ArticleNature communications2022
Pan-African genome demonstrates how population-specific genome graphs improve high-throughput sequencing data analysis.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
19 citing papers in PubMed.
- Pangenomes aid accurate detection of large insertions and deletions from targeted sequencing: the case of cardiomyopathies.Genome medicine · 2026Article
- Rare disease genomics in an era of human pangenomics and telomere-to-telomere genome references.European journal of human genetics : EJHG · 2026Review
- Assembling unmapped reads reveals hidden variation in South Asian genomes.Nature communications · 2026Article
- Dynamics of genome evolution in the era of pangenome analysis.Cell genomics · 2026Review
- Long read and preliminary pangenome analyses reveal breed-specific structural variations and novel sequences in Holstein and Jersey cattle.Journal of advanced research · 2026Article
- Recommendations for responsible use of population descriptors in polygenic risk score development.Nature genetics · 2025Review
- Systemic barriers and opportunities for equity in early implementation of genetic testing and counseling for cardiomyopathies in Tanzania.Communications medicine · 2025Review
- GViNC: an innovative framework for genome graph comparison reveals hidden patterns in the genetic diversity of human populations.NAR genomics and bioinformatics · 2025Article
- Phased genome assemblies and pangenome graphs of human populations of Japan and Saudi Arabia.Scientific data · 2025Article
- Accurate human genome analysis with element avidity sequencing.BMC bioinformatics · 2025Article
- A Pangenomic Approach to Improve Population Genetics Analysis and Reference Bias in Underrepresented Middle Eastern and Horn of Africa Populations.Biomolecules · 2025Article
- Beyond single references: pangenome graphs and the future of genomic medicine.Frontiers in genetics · 2025Review
- Pangenome graphs and their applications in biodiversity genomics.Nature genetics · 2025Review
- A gentle introduction to pangenomics.Briefings in bioinformatics · 2024Review
- Pig pangenome graph reveals functional features of non-reference sequences.Journal of animal science and biotechnology · 2024Article
- Challenges of Diagnosing Mendelian Susceptibility to Mycobacterial Diseases in South Africa.International journal of molecular sciences · 2023Review
- Variant calling and benchmarking in an era of complete human genome sequences.Nature reviews. Genetics · 2023Review
- Personalizing medicine in Africa: current state, progress and challenges.Frontiers in genetics · 2023Review
- Exome variant discrepancies due to reference-genome differences.American journal of human genetics · 2021Article
Corrections and comments
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Authors and funding
12 authors.
Funding
Abstract
Graph-based genome reference representations have seen significant development, motivated by the inadequacy of the current human genome reference to represent the diverse genetic information from different human populations and its inability to maintain the same level of accuracy for non-European ancestries. While there have been many efforts to develop computationally efficient graph-based toolkits for NGS read alignment and variant calling, methods to curate genomic variants and subsequently construct genome graphs remain an understudied problem that inevitably determines the effectiveness of the overall bioinformatics pipeline. In this study, we discuss obstacles encountered during graph construction and propose methods for sample selection based on population diversity, graph augmentation with structural variants and resolution of graph reference ambiguity caused by information overload. Moreover, we present the case for iteratively augmenting tailored genome graphs for targeted populations and demonstrate this approach on the whole-genome samples of African ancestry. Our results show that population-specific graphs, as more representative alternatives to linear or generic graph references, can achieve significantly lower read mapping errors and enhanced variant calling sensitivity, in addition to providing the improvements of joint variant calling without the need of computationally intensive post-processing steps.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.