Illumina Inc. Unveils PromoterAI, Groundbreaking Algorithm to Accelerate Insights for Rare Disease Diagnosis

Published: 2025-05-29 15:20:28 ET ILMN

Published on 05/29/2025 at 15:20

Illumina Inc. unveiled PromoterAI, a new AI algorithm that accurately deciphers pathogenic regulatory genetic variants in the noncoding regions of the human genome. A study published in Science illustrates how this deep learning technology discovered regulatory variants in noncoding "promoter" segments that contribute up to 6% of the genetic causes of rare diseases. By turning data into insights, this technology is expected to help researchers accelerate new breakthroughs in diagnosis for rare diseases.

When promoters are disrupted by genetic mutations, it can have profound consequences for downstream gene expression. The PromoterAI algorithm interprets the genetic sequence of promoters, thus opening the door to precise diagnoses for more patients with rare diseases. With PromoterAI applied to whole-genome sequencing (WGS) data analysis, clinical researchers are empowered to better understand the etiology and drug target potential for rare genetic diseases, common diseases, and oncology.

PromoterAI is the latest genomic AI algorithmic innovation from Illumina. In 2019, the Illumina Artificial Intelligence Lab released SpliceAI, a deep learning tool for interpreting noncoding cryptic splice mutations. In 2023, Illumina released PrimateAI-3D, which predicts the pathogenicity of protein-coding variants based on evolutionary conservation and protein structure.

The study demonstrates that when used together, Illumina's AI classification prediction tools--PromoterAI, PrimateAI-3 D, and SpliceAI--effectively double the diagnostic yield compared to using protein-truncating variants alone. PromoterAI will be accessible through Illumina Connected Software and it is available as part of DRAGEN?? secondary analysis.

Precomputed PromoterAI scores for all human promoter single-nucleotide variants are freely available for academic and noncommercial research use. Illumina Connected Software supports seamless integration with next-generation sequencing and array workflows for genomics and multiomics. Researchers, bioinformaticians, and clinical geneticists can use Illumina Connected Software to prioritize variants that are important to a case, gain critical insights, and accelerate their precision medicine dry lab operations.