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
Authors: Millán Esteban, David, Reyes García, Diana, García Casado, Zaida, Bañuls Roca, José, López Guerrero, José Antonio, Requena Caballero, Celia, Rodríguez Hernández, Aranzazu, Traves, Víctor, Nagore Enguidanos, Eduardo
Format: article
Publication Date:2018
Country:España
Institution:Universidad Católica de Valencia San Vicente Mártir
Repository:RIUCV. Repositorio de la Universidad Católica de Valencia San Vicente Mártir
Language:English
OAI Identifier:oai:riucv.ucv.es:20.500.12466/3223
Online Access:http://hdl.handle.net/20.500.12466/3223
Access Level:Open access
Keyword:Melanoma
Formalin-fixed paraffin-embedded
DNA integrity number
32 Ciencias Médicas
Description
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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