ArticleHuman molecular genetics2014
Expression QTL-based analyses reveal candidate causal genes and loci across five tumor types.
Article in Human molecular genetics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers, 7 of them syntheses 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
55 citing papers in PubMed, 7 syntheses or guidelines pooled it.
- Prostate cancer risk SNP rs10993994 is a trans-eQTL for SNHG11 mediated through MSMB.Human molecular genetics · 2020Pooled it
- Pooled it
- Cis-eQTL-based trans-ethnic meta-analysis reveals novel genes associated with breast cancer risk.PLoS genetics · 2017Pooled it
- Pooled it
- Fine-scale mapping of 8q24 locus identifies multiple independent risk variants for breast cancer.International journal of cancer · 2016Pooled it
- Gene regulatory mechanisms underpinning prostate cancer susceptibility.Nature genetics · 2016Pooled it
- Identification of six new susceptibility loci for invasive epithelial ovarian cancer.Nature genetics · 2015Pooled it
- Article
- A biallelic multiple nucleotide length polymorphism explains functional causality at 5p15.33 prostate cancer risk locus.Nature communications · 2023Article
- Epigenetic germline variants predict cancer prognosis and risk and distribute uniquely in topologically associating domains.F1000Research · 2023Article
- Prostate Cancer Transcriptomic Regulation by the Interplay of Germline Risk Alleles, Somatic Mutations, and 3D Genomic Architecture.Cancer discovery · 2022Article
- Whole genome DNA and RNA sequencing of whole blood elucidates the genetic architecture of gene expression underlying a wide range of diseases.Scientific reports · 2022Article
- IsomiR-eQTL: A Cancer-Specific Expression Quantitative Trait Loci Database of miRNAs and Their Isoforms.International journal of molecular sciences · 2022Article
- Allelic imbalance of chromatin accessibility in cancer identifies candidate causal risk variants and their mechanisms.Nature genetics · 2022Article
- Whole Genome DNA and RNA Sequencing of Whole Blood Elucidates the Genetic Architecture of Gene Expression Underlying a Wide Range of Diseases.Research square · 2022Article
- Whole Genome DNA and RNA Sequencing of Whole Blood Elucidates the Genetic Architecture of Gene Expression Underlying a Wide Range of Diseases.medRxiv : the preprint server for health sciences · 2022Article
- Deciphering the Role of 3D Genome Organization in Breast Cancer Susceptibility.Frontiers in genetics · 2021Article
- Identification of Candidate Genes Associated with Susceptibility to Ovarian Clear Cell Adenocarcinoma UsingJournal of clinical medicine · 2020Article
- DNA methylation and cis-regulation of gene expression by prostate cancer risk SNPs.PLoS genetics · 2020Article
- Integrative comparison of the genomic and transcriptomic landscape between prostate cancer patients of predominantly African or European genetic ancestry.PLoS genetics · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors.
Funding
Abstract
The majority of trait-associated loci discovered through genome-wide association studies are located outside of known protein coding regions. Consequently, it is difficult to ascertain the mechanism underlying these variants and to pinpoint the causal alleles. Expression quantitative trait loci (eQTLs) provide an organizing principle to address both of these issues. eQTLs are genetic loci that correlate with RNA transcript levels. Large-scale data sets such as the Cancer Genome Atlas (TCGA) provide an ideal opportunity to systematically evaluate eQTLs as they have generated multiple data types on hundreds of samples. We evaluated the determinants of gene expression (germline variants and somatic copy number and methylation) and performed cis-eQTL analyses for mRNA expression and miRNA expression in five tumor types (breast, colon, kidney, lung and prostate). We next tested 149 known cancer risk loci for eQTL effects, and observed that 42 (28.2%) were significantly associated with at least one transcript. Lastly, we described a fine-mapping strategy for these 42 eQTL target-gene associations based on an integrated strategy that combines the eQTL level of significance and the regulatory potential as measured by DNaseI hypersensitivity. For each of the risk loci, our analyses suggested 1 to 81 candidate causal variants that may be prioritized for downstream functional analysis. In summary, our study provided a comprehensive landscape of the genetic determinants of gene expression in different tumor types and ranked the genes and loci for further functional assessment of known cancer risk loci.
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.