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Improving DNA Analysis for Correct Healthcare

Periodic Reporting for period 2 - IMPACT (Improving DNA Analysis for Correct Healthcare)

Reporting period: 2020-05-01 to 2021-04-30

Samplix has developed a novel microfluidic technology (Xdrop™) enabling scientists to indirectly capture genomic regions, which have been inaccessible until now. The technology can potentially help to understand complex diseases such as cancer, immunological diseases, and neurological diseases, but since this is a new technology, it requires many user interactions including on-site visits, seminars, and conference presentations. The grant from the European Commission’s prestigious Horizon 2020 SME program has enabled Samplix to establish collaborations, visit user sites, and extensively interact with the potential market. Based on the feedback collected, Samplix has optimized the Xdrop™ technology in many ways to improve the performance and user experience. In addition, Samplix has reached new target groups within high throughput screening and the feedback on the technology has been very positive. Using the Xdrop™ technology, CRISPR modifications have been validated or unintended edits have been found, cancer genes have been studied, unknown genomic regions in plants and animals have been resolved, and the technology has successfully been employed for high throughput screening of bacteria and enzymatic activities.
Since the beginning of the project, Samplix has visited several user-sites, presented at conferences, and made different outreach activities. Users of the technology have also presented at conferences, contributed to tech notes, and have published in peer-reviewed journals. Feedback has been collected, which has been used to make valuable improvements to the product. Guidelines for the most compatible DNA extraction methods have been made to make it easier for users to start Xdrop™ experiments as well as detailed recommendations for the experimental setup, for improving droplets sorting, and for result evaluation and interpretation. The workflow has been optimized and new protocols and videos have been generated to support users. As a response to user feed-back, Samplix is integrating droplet sorting into the Xdrop instrument, greatly improving the workflow for the users. As part of this project, the sorting parameters have been optimized and the technology demonstrated.
The Xdrop™ workflow includes DNA sequencing, and we have therefore tested and developed recommendations for sequencing setups. We have also built data analysis pipelines, analyzed strategies for analysis of unknown regions, and we now provide data analysis recommendations and data analysis service for users. We are currently working on making the developed data analysis solutions available locally on user servers. All this has significantly improved the Xdrop™ workflow and facilitated a fully supported user-experience. Recommendations, application notes, publications, webinars, and tools can be found at https://samplix.com/applications https://samplix.com/webinar https://samplix.com/support and https://samplix.com/tools
The Xdrop™ technology provides new opportunities for genomic analysis. Long regions of ~ 100 kb can be captured and sequenced based on very limited genomic information. In this way, any genomic regions, including insertions, deletions, repeats, gaps, and any structural variation, can be investigated. This is especially valuable in the context of large genomes, genomes for which a reference is not available, or those regions in the human genome underlying the genetic cause of diseases. Basic research questions will be answered, but the technology has also already been used by our partners on clinical samples. Our experience from the project highlights the importance of investing time and effort in user interaction, deeply understanding their needs, and developing new features accordingly. Accordingly, the Xdrop™ technology has been optimized in the project to solve different applications such as CRISPR editing verification, amplification of the whole genome from single human cells, and high throughput screening of cells.
The Xdrop™ technology has the potential to solve many more questions. The ultra-high throughput screening capacity of up to 1 billion compartments per day, that can be achieved with the new Xdrop Sort, has made the technology relevant for a broader market including also high throughput screening of bacterial and mammalian cells. Thus, we will continue expanding the use and work towards “Improving DNA Analysis for Correct Healthcare”.
New workflow for high throughput screening of cells developed based on feedback from users.
The new Xdrop Sort instrument with integrated droplet sorting and the single-use dSort cartrigde.