In the January publication of Nature, scientists at Google DeepMind in London published the paper “Advancing regulatory variant effect prediction with AlphaGenome.” This paper details the creation of AlphaGenome, a deep learning algorithm designed to predict the effect of mutations genome-wide regulatory processes. The predictive capacity of AlphaGenome is particularly applicable in the study of cancer-causing mutations. AlphaGenome takes base-pair sequences (genetic code) as input and predicts the molecular properties of its regulation, such as the systemic expression of the gene it codes for within different tissues and cells.
As a predictive tool, AlphaGenome grants insight into rare genetic disorders by outputting the specific consequences of the mutations that cause them, including differing RNA expression levels and splicing due to position within the genome. AlphaGenome was trained using references to the genomes of multiple organisms, including mice and humans, and it outperforms previous models in its ability to analyze the effects of changes in non-coding regions of the genome.
AlphaGenome is a relevant progression of Google DeepMind’s advancements in the field of computational biology. Rather than analyzing the resulting protein structures of protein coding genes, which consist of less than 2% of the genome, AlphaGenome analyzes the vast sea of information that the non-coding part of a genome contains. The non-coding genome influences expression of genes, facilitates proper management of the genome, and codes for functional RNA rather than proteins. In some ways, the non-coding genome is just as important as the protein coding genome within an organism, breaking free of its previous labeling as “junk DNA”. Predicting and understanding the effects of mutations in the non-coding genome is essential to understand rare-genetic disorders as well as systems biology for genetic engineering.
Computational models such as AlphaGenome are built upon vast experimental data compiled over many years as well as major breakthroughs in molecular biology, and they would not be possible without the hard work of countless researchers. AlphaGenome is a testament to the progress of molecular systems biology and helps scientists better comprehend the vast and seemingly undecipherable sea of genetic code.
