Hardware-efficient on-chip nanopore signal processor for ultra high-throughput single-molecule sensing

DNA sequencing plays an essential role in advancing biological research and in various applications such as virology and medical diagnosis. Nanopores are at the forefront of advanced single molecule sequencing technology, providing long reads, cost-effective and high-throughput DNA analysis. In addition, nanopore based single molecule sensing is viewed as the key to unlock the potentially even more impactful proteomics field.  Advancements in this field are happening at a very fast pace thanks to the improvements of both sensor technologies as well as of the assisting microelectronic CMOS readout circuitry. Currently, it is possible to generate very large quantities of nanopore data at extremely fast data rates (e.g., 4 TB/day), which is expected to keep increasing in the coming years due to the push for even higher throughput. Although very recent base-calling algorithms can potentially keep up with the data stream, researchers are generating datasets much faster than they can be transmitted to online files. These datasets are so large that it is a practical challenge to store them locally. As a result, large-scale genome processing, transmission and storage pose problems from an algorithmic and systems perspective. Based on the current trends, it is likely that storage and transmission of the complete data will soon become infeasible.

Imec is currently leveraging its CMOS process expertise and infrastructure to develop and manufacture silicon-based solid-state nanopores for high-throughput single-molecule sensing. Thus, the main goal of this PhD is to investigate and implement ultra-low-power hardware algorithms and CMOS circuits to process on-chip the enormous amount of data coming from large nanopore arrays. The signal processing will either compress and/or interpreted the data before it is transmitted to a computer, thus enabling future ‘smart’ nanopore systems. The candidate will design innovative chip prototypes that will be integrated with imec nanopore arrays. The candidate will also contribute to the electrical characterization of these nanopore prototype systems in real biological applications.

Skills and background:

• Digital and/or mixed-signal CMOS IC design
• Signal-processing theory and hardware algorithms
• Knowledge of VHDL, embedded firmware design and/or programmable logic (FPGA)
• Knowledge of PCB design