Princess Máxima Center for Pediatric Oncology chooses PetaSuite for genomic oncology data compression

Posted on October 22, 2019
Princess Máxima Center news story

We are pleased to announce that Princess Máxima Center for Pediatric Oncology, the largest pediatric cancer center in Europe, has chosen to use PetaGene’s transparent, lossless genomic data compression software, called PetaSuite, to reduce its data storage costs while accelerating access to the data. Next-generation sequencing plays an integral role in the Center’s diagnostics and research discoveries. These valuable genomic datasets are large, and their volumes are growing. As such the Center sought to find a compression technology that can store genomic data for longer at a much lower cost while removing bottlenecks in genomic sequence analysis.

PetaGene’s PetaSuite software was evaluated by the Center against other compression techniques and unlike these, PetaSuite met and exceeded the criteria for a simple to implement and high compression performance solution, supported to a commercial standard.

Positive evaluation results

Senior Principal Investigator Dr. Patrick Kemmeren at the Princess Máxima Center describing the process, said: “Our tests with PetaGene’s compression software gave very positive results. We tested whole exome samples, RNA-Seq and whole genome sequencing data for different tumor samples. Implementing the software on our high-performance compute cluster is easy, the compression ratios are larger than what we obtain compared to CRAM compression, and accessing data is actually slightly faster compared to non-compressed BAM files. This on top of the added benefits of not having to switch to a different file format, a perpetual license for decompression and the time gains in not doing the BAM to CRAM conversion/retooling (and vice versa for some tools). As a result, we decided to implement PetaGene’s compression software within our computational infrastructure.

Oncology data compression quote
The right software at the right time

Jos Leendertse, Manager Research IDT at Princess Máxima Center, commented “By implementing PetaGene’s compression software we are also able to speed up the migration process to our new storage infrastructure. It’s not only the right software but also at the right time.”

Vaughan Wittorff, Ph.D., Cofounder and Chief Commercial Officer at PetaGene added, “During the evaluation process, the researchers found PetaSuite’s transparent access technology particularly compelling since it meant that the compressed data could integrate seamlessly with the bioinformatics structure Princess Máxima Center’s already had in place. A key challenge with compression is to ensure that end-users can continue working with the compressed files without having to change their existing, optimised workflows. PetaGene has solved this by ensuring that the compressed files are readable to existing tools and pipelines in the compressed state. This means our customers do not have to change any of their tools and pipelines, making it easy to integrate our compression technology within their infrastructure.”

About Princess Máxima Center for Pediatric Oncology

Opened in 2018, the Princess Máxima Center for Pediatric Oncology, based in Utrecht, The Netherlands, consolidated the work of seven different academic centers across the Netherlands into the largest pediatric cancer center in Europe. As both a hospital and a research institute, the Center has a combination of world-class facilities, leading clinicians and researchers all driven by a passion to cure pediatric cancers. By integrating the research facilities with the hospital, the Center is better equipped to implement novel discoveries into clinical care. For more information, visit www.prinsesmaximacentrum.nl/en.

Case study: Storing genomic data for clinical research facilities

Posted on May 1, 2019
Scientist working in laboratory

Scientist working in a clinical research laboratory

In clinical research, next generation sequencing (NGS) allows production of genomic data files at an ever increasing rate. Storing genomic data effectively is critical, and while sequencing costs are falling, the cost of storage for the resulting files is increasing. As the amount of data sequenced grows, genomic data storage costs and transfer times matter.

Clinical Genomics Gothenburg is a translational clinical research facility, performing bioinformatics and sequencing to provide an end-to-end solution to genomic data analysis. Increase in storage requirements was about to place existing infrastructure under considerable strain. Clinical Genomics Gothenburg found a solution to their data storage problem in PetaGene’s PetaSuite genomic data compression software.

Read more about how genomic data compression allowed Clinical Genomics Gothenburg to increase their storage capacity without modifying their workflows in our case study.

PetaSuite genomic data compression allows 60-90% storage cost and transfer time reductions, increasing storage capacity without adding to it. PetaGene’s software works with existing tools and pipelines, so can be used without workflow disruption. Data is quickly and easily accessed.

Compression is an effective method for managing genomic data generated in clinical research. By compressing genomic data, storage and transfer times can be reduced, facilitating analysis and saving valuable resources.  To find out more, get in touch using our contact form.

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