AI-based platform to identify causal, genetically-defined therapeutic targets for Alzheimer's disease

Genetic Intelligence (GI) will analyze de-identified whole genome sequences (WGS) from Alzheimer’s disease (AD) and healthy patients using it’s AI-based platform to discover novel causal genes and variants for AD.

GI has previously obtained a NSF Phase I SBIR grant (#1819331) to develop and validate it’s computational platform using Amyotrophic Lateral Sclerosis (ALS) WGS (obtained from our partner the New York Genome Center) as a proof-of-principle. GI successfully validated the platform by rediscovering known ALS genes SOD1 and C9orf72, as well as discovering new ALS genes including STMN2, which was independently discovered by two labs this year using experimental approaches. We are currently validating two additional ALS targets experimentally. We plan to focus on applying our platform to uncover novel genes and variants in AD using a similar study design as ALS.

Objective 1: Obtain de-identified WGS data (e.g., ADSP and ADNI) from NIAGADS and preprocess them for input into GI’s computational pipeline.
Objective 2: Run the AD WGS through our in-house genetic background dissector tool, Cato, that uses several machine learning systems to stratify genomes before analysis to avoid spurious results arising from differences in case and control backgrounds.
Objective 3: Rediscover known AD genes. Chromosomes containing known AD genes (e.g., APOE, PSEN1 and PSEN2) will be input into our causal gene discovery platform, Bergspitze, to confirm if it can rediscover the known AD genes. The output from Bergspitze will be input into Franklin, GI’s interpretation module that provides a coherent etiology model for the disease with awareness of alternative etiologies advanced in the literature.
Objective 4: Discovery of new AD genes. Run the full genomes from all cluster groups and ancestry cohorts in Bergspitze and Franklin to identify and prioritize new AD genes and variants.
There are no plans to collaborate with other institutions.

Alzheimer’s disease (AD) is the leading cause of dementia affecting over 44 million people worldwide, and for which currently there are no effective prevention or cures. Enormous efforts and funding have been put into the discovery of the root cause of AD so as to find an effective treatment, but even with advancing genetic sequencing and analysis technology, no smoking gun has been found yet. Part of the issue has been scientific focus on analyzing the human exome, the ~1% of the human genome that codes for proteins, due to ease of analysis and lower noise in the data. However, this methodology precludes ~99% of the rest of the human genome, which harbors critical regulatory features that affect many of the processes in the body. Genetic Intelligence (GI) aims to solve this problem using its novel whole genome analysis platform that blends advanced genetic principles with state-of-the-art machine learning to identify causal disease targets. This information can then be used to create new drug candidates that are not only effective and precise, but also affordable.