ArticlePloS one2014
Comparison of pre-analytical FFPE sample preparation methods and their impact on massively parallel sequencing in routine diagnostics.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
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- Protein Expression, Amplification, and Mutation ofAnimals : an open access journal from MDPI · 2024Article
- Analysis of quality metrics in comprehensive cancer genomic profiling using a dual DNA-RNA panel.Practical laboratory medicine · 2024Article
- Optimizing genomic DNA extraction from long-term preserved formalin-fixed and paraffin-embedded lung cancer and lymph node tissues.Brazilian journal of medical and biological research = Revista brasileira de pesquisas medicas e biologica · 2024Article
- The ideal reporting ofPathologica · 2023Review
- Overview of Molecular Detection Technologies forCancers · 2023Review
- Validation of p53 Immunohistochemistry (PAb240 Clone) in Canine Tumors with Next-Generation Sequencing (NGS) Analysis.Animals : an open access journal from MDPI · 2023Article
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- Results and lessons from dual extraction of DNA and RNA from formalin-fixed paraffin-embedded breast tumor tissues for a large Cancer epidemiologic study.BMC genomics · 2022Article
- Comparison between Fluorimetry (Qubit) and Spectrophotometry (NanoDrop) in the Quantification of DNA and RNA Extracted from Frozen and FFPE Tissues from Lung Cancer Patients: A Real-World Use of Genomic Tests.Medicina (Kaunas, Lithuania) · 2021Article
- Article
- Bioinformatics and DNA-extraction strategies to reliably detect genetic variants from FFPE breast tissue samples.BMC genomics · 2019Article
- DNA extraction from FFPE tissue samples - a comparison of three procedures.Contemporary oncology (Poznan, Poland) · 2019Article
- Article
- Article
- Evaluation of commercial DNA and RNA extraction methods for high-throughput sequencing of FFPE samples.PloS one · 2018Article
- Use of the GeneReader NGS System in a clinical pathology laboratory: a comparative study.Journal of clinical pathology · 2017Article
- [BRCA diagnostics of ovarian cancer : Molecular tumor testing since the introduction of PARP inhibitor therapy].Der Pathologe · 2017Article
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Over the last years, massively parallel sequencing has rapidly evolved and has now transitioned into molecular pathology routine laboratories. It is an attractive platform for analysing multiple genes at the same time with very little input material. Therefore, the need for high quality DNA obtained from automated DNA extraction systems has increased, especially to those laboratories which are dealing with formalin-fixed paraffin-embedded (FFPE) material and high sample throughput. This study evaluated five automated FFPE DNA extraction systems as well as five DNA quantification systems using the three most common techniques, UV spectrophotometry, fluorescent dye-based quantification and quantitative PCR, on 26 FFPE tissue samples. Additionally, the effects on downstream applications were analysed to find the most suitable pre-analytical methods for massively parallel sequencing in routine diagnostics. The results revealed that the Maxwell 16 from Promega (Mannheim, Germany) seems to be the superior system for DNA extraction from FFPE material. The extracts had a 1.3-24.6-fold higher DNA concentration in comparison to the other extraction systems, a higher quality and were most suitable for downstream applications. The comparison of the five quantification methods showed intermethod variations but all methods could be used to estimate the right amount for PCR amplification and for massively parallel sequencing. Interestingly, the best results in massively parallel sequencing were obtained with a DNA input of 15 ng determined by the NanoDrop 2000c spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). No difference could be detected in mutation analysis based on the results of the quantification methods. These findings emphasise, that it is particularly important to choose the most reliable and constant DNA extraction system, especially when using small biopsies and low elution volumes, and that all common DNA quantification techniques can be used for downstream applications like massively parallel sequencing.
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