Liquid Biopsy in Gastric Cancer: Analysis of Somatic Cancer Tissue Mutations in Plasma Cell-Free DNA for Predicting Disease State and Patient Survival

Abstract

Introduction: Gastric cancer (GC) diagnosis in late stages and high mortality rates are the main issues that require new noninvasive molecular tools. We aimed to assess somatic mutational profiles in GC tissue and plasma cell-free DNA (cfDNA), evaluate their concordance rate, and analyze the role of multilayer molecular profiling to predict disease state and prognosis. Methods: Treatment-naive GC patient group (n = 29) was selected. Whole exome sequencing (WES) of GC tissue was performed, and a unique 38-gene panel for deep targeted sequencing of plasma cfDNA was developed. Oncoproteins were measured by enzyme-linked immunosorbent assay, and other variables such as tumor mutational burden and microsatellite instability were evaluated using WES data. Results: The yield of cfDNA was increased 43.6-fold; the integrity of fragments was decreased in GC compared with controls. WES analysis of cancerous tissue and plasma cfDNA (targeted sequencing) mutational profiles revealed 47.8% concordance. The increased quantity of GC tissue–derived alterations detected in cfDNA was associated with worse patients' survival. Analysis of importance of multilayer variables and receiver operating characteristic curve showed that combination of 2 analytes: (i) quantity of tissue matching alterations and (ii) presence of any somatic alteration in plasma cfDNA resulted in area under curve 0.744 when discriminating patients with or without distant metastasis. Furthermore, cfDNA sequence alterations derived from tumor tissue were detected in patients who had even relatively small GC tumors (T1-T2). Discussion: Our results indicate that quantitative and qualitative cfDNA mutational profile analysis is a promising tool for evaluating GC disease status or poorer prognosis.

Comparison of the mutation patterns between tumor tissue and cell-free DNA in stage IV gastric cancer

“…Our results showed that the concordance rate between tumor DNA and cfDNA was 42%, which was similar to previous studies [ 14 ]. Varkalaite et al, [ 14 ] used whole-exome sequencing for mutation analysis; among the 152 mutations in the plasma samples, only 39 mutations were detected in the tissue samples, indicating that the specificity was 25.7%. In our study, the specificity was 100% for cfDNA to predict mutations in tumor samples.…”

“…The difference between our study and a previous study [14] might be due to different technology in mutation detection, differences in tumor stage and races. The quantity of cfDNA was higher in stage IV GC than in stage I-III GC [5], which might increase the detection rate of genetic mutations in cfDNA and make our results more promising.…”

“…To the best of our knowledge, this is the first study to investigate the mutation patterns of different metastatic patterns between cfDNA and tumor DNA for stage IV GC. Our results showed that the concordance rate between tumor DNA and cfDNA was 42%, which was similar to previous studies [14]. Varkalaite et al, [14] used wholeexome sequencing for mutation analysis; among the 152 mutations in the plasma samples, only 39 mutations were detected in the tissue samples, indicating that the specificity was 25.7%.…”

The Role of ctDNA in Gastric Cancer

“…The tissue concordance was 47.8% in this cohort. Even small tumours such as T1-T2 shed ctDNA [ 34 ].…”

“…The GC somatic mutation landscape has been described previously using tissue-based sequencing, but also using ctDNA-based sequencing [ 34 ]. A large comprehensive genomic-profiling study using ctDNA to detect targetable genetic mutations in patients with advanced gastrointestinal (GI) cancers was performed in Japan [ 35 ].…”