Judith Schlanderer

Background: The growing demand for versatile laboratory automation is exemplified in the context of liquid biopsy, where multi-analyte approaches are increasingly recognised for their potential to enhance diagnostic sensitivity in oncology. However, current practice often necessitates the use of dedicated instruments and workflows for the extraction of each analyte, posing financial and logistical barriers for automated multi-analyte liquid biopsy. Methods: Here, we present Robotic Centrifugal Microfluidics (RoCM), an all-in-one platform that combines the versatility of centrifugal microfluidics and operational flexibility of robotic liquid handling. This combination enables the automation of complex micro- and macrofluidic protocols, realised through the use of (1). exchangeable microfluidic cartridges and (2). programmable robotic operations such as in-rotation liquid supply, magnetic bead manipulation, or microfluidic valving. In-rotation robotic liquid manipulation maintains fluid control under centrifugal forces and reduces the cartridge footprint associated with pre-loaded liquid reservoirs. Platform applicability was demonstrated using two exemplary liquid biopsy workflows: the extraction of cell-free DNA (cfDNA) from blood plasma using RoCM-cfDNA slices and the extraction of extracellular vesicles (EVs) from blood plasma using RoCM-EV slices. Results: In a pilot study with patient samples from different cancer entities, the RoCM-cfDNA slices yielded comparable variant allele frequencies to a commercial bead-based instrument, while the RoCM-EV slices achieved a recovery of a greater diversity of EV subpopulations than semi-automated size-exclusion chromatography. Conclusions: By simply exchanging cartridges, RoCM enables the extraction of diverse analytes within a single automated system. Its application can be extended to further analytes, such as circulating tumour cells (CTCs), or to applications beyond liquid biopsies, where versatile micro- and macrofluidic protocols benefit from implementation in a single automation instrument.

Background: The growing demand for versatile laboratory automation is exemplified in the context of liquid biopsy, where multi-analyte approaches are increasingly recognised for their potential to enhance diagnostic sensitivity in oncology. However, current practice often necessitates the use of dedicated instruments and workflows for the extraction of each analyte, posing financial and logistical barriers for automated multi-analyte liquid biopsy. Methods: Here, we present Robotic Centrifugal Microfluidics (RoCM), an all-in-one platform that combines the versatility of centrifugal microfluidics and operational flexibility of robotic liquid handling. This combination enables the automation of complex micro- and macrofluidic protocols, realised through the use of (1.) exchangeable microfluidic cartridges and (2.) programmable robotic operations such as in-rotation liquid supply, magnetic bead manipulation, or microfluidic valving. In-rotation robotic liquid manipulation maintains fluid control under centrifugal forces and reduces the cartridge footprint associated with pre-loaded liquid reservoirs. Platform applicability was demonstrated using two exemplary liquid biopsy workflows: the extraction of cell-free DNA (cfDNA) from blood plasma using RoCM-cfDNA slices and the extraction of extracellular vesicles (EVs) from blood plasma using RoCM-EV slices. Results: In a pilot study with patient samples from different cancer entities, the RoCM-cfDNA slices yielded comparable variant allele frequencies to a commercial bead-based instrument, while the RoCM-EV slices achieved a recovery of a greater diversity of EV subpopulations and up to one magnitude higher recovery than semi-automated size exclusion chromatography. Conclusion: By simply exchanging cartridges, RoCM enables the extraction of diverse analytes within a single automated system. Its application can be extended to further analytes, such as circulating tumor cells (CTCs), or to applications beyond liquid biopsies, where versatile micro- and macrofluidic protocols benefit from implementation in a single automation instrument.

Tuberculosis (TB) is still one of the world’s deadliest infections. Fast detection of the pathogen M. tuberculosis (MTB) and its genetic resistance markers substantially improves treatment success and outcome. A key element for rapid genetic diagnostics is the efficient extraction of DNA from sputum for qPCR detection at the point of care. We present the fully automated sample preparation of MTB DNA from 3 mL of liquefied sputum and qPCR detection of MTB on a centrifugal microfluidic cartridge. Our method achieves a limit of detection (LoD) between 17 and 57 CFU/mL and provides a purified DNA solution for molecular downstream testing, such as targeted NGS.

Globally, tuberculosis (TB) remains the deadliest bacterial infectious disease, and spreading antibiotic resistances is the biggest challenge for combatting the disease. Rapid and comprehensive diagnostics including drug susceptibility testing (DST) would assure early treatment, reduction of morbidity and the interruption of transmission chains. To date, rapid genetic resistance testing addresses only one to four drug groups while complete DST is done phenotypically and takes several weeks. To overcome these limitations, we developed a two-stage workflow for rapid TB diagnostics including DST from a single sputum sample that can be completed within three days. The first stage is qPCR detection of M. tuberculosis complex (MTBC) including antibiotic resistance testing against the first-line antibiotics, isoniazid (Inh) and rifampicin (Rif). The test is automated by centrifugal microfluidics and designed for point of care (PoC). Furthermore, enriched MTBC DNA is provided in a detachable sample tube to enable the second stage: if the PCR detects MTBC and resistance to either Inh or Rif, the MTBC DNA is shipped to specialized facilities and analyzed by targeted next generation sequencing (tNGS) to assess the complete resistance profile. Proof-of-concept testing of the PoC test revealed an analytical sensitivity of 44.2 CFU ml⁻¹, a diagnostic sensitivity of 96%, and a diagnostic specificity of 100% for MTBC detection. Coupled tNGS successfully provided resistance profiles, demonstrated for samples from 17 patients. To the best of our knowledge, the presented combination of PoC qPCR with tNGS allows for the fastest comprehensive TB diagnostics comprising decentralized pathogen detection with subsequent resistance profiling in a facility specialized in tNGS.