Munich Leukemia Laboratory (MLL) Uses Illumina Software on AWS Infrastructure for Genome Sequencing

Half a million lives are lost each year to leukemia. The mission of Munich Leukemia Laboratory (MLL) is to find a cure. That mission includes developing better leukemia diagnostics, improving the knowledge of the disease’s mechanisms, and understanding its context and complexity. The genomic revolution is empowering MLL to achieve those goals.

DNA sequencing—the ability to order, or sequence, the chemical building blocks of human DNA—is helping to shape how cancer is diagnosed and treated. Next-generation sequencing (NGS) describes a method that uses technology to sequence whole human genomes at a much faster rate and at a much lower cost. MLL’s use of the NGS method led to a large increase in the organization’s compute and storage needs. Eventually, those needs exceeded the capacity of MLL’s local infrastructure.

“For MLL, the next, most logical step was to use cloud computing rather than building out our own infrastructure, which would have meant more buildings to house servers and more people to maintain those servers,” explains Niroshan Nadarajah, head of the bioinformatics team for MLL. “We wanted to focus on the research that was most meaningful to our patients, not on infrastructure.”

MLL’s initial move to the cloud was prompted by its 5,000 Genome Project, in which the company sequenced 5,000 genomes with 100X coverage (meaning the number of times a base pair is sequenced). That sequencing process produced petabytes of data. To deal with its growing need for scalable compute and storage while maintaining a high standard for data security, MLL turned to Illumina, an AWS Partner Network (APN) Advanced Technology Partner.

“DNA sequencing requires an amazing amount of computing power and processing. It’s inevitable that organizations will turn to the cloud, simply because of the scale demanded to support NGS,” says Chris Kunard, director of software development in customer collaboration and innovation for Illumina. MLL uses Illumina’s sequencing instruments as well as its software analysis tools, including BaseSpace Sequence Hub.

Illumina’s BaseSpace solution and MLL’s compute and storage needs are underpinned by AWS Cloud infrastructure. Illumina relies on Amazon Simple Storage Service (Amazon S3) to store customer data, as well as its own internal data. Amazon Elastic Compute Cloud (Amazon EC2) provides secure, resizable compute capacity.

Kunard says, “Our customers generate terabytes of data with each sequencing run. That quickly becomes costly to manage internally. The BaseSpace Sequence Hub platform allows our customers to sequence their data and send it directly to the cloud. Utilizing BaseSpace Sequence Hub reduces the cost and complexity associated with building and maintaining a local storage environment, making it easier to scale operations easily while remaining cost-effective.”

“We were initially hesitant to use the cloud,” explains Nadarajah. “Protecting personal health information was critical for us. There is nothing more personal than genome data.”

Illumina shares that concern with its worldwide customer base. The global presence of AWS is crucial to Illumina as it responds to the specific privacy and health data regulations required by its customers. AWS customers benefit from a data center and network architecture built to meet the needs of the most security-sensitive organizations. “We rely heavily on AWS standards of security and information management, such as ISO 27001 and others. Our customers require that level of security so they can maintain their own lab accreditations,” says Anton Tsyganov-Bodounov, manager of commercial bioinformatics for Illumina.

Nadarajah agrees, “Germany accredits diagnostic laboratories. Before MLL, no German lab used cloud computing. During our most recent re-accreditation, AWS and Illumina helped us provide all the relevant information to prove our regulatory compliance.”

Leveraging AWS and the Illumina cloud platform, MLL has a secure environment for processing its genome data. More important, however, is the improved speed of that processing. Before using cloud computing, it took MLL 10–12 hours to process a single sequencing run and could only sequence 70 to 80 samples per day. Now done in the cloud, it takes 30–40 minutes, and the company can run an unlimited number of samples. Previously, MLL needed 24 hours to compute a whole-genome sample with 100X coverage. Now that takes only 4 hours using the Illumina DRAGEN Bio-IT Platform.

Already Nadarajah is contemplating what this means for the future of MLL. “Because of the infinite scalability of the cloud, I think whole-genome sequencing—the ability to process the complete DNA—will soon become the standard workflow of care and diagnostics,” he says. “With the AWS Cloud and Illumina’s sequencing tools, we’ll be able to meet that data management challenge while focusing on our core mission: finding a cure for leukemia.”