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UK Biobank RAP Researcher Spotlight: April 2024

The Monthly Researcher Spotlight is our section highlighting the exciting work of the UK Biobank Research Analysis Platform user community. If you would like to be featured, email ukbiobankrap@dnanexus.com.

This was simultaneously published in the April 2024 UK Biobank RAP Newsletter. You can sign up for future installments here.

This month's Spotlight features the Scientific Insight Engineering Group at Genentech and they collaborate with scientists to power scientific discovery and accelerate decision making using computational methods.

Xiucheng Quek & Sai Reddy Achakkagari

(Left) Xiucheng Quek
Bioinformatics Cloud Software Engineer
Genentech, Inc

(Right) Sai Reddy Achakkagari
Bioinformatician
Genentech, Inc

What are the focus and discovery highlights of your research?

We are a research group that collaborates closely with scientists, employing computational techniques to extract scientific insights from their experiments. We develop, manage and execute large-scale computational workflows and methods in a reproducible framework. Our primary workflow development language is the Workflow Description Language (WDL), and we have constructed a framework enabling highly reproducible development, testing, and execution of our workflows. Our work has helped drive various R&D efforts and drug development in the company.

What are some of the key questions that you are looking to answer using UK Biobank data?

The UK Biobank cohort provides a rich set of phenotypes and has whole exome sequencing data for about 470,000 patients. We are interested in correlating certain known variants to specific phenotypes that are available in the UK Biobank cohort. This will provide our scientists with insights into disease biology and might open up pathways to new treatments.

How has the UK Biobank Research Analysis Platform (UKB-RAP) helped you perform your research?

The UK Biobank Research Analysis Platform (UKB-RAP) allowed us to execute workflows at scale.

We started our development at the end of December. By January, following several rounds of refinement and optimization, we initiated the processing of the entire cohort and successfully completed our runs before the month's end. At peak performance, we were processing 1000 jobs at a time, utilizing up to 8 cpu per job.

Because the UKB-RAP platform can run Workflow Description Language (WDL) workflows, we successfully transferred our internally developed and thoroughly tested workflow to the platform. For further optimization, we employed the smart-reuse feature during the pilot stage. This enabled us to iterate various workflow versions efficiently by re-running only the components that had changed between different versions. Additionally, we used dxFuse to mount our reference data, effectively reducing the time needed for data localization and thus, computation time.

About DNAnexus

DNAnexus the leader in biomedical informatics and data management, has created the global network for genomics and other biomedical data, operating in 33 countries including North America, Europe, China, Australia, South America, and Africa. The secure, scalable, and collaborative DNAnexus Platform helps thousands of researchers across a spectrum of industries — biopharmaceutical, bioagricultural, sequencing services, clinical diagnostics, government, and research consortia — accelerate their genomics programs.

The DNAnexus team is made up of experts in computational biology and cloud computing who work with organizations to tackle some of the most exciting opportunities in human health, making it easier—and in many cases feasible—to work with genomic data. With DNAnexus, organizations can stay a step ahead in leveraging genomics to achieve their goals. The future of human health is in genomics. DNAnexus brings it all together.