ArticleGenome biology2023
Characterization of large-scale genomic differences in the first complete human genome.
Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 21 citations in OpenAlex.
- T2T-CHM13 reference genome reduces mapping bias and enhances alignment accuracy at disease-associated variants.iScience · 2026Article
- A Personalized Haplotype-Resolved Near-Gapless Genome Framework for Somatic Variant Discovery in Hepatocellular Carcinoma.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Genome-wide variation landscape reveals temperature adaptation in Chinese indigenous cattle.Journal of animal science and biotechnology · 2026Article
- Multiplatform comparisons and annotation of structural variants highlight the utility of the T2T reference genome in human diagnostics.GigaScience · 2026Article
- Dark and camouflaged genomic regions remain challenging in CHM13.Scientific reports · 2026Article
- Cell line-matched reference enables high-precision functional genomics.Nature communications · 2025Article
- LIMK1 Deficiency Disrupts Hippocampal-Cortical Memory Consolidation and Attenuates Trauma-Induced PTSD-like Behavior.Biology · 2025Article
- Article
- IMGTNAR genomics and bioinformatics · 2025Article
- Sequencing the gaps: dark genomic regions persist in CHM13 despite long-read advances.bioRxiv : the preprint server for biology · 2025Article
- A refined analysis of Neanderthal-introgressed sequences in modern humans with a complete reference genome.Genome biology · 2025Article
- Interactive visualization and interpretation of pangenome graphs by linear reference-based coordinate projection and annotation integration.Genome research · 2025Article
- Environment-dependent mutualism-parasitism transitions in the incipient symbiosis between Tetrahymena utriculariae and Micractinium tetrahymenae.The ISME journal · 2025Article
- Impact and characterization of serial structural variations across humans and great apes.Nature communications · 2024Article
- Structural variation in humans and our primate kin in the era of telomere-to-telomere genomes and pangenomics.Current opinion in genetics & development · 2024Review
- Beef Cattle Genome Project: Advances in Genome Sequencing, Assembly, and Functional Genes Discovery.International journal of molecular sciences · 2024Review
- Article
- Rapid genomic sequencing for genetic disease diagnosis and therapy in intensive care units: a review.NPJ genomic medicine · 2024Review
- Natural variation in oxytocin receptor signaling causes widespread changes in brain transcription: a link to the natural killer gene complex.bioRxiv : the preprint server for biology · 2023Article
- Characterization of large-scale genomic differences in the first complete human genome.Genome biology · 2023Article
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Authors and funding
19 authors at 4 institutions in 3 countries.
Funding
Abstract
backgroundThe first telomere-to-telomere (T2T) human genome assembly (T2T-CHM13) release is a milestone in human genomics. The T2T-CHM13 genome assembly extends our understanding of telomeres, centromeres, segmental duplication, and other complex regions. The current human genome reference (GRCh38) has been widely used in various human genomic studies. However, the large-scale genomic differences between these two important genome assemblies are not characterized in detail yet.
resultsHere, in addition to the previously reported "non-syntenic" regions, we find 67 additional large-scale discrepant regions and precisely categorize them into four structural types with a newly developed website tool called SynPlotter. The discrepant regions (~ 21.6 Mbp) excluding telomeric and centromeric regions are highly structurally polymorphic in humans, where the deletions or duplications are likely associated with various human diseases, such as immune and neurodevelopmental disorders. The analyses of a newly identified discrepant region-the KLRC gene cluster-show that the depletion of KLRC2 by a single-deletion event is associated with natural killer cell differentiation in ~ 20% of humans. Meanwhile, the rapid amino acid replacements observed within KLRC3 are probably a result of natural selection in primate evolution.
conclusionOur study provides a foundation for understanding the large-scale structural genomic differences between the two crucial human reference genomes, and is thereby important for future human genomics studies.
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