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Targeted deep sequencing of cell‐free DNA in serous body cavity fluids with malignant, suspicious, and benign cytology
Author(s) -
Yang SooRyum,
Mooney Kelly L.,
Libiran Paolo,
Jones Carol D.,
Joshi Rohan,
Lau Hubert D.,
Stehr Henning,
Berry Gerald J.,
Zehnder James L.,
Long Steven R.,
Kong Christina S.,
Kunder Christian A.
Publication year - 2020
Publication title -
cancer cytopathology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.29
H-Index - 57
eISSN - 1934-6638
pISSN - 1934-662X
DOI - 10.1002/cncy.22205
Subject(s) - serous fluid , cell free fetal dna , medicine , genotyping , liquid biopsy , pathology , malignancy , dna sequencing , cytology , cancer , genotype , dna , gene , biology , genetics , prenatal diagnosis , pregnancy , fetus
Background Liquid biopsy using cell‐free DNA (cfDNA) presents new opportunities for solid tumor genotyping. While studies have demonstrated the utility of cfDNA from plasma, cfDNA from other body fluids remains underexplored. Methods We evaluated the molecular features and clinicopathologic correlates of cfDNA from serous body cavity fluids by performing hybrid capture‐based next‐generation sequencing (NGS) on cfDNA isolated from residual effusion supernatants. Twenty‐one serous effusions from pleural (n = 15), peritoneal (n = 5), and pericardial (n = 1) cavity were analyzed. Results The supernatants provided a median cfDNA concentration of 10.3 ng/µL. Notably, all effusions were sequenced successfully to a median depth >1000×, revealing a broad range of genetic alterations including single nucleotide variants, small insertions and deletions, amplifications, and fusions. Specifically, pathogenic alterations were identified in all malignant fluids (13/13), all fluids suspicious for malignancy (2/2), and 1 benign fluid (1/6) from a patient with metastatic cancer. To validate our findings, we examined matching results from 11 patients who underwent additional testing using formalin‐fixed, paraffin‐embedded (FFPE) specimens. In 8 patients, the paired results between FFPE and supernatant testing were concordant, whereas in the remaining 3 patients, supernatant analysis identified additional variants likely associated with resistance to targeted therapies. Additional comparison between FFPE and supernatant testing showed no difference in DNA concentration ( P = .5), depth of coverage ( P = .6), or allele frequency of pathogenic mutations ( P = .7). Conclusion cfDNA isolated from serous body cavity fluids represents a promising source of genomic input for targeted NGS.