ArticlePLoS computational biology2017
Landscape and variation of novel retroduplications in 26 human populations.
Article in PLoS computational biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 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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Who cites it
20 citing papers in PubMed.
- Characterization of retrocopies in 663 individuals with esophageal squamous cell carcinoma.iScience · 2026Article
- From Genomic Fossils to Functional Elements: The Evolving Story of Pseudogenes.Advanced genetics (Hoboken, N.J.) · 2025Review
- Quantitative Analysis of Pseudogene-Associated Errors During Germline Variant Calling.International journal of molecular sciences · 2025Article
- Interchromosomal Colocalization with Parental Genes Is Linked to the Function and Evolution of Mammalian Retrocopies.Molecular biology and evolution · 2023Article
- Whole Genome Analysis of Dizygotic Twins With Autism Reveals Prevalent Transposon Insertion Within Neuronal Regulatory Elements: Potential Implications for Disease Etiology and Clinical Assessment.Journal of autism and developmental disorders · 2023Article
- Discovery of non-reference processed pseudogenes in the Swedish population.Frontiers in genetics · 2023Article
- Ancient segmentally duplicated LCORL retrocopies in equids.PloS one · 2023Article
- Recent, full-length gene retrocopies are common in canids.Genome research · 2022Article
- Review
- Tracing the Origin and Evolutionary Fate of Recent Gene Retrocopies in Natural Populations of the House Mouse.Molecular biology and evolution · 2022Article
- Genomics in medicine: A new era in medicine.World journal of methodology · 2021Article
- The mutational load in natural populations is significantly affected by high primary rates of retroposition.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Pseudogene Profiling for Cancer Subtype Classification.Methods in molecular biology (Clifton, N.J.) · 2021Review
- The Landscape of Micro-Inversions Provide Clues for Population Genetic Analysis of Humans.Interdisciplinary sciences, computational life sciences · 2020Article
- MultipleGenes · 2020Article
- Contribution of retrotransposition to developmental disorders.Nature communications · 2019Article
- PseudoFuN: Deriving functional potentials of pseudogenes from integrative relationships with genes and microRNAs across 32 cancers.GigaScience · 2019Article
- Ultraconserved Elements Occupy Specific Arenas of Three-Dimensional Mammalian Genome Organization.Cell reports · 2018Article
- Transposable elements: genome innovation, chromosome diversity, and centromere conflict.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2018Review
- Network analysis of pseudogene-gene relationships: from pseudogene evolution to their functional potentials.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2018Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Retroduplications come from reverse transcription of mRNAs and their insertion back into the genome. Here, we performed comprehensive discovery and analysis of retroduplications in a large cohort of 2,535 individuals from 26 human populations, as part of 1000 Genomes Phase 3. We developed an integrated approach to discover novel retroduplications combining high-coverage exome and low-coverage whole-genome sequencing data, utilizing information from both exon-exon junctions and discordant paired-end reads. We found 503 parent genes having novel retroduplications absent from the reference genome. Based solely on retroduplication variation, we built phylogenetic trees of human populations; these represent superpopulation structure well and indicate that variable retroduplications are effective population markers. We further identified 43 retroduplication parent genes differentiating superpopulations. This group contains several interesting insertion events, including a SLMO2 retroduplication and insertion into CAV3, which has a potential disease association. We also found retroduplications to be associated with a variety of genomic features: (1) Insertion sites were correlated with regular nucleosome positioning. (2) They, predictably, tend to avoid conserved functional regions, such as exons, but, somewhat surprisingly, also avoid introns. (3) Retroduplications tend to be co-inserted with young L1 elements, indicating recent retrotranspositional activity, and (4) they have a weak tendency to originate from highly expressed parent genes. Our investigation provides insight into the functional impact and association with genomic elements of retroduplications. We anticipate our approach and analytical methodology to have application in a more clinical context, where exome sequencing data is abundant and the discovery of retroduplications can potentially improve the accuracy of SNP calling.
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