Suitability of melanoma FFPE samples for NGS libraries: time and quality thresholds for downstream molecular tests

The use of NGS in clinical practice for precision diagnosis requires a quality starting material. Despite the broadly established use of formalin-fixed paraffin-embedded (FFPE) samples in molecular testing, these usually have low-quality DNA. We established a method to determine the suitability of m...

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Bibliographic Details
Published inBioTechniques Vol. 65; no. 2; pp. 79 - 85
Main Authors Millán-Esteban, David, Reyes-García, Diana, García-Casado, Zaida, Bañuls, José, López-Guerrero, José Antonio, Requena, Celia, Rodríguez-Hernández, Aranzazu, Traves, Víctor, Nagore, Eduardo
Format Journal Article
LanguageEnglish
Published England Future Science Ltd 01.08.2018
Taylor & Francis Group 01.08.2018
Subjects
DIN
FFPE
library
melanoma
NGS
quality
threshold
time
QC
library
FFPE
DIN
melanoma
threshold
NGS
time
quality
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Summary:The use of NGS in clinical practice for precision diagnosis requires a quality starting material. Despite the broadly established use of formalin-fixed paraffin-embedded (FFPE) samples in molecular testing, these usually have low-quality DNA. We established a method to determine the suitability of melanoma FFPE samples for an amplicon-based NGS custom panel analysis. DNA was extracted from unstained melanoma samples and wide local excision samples. Amplicon-based libraries were constructed and tested using time and quality parameters as variables. Time elapsed from sample retrieval >7 years, a quality control value > 5.63 and a DNA integrity value < 2.05 indicated samples were not suitable. A decision tree is provided with rate of samples suitable for analysis according to the combination of these parameters.
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ISSN:0736-6205
1940-9818
DOI:10.2144/btn-2018-0016