Abstract
This paper presents a reconfigurable architecture of a lab-on-chip (LoC) microarray device capable to process data either in genotyping or in gene expression applications in a fraction of the time that is required by the usual software methods running on a standard computer. The entire LoC consists of a microfluidics part for the sample preparation and hybridization, a microsystem part including the application specific array of sensors for the electronic detection, and finally a reconfigurable processing part for the data analysis. The proposed data processing and analysis electronic module are an embedded multicore reconfigurable system-on-chip designed to analyze data from the forthcoming high-density oligonucleotide microarrays. The proposed architecture employs reconfigurable technology and has the capacity to process data from microarrays of various sizes from small size ones used in genotyping up to large-scale gene expression arrays. Additionally, the embedded processing cores feature reconfigurable circuitry for implementing the intense part of the processing, supplementing the various computational needs of the diverse applications for microarray real-time data processing and for a scalable reconfigurable architecture to handle also the future high-density microarrays.
Highlights
Microarrays are a significant part of the lab-on-chip (LoC) research area and are dedicated either for the parallel assessment of gene expressionfor hundreds or thousands of genes in a single experiment,or for genotyping molecular diagnostics applications and for pharmacogenomics
These further data processing steps require a larger number of data to be stored, when the number of spots on the microarray is of several thousands, and to process them for the quality assessment
The proposedmulticore architecturewas prototyped on anFPGA platform (Virtex-4-FX20) and was used to process data from a glass slide microarray
Summary
Microarrays are a significant part of the lab-on-chip (LoC) research area and are dedicated either for the parallel assessment of gene expressionfor hundreds or thousands of genes in a single experiment,or for genotyping molecular diagnostics applications and for pharmacogenomics. This paper presents the architecture of the electronic part of a fully integrated robust biomedical, biodiagnostics electronic microsystem This architecture processes the measurements of the electronic hybridization detection sensors and hosted at a disposable device-cartridge which first extracts the DNA from a blood drop, it amplifies the fragmented tiny DNA samples (using PCR) and runs biological protocols which evaluate the analyzed substance. It can be encapsulated in a single, portable, self-contained device-unit, significantly reducing the risks of cross-contamination inherent in conventional analysis methods.
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