Illumina and Broad Institute announce agreement to co-develop genomic secondary analysis tools

Illumina, Inc. and the Broad Institute of MIT and Harvard today announced they have entered into a collaboration for the co-development of secondary genomic analysis algorithms and software. Top data scientists from both institutions will collaborate to bring together the industry-leading open-source GATK algorithms with the speed and enhanced accuracy of Illumina’s DRAGEN (Dynamic Read Analysis for GENomics) Bio-IT Platform for commonly used methods, including small variant (SNV) and large variant (CNV/SV) detection.

“Broad and Illumina are committed to ensuring labs of all sizes and disciplines have access to the best algorithms,” said Anthony Philippakis, MD, PhD, Chief Data Officer of the Broad Institute of MIT and Harvard. “By bringing our expertise together to improve on our open-source toolkit, we can offer our most advanced comprehensive pipeline, while ensuring it remains widely available, open, and accessible to the global genomics community. This is a long-term partnership – we will innovate together to drive the leading edge of novel variant calling for the advancement of genomics.”

The co-developed secondary analysis software will be open-source and will be distributed through the Broad Institute's usual community support channels, such as GitHub. Illumina intends to develop proprietary, hardware-accelerated versions of the co-developed software on the Illumina DRAGEN-Bio-IT platform. This accelerated version of the software will be complemented with the wide offering of currently available pipelines on the DRAGEN Bio-IT platform. The Broad Institute and Illumina teams will validate that the results of such hardware-accelerated versions are functionally equivalent to those of the co-developed open-source software in order to ensure interoperability of data for downstream analyses.

“Illumina’s goal is to deliver industry leading technologies to our customers, whether that means creating tools ourselves, bringing new technologies and teams in-house or partnering to enhance our offerings,” said Susan Tousi, Senior Vice President of Product Development at Illumina. “This is why we were so thrilled to acquire Edico Genome and DRAGEN last year and in this spirit that we are partnering with the Broad with the goal to deliver best-in-class open-source software for commonly used methods. By creating a suite of algorithms combining the best of DRAGEN and GATK, we believe we can fuel the clinical adoption of sequencing by decreasing the cost and time of analysis.”

The Broad Institute’s GATK is an industry leader for identifying SNPs and indels in germline DNA and RNA sequencing data. These tools were primarily designed to process exomes and whole genomes generated with Illumina sequencing technology. Over time, the scope expanded to include somatic short variant calling, and to tackle copy number variation (CNV) and structural variation (SV). In addition to variant callers, GATK also includes utilities to perform related tasks such as processing and quality control of high-throughput sequencing data.

The Illumina DRAGEN Bio-IT Platform delivers accurate, rapid secondary analysis for germline and somatic SNV, SV, CNV(A) calling as well as methylation, RNA and repeat expansion workflows. DRAGEN pipelines are hardware-accelerated using reconfigurable field-programmable gate array technology (FPGA). DRAGEN Pipelines can be deployed on-premise via a local server and in the cloud through Illumina’s BaseSpace^TM Sequence Hub.

The co-developed secondary analysis software will provide a standardized methodology for processing high-throughput sequencing data and performing variant discovery analysis aiming for best-in-class sensitivity, accuracy and scalability.

“This approach is a positive step for the community and will add to the available choices in data analysis to increase the quality and lower the cost of the current set of analysis methods,” said Ewan Birney, Director, Global Alliance for Genomics and Health (GA4GH) and EMBL’s European Bioinformatics Institute. “The scientific community is well-positioned to benefit from this collaboration toward gold standard analysis methods and file formats which we believe will further enable inter-institution interoperability, research, and insights to maximize the impact of genomics in healthcare.”

Interested parties attending ASHG in Houston are encouraged to visit the Illumina booth or the Broad booth October 15-19, 2019.