ArticleNature genetics2025
Genotyping sequence-resolved copy number variation using pangenomes reveals paralog-specific global diversity and expression divergence of duplicated genes.
Article in Nature genetics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 3 papers.
What it found
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Who cites it
3 citing papers in PubMed.
- HPRC2: A human pangenome reference with near-complete coverage of common genetic variation.bioRxiv : the preprint server for biology · 2026Article
- Building and applying pangenome references to capture genetic diversity.Nature reviews. Genetics · 2026Review
- Multimodal characterisation of the SMN locus in SMA: copy number quantification and hybrid gene identification.NPJ genomic medicine · 2026Article
Corrections and comments
- Erratum issued
- Update of
Authors and funding
2 authors.
Funding
Abstract
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.
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