Fixing reference errors efficiently improves sequencing results

Abstract

The GRCh38 reference is the current standard in human genomics research and clinical applications, but includes errors across 33 protein-coding genes, including 12 with medical relevance. Current studies rely on the correctness of this reference genome and require an accurate and cost-effective way to improve variant calling and expression analysis across these erroneous loci. We identified likely artifacts in GTEx, gnomAD, 1000 Genomes Project, and other important genomic resources leading to wrong interpretations for these genes. Here, we present FixItFelix together with a modified GRCh38 version that improves the subsequent analysis across these genes within minutes for an existing BAM/CRAM file. We showcase these improvements over multi-ethnic control samples across short and long-read DNA-, and RNA-sequencing. Furthermore, applying our approach across thousands of genomes demonstrates improvements for population variant calling as well as eQTL studies. Still, some genes e.g., DUSP22 indicate mixed results due to their complexity.