ArticleGenome biology2013
Systematic biases in DNA copy number originate from isolation procedures.
Article in Genome biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers, 1 of them a synthesis that pooled it.
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
29 citing papers in PubMed, 1 synthesis or guideline pooled it.
- ACMG Standards and Guidelines for constitutional cytogenomic microarray analysis, including postnatal and prenatal applications: revision 2013.Genetics in medicine : official journal of the American College of Medical Genetics · 2013Guideline
- Mapping-based genome size estimation.BMC genomics · 2025Article
- Profiling bacterial communities in feedlot cattle affected with bovine foot rot and bovine digital dermatitis lesions using 16S rRNA gene sequencing and quantitative real-time PCR.BMC microbiology · 2025Article
- Variant calling: Considerations, practices, and developments.Human mutation · 2022Review
- An optimized approach for processing of frozen lung and lavage samples for microbiome studies.PloS one · 2022Article
- Chromosomal microarray analysis, including constitutional and neoplastic disease applications, 2021 revision: a technical standard of the American College of Medical Genetics and Genomics (ACMG).Genetics in medicine : official journal of the American College of Medical Genetics · 2021Article
- Evaluation of a Highly Efficient DNA Extraction Method forMicroorganisms · 2020Article
- Hierarchical discovery of large-scale and focal copy number alterations in low-coverage cancer genomes.BMC bioinformatics · 2020Article
- Somatic mosaicism of sex chromosomes in the blood and brain.Brain research · 2019Article
- Plasmid-normalized quantification of relative mitochondrial DNA copy number.Scientific reports · 2018Article
- Somatic mutations in neurons during aging and neurodegeneration.Acta neuropathologica · 2018Review
- Measuring mutation accumulation in single human adult stem cells by whole-genome sequencing of organoid cultures.Nature protocols · 2018Article
- Whole exome association of rare deletions in multiplex oral cleft families.Genetic epidemiology · 2017Article
- Optimal Fixation Conditions and DNA Extraction Methods for MLPA Analysis on FFPE Tissue-Derived DNA.American journal of clinical pathology · 2017Article
- Article
- CNARA: reliability assessment for genomic copy number profiles.BMC genomics · 2016Article
- Deep landscape update of dispersed and tandem repeats in the genome model of the red jungle fowl, Gallus gallus, using a series of de novo investigating tools.BMC genomics · 2016Article
- Comparison of six commercial kits to extract bacterial chromosome and plasmid DNA for MiSeq sequencing.Scientific reports · 2016Article
- Gene amplification during differentiation of mammalian neural stem cells in vitro and in vivo.Oncotarget · 2015Article
- Lack of major genome instability in tumors of p53 null rats.PloS one · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors.
Funding
Abstract
backgroundThe ability to accurately detect DNA copy number variation in both a sensitive and quantitative manner is important in many research areas. However, genome-wide DNA copy number analyses are complicated by variations in detection signal.
resultsWhile GC content has been used to correct for this, here we show that coverage biases are tissue-specific and independent of the detection method as demonstrated by next-generation sequencing and array CGH. Moreover, we show that DNA isolation stringency affects the degree of equimolar coverage and that the observed biases coincide with chromatin characteristics like gene expression, genomic isochores, and replication timing.
conclusionThese results indicate that chromatin organization is a main determinant for differential DNA retrieval. These findings are highly relevant for germline and somatic DNA copy number variation analyses.
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.