ArticleNature communications2019
GraphTyper2 enables population-scale genotyping of structural variation using pangenome graphs.
Article in Nature communications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 120 papers, 3 of them syntheses that pooled it.
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120 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Missense variants in FRS3 affect body mass index in populations of diverse ancestries.Nature communications · 2025Pooled it
- GWAS meta-analysis reveals key risk loci in essential tremor pathogenesis.Communications biology · 2024Pooled it
- Exome sequencing identifies breast cancer susceptibility genes and defines the contribution of coding variants to breast cancer risk.Nature genetics · 2023Pooled it
- SVPG: a pangenome-based structural variant detection approach and rapid augmentation of pangenome graphs with new samples.Nature methods · 2026Article
- European ash pangenome reveals widespread structural variation and genetic basis of low ash dieback susceptibility.Nature communications · 2026Article
- Inferring the demographic history of Chinese and Indian rhesus macaque (Macaca mulatta) populations from PacBio HiFi long-read sequencing data.Molecular biology and evolution · 2026Article
- Integrating deep learning and pangenomics to recover missing heritability from wild structural variations.BMC genomics · 2026Review
- Rare disease genomics in an era of human pangenomics and telomere-to-telomere genome references.European journal of human genetics : EJHG · 2026Review
- The influence of structural variants from 2445 pigs on gene expression and complex traits.Nature communications · 2026Article
- Computational strategies for copy number variation detection, disease association, and beyond.Genome biology · 2026Review
- PanGraphRNA: An efficient and flexible bioinformatics platform for graph pangenome-based RNA-seq data analysis.Journal of integrative plant biology · 2026Article
- Building and applying pangenome references to capture genetic diversity.Nature reviews. Genetics · 2026Review
- Approaches to Studying Viral Pangenome Variation Graphs.Genomics, proteomics & bioinformatics · 2026Review
- Article
- TriosCompass: a snakemake workflow for integrated detection of SNVs, indels, STRs, and structural de novo variants in parent-child trios.Bioinformatics (Oxford, England) · 2026Article
- Challenges in Bringing Pangenome Research Into Breeding: A Case Study in Rice.Plant biotechnology journal · 2026Review
- Integrated selection scans and cis-eQTL analyses reveal genes and variants associated with milk quality, immunity, and adaptation in endangered Dengchuan cattle.BMC genomics · 2026Article
- Structural variation drives rhizome innovation and adaptive divergence in sister Medicago species.Journal of integrative plant biology · 2026Article
- SVCROWS: a user-defined tool for interpreting significant structural variants in heterogeneous datasets.Nucleic acids research · 2026Article
- Influence of homozygosity on genomic structural variation analyses for predicting ACL rupture risk in the Labrador Retriever and Rottweiler.Frontiers in genetics · 2026Article
60 more citing papers are in PubMed but not listed here.
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10 authors.
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Abstract
Analysis of sequence diversity in the human genome is fundamental for genetic studies. Structural variants (SVs) are frequently omitted in sequence analysis studies, although each has a relatively large impact on the genome. Here, we present GraphTyper2, which uses pangenome graphs to genotype SVs and small variants using short-reads. Comparison to the syndip benchmark dataset shows that our SV genotyping is sensitive and variant segregation in families demonstrates the accuracy of our approach. We demonstrate that incorporating public assembly data into our pipeline greatly improves sensitivity, particularly for large insertions. We validate 6,812 SVs on average per genome using long-read data of 41 Icelanders. We show that GraphTyper2 can simultaneously genotype tens of thousands of whole-genomes by characterizing 60 million small variants and half a million SVs in 49,962 Icelanders, including 80 thousand SVs with high-confidence.
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