Cytology smears for DNA extraction: Practical approach for selecting the best slide.
DNA yield
cytology smears
next generation sequencing
scraping
tumour fraction
Journal
Cytopathology : official journal of the British Society for Clinical Cytology
ISSN: 1365-2303
Titre abrégé: Cytopathology
Pays: England
ID NLM: 9010345
Informations de publication
Date de publication:
01 2019
01 2019
Historique:
received:
08
03
2018
accepted:
15
07
2018
pubmed:
29
7
2018
medline:
20
8
2019
entrez:
29
7
2018
Statut:
ppublish
Résumé
Next generation sequencing (NGS) to detect actionable genetic abnormalities is standard of care in advanced stage lung adenocarcinoma. Many studies have shown that the molecular results obtained from fine needle aspiration cytology material are comparable to those obtained from formalin-fixed tissue samples. We undertook this study to validate DNA extraction from cytology material for molecular studies and to find any correlation between DNA yield, pattern of tumour cells and tumour fraction. DNA was extracted from 34 cytology slides of pulmonary adenocarcinoma cases with predetermined EGFR mutation status. Cytology slides were reviewed for pattern of tumour distribution and tumour fraction. NGS was performed on five slides with variable DNA and compared with original results. There were 14 alcohol-fixed and 20 air-dried smears. The mean DNA yield was 1.74 μg and median of 0.4 μg (range, 0.02-21 μg). Tumour fractions varied from 10% to 90%. No correlation was found between tumour fraction and DNA yield (P = 0.14). The mean DNA yield was high in slides with tumour throughout the slide (sheets or scattered clusters) as compared to rare scattered clusters and/or single cells. EGFR mutation was found in four of the five cases sent for NGS lung panel while one case revealed BRAF mutation. DNA with good quantity and quality can be extracted from the cytology slides for NGS irrespective of type of fixation. DNA yield has better correlation with distribution pattern of tumour cells on the slides rather than tumour fraction.
Sections du résumé
BACKGROUND
Next generation sequencing (NGS) to detect actionable genetic abnormalities is standard of care in advanced stage lung adenocarcinoma. Many studies have shown that the molecular results obtained from fine needle aspiration cytology material are comparable to those obtained from formalin-fixed tissue samples. We undertook this study to validate DNA extraction from cytology material for molecular studies and to find any correlation between DNA yield, pattern of tumour cells and tumour fraction.
METHODS
DNA was extracted from 34 cytology slides of pulmonary adenocarcinoma cases with predetermined EGFR mutation status. Cytology slides were reviewed for pattern of tumour distribution and tumour fraction. NGS was performed on five slides with variable DNA and compared with original results.
RESULTS
There were 14 alcohol-fixed and 20 air-dried smears. The mean DNA yield was 1.74 μg and median of 0.4 μg (range, 0.02-21 μg). Tumour fractions varied from 10% to 90%. No correlation was found between tumour fraction and DNA yield (P = 0.14). The mean DNA yield was high in slides with tumour throughout the slide (sheets or scattered clusters) as compared to rare scattered clusters and/or single cells. EGFR mutation was found in four of the five cases sent for NGS lung panel while one case revealed BRAF mutation.
CONCLUSIONS
DNA with good quantity and quality can be extracted from the cytology slides for NGS irrespective of type of fixation. DNA yield has better correlation with distribution pattern of tumour cells on the slides rather than tumour fraction.
Substances chimiques
EGFR protein, human
EC 2.7.10.1
ErbB Receptors
EC 2.7.10.1
BRAF protein, human
EC 2.7.11.1
Proto-Oncogene Proteins B-raf
EC 2.7.11.1
Types de publication
Journal Article
Langues
eng
Pagination
68-73Informations de copyright
© 2018 John Wiley & Sons Ltd.