Genotyping sequence-resolved copy number variation using pangenomes reveals paralog-specific global diversity and expression divergence of duplicated genes

Copy number variable (CNV) genes are important in evolution and disease, yet their sequence variation remains a blind spot in large-scale studies. We present ctyper, a method that leverages pangenomes to produce allele-specific copy numbers with locally phased variants from next-generation sequencing samples. Benchmarking on 3,351 CNV genes and 212 challenging medically relevant (CMR) genes, ctyper captures 96.5% of phased variants with ≥99.1% correctness of copy number in CNV genes and 94.8% of phased variants in CMR genes. Ctyper takes 1.5 h to genotype a genome on one CPU. The ctyper genotypes give a 4.81-fold improvement in predictions of gene expression compared to known expression quantitative trait locus (eQTL) variants. Allele-specific expression quantified divergent expression in 7.94% of paralogs and tissue-specific biases in 4.68%. We found reduced expression of SMN2 due to SMN1 conversion, potentially affecting spinal muscular atrophy, and increased expression of translocated duplications of AMY2B. Overall, ctyper enables biobank-scale genotyping of CNV and CMR genes. Ctyper is a genotyping method for copy number variation and complex genes that produces sequence-resolved genotypes by directly comparing sequencing reads to pangenome haplotypes, achieving increased robustness and copy number sensitivity with efficiency scalable to biobank analysis.