Background
Circulating tumor cells (CTCs) are rare cancer cells, shed from cancerous lesions into the bloodstream or other bodily fluids. Utilizing genomic characterization of CTCs presents a promising alternative to traditional tissue biopsies for profiling cancer mutations. However, the isolation of these scarce CTCs from whole blood poses significant challenges. Additionally, the limited amount of DNA available falls short of the requirements for next-generation sequencing (NGS) without the implementation of whole genome amplification (WGA). To address these obstacles, we have developed a fully automated solution for CTC enrichment, integrating WGA and targeted gene sequencing panel workflows.
Methods
For this study, blood samples were collected from patients with breast, lung, and other solid tumors using BioFluidica blood collection tubes. The LiquidScan platform, employing microfluidic affinity selection with the EPCAM surface marker, was utilized to enrich CTCs. Cell eluates released from the microfluidic chips underwent further sorting to eliminate white blood cells, and the sorted cells were collected into multiple wells. To analyze the DNA, the cells underwent whole genome amplification using the Takara PicoPLEX single-cell kit and amplicon-based targeted sequencing utilizing the Illumina AmpiSeq Cancer Hotspot Panel v2 and the ArcherDx Solid Tumor Focus v2.
Results
The whole blood samples were directly loaded onto microfluidic chips using a Hamilton robot for automated processing, minimizing manual intervention. The procedure did not require red blood cell lysis, and each sample took approximately 3 hours to process, with up to 8 samples simultaneously processed per instrument. The success rate of DNA amplifications exceeded 90%, and somatic mutations were detected in all patients.
Conclusions
The LiquidScan platform offers a rapid and automated solution for CTC isolation, and we established workflows for detecting downstream somatic mutations. This study demonstrates the feasibility of utilizing CTCs for monitoring clinically relevant cancer mutations throughout a patient’s cancer therapy journey.