Periodic Reporting for period 7 - PHOTO-SENS (A plug and play PHOTOnics based bioSENSing platform for salmon pathogen detection)
Reporting period: 2023-12-01 to 2024-05-31
Aquaculture is expected to play a vital role in solving the challenge of sustainably providing the growing world population with healthy and nutritious food. Pathogen outbreaks are a major risk for the sector, so early detection and a timely response are crucial. This can be enabled by monitoring of pathogen levels in aquaculture facilities.
In PHOTO-SENS, a photonic biosensing platform based on silicon nitride waveguide technology with integrated active components is developed, which can be used for such applications. The project will connect pioneering biosensor technology and scaling-up procedures with aquaculture expertise to establish and a working prototype system for monitoring salmon pathogens. Previous work showed proof of principle of hybrid photonic integrated Circuits (PICs). However, due to lack of scalability, the overall costs of the biosensor remained very high, and it was not used for biosensing. The PHOTO-SENS system will feature significant improvements in terms of:
- miniaturization of the PIC
- development of processes for hybrid integration of active components
- development of processes for surface modification
- integration of the PIC in a microfluidic cartridge
Importantly, these processes will not only be developed and optimized as such, but they will be designed to be mutually compatible, and constitute a coherent workflow for manufacturing functional microfluidic cartridges with hybrid PICs. A prototype desktop readout instrument for the PHOTO-SENS cartridge will be developed. Furthermore, biomarkers for aquaculture pathogens will be identified, and qPCR test for their detection will be developed. Finally, the qPCR biomarkers will be used for pathogen detection on the hybrid PIC.
At the end of the project, it can be concluded that the objectives have been realized. The results obtained in PHOTO-SENS advance the state of the art and contribute to the increasing technology, manufacturing, and market readiness of integrated biophotonics, and brings practical applications of (hybrid) PICs in biosensing one step closer. Using the PHOTO-SENS system, biosensing on the hybrid PIC platform has been demonstrated for the first time. In addition, the qPCR based pathogen tests are readily available for application in aquaculture practice.
In PHOTO-SENS, a photonic biosensing platform based on silicon nitride waveguide technology with integrated active components is developed, which can be used for such applications. The project will connect pioneering biosensor technology and scaling-up procedures with aquaculture expertise to establish and a working prototype system for monitoring salmon pathogens. Previous work showed proof of principle of hybrid photonic integrated Circuits (PICs). However, due to lack of scalability, the overall costs of the biosensor remained very high, and it was not used for biosensing. The PHOTO-SENS system will feature significant improvements in terms of:
- miniaturization of the PIC
- development of processes for hybrid integration of active components
- development of processes for surface modification
- integration of the PIC in a microfluidic cartridge
Importantly, these processes will not only be developed and optimized as such, but they will be designed to be mutually compatible, and constitute a coherent workflow for manufacturing functional microfluidic cartridges with hybrid PICs. A prototype desktop readout instrument for the PHOTO-SENS cartridge will be developed. Furthermore, biomarkers for aquaculture pathogens will be identified, and qPCR test for their detection will be developed. Finally, the qPCR biomarkers will be used for pathogen detection on the hybrid PIC.
At the end of the project, it can be concluded that the objectives have been realized. The results obtained in PHOTO-SENS advance the state of the art and contribute to the increasing technology, manufacturing, and market readiness of integrated biophotonics, and brings practical applications of (hybrid) PICs in biosensing one step closer. Using the PHOTO-SENS system, biosensing on the hybrid PIC platform has been demonstrated for the first time. In addition, the qPCR based pathogen tests are readily available for application in aquaculture practice.
The PHOTO-SENS system consists of a desktop reader, which can be used in combination with disposable microfluidic cartridges containing hybrid PICs. To reduce the manufacturing costs of the cartridge, the price of the PIC has to be reduced and the manufacturing and assembly process has to be improved. Design optimization of the waveguide circuitry and an improved cartridge integration concept enabled a reduction of the PIC footprint by a factor of 8 without sacrificing functionality or sensitivity, resulting in an equivalent reduction of the cost per chip. Wafer scale processes for hybrid integration of components by thermocompression bonding, soldering, and adhesive bonding have been developed based on laser-assisted local heating of substrate wafers. Furthermore, novel processes for wafer scale material-selective chemical surface modification and singulation by stealth dicing have been developed. Together, all of these processes constitute a complete and scalable process flow for wafer scale production of hybrid biosensor PICs.
The next step is the assembly of the PIC in the microfluidic cartridge. First, a basic cartridge has been designed and fabricated, with which the concept of chip-cartridge integration has been validated. Leak tightness, and optical and electrical functionality of the basic cartridge has been confirmed. Next, a microfluidic cartridge for DNA assays has been developed, comprising a sample injection port, and blister pouches with assay buffers and reagents. The cartridge also features a heating element, degassing functionality, cavities for flow front detection, and a waste reservoir. Moreover, the cartridge provides electrical, mechanical, and fluidic interfaces with the tabletop readout instrument.
The instrument contains mechanics, electronics, and software for cartridge handling, heating, optical actuation and readout of the PIC, and controlling liquid flows. Three prototype instruments have been built, and were tested in combination with the microfluidic cartridge. Measurements using solutions with different salt concentrations have confirmed the functionality of the instrument, the microfluidic cartridge, and the hybrid PICs.
Three bacterial aquaculture pathogens were selected for assay development. DNA biomarkers were identified, corresponding primer-probe sets were designed, and qPCR assays were developed that could detect biomarker concentrations down to 5 copies/µL. One pathogen biomarker was also detected using the hybrid PIC platform. This is the first successful demonstration of biosensing on the hybrid PIC platform.
Dissemination of project results has taken place through different channels. The main dissemination publications are:
- 3 theses
- 3 white papers
- 6 conference presentations
- 1 project poster
- 1 peer reviewed scientific paper
Despite the impressive technical progress, the system as a whole is not yet sufficiently advanced to be commercialized shortly after finalization of the project. This also has an impact on the exploitation plans of the project partners. In particular, the first generation of PIC biosensor products will be based on passive PICs. Furthermore, Surfix has decided to focus on medical (cancer) diagnostics as their primary target market. TunaTech will serve the aquaculture market with their qPCR based solutions, while looking for opportunities to continue the development towards chip-based testing. For PHIX, CSEM, and LRE, their participation in PHOTO-SENS has resulted in the development of new exploitable processes and knowledge, which enables them to expand their portfolio of services. Thus, the consortium will not jointly market hybrid PIC based pathogen detection tests. Instead, the partners will focus on their individual plans to exploit and commercialize the project results.
The next step is the assembly of the PIC in the microfluidic cartridge. First, a basic cartridge has been designed and fabricated, with which the concept of chip-cartridge integration has been validated. Leak tightness, and optical and electrical functionality of the basic cartridge has been confirmed. Next, a microfluidic cartridge for DNA assays has been developed, comprising a sample injection port, and blister pouches with assay buffers and reagents. The cartridge also features a heating element, degassing functionality, cavities for flow front detection, and a waste reservoir. Moreover, the cartridge provides electrical, mechanical, and fluidic interfaces with the tabletop readout instrument.
The instrument contains mechanics, electronics, and software for cartridge handling, heating, optical actuation and readout of the PIC, and controlling liquid flows. Three prototype instruments have been built, and were tested in combination with the microfluidic cartridge. Measurements using solutions with different salt concentrations have confirmed the functionality of the instrument, the microfluidic cartridge, and the hybrid PICs.
Three bacterial aquaculture pathogens were selected for assay development. DNA biomarkers were identified, corresponding primer-probe sets were designed, and qPCR assays were developed that could detect biomarker concentrations down to 5 copies/µL. One pathogen biomarker was also detected using the hybrid PIC platform. This is the first successful demonstration of biosensing on the hybrid PIC platform.
Dissemination of project results has taken place through different channels. The main dissemination publications are:
- 3 theses
- 3 white papers
- 6 conference presentations
- 1 project poster
- 1 peer reviewed scientific paper
Despite the impressive technical progress, the system as a whole is not yet sufficiently advanced to be commercialized shortly after finalization of the project. This also has an impact on the exploitation plans of the project partners. In particular, the first generation of PIC biosensor products will be based on passive PICs. Furthermore, Surfix has decided to focus on medical (cancer) diagnostics as their primary target market. TunaTech will serve the aquaculture market with their qPCR based solutions, while looking for opportunities to continue the development towards chip-based testing. For PHIX, CSEM, and LRE, their participation in PHOTO-SENS has resulted in the development of new exploitable processes and knowledge, which enables them to expand their portfolio of services. Thus, the consortium will not jointly market hybrid PIC based pathogen detection tests. Instead, the partners will focus on their individual plans to exploit and commercialize the project results.
In PHOTO-SENS, several advances over the state of the art are achieved:
- miniaturization of the hybrid biosensor PIC by a factor of 8
- wafer level processes for hybrid integration of light source, detector, and temperature sensor on the PIC
- wafer level processes for material-selective chemical and biological surface modification of the PIC
- scalable processes for integration of the PIC in a microfluidic cartridge
- biosensing using hybrid PICs
Together, all of these processes constitute a complete and scalable process flow for wafer scale production of hybrid biosensor PICs.
Aquaculture is expected to play a vital role in providing the growing world population with healthy and nutritious food. Pathogen outbreaks are a major risk for the sector, so early detection and a timely response are crucial. This can be enabled by biosensor based monitoring of pathogen levels in aquaculture facilities. The PIC biosensing technology developed in PHOTO-SENS could be used for such applications. The results obtained in PHOTO-SENS bring practical applications of PICs in biosensing one step closer. As a generic platform technology, the potential of PIC based biosensing goes beyond aquaculture, and is expected to also have a significant impact on other application areas, such as healthcare.
- miniaturization of the hybrid biosensor PIC by a factor of 8
- wafer level processes for hybrid integration of light source, detector, and temperature sensor on the PIC
- wafer level processes for material-selective chemical and biological surface modification of the PIC
- scalable processes for integration of the PIC in a microfluidic cartridge
- biosensing using hybrid PICs
Together, all of these processes constitute a complete and scalable process flow for wafer scale production of hybrid biosensor PICs.
Aquaculture is expected to play a vital role in providing the growing world population with healthy and nutritious food. Pathogen outbreaks are a major risk for the sector, so early detection and a timely response are crucial. This can be enabled by biosensor based monitoring of pathogen levels in aquaculture facilities. The PIC biosensing technology developed in PHOTO-SENS could be used for such applications. The results obtained in PHOTO-SENS bring practical applications of PICs in biosensing one step closer. As a generic platform technology, the potential of PIC based biosensing goes beyond aquaculture, and is expected to also have a significant impact on other application areas, such as healthcare.