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

Posted on October 22, 2019
Princess Máxima Center logo

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.

Genique Lifesciences appointed exclusive PetaGene distributor for India

Posted on October 3, 2019

We are pleased to announce that PetaGene has signed an agreement appointing Genique Lifesciences as the exclusive distributor of our genomic data management software in India.

The agreement will allow India-based Genique Lifesciences to act as the exclusive sales channel for PetaGene’s genomic data compression software for the growing Indian market. Genique’s founding team has extensive experience with distribution of Next Generation sequencers in India.

“Genique already possesses significant expertise in sequencing technology sales and the consumer DNA testing market, making it an ideal partner for us in India, one of the fastest growing genomics markets,” commented Vaughan Wittorff, Ph.D., Cofounder and Chief Commercial Officer of PetaGene. “We are excited to be working with Genique to bring PetaGene’s software to genomics researchers in India, so that they can access their genomic data faster, more efficiently, and store it more cost-effectively.”

Speaking for Genique Lifesciences, Cofounder and CEO, Abhishek Das said, “We are delighted to represent PetaGene in India. Their innovative technology will help organisations optimise their on-site or cloud storage costs for the growing volume of genomic data in India.”

Significant developments in India include the Department of Biotechnology launching the Genome India project later this year with the target of sequencing the genome of 10,000 Indian citizens.

To contact Genique, visit their website.

New genomic data storage and analysis guide

Posted on July 11, 2019
Laptop showing data compression report

One year ago, Frontline Genomics published Genomic Data 101, its guide to the technology and hardware landscape for genomic data storage and analysis. It proved a valuable primer for anyone looking to find out about compression and general management of genomic data.

The data infrastructure to support genomic research, including compression, has evolved since the original guide. Frontline Genomics have published a new version. It’s called Biodata Analysis and Management – Genome Analytics, Interoperability, and Data Life Cycle.

The new publication addresses key issues:

  • The landscape of compression options and the enhanced benefits of techniques developed specifically for genomics.
  • The state of the art.
  • Technical considerations when choosing a compression solution.
  • Commercial considerations – ROI.
  • Specific considerations when storing data in the cloud
  • How different compression techniques integrate with existing and new analysis workflows.

There is new information on the innovations and developments in genomic compression, which include:

  • The improved compression ratios now being achieved.
  • Data to show how efficient commercially available compression gives better savings than would be obtained using a free open source tool.
  • How the plateauing of storage costs mean it’s no longer possible to rely on the historical trend for reductions in storage costs.

You can download the paper here to discover the latest on compression and other aspects of genomic data management.

Bio-IT World 2019 Best of Show winners

Posted on April 26, 2019
PetaGene celebrate their Best of Show award
The PetaGene team toast their Best of Show award

The latest addition to our product range, PetaSuite Protect, won “Best of Show” earlier this month at BioIT World Conference & Expo 2019, the premier conference for IT in Life Sciences. This is our third “Best of Show” win, previously winning in 2016 and 2018. This year, 31 new products were considered by an expert panel of judges who awarded PetaSuite Protect  the ‘Nailed It’ award.

In the award citation, Phillips Kuhl, President at Cambridge Healthtech Institute said, “Our judges believe this is a new, powerful and highly relevant approach to security, driven by a passionate and invested team”.

PetaSuite Protect provides users with the tools to encrypt their genomic data; manage fine-grain access to it, and demonstrate compliance with applicable regulations. As with the established PetaSuite compression technology, the new encryption and access capabilities are completely transparent to genomic tools and analysis pipelines.

Dan Greenfield, our co-founder and CEO said, “We’re thrilled to win this illustrious award for the third time. We’re particularly grateful to the judges for recognizing the relevance of our approach to this important element of genomic data management.”

To find out more about PetaSuite Protect please get in touch via our contact us page.

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PetaGene is hiring

Posted on February 21, 2019

Would you like to join a funded, award-winning and growing Cambridge start-up working in the increasingly vital field of genomic data?   

We are looking for developers and a business support administrator.  For the developer roles you’ll need to be proficient in C/C++ and it would help if you’re comfortable working with algorithms.

For the business support administrator position, we’re looking for someone with experience in a business support role. You will need to be well-organised, persistent and accurate to help make our sales operation as effective as possible.

We’ll be at the Cambridge Network Recruitment Evening on 26th February, so come along to talk about how you could fit into our team.

Full job descriptions are on our careers page, with information on how to apply.  We’d love to hear from you.

 

Photo by Tim Mossholder on Unsplash

Start solving your data challenges at ASHG 2018 in San Diego

Posted on September 6, 2018
ASHG 2018 graphic - see us on booth 819
ASHG 2018 Banner - see us on booth 819

Every year the ASHG annual meeting attracts the thought leaders in the field of human genetics. Will you be among them at ASHG 2018 in San Diego? If so, visit us on booth #819 during the three days of the exhibition, October 17th to 19th, to let us know about the data challenges you face.

Our team has extensive experience in health information technologies, systems development and large-scale genomics. We’ll be delighted to discuss how to address the frustrations caused by ever increasing volumes of genomic data.

Those challenges go beyond the simple cost of on-premises or cloud storage. There’s the transfer and analysis times for large data sets to consider too. Speeding those up can give a great boost to your research. Our PetaSuite compression software integrates seamlessly with analysis pipelines, reduces I/O demand and facilitates collaboration.

We’ll also be hosting a session in CoLab Theater 3 on Thursday 18th from 4:00 to 4:15pm to present on how using appropriate compression technology can benefit commercial and research organizations working with genomic data.

If you’re attending ASHG 2018 in San Diego, drop by booth #819 or book a meeting in advance of the show to make sure we fit into your schedule. We look forward to seeing you there.

If you’d like to know more about the ASHG meeting or register to attend, visit the website.

Second win at Bio-IT World.

Posted on June 12, 2018
Bio-IT World Best of Show 2018 winner logo
The PetaGene team celebrating their win
From left: Vaughan Wittorff, Co-Founder & Chief Commercial Officer; Dan Greenfield, Co-Founder and CEO; Mar Sanchez Gadea, Business Support Administrator and Michael Hultner SVP Strategy & GM US Operations

We launched PetaSuite Cloud Edition (CE) at Bio-IT World 2018, the premiere conference for IT in the Life Sciences.  Its benefits for organisations working with genomic data in terms of reduced storage cost, shorter data transfer times and quicker analysis were immediately recognised by the judges of the Best in Show awards; they awarded it top prize in the storage infrastructure and hardware category.  This is the second time we have won this influential award.  The original version of PetaSuite picked up Best of Show in the category for optimising speed and storage at the same event in 2016.

In her award citation for PetaSuite CE, Allison Proffit, Bio-IT World Editor, said: “the judges were very impressed with an offering that lets users access data compression, objects in storage or an s3 bucket, all from the command line.”

Petasuite CE allows a user’s software tools and next generation sequencing (NGS) pipelines to seamlessly integrate with a wide variety of cloud storage platforms without modification.  Amazon Web Services (AWS), Microsoft Azure, Google Cloud Platform (GCP), private cloud and hybrid cloud are all supported transparently.

PetaSuite CE also delivers significantly improved, high-performance, scalable genomic compression technology.  Lossless compression ratios of up to 10x for GATK BAM files are now possible. Other NGS file types such as FASTQ.gz can now also achieve much better compression ratios.  For FASTQ.gz files, the ratio is up to 4.3 times compression.  This represents a potential space saving of 77%, which brings dramatic cost and transfer time reductions without compromising the quality of the original genomic data.

Dan Greenfield, our co-founder and CEO said: “We are honoured to win this prestigious award for the second time. The fact that the judges acknowledged the importance of our seamless cloud integration, with its implications for scaling and collaboration, was particularly pleasing.  We will continue to strive to create solutions which speed up cooperation and analysis for our research and diagnostic customers.”

Find out more about PetaSuite Cloud Edition on the products page or get in touch via our contact page.