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Gilead Sciences, Second Genome Partner for Microbiome-Based IBD Biomarker, Drug Discovery

NEW YORK – Gilead Sciences and Second Genome have launched a collaboration to identify biomarkers linked to clinical response in up to five of Gilead's pipeline compounds in inflammation, fibrosis, and other diseases. The team aims to also identify potential targets and drug candidates for treating inflammatory bowel disease (IBD).

As part of the project, South San Francisco-based Second Genome will use its Microbiome Analytics Platform to identify novel biomarkers associated with clinical responses to Gilead's investigational medicines.

According to Second Genome's site, its platform prioritizes confirmatory assays by integrating 16S rRNA gene community profiling, PhyloChip, metagenomics meta-transcriptomics, and inferred functional profiles.

The firm uses its SG KnowledgeBase to organize -omics data and clinical metadata for systematic mining. Using a defined in-house hierarchical ontology, the database curates data to allow cross-study analyses. Processed data is further refined to identify novel gene products from microbial dark matter and to identify bacterial and archaeal strains present.

From there, the firm evaluates quantitative taxonomic and functional profiles of the microbiome and connects them to its microbiome therapeutic database.

Second Genome's platform then tests selected peptides, proteins, and metabolites from the informatics analyses for activity in traditional pharmaceutical in vitro assays and in vivo models. After being optimized to improve potency, stability, manufacturability, and safety, the molecules undergo drug development processes for additional characterization in in pre-clinical and investigational new drug-enabling studies.

Second Genomics' platform will also analyze new targets and drug candidates linked to IBD. The firm believes that the platform will help inform patient stratification and improve potential future treatments.

"There is a growing body of evidence that the microbiome plays an important role in disease progression and treatment response in inflammatory diseases," William Lee, executive VP of research at Gilead, said in a statement. "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."

Second Genome will receive $38 million in an upfront payment, and up to about $300 million in success-based preclinical, clinical regulatory, and commercial milestones for each of the five target discovery programs, in addition to low double-digit royalties for approved products. The firm will also receive success-based milestones for each validated biomarker delivered as part of the agreement.

"The Second Genome platform seeks to redefine diseases through the lens of the microbiome, utilizing this incredible resource to identify potential biomarkers and therapeutics," Second Genome CEO Karim Dabbagh said in a statement. "We believe the microbiome holds insights into patient heterogeneity, as well as response to specific therapies. These differences enable the identification of important biomarkers to enhance precision medicine for better patient segmentation as well as potential combination therapies."

Gilead will have the option to worldwide rights for up to five programs for all diseases, as well as exclusive rights to all biomarkers developed under the collaboration.