Variant discovery with a tumor-informed workflow followed by the xGen Custom MRD Workflow
Researchers use biomarkers to track ctDNA found in circulating cfDNA, and/or formalin fixed paraffin embedded (FFPE) samples to research cancer. Initial analysis involves identifying the specific somatic variants found in a sample. Common MRD research approaches for identifying such variants involve preparing libraries from extracted cfDNA and FFPE, then performing hybridization capture using larger custom or predesigned panels with a broad number of targets to find unique signatures for each research sample. This approach is used during the early research stage and discovery phase to identify somatic and germline mutations, but due to the larger size of the panel and associated sequencing depth required, it is not used to identify ultra-low variants in MRD research samples.
For rare variant discovery, IDT offers an xGen Custom MRD Workflow to assist you in your MRD research needs. Easily prepare high complexity libraries from extracted cfDNA using the xGen cfDNA & FFPE DNA Library Prep Kit. For target enrichment and accurate ultra-low variant identification, design your xGen MRD Hybridization Panels with up to 2000 probes per panel and order up to 50 panels at once. These customizable panels can enable reliable variant identification at ≤1% variant allele frequency (VAF) if input cfDNA quantity and sequencing depth requirements are met (see Table 3).
Comprehensive conversion and error correction enables ultra-low variant identification with cell-free DNA
The unique, single-stranded ligation strategy of the IDT xGen cfDNA & FFPE DNA Library Prep Kit and workflow delivers high conversion of input DNA molecules to sequencing data. This high conversion rate is critical for identification of ultra-low frequency variants, which is common in the analysis of cfDNA samples. A higher conversion rate translates to higher complexity and coverage than other DNA library prep kits for cfDNA (Figure 1). In addition, the xGen cfDNA & FFPE DNA Library Prep Kit includes adapters that contain unique molecular identifiers (UMIs), which enable bioinformatic error correction. Combining higher complexity and coverage with stringent error correction better enables the identification of ultra-low frequency variants (Table 3). For target enrichment, two different custom panels containing a target size of 61 kb (Figure 1), or 180 kb (Table 3) were designed and utilized in the data shown.