Concurrent fine needle aspirations and core needle biopsies: a comparative study of substrates for next-generation sequencing in solid organ malignancies.
Author(s): Roy-Chowdhuri S, Chen H, Singh RR, Krishnamurthy S, Patel KP, Routbort MJ, Manekia J, Barkoh BA, Yao H, Sabir S, Broaddus RR, Medeiros LJ, Staerkel G, Stewart J, Luthra R
Publication: Mod Pathol, 2017, Vol. 30, Page 499-508
PubMed ID: 28084342 PubMed Review Paper? No
Purpose of Paper
This paper compared the cellularity, tumor content, DNA yield, and next generation sequencing (NGS) results in matched fine-needle aspiration (FNA) and core needle biopsies (CNB).
Conclusion of Paper
FNA specimens had significantly higher cellularity and tumor fraction than CNB, regardless of tumor type or location. FNA specimens had lower DNA yield than matched CNB specimens but higher average coverage for the panel as a whole and for nine genes of interest. Importantly, all somatic mutations found in FNA specimens were also found in the matched CNB.
Studies
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Study Purpose
This study compared the cellularity and tumor content of 100 matched FNA and CNB specimens and investigated the effects of neoplasm type (adenocarcinoma, squamous cell carcinoma, poorly differentiated carcinoma, or neuroendocrine carcinoma/small cell carcinoma) and location. Two to three FNA specimens were obtained using 20-25 gauge (G) needles under computed tomography (CT) or ultrasound guidance with a 17-19 G guide needle. Three to four cores were obtained using the guide needle with a 16-20 G needle. The FNA was obtained first for most tumors but the CNB was obtained first for subcentimeter tumors. FNA specimens were smeared and Diff-Quik and Papanicolaou stained. CNB slides were prepared and H&E stained. Cellularity was described as high for >5000 cells per FNA slide or >2000 cells per CNB slide, moderate for 1000-5000 cells per FNA slide or 300-2000 cells per CNB slide and low for <1000 cells per FNA slide or <300 cells per CNB slide. Tumor fraction was determined independently by two cytopathologists and then reviewed together in cases with >10% discordance.
Summary of Findings:
In 100 matched specimens, the cellularity of FNA was more likely than CNB to be defined as high (60% versus 15%) and less likely to be defined as moderate (33% versus 58%) or low (7% versus 27%). Further, the overall cellularity was significantly higher in FNA specimens than in matched CNB specimens (P<0.001), and this held true when broken down by diagnosis (adenocarcinoma, squamous cell carcinoma, poorly differentiated carcinoma, and neuroendocrine carcinoma/small cell carcinoma) and lesion site. Further, a higher percentage of FNA than CNB specimens had >40% tumor fraction (83% versus 54%) and a lower percentage had <20% tumor (14% versus 2%, P<0.001). Importantly, the majority of the CNB specimens with low <25% tumor fraction had matched FNA with high or moderate cellularity.
Biospecimens
Preservative Types
- Ethanol
- Formalin
Diagnoses:
- Neoplastic - Carcinoma
Platform:
Analyte Technology Platform Morphology Light microscopy Morphology H-and-E microscopy Pre-analytical Factors:
Classification Pre-analytical Factor Value(s) Biospecimen Acquisition Method of tissue acquisition Core needle biopsy
Fine needle aspiration
Preaquisition Diagnosis/ patient condition Adenocarcinoma
Squamous cell carcinoma
Poorly differentiated carcinoma
Neuroendocrine carcinoma
Small cell carcinoma
Biospecimen Acquisition Biospecimen location Lung
Liver
Bone/soft tissue
Lymph node
Other
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Study Purpose
This study compared the tumor content, DNA yield, and NGS sequencing coverage of 100 matched FNA and CNB specimens. Matched image-guided CNB and FNA specimens from 17 adenocarcinomas, four carcinomas not specified, two squamous cell carcinomas, and one melanoma. Two to three FNA specimens were obtained using 20-25 G needles under computed tomography (CT) or ultrasound guidance with a 17-19 G guide needle. Three to four cores were obtained using the guide needle with a 16-20 G needle. The FNA was obtained first for most tumors but the CNB was obtained first for subcentimeter tumors. FNA specimens were smeared and Diff-Quik and Papanicolaou stained. CNB slides were prepared and H&E stained. Tumor fraction was determined independently by two cytopathologists and then reviewed together in cases with >10% discordance. DNA was extracted from tumor-enriched areas of smears and FFPE sections using PicoPure. DNA was quantified using Qubit. NGS was conducted on an Ion Torrent using the Ampliseq Cancer panel primers.
Summary of Findings:
H&E stained CNB sections had lower estimated tumor fraction compared to stained FNA smears (39% versus 54%, P=0.003) but higher DNA yield (17.5 ng/µL versus 6.6 ng/µL, P=0.01). FNA specimens had higher average coverage for the panel as a whole (50 genes) and for nine selected genes of interest than matched CNB specimens (2177 reads verses 1785 reads, P=0.025 and 2415 versus 1933 reads, P=0.014, respectively). More under-performing amplicons occurred in CNB than FNA specimens (2.25 versus 0.46, significance not specified). Importantly, all somatic mutations found in FNA specimens were also found in the matched CNB.
Biospecimens
Preservative Types
- Ethanol
- Formalin
Diagnoses:
- Neoplastic - Melanoma
- Neoplastic - Carcinoma
Platform:
Analyte Technology Platform DNA Fluorometry Morphology Light microscopy Morphology H-and-E microscopy DNA Next generation sequencing Pre-analytical Factors:
Classification Pre-analytical Factor Value(s) Biospecimen Acquisition Method of tissue acquisition Core needle biopsy
Fine needle aspiration