Periodic Reporting for period 1 - IMPACT (Improving DNA Analysis for Correct Healthcare)
Reporting period: 2019-05-01 to 2020-04-30
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 different ways to improve the performance and user experience. Thanks to the possibility to mature the Xdrop™ technology, it can help to provide valuable genomic insights. Using the Xdrop™ technology, CRISPR modifications, genomic gaps, unknown regions, and other complex genomic landscapes have been successfully investigated.
Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far
Since the beginning of the project, Samplix has visited several user-sites, presented at conferences, and made different outreach activities. A lot of feedback has been collected, which has been used to improve 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. The Xdrop™ workflow includes sequencing, and we have therefore tested and developed recommendations for sequencing setups. All this has significantly improved the Xdrop™ workflow and facilitated a fully supported user-experience.
Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)
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 on clinical samples. Our experience from the first year of the project highlights the importance of investing time and effort in users’ 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, understand viral integration sites, investigate repeat regions in e.g. cancer genes, phase mutations, and do improved whole genome amplification, when very limited sample sizes are available. The Xdrop™ technology has the potential to solve many more genomic questions and, in this way, we will continue expanding the use and work towards “Improving DNA Analysis for Correct Healthcare”.