ArticleG3 (Bethesda, Md.)2020
Challenges and Approaches to Genotyping Repetitive DNA.
Article in G3 (Bethesda, Md.), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
What it found
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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
20 citing papers in PubMed.
- rDNAmine: A New Tool for the Analysis of Long Repetitive Sequences.Yeast (Chichester, England) · 2026Article
- Oligonucleotide Selective Detection by Levitated Optomechanics.ACS nanoscience Au · 2026Article
- Digital droplet PCR is an accurate and precise method to measure DNA copy number.Scientific reports · 2025Article
- rDNA copy number variation affects yeast fitness in response to different environments.Genetics · 2025Article
- Phenotypic tolerance for rDNA copy number variation within the natural range of C. elegans.PLoS genetics · 2025Article
- Assessing Human Ribosomal DNA Variation and Its Association With Phenotypic Outcomes.BioEssays : news and reviews in molecular, cellular and developmental biology · 2025Review
- Design and validation of a clinical whole genome sequencing-based assay for patient screening in a large healthcare system.Frontiers in molecular biosciences · 2025Article
- Comparative analysis of predicted DNA secondary structures infers complex human centromere topology.American journal of human genetics · 2024Article
- Copy number and sequence variation in rDNA of Daphnia pulex from natural populations: insights from whole-genome sequencing.G3 (Bethesda, Md.) · 2024Article
- The Use of CGH Arrays for Identifying Copy Number Variations in Children with Autism Spectrum Disorder.Brain sciences · 2024Article
- Ribosomal DNA Copy Number Variation is Coupled with DNA Methylation Changes at the 45S rDNA Locus.Epigenetics · 2023Article
- Contribution of Spontaneous Mutations to Quantitative and Molecular Variation at the Highly Repetitive rDNA Locus in Yeast.Genome biology and evolution · 2023Article
- Substantial rDNA copy number reductions alter timing of development and produce variable tissue-specific phenotypes in C. elegans.Genetics · 2023Article
- Ribosomal DNA replication time coordinates completion of genome replication and anaphase in yeast.Cell reports · 2023Article
- A genome sequence for Biomphalaria pfeifferi, the major vector snail for the human-infecting parasite Schistosoma mansoni.PLoS neglected tropical diseases · 2023Article
- Under the magnifying glass: The ups and downs of rDNA copy number.Seminars in cell & developmental biology · 2023Review
- First discovered, long out of sight, finally visible: ribosomal DNA.Trends in genetics : TIG · 2022Review
- Expanding studies of chromosome structure and function in the era of T2T genomics.Human molecular genetics · 2021Review
- An essential role for the piRNA pathway in regulating the ribosomal RNA pool in C. elegans.Developmental cell · 2021Article
- Thousands of high-quality sequencing samples fail to show meaningful correlation between 5S and 45S ribosomal DNA arrays in humans.Scientific reports · 2021Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
Individuals within a species can exhibit vast variation in copy number of repetitive DNA elements. This variation may contribute to complex traits such as lifespan and disease, yet it is only infrequently considered in genotype-phenotype associations. Although the possible importance of copy number variation is widely recognized, accurate copy number quantification remains challenging. Here, we assess the technical reproducibility of several major methods for copy number estimation as they apply to the large repetitive ribosomal DNA array (rDNA). rDNA encodes the ribosomal RNAs and exists as a tandem gene array in all eukaryotes. Repeat units of rDNA are kilobases in size, often with several hundred units comprising the array, making rDNA particularly intractable to common quantification techniques. We evaluate pulsed-field gel electrophoresis, droplet digital PCR, and Nextera-based whole genome sequencing as approaches to copy number estimation, comparing techniques across model organisms and spanning wide ranges of copy numbers. Nextera-based whole genome sequencing, though commonly used in recent literature, produced high error. We explore possible causes for this error and provide recommendations for best practices in rDNA copy number estimation. We present a resource of high-confidence rDNA copy number estimates for a set of
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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.