CN-RNN: a Deep Learning Framework for Copy Number Variation Detection with Exome Sequencing Data

Copy number variations (CNVs) are major structural genomic variants that contribute to a wide range of human diseases. Accurate detection of CNVs from whole-exome sequencing (WES) data has been a long-sought goal for clinical and population genetic studies. Despite recent progress, existing WES-based CNV callers still suffer from high false-positive rates and reduced recall for short-length variants, and current deep learning methods have not fully used complementary information in region-level genomic features. Here we present CN-RNN, a deep learning-based CNV caller for WES data. The model combines a bidirectional long short-term memory (BiLSTM) branch that captures local depth changes and contextual dependencies across neighboring exons with a parallel multi-layer perceptron (MLP) branch that encodes region-level metadata such as GC content, mappability, and exon length. CN-RNN was trained on the Autism Sequencing Consortium (ASC) parent-child trio cohort using the Mendelian rule of inheritance to ensure high-quality training sets. It was evaluated across three independent datasets, in which we showed that CN-RNN outperformed existing WES-based CNV callers and deep learning methods. CN-RNN offers a scalable, accurate tool for CNV profiling in WES-based studies and supports broader application of CNV analysis in population and clinical research. CN-RNN is available at https://github.com/FeifeiXiao-lab/CN-RNN.