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New AI algorithm accurately deciphers pathogenic regulatory genetic variants in the noncoding regions of the human genome at scale for the first time
SAN DIEGO , May 29, 2025 /PRNewswire/ -- Illumina Inc. (NASDAQ: ILMN ) today unveiled PromoterAI, a new AI algorithm that accurately deciphers pathogenic regulatory genetic variants in the noncoding regions of the human genome. A study published today 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.
Currently, only about 30% of rare disease patients receive an accurate diagnosis from exome sequencing. For many patients, insights may be hidden in what are known as "noncoding regions," which comprise over 98% of the genome and may hold the key to increasing the diagnostic rate.
Promoters are key noncoding elements that define where transcription of a gene begins. 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.
"Illumina is breaking new ground with this AI technology," said Kyle Farh , MD, PhD, vice president, distinguished scientist, and head of the Illumina Artificial Intelligence Lab. "Combined with whole-genome sequencing, we believe PromoterAI holds the power to improve the rate of rare disease diagnosis by identifying previously overlooked variants in the noncoding genome. One of the challenges of searching for the genetic causes of rare disease is that, even if the protein-coding sequence of a gene is free from variants, mutations in that gene's promoter region can prevent it from being properly expressed."
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-3D, and SpliceAI—effectively double the diagnostic yield compared to using protein-truncating variants alone.
"PromoterAI is the latest addition to our AI and software portfolio, which has delivered leading quality, prediction accuracy, and comprehensiveness to turn data into valuable insights for our customers," said Rami Mehio , vice president, and global head of Software and Informatics.
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