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Published on: April 17, 2015
Impact of serous fluid volume on next-generation sequencing: a significant step forward for optimization of serous
Shaham Beg1, Kemin Xu1, James P Solomon1
1Department of Pathology and Laboratory Medicine, New York Presbyterian-Weill Cornell Medicine, New York, New York.
Introduction:
Current literature lacks data regarding the influence of serous fluid volume (SFV) on next-generation sequencing (NGS) performed on malignant cases. In this study, we highlight the impact of SFV and other parameters influencing the outcome of NGS analysis.
Materials And Methods:
We evaluated 827 samples of serous fluids from 607 patients. Of these, 72 samples underwent NGS analysis. Effusion volume, tumor cellularity, DNA, and RNA quality metrics, as well as clinicopathologic and molecular data were evaluated. Pleural fluid accounted for 56.3% of the fluid samples collected. The most common primary tumor site was gastrointestinal/pancreatobiliary, adenocarcinoma was the most common histologic type. Overall mean volume was 293 mL. The mean Qubit DNA of the 72 effusion samples that underwent NGS analysis was 14.3 ng/μL and mean Qubit RNA was 28.2 ng/μL. The mean Qubit DNA concentration increases in SFV up to 100 mL only.
Results:
No correlation exists between SFV and mean tumor cellularity. In addition, 74.6% (50 of 67) of sequenced samples showed oncogenic drivers; KRAS was the most common driver followed by EGFR. Three cases displayed ALK fusions, and 1 case displayed NTRK1 fusion. The DNA yield is higher in SFV of 100 mL as a cutoff. Beyond 100 mL, there is no impact of SFV on DNA yield. SFV does not impact RNA yield and mean tumor cellularity. Effusion samples should be submitted for molecular testing despite low tumor cellularity.
Conclusions:
Our results as a pilot study are important in optimization of SFV for both diagnosis as well as NGS analysis for improving management.
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