Molecular features of tumor-derived genetic alterations in circulating cell-free DNA in virtue of autopsy analysis

Hayato Koba,Kazuo Kasahara,Atsushi Tajima,Taro Yoneda,Kazuyoshi Hosomichi,Hideharu Kimura,Johsuke Hara,Noriyuki Ohkura,Takashi Sone

doi:10.1038/s41598-021-87094-1

Hayato Koba, Kazuo Kasahara + Show 7 more

Open Access

https://doi.org/10.1038/s41598-021-87094-1

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Abstract

In cancer patients, circulating cell-free DNA (cfDNA) includes tumor-derived DNA (tDNA). cfDNA has been used clinically for non-invasive gene mutation testing. The aim of this study was to characterize the features of the genetic alterations detected in cfDNA. This study included 6 patients with primary lung cancer who died due to cancer progression. Tumors were biopsied at autopsy. Genetic alteration profiles were obtained using next generation sequencing. The features of the tDNA genetic alterations detected in cfDNA included a higher frequency of being present in multiple tumors (67% truncal mutations, 36% shared mutations, and 4% individual mutations) and a higher variant allele frequency (VAF; 47.6% versus 4.1% for tDNA alterations detected in cfDNA versus not detected in cfDNA, respectively). The data revealed that the tumor-derived genetic alterations most easily detected in cfDNA were truncal mutations with a high VAF. These results showed that essential genetic alterations enriched in cfDNA could help to characterize cancer cells and that genetic testing using cfDNA has advantages in the detection of fundamental regulatory aberrations occurring during tumorigenesis.

Highlights

Circulating cell-free DNA is present at very low levels as fragments in the bloodstream. cfDNA includes circulating tumor-derived DNA in patients with malignancies
We evaluated the correlations between the genetic alteration profiles detected in cfDNA and those detected in whole tumor lesions, including distant metastases obtained from autopsy samples
The tumor-derived genetic alterations used as a control for mutation analyses in cfDNA reflect only a small portion of the overall alterations in all tumors of a patient with advanced non-small cell lung cancer (NSCLC)

Summary

Introduction

Circulating cell-free DNA (cfDNA) is present at very low levels as fragments in the bloodstream. cfDNA includes circulating tumor-derived DNA (ctDNA) in patients with malignancies. CfDNA-based mutation tests of the epidermal growth factor receptor (EGFR) gene have been approved as in vitro diagnostic tests in clinical settings worldwide, including in Japan. They are used in treatment decision-making for patients with advanced non-small cell lung cancer (NSCLC). Samples obtained from transbronchial biopsy, which is one of the most widely used methods of tumor collection in advanced NSCLC, are very limited and represent a small fraction of the tumor lesion. We expect that cfDNA-based genetic testing using NGS should yield promising information by visualizing all of the genetic alterations present in a patient, including those among multiple tumor lesions

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