Basepair’s SaaS Platform Orchestrates Nkarta’s Use of Its Own AWS Resources to Democratize Genomic Data Analysis

As a research scientist at Harvard Medical School, Sinha saw firsthand how scientists sometimes had to wait months for bioinformaticians to complete their analyses of NGS data. “We had more samples year over year at a lower price, generating bigger files and taking on more collaborators, but the analysis was the bottleneck,” says Sinha. “The vision was to create software so that all scientists, from bioinformaticians to bench biologists, could do their own analyses and get results within minutes.”

Basepair helps its customers to securely deploy, scale, and run bioinformatics tools and pipelines in a cost-effective way that is HIPAA and General Data Protection Regulation compliant. The solution uses Amazon Elastic Compute Cloud (Amazon EC2), which provides secure and resizable compute capacity for virtually any workload. It efficiently processes huge datasets, where the size of a single sample ranges to several gigabytes. “Traditional commercial data sharing and analysis approaches involve the movement of sensitive data into centralized bioinformatics products, increasing risk,” says Sinha. “It made sense to build a scalable cloud-native solution, and AWS was the obvious choice. Compute and storage capabilities no longer max out.”

Basepair’s intuitive interface lets bench scientists, who might lack programming expertise, run complex analyses simply. “They get results within minutes and can play with their own data: run quality control, slice and dice it, and look at it in different ways,” says Sinha. “AWS was leaps and bounds ahead of any other cloud providers in terms of resources to build on. We can continue to innovate and build features that our customers will use. If there were no AWS, there would be no Basepair.”

Founded in 2015, the biotech company Nkarta—Nk from the abbreviation for natural killer (NK) cells—was looking for a user-friendly, scalable bioinformatics solution to accelerate the development of NK cell therapies for cancer patients. “As a startup, it did not have enough bandwidth to adequately manage all its compute resources,” says Valentine. “This meant that it wasn’t efficiently spinning down or optimizing instances.”

Nkarta adopted Basepair’s NGS Analysis and Visualization Software and off-loaded routine DevOps tasks, such as compute optimization, job handling, and access permissions. Instead of a multiday training course, Nkarta bench scientists needed 1–2 hours of training to interpret results using Basepair’s built-in interactive visualizations and reports. “We have freed about 25 percent of the time for our small team to focus on more valuable data-mining tasks,” says Sombeet Sahu, Nkarta’s associate director of bioinformatics. “What’s more, bench scientists now come to my team with an informed question rather than a request to work on small, repetitive tasks.”

Nkarta has increased operational resilience, cutting internal response time by 50 percent and accelerating time to market for therapies. Additionally, Nkarta saves the equivalent of three to five full-time engineers who otherwise would have to configure, connect, and maintain the technology behind the pipeline. “The resources can be better allocated for scientific innovation and other core business areas, like exploring the power of artificial intelligence and machine learning for R&D,” says Valentine.

Basepair has helped Nkarta cut compute costs in half by automatically selecting the right instances to improve performance. The platform uses its own Amazon EC2 Spot Instances, which take advantage of unused Amazon EC2 capacity on AWS. For storage, Basepair uses Nkarta’s instances of Amazon Simple Storage Service (Amazon S3), an object storage service offering industry-leading scalability, data availability, security, and performance. Basepair estimates that the automated data archival and dynamic retrieval capabilities could cut storage costs by up to 80 percent.

For added data privacy and security, Nkarta connects to Basepair’s compute and storage resources from its own AWS account. “Organizations can keep all the data in their own environments and use Basepair to automate the management of the building blocks,” says Valentine. “It opens new horizons to use NGS for discovery and development of therapies. We accelerate time to scientific insight for researchers and diagnostic insights for patients while eliminating the need for data movement.”

Basepair has started to incorporate AWS HealthOmics, which helps healthcare and life science organizations build at scale to store, query, and analyze genomic, transcriptomic, and other omics data. Basepair plans to use Amazon Omics for even more cost-effective storage of genomic data and to help customers perform cohort-level clinical-genomics–based queries across patient datasets.

Basepair became an AWS Partner in May 2023 after completing the AWS Foundational Technical Review, which helps organizations identify and remediate risks in software or solutions. Basepair’s NGS Analysis and Visualization Software is available in AWS Marketplace, a curated digital catalog that simplifies procurement, provisioning, and governance of third-party software. “We want to democratize the use of NGS by helping more people analyze the data without replacing bioinformaticians’ valuable work,” says Valentine. “When we combine improved cross-team collaboration with effective use of the power of AWS, we will definitely accelerate the discovery process.”