ArticleGenes2018
De Novo Assembly of Two Swedish Genomes Reveals Missing Segments from the Human GRCh38 Reference and Improves Variant Calling of Population-Scale Sequencing Data.
Article in Genes, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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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
37 citing papers in PubMed, 63 citations in OpenAlex.
- The Pan-Genome of 1107 Spotted Sea Bass Accessions Reveals Gene Evolution Patterns During Domestication Selection.Molecular ecology resources · 2026Article
- Adoption of Standard Reference SNP Identifiers in Agricultural Genomics for Interoperability and Data Reuse.Scientific data · 2026Article
- Genome-wide association study bridging genomics-phenomics gap in natural plant populations.Journal of applied genetics · 2026Review
- T2T-CHM13 improves read mapping and detection of clinically relevant genetic variation in the Swedish population.Genome research · 2025Article
- JG2: an updated version of the Japanese population-specific reference genome.Human genome variation · 2025Article
- Article
- Constructing a draft Indian cattle pangenome using short-read sequencing.Communications biology · 2025Article
- Leveraging the T2T assembly to resolve rare and pathogenic inversions in reference genome gaps.Genome research · 2024Article
- De Novo Genome Assemblies From Two Indigenous Americans from Arizona Identify New Polymorphisms in Non-Reference Sequences.Genome biology and evolution · 2024Article
- Human pangenome analysis of sequences missing from the reference genome reveals their widespread evolutionary, phenotypic, and functional roles.Nucleic acids research · 2024Article
- Article
- The complete and fully-phased diploid genome of a male Han Chinese.Cell research · 2023Article
- Transposable element insertions in 1000 Swedish individuals.PloS one · 2023Article
- Assembly-free discovery of human novel sequences using long reads.DNA research : an international journal for rapid publication of reports on genes and genomes · 2022Article
- Complex genomic rearrangements: an underestimated cause of rare diseases.Trends in genetics : TIG · 2022Review
- InnovativeFrontiers in genetics · 2022Review
- Towards population-scale long-read sequencing.Nature reviews. Genetics · 2021Review
- Novel functional sequences uncovered through a bovine multiassembly graph.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- A novel canine reference genome resolves genomic architecture and uncovers transcript complexity.Communications biology · 2021Article
- Construction and integration of three de novo Japanese human genome assemblies toward a population-specific reference.Nature communications · 2021Article
Corrections and comments
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Authors and funding
12 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The current human reference sequence (GRCh38) is a foundation for large-scale sequencing projects. However, recent studies have suggested that GRCh38 may be incomplete and give a suboptimal representation of specific population groups. Here, we performed a de novo assembly of two Swedish genomes that revealed over 10 Mb of sequences absent from the human GRCh38 reference in each individual. Around 6 Mb of these novel sequences (NS) are shared with a Chinese personal genome. The NS are highly repetitive, have an elevated GC-content, and are primarily located in centromeric or telomeric regions. Up to 1 Mb of NS can be assigned to chromosome Y, and large segments are also missing from GRCh38 at chromosomes 14, 17, and 21. Inclusion of NS into the GRCh38 reference radically improves the alignment and variant calling from short-read whole-genome sequencing data at several genomic loci. A re-analysis of a Swedish population-scale sequencing project yields > 75,000 putative novel single nucleotide variants (SNVs) and removes > 10,000 false positive SNV calls per individual, some of which are located in protein coding regions. Our results highlight that the GRCh38 reference is not yet complete and demonstrate that personal genome assemblies from local populations can improve the analysis of short-read whole-genome sequencing data.
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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.