ArticleGenome research2018
Detection and analysis of ancient segmental duplications in mammalian genomes.
Article in Genome research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
25 citing papers in PubMed, 51 citations in OpenAlex.
- Emergence and evolution of chimeric pseudogenes (φgenes) contribute to genetic and functional diversity of the human genome.Nucleic acids research · 2026Article
- Heritable changes in chromatin contacts associated with transgenerational susceptibility to diet-induced insulin dysregulation and obesity.Nature communications · 2026Article
- SDrecall: a sensitive approach for variant detection in segmental duplications.Genome biology · 2026Article
- The role of unbalanced segmental duplication in sex chromosome evolution in Australian ridge-tailed goannas.Scientific reports · 2025Article
- GenomeDecoder: inferring segmental duplications in highly repetitive genomic regions.Bioinformatics (Oxford, England) · 2025Article
- Transposable elements shape the landscape of heterozygous structural variation in a bird genome.Zoological research · 2025Article
- Detection of an 8p23.1 Inversion Using High-Resolution Optical Genome Mapping.Maternal-fetal medicine (Wolters Kluwer Health, Inc.) · 2024Article
- Multiscale analysis of pangenomes enables improved representation of genomic diversity for repetitive and clinically relevant genes.Nature methods · 2023Article
- Three amphioxus reference genomes reveal gene and chromosome evolution of chordates.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Characterization of the immunoglobulin lambda chain locus from diverse populations reveals extensive genetic variation.Genes and immunity · 2023Article
- Article
- Methodologies for theGenes · 2022Review
- Fast characterization of segmental duplication structure in multiple genome assemblies.Algorithms for molecular biology : AMB · 2022Article
- Towards the detection of copy number variation from single sperm sequencing in cattle.BMC genomics · 2022Article
- A custom ddPCR method for the detection of copy number variations in the nebulin triplicate region.PloS one · 2022Article
- Quantitative assessment reveals the dominance of duplicated sequences in germline-derived extrachromosomal circular DNA.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Prenatal Diagnosis of True Fetal Mosaicism with Small Supernumerary Marker Chromosome Derived from Chromosome 16 by Funipuncture and Molecular Cytogenetics Including Chromosome Microarray.Diagnostics (Basel, Switzerland) · 2021Article
- Modelling segmental duplications in the human genome.BMC genomics · 2021Article
- Fatal perinatal mitochondrial cardiac failure caused by recurrentMed (New York, N.Y.) · 2021Article
- Current understanding of extrachromosomal circular DNA in cancer pathogenesis and therapeutic resistance.Journal of hematology & oncology · 2020Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Although segmental duplications (SDs) represent hotbeds for genomic rearrangements and emergence of new genes, there are still no easy-to-use tools for identifying SDs. Moreover, while most previous studies focused on recently emerged SDs, detection of ancient SDs remains an open problem. We developed an SDquest algorithm for SD finding and applied it to analyzing SDs in human, gorilla, and mouse genomes. Our results demonstrate that previous studies missed many SDs in these genomes and show that SDs account for at least 6.05% of the human genome (version hg19), a 17% increase as compared to the previous estimate. Moreover, SDquest classified 6.42% of the latest GRCh38 version of the human genome as SDs, a large increase as compared to previous studies. We thus propose to re-evaluate evolution of SDs based on their accurate representation across multiple genomes. Toward this goal, we analyzed the complex mosaic structure of SDs and decomposed mosaic SDs into elementary SDs, a prerequisite for follow-up evolutionary analysis. We also introduced the concept of the breakpoint graph of mosaic SDs that revealed SD hotspots and suggested that some SDs may have originated from circular extrachromosomal DNA (ecDNA), not unlike ecDNA that contributes to accelerated evolution in cancer.
Indexed as
Identifiers
What OpenQuestion holds
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.