Evidence map›Paper›PMID 21862627›Full record

ArticleGenome research2011

Relating CNVs to transcriptome data at fine resolution: assessment of the effect of variant size, type, and overlap with functional regions.

Andreas Schlattl, Simon Anders, Sebastian M Waszak, Wolfgang Huber, Jan O Korbel

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 papers.

0numbers the graph read from it
0cells of the map it votes in
70citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from 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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

70 citing papers in PubMed.

  1. Article
  2. Mapping copy number variable regions correlated with reproduction and production traits in Karan Fries cattle mammalian genomics.Mammalian genome : official journal of the International Mammalian Genome Society · 2025
    Article
  3. Article
  4. Article
  5. Characterization of Exhausted T Cell Signatures in Pan-Cancer Settings.International journal of molecular sciences · 2025
    Article
  6. Copy Number Variation in Asthma: An Integrative Review.Clinical reviews in allergy & immunology · 2025
    Review
  7. Heliyon · 2024
    Article
  8. Article
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10 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

5 authors.

Andreas SchlattlEuropean Molecular Biology Laboratory (EMBL), Genome Biology Research Unit, 69117 Heidelberg, Germany.
Simon Anders
Sebastian M Waszak
Wolfgang Huber
Jan O Korbel

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Copy-number variants (CNVs) form an abundant class of genetic variation with a presumed widespread impact on individual traits. While recent advances, such as the population-scale sequencing of human genomes, facilitated the fine-scale mapping of CNVs, the phenotypic impact of most of these CNVs remains unclear. By relating copy-number genotypes to transcriptome sequencing data, we have evaluated the impact of CNVs, mapped at fine scale, on gene expression. Based on data from 129 individuals with ancestry from two populations, we identified CNVs associated with the expression of 110 genes, with 13% of the associations involving complex, multiallelic CNVs. Categorization of CNVs according to variant type, size, and gene overlap enabled us to examine the impact of different CNV classes on expression variation. While many small (<4 kb) CNVs were associated with expression variation, overall we observed an enrichment of large duplications and deletions, including large intergenic CNVs, relative to the entire set of expression-associated CNVs. Furthermore, the copy number of genes intersecting with CNVs typically correlated positively with the genes' expression, and also was more strongly correlated with expression than nearby single nucleotide polymorphisms, suggesting a frequent causal role of CNVs in expression quantitative trait loci (eQTLs). We also elucidated unexpected cases of negative correlations between copy number and expression by assessing the CNVs' effects on the structure and regulation of genes. Finally, we examined dosage compensation of transcript levels. Our results suggest that association studies can gain in resolution and power by including fine-scale CNV information, such as those obtained from population-scale sequencing.

Indexed as

GenotypeModels, GeneticDNA Copy Number VariationsFemaleGene DosageGene Expression RegulationHumansMalePolymorphism, Single NucleotideTranscriptome

Identifiers

PMID21862627
PMCPMC3227091

What OpenQuestion holds

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Registered trials

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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.