Gilead taps Second Genome for microbiome biomarker help in a potential $1.5B deal

green bacteria
Second Genome's platforms include next-generation sequencing analyses and high-throughput assays for mapping out the microbiome, as well as an integrated informatics program for drug R&D. (Gerd Altmann)

Gilead launched a four-year collaboration with the microbiome-focused Second Genome, to develop new biomarkers that can track clinical responses to its drugs aimed at inflammation, fibrosis and more. 

The two companies also plan to identify new potential targets and therapeutic candidates for inflammatory bowel disease, or IBD. 

Second Genome will receive $38 million upfront for providing its Microbiome Analytics Platform to the clinical development of Gilead’s pipeline compounds. It could also net up to about $300 million in milestone-based payments per drug, up to five in all, based on the success of each one's preclinical and clinical development or eventual commercialization—for a potential total of about $1.5 billion.

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“There is a growing body of evidence that the microbiome plays an important role in disease progression and treatment response in inflammatory diseases,” said Gilead’s William Lee, executive vice president of research. 

“We look forward to working with Second Genome to investigate the microbiome’s role in inflammatory disease and particularly IBD, where patients can face significant challenges in achieving long-term remission with conventional therapies,” Lee said.

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Additionally, Second Genome will receive extra payments for each clinically validated biomarker it delivers, parsing the microbiome for signs that could be used to optimize treatment courses or assign patients within clinical trials. The collaboration also includes an option for a two-year extension.

“The Second Genome platform seeks to redefine diseases through the lens of the microbiome, utilizing this incredible resource to identify potential biomarkers and therapeutics,” said Second Genome CEO Karim Dabbagh. 

This includes next-generation sequencing analyses and high-throughput assays, as well as an integrated informatics program.

“We believe the microbiome holds insight into patient heterogeneity as well as response to specific therapies,” Dabbagh added. “These differences enable the identification of important biomarkers to enhance precision medicine for better patient segmentation as well as potential combination therapies.”

Editor's note: This story has been corrected to show the $300 million in milestone-based payments are per drug, and not $300 million in total.

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