SynthesisPLoS genetics2013
DeepSAGE reveals genetic variants associated with alternative polyadenylation and expression of coding and non-coding transcripts.
Synthesis in PLoS genetics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 25 papers, 2 of them syntheses that pooled it.
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.
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, 2 syntheses or guidelines pooled it, 42 citations in OpenAlex.
- Genome-wide association reveals contribution of MRAS to painful temporomandibular disorder in males.Pain · 2019Pooled it
- Cell Specific eQTL Analysis without Sorting Cells.PLoS genetics · 2015Pooled it
- RNA Sequencing in Disease Diagnosis.Annual review of genomics and human genetics · 2024Review
- Review
- An atlas of alternative polyadenylation quantitative trait loci contributing to complex trait and disease heritability.Nature genetics · 2021Article
- Statistical method for modeling sequencing data from different technologies in longitudinal studies with application to Huntington disease.Biometrical journal. Biometrische Zeitschrift · 2021Article
- Impact of Natural OccurringInternational journal of molecular sciences · 2020Review
- Genetic effects on promoter usage are highly context-specific and contribute to complex traits.eLife · 2019Article
- The Length of the Expressed 3' UTR Is an Intermediate Molecular Phenotype Linking Genetic Variants to Complex Diseases.Frontiers in genetics · 2019Article
- Single-cell RNA sequencing identifies celltype-specific cis-eQTLs and co-expression QTLs.Nature genetics · 2018Article
- Cancer transcriptome profiling at the juncture of clinical translation.Nature reviews. Genetics · 2018Review
- A Genome-Wide Association Study and Complex Network Identify Four Core Hub Genes in Bipolar Disorder.International journal of molecular sciences · 2017Article
- Context-specific effects of genetic variants associated with autoimmune disease.Human molecular genetics · 2017Review
- The roles of RNA processing in translating genotype to phenotype.Nature reviews. Molecular cell biology · 2017Review
- Undiscovered Physiology of Transcript and Protein Networks.Comprehensive Physiology · 2016Review
- Consistency of biological networks inferred from microarray and sequencing data.BMC bioinformatics · 2016Article
- Refined mapping of autoimmune disease associated genetic variants with gene expression suggests an important role for non-coding RNAs.Journal of autoimmunity · 2016Article
- Identification of common genetic variants controlling transcript isoform variation in human whole blood.Nature genetics · 2015Article
- Article
- Calling genotypes from public RNA-sequencing data enables identification of genetic variants that affect gene-expression levels.Genome medicine · 2015Article
Corrections and comments
- Erratum issued
Authors and funding
19 authors at 6 institutions in 1 country.
Funding
Abstract
Many disease-associated variants affect gene expression levels (expression quantitative trait loci, eQTLs) and expression profiling using next generation sequencing (NGS) technology is a powerful way to detect these eQTLs. We analyzed 94 total blood samples from healthy volunteers with DeepSAGE to gain specific insight into how genetic variants affect the expression of genes and lengths of 3'-untranslated regions (3'-UTRs). We detected previously unknown cis-eQTL effects for GWAS hits in disease- and physiology-associated traits. Apart from cis-eQTLs that are typically easily identifiable using microarrays or RNA-sequencing, DeepSAGE also revealed many cis-eQTLs for antisense and other non-coding transcripts, often in genomic regions containing retrotransposon-derived elements. We also identified and confirmed SNPs that affect the usage of alternative polyadenylation sites, thereby potentially influencing the stability of messenger RNAs (mRNA). We then combined the power of RNA-sequencing with DeepSAGE by performing a meta-analysis of three datasets, leading to the identification of many more cis-eQTLs. Our results indicate that DeepSAGE data is useful for eQTL mapping of known and unknown transcripts, and for identifying SNPs that affect alternative polyadenylation. Because of the inherent differences between DeepSAGE and RNA-sequencing, our complementary, integrative approach leads to greater insight into the molecular consequences of many disease-associated variants.
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.