New genome analytics platform makes clinical genomics affordable for daily use in hospital

02/05/2019

Together with 2 other Leuven MindGate members - KU Leuven and UZ Leuven - and a range of exterior partners, imec has developed a unique hybrid cloud platform for fast and cost-efficient whole genome sequencing and analysis. Imec’s Genome Analytics Platform (GAP) platform can now perform a full genome analysis of 48 samples in only 48 hours and at an acceptable cost.

The platform paves the way to genome sequencing as a daily practice in hospitals, for diagnosing and treating genetic diseases, including cancer and rare diseases, and for better treating newborns with complex disorders.

When the first human genome was published in 2000, the scientific community agreed that they, together with the industry, had to set a goal – the ‘1,000dollar genome’.

They believed that when sequencing the genome would only cost 1,000 USD, it would become feasible to sequence the genome of every patient that needed it for a better, personalized treatment.

Today, this 1,000-dollar genome is almost a reality. However, it becomes clear that just cost-efficient sequencing is not the whole answer to realizing personalized medicine.

Turning the raw sequencing data into ‘knowledge’ and useful information for doctors, requires a lot of compute and storage power. Previously, the analysis and storage of the genome data had been too expensive and could take up to several weeks.

Researchers and industry leaders in Belgium have now tackled this genome analytics challenge, making whole genome sequencing process cost- and time-effective for hospitals – not only for research purposes, but also for the treatment of patients in everyday care.

The platform consists of a combined compute cluster and ActiveScale™ cloud object storage system from Western Digital, which runs a heavily optimized genomics software platform and that can also tap into the cloud as needed (BlueBee Genomics Platform). This solution can process the full output of a sequencing machine (48 genomes) within 48 hours, the same time it takes the sequencing machine to produce the raw genome data.

Scalable to 63PB (raw) in a single namespace, and up to 19 nines of data durability, Western Digital’s ActiveScale system provides the capacity, data durability and scaling capabilities required to accomplish imec’s extreme data-driven GAP goals – now and into the future.

Its unified data access enables the project architects to streamline the interaction between ActiveScale and the process for ingesting and analyzing the massive amounts of genome data. Western Digital NVMe SSDs sustain the velocity of data required to support the processing power of the compute cluster for balanced system design.

Up until now, there was no real ecosystem or workflow available for clinical genomics, and discussions were ongoing on whether local or cloud computing were the best answer. With this new platform, a hybrid solution, combines the best of both worlds: cost-effective analysis at a local site, and faster analysis involving cloud computing.

One of the project partners, Agilent, has already integrated the hybrid platform solution into a first product – Alissa OnePGT solution – which is being tested by the University Hospital of Leuven (UZ Leuven) and the Human Genetics Group of KU Leuven, to better treat patients.


Source: Electronics Weekly


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