Oncomine Cell-Free Assays for Liquid Biopsy Clinical Research

Liquid biopsies offer several advantages over conventional solid tumor samples: 

• Less invasive to obtain, enabling tumor content to be sampled multiple times
• Lower cost compared to traditional tissue samples
• Faster turnaround time from sample to results
• Help capture more of the heterogeneity of the tumor
• May lead to improvements in standard of care in the future

We now know that cancer is a molecular disease. To better advance cancer research in the future, we need a clearer understanding of how those oncogenes and oncoproteins change in both time and space. Liquid biopsy applications enable clinical researchers to investigate tumors in ways not previously possible.

In the past, clinical cancer research on cfDNA focused on digital PCR or droplet digital PCR applications to analyze samples with low-frequency mutations. These approaches, while sensitive, limit the number of target genes, thereby limiting the field of vision of the researcher.

The Oncomine Cell-Free Research Assays and the Ion GeneStudio S5 Systems enable tumor heterogeneity research, therapy selection research, therapy monitoring research, and reoccurrence research studies from as little as 1ng of sample input.

In verification studies, the assays demonstrate high correlation between the variants called in formalin-fixed, paraffin-embedded (FFPE) samples and those called in plasma (Table 1). As expected, there is a higher mutant allelic fraction in the FFPE tumor sample compared to that measured in plasma, and germline variants are seen at expected levels of ~50% in both FFPE and plasma. 

Table 1. Correlation of FFPE and matched plasma sample results (late-stage lung cancer samples). Oncomine cell-free assays demonstrate high correlation between variants called in FFPE samples and those called in matched plasma samples. The above data was obtained using the Oncomine Lung cfDNA Assay. Bolded values indicate somatic mutations. Non-bolded values indicate germline mutations.

Overall, Oncomine cell-free assays enable results from more samples, with demonstrated, repeatable results using clinical research samples at 0.1% limit of detection with 90% sensitivity and >98% specificity across our whole portfolio of Oncomine cell-free assays.

Table 2. Variants called from Horizon cfDNA Multiplex Reference Set. All 8 mutant hotspots were called at 0.1%. Data obtained using the Oncomine Lung cfDNA Assay.

Running up to 8 samples on an Ion 530 chip or up to 32 samples on an Ion 540 chip, the Oncomine cell-free assays enable efficiently multiplexed PCR analysis of single nucleotide variants (SNVs) , short indels, copy number variations, and fusions across our whole portfolio of Oncomine cell-free assays. frequently mutated in common tumor types, tolerating sample input variability and accommodating flexible input amounts as low as 1 ng.

The entire workflow (Figure 2), from isolation of cell-free nucleic acids using the appropriate Applied Biosystems MagMAX Cell-Free Isolation Kit to analysis of samples, can be accomplished in just 2 days on the Ion GeneStudio S5 Prime system.

Oncomine cell-free assays are part of a complete workflow designed for liquid biopsy clinical research, which includes:

Oncomine cell-free assays

A kit containing reagents for library construction and a single pool of multiplex PCR primers to prepare amplicon libraries from cell-free nucleic acids found in the plasma fraction of whole blood.

Tag Sequencing Barcode Sets 1–24 and 25–48

A set of unique barcode adapters specifically designed for optimal performance with our technology. The unique barcode adapters are compatible with the Ion S5, Ion PGM, and Ion Proton systems. When used in combination with kits, this set enables you to pool up to 24 amplicon libraries and conduct multiplex sequencing analysis, which helps reduce the sequencing cost per sample.

Ion GeneStudio S5 Series

The Ion GeneStudio S5 Series supports five different chip types, so you can run multiple applications on a single sequencer. This flexibility eliminates the need to batch samples in order to achieve the optimum cost efficiency. Just choose the chip type that matches your specific throughput or application needs. 

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