Multi-megabase scale genome interpretation with genetic language models

Understanding how molecular changes caused by genetic variation drive disease risk is crucial for deciphering disease mechanisms. However, interpreting genome sequences is challenging because of the vast size of the human genome, and because its consequences manifest across a wide range of cells, tissues and scales -- spanning from molecular to whole organism level. Here, we present Phenformer, a multi-scale genetic language model that learns to generate mechanistic hypotheses as to how differences in genome sequence lead to disease-relevant changes in expression across cell types and tissues directly from DNA sequences of up to 88 million base pairs. Using whole genome sequencing data from more than 150 000 individuals, we show that Phenformer generates mechanistic hypotheses about disease-relevant cell and tissue types that match literature better than existing state-of-the-art methods, while using only sequence data. Furthermore, disease risk predictors enriched by Phenformer show improved prediction performance and generalisation to diverse populations. Accurate multi-megabase scale interpretation of whole genomes without additional experimental data enables both a deeper understanding of molecular mechanisms involved in disease and improved disease risk prediction at the level of individuals.

Generalising sequence models for epigenome predictions with tissue and assay embeddings

Sequence modelling approaches for epigenetic profile prediction have recently expanded in terms of sequence length, model size, and profile diversity. However, current models cannot infer on many experimentally feasible tissue and assay pairs due to poor usage of contextual information, limiting $\textit{in silico}$ understanding of regulatory genomics. We demonstrate that strong correlation can be achieved across a large range of experimental conditions by integrating tissue and assay embeddings into a Contextualised Genomic Network (CGN). In contrast to previous approaches, we enhance long-range sequence embeddings with contextual information in the input space, rather than expanding the output space. We exhibit the efficacy of our approach across a broad set of epigenetic profiles and provide the first insights into the effect of genetic variants on epigenetic sequence model training. Our general approach to context integration exceeds state of the art in multiple settings while employing a more rigorous validation procedure.