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Cancer biomarker research using complementary NGS technologies

Identify and confirm cancer biomarkers

IDT targeted next generation sequencing workflows complement each other when applied to cancer biomarker discovery research. Using low-input DNA derived from cell-free DNA (cfDNA) and formalin-fixed, paraffin embedded (FFPE) tumor samples, both the xGen hybridization capture system and the rhAmpSeq amplicon sequencing system reveal low frequency variants with Illumina sequencing. Download Combining NGS technologies for biomarker identification and confirmation research to read more.

Next generation sequencing (NGS) has moved cancer research forward in many ways, from biomarker discovery research to early cancer screening. Targeted NGS, high-throughput, parallel sequencing that focuses on specific areas of the genome, can characterize diseases quickly and economically. Previously, we published an application note that demonstrated how the xGen™ Prism DNA Library Prep Kit can be used in biomarker discovery research: Biomarker discovery research—Cancer molecular profiling.

Building on the idea that comprehensive tumor profiling can be achieved using hybridization capture with the novel IDT xGen Prism DNA Library Prep Kit and xGen hybridization capture system, we complement the hyb capture approach with the rhAmpSeq™ amplicon sequencing system. The fast and easy rhAmpSeq workflow, based on our proprietary RNase H2-dependent PCR (rhAmp™ PCR) technology, generates NGS-ready amplicon libraries for deep, targeted resequencing. In this study, cell-free DNA (cfDNA) and formalin-fixed, paraffin embedded (FFPE) tumor samples from lung cancer patients were used to identify biomarkers, which were correlated between the xGen hybridization capture system and the rhAmpSeq amplicon sequencing system. Both systems showed sensitivity down to 1% VAF (variant allele frequency) starting from low quantities of DNA input. To read the full application note, download Combining NGS technologies for biomarker identification and confirmation research.

Published Aug 21, 2020