.lastname: Stickeler
authors.forename: Guido
authors.initials: G
authors.lastname: Reifenberger
authors.forename: Bastian
authors.initials: B
authors.lastname: Malzkorn
authors.forename: Martina
authors.initials: M
authors.lastname: Oberländer
authors.forename: Jens K
authors.initials: JK
authors.lastname: Habermann
authors.forename: Hans-Peter
authors.initials: HP
authors.lastname: Bruch
authors.forename: Michael
authors.initials: M
authors.lastname: Linnebacher
authors.forename: Dirk
authors.initials: D
authors.lastname: Schadendorf
authors.forename: Michael
authors.initials: M
authors.lastname: Neumaier
mesh_terms: D004247:DNA / Q000235:genetics / Q000302:isolation & purification* / Q000592:standards; D005557:Formaldehyde / Q000737:chemistry*; D006801:Humans; D016612:Paraffin Embedding / Q000592:standards; D011786:Quality Control; D014015:Tissue Banks / Q000592:standards*
chemical_list: D005557:Formaldehyde; D004247:DNA