Innovative tools for genomics research
Leymus Genomics, based in Copenhagen (Denmark), is a next-generation sequencing company working with Nordic and German institutions. The company, founded in 2017, provides hardware and software for data storage, whole genome sequencing (WGS) data analysis and AI for large genomic datasets.
Leymus Genomics, founded by CEO Rasmus Brøndum, was launched at the European Society of Human Genetics meeting in Copenhagen, Denmark in May 2017.
"I have worked in the genomic tools and diagnostics industries since 2005. Working for Illumina, Thermo and Roche Diagnostics, three of the leading genomics companies, I realised that there was a need for big data and genomics solutions. The complexity and data amount of the whole genome sequencing [WGS] ecosystem is daunting, and to advance the field the next-generation sequencing [NGS] tools and solutions companies must provide novel, simple, fast, and flexible solutions," said Brøndum.
Bringing big data hardware and software solutions to Nordic genomic labs
Big data plays an increasingly important part in healthcare and in drug research and development, where fast, scalable, secure and encrypted data storage is vital. However, pulling data from storage for analysis is becoming a bottleneck, which will increase with the use of WGS data and the increased data footprint.
"Sequencing technologies like Illumina's NovaSeq can put out three terabytes of data every two days. Hospitals and clinics may not be prepared to deal with this amount of data," said Brøndum.
Speed is crucial for some patient groups. In a neonatal ward, for example, NGS screening and analysis could pick up a rare mutation behind a metabolic disorder. Any delays in pulling data down from storage and then analysing it could mean a fatal delay in treatment. Security and data quality are also important, when handling patients' personal data.
To solve these challenges, Leymus provides scientists with access to tools and solutions through its partnerships and internal software and AI developers. The key partners in large data handling in WGS are DDN-DataDirect Networks, NVIDIA and Parabricks.
DDN provides large-scale data storage for sequencing applications, genomic pipelines and data collaboration solutions. Storage is typically from 250 TB and up, and DDN runs the world's fastest data pipelines, as demonstrated by the fact that DDN supplies 60% of the world's supercomputers. Through its partnership with DDN in the Nordic countries, Leymus Genomics can meet the needs for infinitely-scalable storage, to avoid the need for data migration, and maintain rapid and secure access to speed up research and diagnosis
"DDN is a leader in high performance computing, and is used by leading genomics sites including the Wellcome Trust Sanger Institute, the Institute of Cancer Research, Public Health England, DKFZ, Edinburgh Genomics and most recently SciLife Clinical Genomics Stockholm," said Brøndum.
NVIDIA powers AI solutions, and Parabricks provides a novel way of analysing whole genome data files. The partnerships with NVDIA and Parabricks can shorten the whole genome sequencing secondary analysis workflow.
Processing a GATK4 pipeline relying on CPUs can take over 24 hours. NVIDIA uses graphics processing units (GPUs) that can cut the runtime to less than one hour. The analysis can run in-house on a NVDIA GPU unit or as a cloud solution with Azure, AWS or Google Cloud.
Under the new partnership with Parabricks, Leymus brought on board two new AI data scientists, Niels Buus Lassen and Rene Madsen, who have a long track-record of working with statistical modelling, software development and AI, and who will collaborate on customized solutions for NVDIA and DDN costumers.
"Buus Lassen and Madsen will ensure that we can help companies to decide what data infrastructure and software they need to increase their whole genome data flow," said Brøndum.
Focusing on large scale data into the future
"Most of the Nordic countries have national whole genome population data projects under way. These national projects generate a lot of information, and analysing the data could provide major benefits for the population, such as new findings for precision medicine, or tailoring individual patients' medications. My passion is the analysis of DNA and to help scientist,patients and physicians to find the answers by delivering the best possible genomic analysis and solutions," said Brøndum.