Happy 10-Year Anniversary to BaseSpace® Correlation Engine

Deep sequencing and high throughput microarray technologies have enabled scientists to routinely generate hundreds of thousands if not millions of new data points in a single experiment. The extraordinary rate of data generation, finite resources, and focused research interests limit most investigations to follow up on only a small fraction of the data generated from next-generation sequencing (NGS) instruments.

Ten years ago, there were no services available to curate data. Researchers relied on home grown tools to perform the cumbersome task of matching information to publications, but they didn’t have the expertise to do a re-analysis. A group of entrepreneurial scientists and bioinfomaticists envisioned a need for solutions to handle the deluge of data that was coming as more and more genomes, from different kinds of species, were being sequenced. That vision manifested into NextBio® Research, a genomics software platform that could match variant to variant sets and gene expression to DNA methylation to protein-DNA binding across a spectrum of organisms, saving researchers time and resources. By leveraging biomedical ontologies coupled with proto-machine learning algorithms, dynamic data-driven applications were added to aid in the discovery of novel relationships among diseases, compounds, gene perturbations, and pathways.

After the acquisition of NextBio by Illumina in 2014, one of the primary NextBio Research utilities was rebranded as BaseSpace® Correlation Engine. Today it stands as a key pillar in the BaseSpace® Informatics Suite.

The BaseSpace Correlation Engine public study library has steadily grown over the years, approaching 21,000 studies, with more than 130,000 experimental gene signatures that have been collected and curated by a highly skilled team of scientists.* Illumina has been working hard to engage with ecosystem partners  to improve the quality of the user experience. Illumina has partnered with Elsevier over the past year to create connectivity between BaseSpace Correlation Engine and Elsevier’s Pathway Studio. Users can apply data filters to their results or work with the public data and visualize functional relationships among genes found in an experiment.

BaseSpace Correlation Engine results have found their way into hundreds of peer-reviewed citations from distinguished universities around the world and from many of the top 25 large pharmaceutical organizations including:


Pharmaceutical Organizations

Sanford Burnham Celgene
Mayo Clinic Sanofi
University of Pittsburgh Regeneron
University of Southern California Boehringer-Ingelheim
Stanford Pfizer
Harvard Johnson & Johnson
Cornel Weil Medical College Merck
Karolinska Institute Medimmune
Emory University
Kyoto University

Government Organizations

Vanderbilt NIH-National Institute
of Environmental Health Sciences
Yale Health Canada
University of California – Davis Environmental Protection Agency

If you would like to learn more about BaseSpace Correlation Engine:

*Based on internal database read as of 5/2017.

For Research Use Only. Not for use in diagnostic procedures.

One comment

Leave a Reply

This site uses Akismet to reduce spam. Learn how your comment data is processed.