Addressing False Positive Variants Arising from Pseudogenes

Clinical genetic testing has been transformed in recent years by the introduction of Next-Generation Sequencing (NGS). Targeted gene panels have made it possible to simultaneously analyse hundreds of genes with high confidence. However, since current aligners lack the sensitivity to distinguish reads that come from homologous parts of the genome, it is a challenge to work with genes with paralogues or pseudogenes. Pseudogenes arise from duplication of protein-coding genes, and have been considered to be degraded paralogues, due to loss of functionality.