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Article

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

Nature genetics - 1 Nov 2025

Ma Walfred, Chaisson Mark J P

Abstract excerpt

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%...

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Methodology Data sources Editorial policy Privacy About Contact Helena Bioinformatics

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Identifiers

PMID: 41107550
DOI: 10.1038/s41588-025-02346-4
PMCID: PMC12597824

Genes

AMY2B
SMN1
SMN2

Provenance

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