Unlocking the immune system with high-throughput lab automation

Adaptive Biotechnologies, a Seattle-based biopharma leader with 600+ employees, is redefining how diseases like cancer, autoimmune disorders, and infectious diseases are diagnosed and treated. By decoding the adaptive immune system with their proprietary immune profiling platform, they’re turning biology’s most powerful detection system into precision medicine tools.

Manual error-prone processes block scientific speed

Adaptive’s high-throughput molecular research team works extensively with techniques like NGS and PCR. But despite their scientific innovation, lab operations were held back by manual, error-prone workflows.

Scientists had to manually build templates and CSV files for every assay run. Data was copied and pasted between systems, causing frequent errors. These errors sometimes caused their Hamilton liquid handlers to stall or crash, risking valuable, time-sensitive samples.

Misplaced or misformatted files disrupted downstream NGS analysis, sometimes causing days of delay. Weekly audits were necessary to find and fix mistakes, costing valuable time and delaying results. Even a small error in a sample sheet could take anywhere from 30 minutes to several hours to troubleshoot. Altogether, these challenges created a fragile system that couldn’t scale with the pace or precision Adaptive’s research demanded.

Connecting data, instruments, and people

Adaptive turned to Benchling to modernize and unify their molecular research teams operations. With Benchling and Benchling Connect they built seamless automated links between digital workflows and lab instruments. Hamilton liquid handlers and other lab instruments are now directly integrated into Benchling through Benchling Connect, enabling data to flow bi-directionally without manual intervention. 

Benchling Connect automates the registration, tracking, and retrieval of samples and reagents and sends them to the liquid handlers directly, eliminating manual data wrangling between spreadsheets. Output from those instruments flows automatically into Benchling’s Registry and Results schemas, pre-formatted for downstream analysis and removing the risk of mismatches or manual re-entry. 

For NGS workflows, Benchling Connect also auto-generates and formats the required metadata CSVs, ensuring it’s ready for downstream omics pipelines. This eliminates the need for manual copy and pasting across different data sources and decreases data analysis delays due to human error.

Fewer errors, faster science

Since deploying Benchling, Adaptive has transformed how their high-throughput molecular workflows operate:

• Errors eliminated: Weekly file-handling mistakes have dropped to nearly zero, saving the team over 20 hours a month.

• Faster resolutions: Data issues that once took hours to troubleshoot are now solved instantly–or never occur.

• More science, less busywork: Scientists focus on discovery instead of manual data wrangling.

• Accelerate research: NGS workflow throughput has surged nearly 1.5x, speeding research cycles.

• Data you can trust: Every dataset is now fully traceable, easy to find, and instantly shareable across teams.

Benchling is now integral to Adaptive’s molecular research improving efficiency, and scalability—turning complex innovations into simplified, cost-effective processes.