Sensitive Detection of Cell-Free Tumour DNA Using Optimised Targeted Sequencing Can Predict Prognosis in Gastro-Oesophageal Cancer

• Published in: Cancers 2023, Vol.15 (4), p.1160
• Main Authors: Wallander, Karin, Haider, Zahra, Jeggari, Ashwini, Foroughi-Asl, Hassan, Gellerbring, Anna, Lyander, Anna, Chozhan, Athithyan, Cuba Gyllensten, Ollanta, Hägglund, Moa, Wirta, Valtteri, Nordenskjöld, Magnus, Lindblad, Mats, Tham, Emma
• Format: Article
• Language: English
• Subjects: Biomarkers; Biopsy; Blood & organ donations; Cancer; Cancer therapies; cell-free (tumour) DNA; Chemotherapy; Deoxyribonucleic acid; DNA; DNA sequencing; Esophageal cancer; Esophagus; gastric; Gastrointestinal cancer; Gastrointestinal surgery; Genes; Genetic analysis; Genetic aspects; Genetic diversity; Genomics; Hospitals; Leukocytes; liquid biopsy; Mathematical optimization; Medical prognosis; Medicin och hälsovetenskap; Metastasis; Methods; Mutation; Nucleotide sequencing; oesophageal; Plasma; Prognosis; prognostic biomarker; Tumors
• ISSN: 2072-6694; 2072-6694
• DOI: 10.3390/cancers15041160

In this longitudinal study, cell-free tumour DNA (a liquid biopsy) from plasma was explored as a prognostic biomarker for gastro-oesophageal cancer. Both tumour-informed and tumour-agnostic approaches for plasma variant filtering were evaluated in 47 participants. This was possible through sequencing of DNA from tissue biopsies from all participants and cell-free DNA from plasma sampled before and after surgery (n = 42), as well as DNA from white blood cells (n = 21) using a custom gene panel with and without unique molecular identifiers (UMIs). A subset of the plasma samples (n = 12) was also assayed with targeted droplet digital PCR (ddPCR). In 17/31 (55%) diagnostic plasma samples, tissue-verified cancer-associated variants could be detected by the gene panel. In the tumour-agnostic approach, 26 participants (59%) had cancer-associated variants, and UMIs were necessary to filter the true variants from the technical artefacts. Additionally, clonal haematopoietic variants could be excluded using the matched white blood cells or follow-up plasma samples. ddPCR detected its targets in 10/12 (83%) and provided an ultra-sensitive method for follow-up. Detectable cancer-associated variants in plasma correlated to a shorter overall survival and shorter time to progression, with a significant correlation for the tumour-informed approaches. In summary, liquid biopsy gene panel sequencing using a tumour-agnostic approach can be applied to all patients regardless of the presence of a tissue biopsy, although this requires UMIs and the exclusion of clonal haematopoietic variants. However, if sequencing data from tumour biopsies are available, a tumour-informed approach improves the value of cell-free tumour DNA as a negative prognostic biomarker in gastro-oesophageal cancer patients.