Peripheral Monitoring | Thermo Fisher Scientific

Cancer research applications in peripheral monitoring

Analysis of retrospectively collected whole-blood samples opens up opportunities to identify new biomarkers, to potentially develop future tests, and to conduct research that may impact tumor detection, response to therapy, and recurrence in the future. To effectively conduct this type of analysis, you need a reliable method to identify, capture, and analyze rare target cells.

Using cell-free DNA (cfDNA) is a common approach, but cfDNA is incompatible with expression of some fusion genes like AR-V7 or ALK. While circulating tumor cell (CTC) enumeration has been shown to be associated with disease progression (Cristofanilli et al., 2004; N Engl J Med 351:781), it does not help characterize the biology of the CTC. A comprehensive approach that enables next-generation sequencing (NGS) analysis of both cfDNA and CTCs from one sample may help address these issues.

The Ion Torrent™ LiquidBiopsy™ Platform enables translational professionals to add CTC analysis to existing cfDNA research. From one whole-blood sample, the LiquidBiopsy Platform automates molecular characterization of CTCs, cfDNA, and germline DNA to help maximize blood sample utility.

LiquidBiopsy Platform

The LiquidBiopsy Platform automates isolation of CTCs from blood samples. Achieving high target cell recovery and exceptional purity, the platform enables both enumeration and downstream molecular characterization of rare cells using the LiquidBiopsy Platform:

Along with the Ion sequencer, it offers a comprehensive, cost-effective sample-to-sequence workflow
Is uniquely suited to low-input DNA sequencing without the need for whole-genome amplification
Enables highly multiplexed analyses on serially collected blood samples
Achieves <1% limit of detection critical to CTC research
Offers rapid turnaround time; sample-to-sequence workflow typically completed in 2 days

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Comprehensive sample-to-sequence automated workflow

The LiquidBiopsy Platform is part of a comprehensive, two-day workflow that enables genomic research reporting data on CTCs, cfDNA, and germline whole blood cells from a single blood sample in a single cycle. Captured cells are pooled on a single Ion 318™ Chip and sequenced on the Ion PGM™ Sequencer. Resulting data may be analyzed using Ion Reporter™ Software.

Workflow components:

Blood Collection Kit—collect and stabilize whole-blood samples for up to 96 hours
LiquidBiopsy Instrument—isolates CTCs
Ion 318 Chip—cfDNA, germline whole blood cells, and CTCs are pooled on one chip
Ion PGM Sequencer—sequence highly multiplexed samples
Genomic research reporting—analyze mutations across cfDNA, germline cells, and CTCs

High capture rate and sample purity with the LiquidBiopsy™ Flow Chip

At the center of the LiquidBiopsy Platform is a proprietary flow chip that uses antibody-based positive selection to enable CTC enumeration and downstream molecular analysis using NGS, eliminating the need for whole-genome amplification, a process that typically introduces false positives in the data.

The flow chip processes reagents for the selection and immunomagnetic isolation of target cells, enabling a highly pure capture of CTCs—capture rates of up to 40% facilitate downstream NGS analysis. The high capture rate is the result of an EpCAM-based methodology that also allows for a cocktail of antibodies to be used for a more diverse cell recovery. The design helps ensure a high rate of capture of mutation-bearing tumor cells while avoiding impurity, or the unwanted binding of nontarget cells to the surfaces of the separation device.

2–7.5 mL (whole-blood) sample input
Throughput of 5 mL/hr for 1.5–3 hours on-platform assay time

Low-DNA input capability

Using the power of Ion AmpliSeq™ technology, the platform allows for multiplexing samples and yields more data from low DNA input commonly obtained from CTCs. The LiquidBiopsy™ Instrument’s manifold houses four flow chips, accelerating turnaround time for higher-throughput laboratories.

Highly sensitive multiplexing

Combined with Ion AmpliSeq technology and the Ion PGM System, the LiquidBiopsy Platform achieves up to 100% sensitivity down to <1% allele frequency at 2,000x read depth. The Ion PGM Sequencer is a scalable, cost-effective sequencing solution that allows analysis of incremental numbers of samples, to effectively support research applications without the need to batch samples.