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Assessing quality and functionality of DNA isolated from FFPE tissues through external quality assessment in tissue banks

  • Parviz Ahmad-Nejad , Angelika Duda , Antje Sucker , Martin Werner , Peter Bronsert , Elmar Stickeler , Guido Reifenberger , Bastian Malzkorn , Martina Oberländer , Jens K. Habermann , Hans-Peter Bruch , Michael Linnebacher , Dirk Schadendorf and Michael Neumaier EMAIL logo
Published/Copyright: June 6, 2015
Clinical Chemistry and Laboratory Medicine (CCLM)
From the journal Clinical Chemistry and Laboratory Medicine (CCLM) Volume 53 Issue 12

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.

Keywords: biobanking; DNA fragmentation; FFPE quality
Corresponding author: Prof. Dr. Michael Neumaier, University Medical Centre Mannheim, Medical Faculty Mannheim, University of Heidelberg, Institute for Clinical Chemistry, Theodor Kutzer Ufer 1-3, 68167 Mannheim, Germany, Phone: +49 621 383 2222, Fax: +49 621 383 3819, E-mail:

References

1. Riegman PH, Morente MM, Betsou F, de Blasio P, Geary P. Biobanking for better healthcare. Mol Oncol 2008;2:213–22.10.1016/j.molonc.2008.07.004Search in Google Scholar PubMed PubMed Central

2. Ringborg U, de Valeriola D, van Harten W, Bosch AL, Lombardo C, Nilsson K, et al. Improvement of European translational cancer research. Collaboration between comprehensive cancer centers. Tumori 2008;94:143–6.10.1177/030089160809400202Search in Google Scholar

3. Yuille M, van Ommen GJ, Brechot C, Cambon-Thomsen A, Dagher G, Landegren U, et al. Biobanking for Europe. Brief Bioinform 2008;9:14–24.10.1093/bib/bbm050Search in Google Scholar PubMed

4. Wichmann HE, Kuhn KA, Waldenberger M, Schmelcher D, Schuffenhauer S, Meitinger T, et al. Comprehensive catalog of European biobanks. Nat Biotechnol 2011;29:795–7.10.1038/nbt.1958Search in Google Scholar PubMed

5. Bezemer ID, Bare LA, Doggen CJ, Arellano AR, Tong C, Rowland CM, et al. Gene variants associated with deep vein thrombosis. J Am Med Assoc 2008;299:1306–14.10.1001/jama.299.11.1306Search in Google Scholar PubMed

6. Chapman PB, Hauschild A, Robert C, Haanen JB, Ascierto P, Larkin J, et al. Improved survival with vemurafenib in melanoma with braf v600e mutation. N Engl J Med 2011;364:2507–16.10.1056/NEJMoa1103782Search in Google Scholar PubMed PubMed Central

7. Clarke R, Peden JF, Hopewell JC, Kyriakou T, Goel A, Heath SC, et al. Genetic variants associated with lp(a) lipoprotein level and coronary disease. N Engl J Med 2009;361:2518–28.10.1056/NEJMoa0902604Search in Google Scholar PubMed

8. Khor CC, Chapman SJ, Vannberg FO, Dunne A, Murphy C, Ling EY, et al. A mal functional variant is associated with protection against invasive pneumococcal disease, bacteremia, malaria and tuberculosis. Nat Genet 2007;39:523–8.10.1038/ng1976Search in Google Scholar PubMed PubMed Central

9. Moffatt MF, Gut IG, Demenais F, Strachan DP, Bouzigon E, Heath S, et al. A large-scale, consortium-based genomewide association study of asthma. N Engl J Med 2010;363:1211–21.10.1056/NEJMoa0906312Search in Google Scholar PubMed PubMed Central

10. Morente MM, Mager R, Alonso S, Pezzella F, Spatz A, Knox K, et al. Tubafrost 2: standardising tissue collection and quality control procedures for a European virtual frozen tissue bank network. Eur J Cancer 2006;42:2684–91.10.1016/j.ejca.2006.04.029Search in Google Scholar PubMed

11. Riegman PH, Bosch AL. Oeci tubafrost tumor biobanking. Tumori 2008;94:160–3.10.1177/030089160809400205Search in Google Scholar

12. http://www.iarc.fr/en/publications/pdfs-online/wrk/wrk2/standardsBRC-1.pdf.Search in Google Scholar

13. Lin J, Kennedy SH, Svarovsky T, Rogers J, Kemnitz JW, Xu A, et al. High-quality genomic DNA extraction from formalin-fixed and paraffin-embedded samples deparaffinized using mineral oil. Anal Biochem 2009;395:265–7.10.1016/j.ab.2009.08.016Search in Google Scholar PubMed PubMed Central

14. Okayama N, Nishioka M, Hazama S, Sakai K, Suehiro Y, Maekawa M, et al. The importance of evaluation of DNA amplificability in kras mutation testing with dideoxy sequencing using formalin-fixed and paraffin-embedded colorectal cancer tissues. Jpn J Clin Oncol 2011;41:165–71.10.1093/jjco/hyq173Search in Google Scholar PubMed

15. Miller SA, Dykes DD, Polesky HF. A simple salting out procedure for extracting DNA from human nucleated cells. Nucleic Acids Res 1988;16:1215.10.1093/nar/16.3.1215Search in Google Scholar PubMed PubMed Central

16. Orlando C, Verderio P, Maatman R, Danneberg J, Ramsden S, Neumaier M, et al. Equal-qual: A European program for external quality assessment of genomic DNA extraction and PCR amplification. Clin Chem 2007;53:1349–57.10.1373/clinchem.2006.084004Search in Google Scholar PubMed

17. Ahmad-Nejad P, Dorn-Beineke A, Pfeiffer U, Brade J, Geilenkeuser WJ, Ramsden S, et al. Methodologic European external quality assurance for DNA sequencing: the equalseq program. Clin Chem 2006;52:716–27.10.1373/clinchem.2005.061572Search in Google Scholar PubMed

18. Dorn-Beineke A, Ahmad-Nejad P, Pfeiffer U, Ramsden S, Pazzagli M, Neumaier M. Improvement of technical and analytical performance in DNA sequencing by external quality assessment-based molecular training. Clin Chem 2006;52:2072–8.10.1373/clinchem.2006.072405Search in Google Scholar PubMed

19. Lewis SM. Eqa for general haematology in the United Kingdom. Ann Ist Super Sanita 1995;31:71–5.Search in Google Scholar

20. Ramsden SC, Daly S, Geilenkeuser WJ, Duncan G, Hermitte F, Marubini E, et al. Equal-quant: an international external quality assessment scheme for real-time PCR. Clin Chem 2006;52:1584–91.10.1373/clinchem.2005.066019Search in Google Scholar PubMed

21. Sciacovelli L, Secchiero S, Zardo L, Zaninotto M, Plebani M. External quality assessment: an effective tool for clinical governance in laboratory medicine. Clin Chem Lab Med 2006;44:740–9.10.1515/CCLM.2006.133Search in Google Scholar PubMed

22. Kruse R, Geilenkeuser WJ, Rohle G. Overview: quality control of tumor marker assays. Int J Biol Markers 1998;13:238–40.10.1177/172460089801300412Search in Google Scholar

Supplemental Material:

The online version of this article (DOI: 10.1515/cclm-2014-1202) offers supplementary material, available to authorized users.

Received: 2014-12-5
Accepted: 2015-4-30
Published Online: 2015-6-6
Published in Print: 2015-11-1

©2015 by De Gruyter

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https://doi.org/10.1515/cclm-2014-1202
Keywords for this article
biobanking; DNA fragmentation; FFPE quality

Articles in the same Issue

  1. Frontmatter
  2. Editorial
  3. Biomarkers of inflammatory bowel disease: ready for prime time?
  4. Review
  5. Discriminant indices for distinguishing thalassemia and iron deficiency in patients with microcytic anemia: a meta-analysis
  6. Mini Reviews
  7. Cell-free DNA for diagnosing myocardial infarction: not ready for prime time
  8. The Laboratory Medicine and the care of patients infected by the Ebola virus. Experience in a reference hospital of Madrid, Spain
  9. Opinion Papers
  10. Theranos phenomenon − part 2
  11. Considerations in parathyroid hormone testing
  12. Quantity quotient reporting. Comparison of various models
  13. Genetics and Molecular Diagnostics
  14. Assessing quality and functionality of DNA isolated from FFPE tissues through external quality assessment in tissue banks
  15. 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
  16. Non-invasive fetal ABO genotyping in maternal plasma using real-time PCR
  17. Screening non-deletion α-thalassaemia mutations in the HBA1 and HBA2 genes by high-resolution melting analysis
  18. General Clinical Chemistry and Laboratory Medicine
  19. European views on patients directly obtaining their laboratory test results
  20. Diagnostic performances of clinical laboratory tests using Triton X-100 to reduce the biohazard associated with routine testing of Ebola virus-infected patients
  21. Thrombin generation, D-dimer and protein S in uncomplicated pregnancy
  22. Multi-analyte analysis of non-vitamin K antagonist oral anticoagulants in human plasma using tandem mass spectrometry
  23. Second generation analysis of antinuclear antibody (ANA) by combination of screening and confirmatory testing
  24. Faecal leukocyte esterase activity is an alternative biomarker in inflammatory bowel disease
  25. Reference Values and Biological Variations
  26. Total folate and 5-methyltetrahydrofolate in the cerebrospinal fluid of children: correlation and reference values
  27. Effect of age and gender on reference intervals of red blood cell distribution width (RDW) and mean red cell volume (MCV)
  28. Infectious Diseases
  29. Inosine triphosphate pyrophosphohydrolase activity: more accurate predictor for ribavirin-induced anemia in hepatitis C infected patients than ITPA genotype
  30. The ratio of calprotectin to total protein as a diagnostic and prognostic marker for spontaneous bacterial peritonitis in patients with liver cirrhosis and ascites
  31. Letter to the Editors
  32. Misleading high-sensitivity troponin algorithm for NSTEMI in the ESC guidelines
  33. Adjustment of serum potassium for age and platelet count. A simple step forward towards personalized medicine
  34. The impact of Tween 20 on repeatability of amyloid β and tau measurements in cerebrospinal fluid
  35. Effect of storage time and temperature on the generation of reactive oxygen species in peripheral blood leukocytes
  36. Iohexol interference in the α2-globulin fraction of the serum protein capillary electrophoresis
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