Suitability of melanoma FFPE samples for NGS libraries: time and quality thresholds for downstream molecular tests.
Biotechniques
; 65(2): 79-85, 2018 08.
Article
em En
| MEDLINE
| ID: mdl-30091391
ABSTRACT
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.
Palavras-chave
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
DNA
/
Biblioteca Gênica
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Fixação de Tecidos
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Inclusão em Parafina
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Sequenciamento de Nucleotídeos em Larga Escala
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Melanoma
Tipo de estudo:
Prognostic_studies
Limite:
Humans
Idioma:
En
Revista:
Biotechniques
Ano de publicação:
2018
Tipo de documento:
Article