Suitability of melanoma FFPE samples for NGS libraries: time and quality thresholds for downstream molecular tests.
Por:
Millán-Esteban D, Reyes-García D, García-Casado Z, Bañuls J, López-Guerrero JA, Requena C, Rodríguez-Hernández A, Traves V and Nagore E
Publicada:
1 ago 2018
Resumen:
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.
Filiaciones:
Millán-Esteban D:
Laboratorio de Biología Molecular, Instituto Valenciano de Oncología, Valencia, Spain
Reyes-García D:
Universidad Católica de Valencia San Vicente Mártir, Valencia, Spain
García-Casado Z:
Laboratorio de Biología Molecular, Instituto Valenciano de Oncología, Valencia, Spain
:
Servicio de Dermatología, Hospital General Universitario de Alicante, Alicante, Spain
López-Guerrero JA:
Laboratorio de Biología Molecular, Instituto Valenciano de Oncología, Valencia, Spain
Requena C:
Servicio de Dermatología, Instituto Valenciano de Oncología, Valencia, Spain
Rodríguez-Hernández A:
Servicio de Dermatología, Instituto Valenciano de Oncología, Valencia, Spain
Traves V:
Servicio de Anatomía Patológica, Instituto Valenciano de Oncología, Valencia, Spain
Nagore E:
Servicio de Dermatología, Instituto Valenciano de Oncología, Valencia, Spain
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