The journal of liquid biopsy · 2026
Development of a LiDia-SEQ™ platform compatible breast cancer panel and testing with metastatic breast cancer patient samples: A rapid, sample-to-result, fully integrated next-generation sequencing (NGS)-based platform, LiDia-SEQ, for use at the point-of-need.
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Ramsheh Mohammadali Yavari, Fraccari Raquel L, Christova Rossitza, Killpack Jarrett, Acquah Jean-Rene, Nteliopoulos Georgios, Wren Evie, Rehman Farah, Page Karen, Shaw Jacqueline A, Saha Atreyee, Wong Ryan, Pradhan Subhas, Novotny Peter, Peras Marie, Arnold Beth, Wisniewski Michele, Joshi Hrishikesh, Coombes R Charles, Reed Samuel
Аннотация
BACKGROUND: Plasma circulating tumour DNA (ctDNA) analysed using next generation sequencing (NGS) reflects the evolving tumour molecular landscape. However, barriers to routine adoption of NGS ctDNA analysis in clinical settings to detect breast cancer recurrence and therapy selection and monitoring include high costs, the need for highly trained personnel to perform complex workflows and specialised laboratories. DNAe is addressing this with its sample-to-result NGS-based LiDia-SEQ™ platform. This benchtop platform is simple to operate, rapid, fully automated and likely cost-effective.
MATERIALS AND METHODS: A clinically relevant panel (DNAe panel) covering 127-point mutations on three key genes - ESR1, PIK3CA and TP53 was designed and optimised with commercially available reference material. Once sufficiently optimised, the panel was validated using 32 clinical samples from metastatic breast cancer patients in a side-by-side comparison with the Oncomine™ Breast cfDNA Assay. Results from the Oncomine assay were analysed with the Oncomine standard pipeline while results from the DNAe panel were analysed using DNAe's custom bioinformatics pipeline.
RESULTS: Out of the 32 clinical samples tested with the two panels, 12 samples had no mutations, and 20 samples contained mutations. Fifteen samples had mutations detected by both panels and five had a single mutation detected by one or the other panel.
CONCLUSION: Using clinical samples, we show that the DNAe panel with analysis using DNAe's pipeline detects mutations comparably to the commercial Oncomine-Assay. This paves the way for development of the DNAe panel into a test for the LiDia-SEQ platform.
MATERIALS AND METHODS: A clinically relevant panel (DNAe panel) covering 127-point mutations on three key genes - ESR1, PIK3CA and TP53 was designed and optimised with commercially available reference material. Once sufficiently optimised, the panel was validated using 32 clinical samples from metastatic breast cancer patients in a side-by-side comparison with the Oncomine™ Breast cfDNA Assay. Results from the Oncomine assay were analysed with the Oncomine standard pipeline while results from the DNAe panel were analysed using DNAe's custom bioinformatics pipeline.
RESULTS: Out of the 32 clinical samples tested with the two panels, 12 samples had no mutations, and 20 samples contained mutations. Fifteen samples had mutations detected by both panels and five had a single mutation detected by one or the other panel.
CONCLUSION: Using clinical samples, we show that the DNAe panel with analysis using DNAe's pipeline detects mutations comparably to the commercial Oncomine-Assay. This paves the way for development of the DNAe panel into a test for the LiDia-SEQ platform.