Integration of GWAS SNPs and tissue specific expression profiling reveal discrete eQTLs for human traits in blood and brain.
paper
Cited
Public
- Authors
- Hernandez, Dena G; Nalls, Mike A; Moore, Matthew; Chong, Sean; Dillman, Allissa; Trabzuni, Daniah; Gibbs, J Raphael; Ryten, Mina; Arepalli, Sampath; Weale, Michael E; Zonderman, Alan B; Troncoso, Juan; O'Brien, Richard; Walker, Robert; Smith, Colin; Bandinelli, Stefania; Traynor, Bryan J; Hardy, John; Singleton, Andrew B; Cookson, Mark R
- Year
- 2012
- Journal
- Neurobiology of disease
- PMID
- 22433082
- DOI
- 10.1016/j.nbd.2012.03.020
- PMCID
- PMC3358430
Genome-wide association studies have nominated many genetic variants for common human traits, including diseases, but in many cases the underlying biological reason for a trait association is unknown. Subsets of genetic polymorphisms show a statistical association with transcript expression levels, and have therefore been nominated as expression quantitative trait loci (eQTL). However, many tissue and cell types have specific gene expression patterns and so it is not clear how frequently eQTLs found in one tissue type will be replicated in others. In the present study we used two appropriately powered sample series to examine the genetic control of gene expression in blood and brain. We find that while many eQTLs associated with human traits are shared between these two tissues, there are also examples where blood and brain differ, either by restricted gene expression patterns in one tissue or because of differences in how genetic variants are associated with transcript levels. These observations suggest that design of eQTL mapping experiments should consider tissue of interest for the disease or other traits studied.
No figures extracted from this document.
No entities extracted from this document yet.
No uploaded files.
Not in any collection.
In this knowledge base
External
| Title | Authors | Journal | Year | Link |
|---|---|---|---|---|
| Decoding Alzheimer's Disease One Cell Class at a Time. | Darvas M et al. | β | 2026 | β |
| Genetic evidence for causal relationship between general cognition and treatment resistance in schizophrenia. | Li C et al. | β | 2026 | β |
| Genome-wide meta-analyses of non-response to antidepressants provide insights into underlying molecular genetics and suggest potential pharmacotherapies. | Koch E et al. | β | 2026 | β |
| An Introduction to Causal Inference Methods with Multi-omics Data. | Yao M et al. | β | 2025 | β |
| Dosage effect of copy number variation in epilepsy and ten regions of the human brain. | De T et al. | β | 2025 | β |
| Dosage effect of Copy Number Variation in Epilepsy and ten regions of the human brain Β | De T et al. | β | 2025 | β |
| Expression quantitative trait loci (eQTL): from population genetics to precision medicine. | Wong ZQ et al. | β | 2025 | β |
| Identifying Age-Modulating Compounds Using a Novel Computational Framework for Evaluating Transcriptional Age. | Zhang C et al. | β | 2025 | β |
| Integration of summary data from GWAS and eQTLs studies predicts causality of S1PR1 and breast cancer. | Shi H et al. | β | 2025 | β |
| Unveiling novel potential drug targets for lung cancer through Mendelian randomization analysis. | Huang Y et al. | β | 2025 | β |
| Comprehensive transcriptome analysis reveals altered mRNA splicing and post-transcriptional changes in the aged mouse brain. | Kumar NH et al. | β | 2024 | β |
| Integration of Mendelian randomisation and systems biology models to identify novel blood-based biomarkers for stroke. | Islam T et al. | β | 2023 | β |
| Polygenic overlap with body-mass index improves prediction of treatment-resistant schizophrenia. | O'Connell KS et al. | β | 2023 | β |
| Sex, Age, and Regional Differences in <i>CHRM1</i> and <i>CHRM3</i> Genes Expression Levels in the Human Brain Biopsies: Potential Targets for Alzheimer's Disease-related Sleep Disturbances. | Sanfilippo C et al. | β | 2023 | β |
| Single-cell RNA sequencing analysis of human Alzheimer's disease brain samples reveals neuronal and glial specific cells differential expression. | Soreq L et al. | β | 2023 | β |
| DIALOGUE maps multicellular programs in tissue from single-cell or spatial transcriptomics data. | Jerby-Arnon L et al. | β | 2022 | β |
| Genetic associations at regulatory phenotypes improve fine-mapping of causal variants for 12 immune-mediated diseases. | Kundu K et al. | β | 2022 | β |
| Human prefrontal cortex gene regulatory dynamics from gestation to adulthood at single-cell resolution. | Herring CA et al. | β | 2022 | β |
| Integrated analysis of mRNA-single nucleotide polymorphism-microRNA interaction network to identify biomarkers associated with prostate cancer. | Wang Z et al. | β | 2022 | β |
| Limited evidence for blood eQTLs in human sexual dimorphism. | Porcu E et al. | β | 2022 | β |
| Allele-specific expression of Parkinson's disease susceptibility genes in human brain. | Langmyhr M et al. | β | 2021 | β |
| Brain <i>CHID1</i> Expression Correlates with <i>NRGN</i> and <i>CALB1</i> in Healthy Subjects and AD Patients. | Castrogiovanni P et al. | β | 2021 | β |
| Causal Inference Methods to Integrate Omics and Complex Traits. | Porcu E et al. | β | 2021 | β |
| Differentially expressed genes reflect disease-induced rather than disease-causing changes in the transcriptome. | Porcu E et al. | β | 2021 | β |
| Effects of caloric restriction on the antagonistic and integrative hallmarks of aging. | Erbaba B et al. | β | 2021 | β |
| GNG13 Is a Potential Marker of the State of Health of Alzheimer's Disease Patients' Cerebellum. | Sanfilippo C et al. | β | 2021 | β |
| <i>Alu</i> insertion variants alter gene transcript levels. | Payer LM et al. | β | 2021 | β |
| Molecular Mechanisms Underlying Synaptic and Axon Degeneration in Parkinson's Disease. | Gcwensa NZ et al. | β | 2021 | β |
| Network modules linking expression and methylation in prefrontal cortex of schizophrenia. | Lin D et al. | β | 2021 | β |
| Sex-dependent monoamine oxidase isoforms expression patterns during human brain ageing. | Sanfilippo C et al. | β | 2021 | β |
| An atlas of genetic correlations between psychiatric disorders and human blood plasma proteome. | Cheng S et al. | β | 2020 | β |
| A practical view of fine-mapping and gene prioritization in the post-genome-wide association era. | Broekema RV et al. | β | 2020 | β |
| CHI3L2 Expression Levels Are Correlated with AIF1, PECAM1, and CALB1 in the Brains of Alzheimer's Disease Patients. | Sanfilippo C et al. | β | 2020 | β |
| Expression quantitative trait loci-derived scores and white matter microstructure in UK Biobank: a novel approach to integrating genetics and neuroimaging. | Barbu MC et al. | β | 2020 | β |
| Genetic Predisposition to Glioma Mediated by a MAPKAP1 Enhancer Variant. | Huang L et al. | β | 2020 | β |
| Immune and Inflammatory Pathways Implicated by Whole Blood Transcriptomic Analysis in a Diverse Ancestry Alzheimer's Disease Cohort. | Griswold AJ et al. | β | 2020 | β |
| Missing heritability in Parkinson's disease: the emerging role of non-coding genetic variation. | Ohnmacht J et al. | β | 2020 | β |
| Transcriptomic landscape, gene signatures and regulatory profile of aging in the human brain. | GonzΓ‘lez-Velasco O et al. | β | 2020 | β |
| An epistasis between dopaminergic and oxytocinergic systems confers risk of post-traumatic stress disorder in a traumatized Chinese cohort. | Zhang K et al. | β | 2019 | β |
| A regulatory variant of CHRM3 is associated with cannabis-induced hallucinations in European Americans. | Cheng Z et al. | β | 2019 | β |
| Beyond genome-wide significance: integrative approaches to the interpretation and extension of GWAS findings for alcohol use disorder. | Salvatore JE et al. | β | 2019 | β |
| Brain microstructural abnormalities correlate with KCC2 downregulation in refractory epilepsy. | Gharaylou Z et al. | β | 2019 | β |
| Human gene expression variability and its dependence on methylation and aging. | Bashkeel N et al. | β | 2019 | β |
| Mendelian randomization integrating GWAS and eQTL data reveals genetic determinants of complex and clinical traits. | Porcu E et al. | β | 2019 | β |
| Sex difference in CHI3L1 expression levels in human brain aging and in Alzheimer's disease. | Sanfilippo C et al. | β | 2019 | β |
| Transcriptomic metaanalyses of autistic brains reveals shared gene expression and biological pathway abnormalities with cancer. | ForΓ©s-Martos J et al. | β | 2019 | β |
| Translating Alzheimer's disease-associated polymorphisms into functional candidates: a survey of IGAP genes and SNPs. | Katsumata Y et al. | β | 2019 | β |
| A powerful approach reveals numerous expression quantitative trait haplotypes in multiple tissues. | Ying D et al. | β | 2018 | β |
| Genome-wide Association Study Identifies a Regulatory Variant of RGMA Associated With Opioid Dependence in European Americans. | Cheng Z et al. | β | 2018 | β |
| Human Genetics of Addiction: New Insights and Future Directions. | Hancock DB et al. | β | 2018 | β |
| Identification of expression quantitative trait loci of <i>MTOR</i> associated with the progression of glioma. | Huang L et al. | β | 2018 | β |
| Integrating GWAS and gene expression data for functional characterization of resistance to white mould in soya bean. | Wen Z et al. | β | 2018 | β |
| Variation among intact tissue samples reveals the core transcriptional features of human CNS cell classes. | Kelley KW et al. | β | 2018 | β |
| brain-coX: investigating and visualising gene co-expression in seven human brain transcriptomic datasets. | Freytag S et al. | β | 2017 | β |
| Comprehensive Computational Analysis of GWAS Loci Identifies CCR2 as a Candidate Gene for Celiac Disease Pathogenesis. | Banaganapalli B et al. | β | 2017 | β |
| Gene-based association study of genes linked to hippocampal sclerosis of aging neuropathology: GRN, TMEM106B, ABCC9, and KCNMB2. | Katsumata Y et al. | β | 2017 | β |
| Genome-wide mapping of genetic determinants influencing DNA methylation and gene expression in human hippocampus. | Schulz H et al. | β | 2017 | β |
| Inherited variation in circadian rhythm genes and risks of prostate cancer and three other cancer sites in combined cancer consortia. | Gu F et al. | β | 2017 | β |
| Integrating genome-wide association study and expression quantitative trait loci data identifies multiple genes and gene set associated with neuroticism. | Fan Q et al. | β | 2017 | β |
| Neuregulin signaling pathway in smoking behavior. | Gupta R et al. | β | 2017 | β |
| NeuroChip, an updated version of the NeuroX genotyping platform to rapidly screen for variants associated with neurological diseases. | Blauwendraat C et al. | β | 2017 | β |
| A20 Inhibits Ξ²-Cell Apoptosis by Multiple Mechanisms and Predicts Residual Ξ²-Cell Function in Type 1 Diabetes. | Fukaya M et al. | β | 2016 | β |
| Aging Shapes the Population-Mean and -Dispersion of Gene Expression in Human Brains. | Brinkmeyer-Langford CL et al. | β | 2016 | β |
| AlzBase: an Integrative Database for Gene Dysregulation in Alzheimer's Disease. | Bai Z et al. | β | 2016 | β |
| A Population-Based Study of Four Genes Associated with Heroin Addiction in Han Chinese. | Li Y et al. | β | 2016 | β |
| Blood gene expression studies in migraine: Potential and caveats. | Gerring Z et al. | β | 2016 | β |
| Data sources for in vivo molecular profiling of human phenotypes. | Cardozo T et al. | β | 2016 | β |
| Expression of asthma susceptibility genes in bronchial epithelial cells and bronchial alveolar lavage in the Severe Asthma Research Program (SARP) cohort. | Li X et al. | β | 2016 | β |
| Genomics and CSF analyses implicate thyroid hormone in hippocampal sclerosis of aging. | Nelson PT et al. | β | 2016 | β |
| Next-generation sequencing reveals substantial genetic contribution to dementia with Lewy bodies. | Geiger JT et al. | β | 2016 | β |
| A multiancestry study identifies novel genetic associations with CHRNA5 methylation in human brain and risk of nicotine dependence. | Hancock DB et al. | β | 2015 | β |
| Common genetic variants influence human subcortical brain structures. | Hibar DP et al. | β | 2015 | β |
| Fast eQTL Analysis for Twin Studies. | Yin Z et al. | β | 2015 | β |
| Genome-wide differential expression of synaptic long noncoding RNAs in autism spectrum disorder. | Wang Y et al. | β | 2015 | β |
| Genomic approaches for understanding the genetics of complex disease. | Lowe WL et al. | β | 2015 | β |
| Pathways to Parkinsonism Redux: convergent pathobiological mechanisms in genetics of Parkinson's disease. | Kumaran R et al. | β | 2015 | β |
| Peripheral Biomarker Candidates of Posttraumatic Stress Disorder. | Kang HJ et al. | β | 2015 | β |
| RNA sequencing of transcriptomes in human brain regions: protein-coding and non-coding RNAs, isoforms and alleles. | Webb A et al. | β | 2015 | β |
| Systematic annotation of celiac disease loci refines pathological pathways and suggests a genetic explanation for increased interferon-gamma levels. | Kumar V et al. | β | 2015 | β |
| Systematic noise degrades gene co-expression signals but can be corrected. | Freytag S et al. | β | 2015 | β |
| A quantitative framework to evaluate modeling of cortical development by neural stem cells. | Stein JL et al. | β | 2014 | β |
| Bayesian test for colocalisation between pairs of genetic association studies using summary statistics. | Giambartolomei C et al. | β | 2014 | β |
| Blood cis-eQTL analysis fails to identify novel association signals among sub-threshold candidates from genome-wide association studies in restless legs syndrome. | Schulte EC et al. | β | 2014 | β |
| Cross-tissue and tissue-specific eQTLs: partitioning the heritability of a complex trait. | Torres JM et al. | β | 2014 | β |
| Genetic evidence for a pathogenic role for the vitamin D3 metabolizing enzyme <i>CYP24A1</i> in multiple sclerosis. | Ramasamy A et al. | β | 2014 | β |
| Genetic variability in the regulation of gene expression in ten regions of the human brain. | Ramasamy A et al. | β | 2014 | β |
| Genome-wide identification of expression quantitative trait loci (eQTLs) in human heart. | Koopmann TT et al. | β | 2014 | β |
| Overlap of expression quantitative trait loci (eQTL) in human brain and blood. | McKenzie M et al. | β | 2014 | β |
| Peripheral biomarkers revisited: integrative profiling of peripheral samples for psychiatric research. | Hayashi-Takagi A et al. | β | 2014 | β |
| Sex- and age-interacting eQTLs in human complex diseases. | Yao C et al. | β | 2014 | β |
| Age-associated changes in gene expression in human brain and isolated neurons. | Kumar A et al. | β | 2013 | β |
| Analytical strategies for large imaging genetic datasets: experiences from the IMAGEN study. | Nymberg C et al. | β | 2013 | β |
| Application of genomics, proteomics and metabolomics in drug discovery, development and clinic. | Russell C et al. | β | 2013 | β |
| Cis-regulatory variants affect CHRNA5 mRNA expression in populations of African and European ancestry. | Wang JC et al. | β | 2013 | β |
| Genetic analysis in neurology: the next 10 years. | Pittman A et al. | β | 2013 | β |
| Genetics of human gene expression. | Stranger BE et al. | β | 2013 | β |
| GLiMMPS: robust statistical model for regulatory variation of alternative splicing using RNA-seq data. | Zhao K et al. | β | 2013 | β |
| Integrative genomics in cardiovascular medicine. | Ware JS et al. | β | 2013 | β |
| Mapping eQTLs in the Norfolk Island genetic isolate identifies candidate genes for CVD risk traits. | Benton MC et al. | β | 2013 | β |
| Resolving the polymorphism-in-probe problem is critical for correct interpretation of expression QTL studies. | Ramasamy A et al. | β | 2013 | β |
| Widespread sex differences in gene expression and splicing in the adult human brain. | Trabzuni D et al. | β | 2013 | β |
| Lung eQTLs to help reveal the molecular underpinnings of asthma. | Hao K et al. | β | 2012 | β |
| MAPT expression and splicing is differentially regulated by brain region: relation to genotype and implication for tauopathies. | Trabzuni D et al. | β | 2012 | β |