Leveraging molecular quantitative trait loci to comprehend complex diseases/traits from the omics perspective

Alasoo K et al (2018) Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response. Nat Genet 50(3):424–431

Article  CAS  PubMed  PubMed Central  Google Scholar 

Astle WJ et al (2016) The allelic landscape of human blood cell trait variation and links to common complex disease. Cell 167(5):1415–1429

Article  CAS  PubMed  PubMed Central  Google Scholar 

Aznaourova M et al (2022) Single-cell RNA sequencing uncovers the nuclear decoy lincRNA PIRAT as a regulator of systemic monocyte immunity during COVID-19. Proc Natl Acad Sci USA 119(36):e2120680119

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bannister AJ, Kouzarides T (2011) Regulation of chromatin by histone modifications. Cell Res 21(3):381–395

Article  CAS  PubMed  PubMed Central  Google Scholar 

Barbeira AN et al (2018) Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics. Nat Commun 9(1):1825

Article  PubMed  PubMed Central  Google Scholar 

Beckmann ND et al (2020) Multiscale causal networks identify VGF as a key regulator of Alzheimer’s disease. Nat Commun 11(1):3942

Article  CAS  PubMed  PubMed Central  Google Scholar 

Benner C et al (2016) FINEMAP: efficient variable selection using summary data from genome-wide association studies. Bioinformatics 32(10):1493–1501

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bonder MJ et al (2017) Disease variants alter transcription factor levels and methylation of their binding sites. Nat Genet 49(1):131–138

Article  CAS  PubMed  Google Scholar 

Bruscadin JJ et al (2021) Muscle allele-specific expression QTLs may affect meat quality traits in Bos indicus. Sci Rep 11(1):7321

Article  CAS  PubMed  PubMed Central  Google Scholar 

Byars SG et al (2017) Genetic loci associated with coronary artery disease harbor evidence of selection and antagonistic pleiotropy. PLoS Genet 13(6):e1006328

Article  PubMed  PubMed Central  Google Scholar 

Chamberlain LH, Shipston MJ (2015) The physiology of protein S-acylation. Physiol Rev 95(2):341–376

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chandra V et al (2021) Promoter-interacting expression quantitative trait loci are enriched for functional genetic variants. Nat Genet 53(1):110–119

Article  CAS  PubMed  Google Scholar 

Chang L, Zhou G, Xia J (2023) mGWAS-Explorer 20: causal analysis and interpretation of metabolite-phenotype associations. Metabolites 13(7):826

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chen W et al (2015) Fine mapping causal variants with an approximate Bayesian method using marginal test statistics. Genetics 200(3):719–736

Article  PubMed  PubMed Central  Google Scholar 

Chen L et al (2016) Genetic drivers of epigenetic and transcriptional variation in human immune cells. Cell 167(5):1398–1414

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chen C et al (2022) Pan-cancer analysis of microbiome quantitative trait loci. Cancer Res 82(19):3449–3456

Article  CAS  PubMed  Google Scholar 

Chun S et al (2017) Limited statistical evidence for shared genetic effects of eQTLs and autoimmune-disease-associated loci in three major immune-cell types. Nat Genet 49(4):600–605

Article  CAS  PubMed  PubMed Central  Google Scholar 

Consortium G.T (2015) Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. Science 348(6235):648–660

Article  Google Scholar 

Consortium, G.T (2013) The Genotype-Tissue Expression (GTEx) project. Nat Genet 45(6):580–585

Article  Google Scholar 

Cookson W et al (2009) Mapping complex disease traits with global gene expression. Nat Rev Genet 10(3):184–194

Article  CAS  PubMed  PubMed Central  Google Scholar 

Corces MR et al (2020) Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer’s and Parkinson’s diseases. Nat Genet 52(11):1158–1168

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cuddleston WH et al (2022) Cellular and genetic drivers of RNA editing variation in the human brain. Nat Commun 13(1):2997

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cui Y et al (2022) 3’aQTL-atlas: an atlas of 3’UTR alternative polyadenylation quantitative trait loci across human normal tissues. Nucleic Acids Res 50(D1):D39–D45

Article  CAS  PubMed  Google Scholar 

Currin KW et al (2021) Genetic effects on liver chromatin accessibility identify disease regulatory variants. Am J Hum Genet 108(7):1169–1189

Article  CAS  PubMed  PubMed Central  Google Scholar 

Degner JF et al (2012) DNase I sensitivity QTLs are a major determinant of human expression variation. Nature 482(7385):390–394

Article  CAS  PubMed  PubMed Central  Google Scholar 

Denault WRP, Jugessur A (2021) Detecting differentially methylated regions using a fast wavelet-based approach to functional association analysis. BMC Bioinformatics 22(1):61

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dowell RD (2010) Transcription factor binding variation in the evolution of gene regulation. Trends Genet 26(11):468–475

Article  CAS  PubMed  Google Scholar 

Draisma HHM et al (2015) Genome-wide association study identifies novel genetic variants contributing to variation in blood metabolite levels. Nat Commun 6:7208

Article  CAS  PubMed  Google Scholar 

Elkon R, Ugalde AP, Agami R (2013) Alternative cleavage and polyadenylation: extent, regulation and function. Nat Rev Genet 14(7):496–506

Article  CAS  PubMed  Google Scholar 

Emdin CA, Khera AV, Kathiresan S (2017) Mendelian randomization. JAMA 318(19):1925–1926

Article  PubMed  Google Scholar 

Ernst CW, Steibel JP (2013) Molecular advances in QTL discovery and application in pig breeding. Trends Genet 29(4):215–224

Article  CAS  PubMed  Google Scholar 

Evans DM, Davey Smith G (2015) Mendelian randomization: new applications in the coming age of hypothesis-free causality. Annu Rev Genomics Hum Genet 16:327–350

Article  CAS  PubMed  Google Scholar 

Farashi S et al (2019) Post-GWAS in prostate cancer: from genetic association to biological contribution. Nat Rev Cancer 19(1):46–59

Article  CAS  PubMed  Google Scholar 

Fazel-Najafabadi M et al (2022) Discovery and functional characterization of two regulatory variants underlying lupus susceptibility at 2p13.1. Genes (basel) 13(6):1016

Article  CAS  PubMed  Google Scholar 

Fleige S, Pfaffl MW (2006) RNA integrity and the effect on the real-time qRT-PCR performance. Mol Aspects Med 27(2–3):126–139

Article  CAS  PubMed  Google Scholar 

Flint J, Mott R (2001) Finding the molecular basis of quantitative traits: successes and pitfalls. Nat Rev Genet 2(6):437–445

Article  CAS  PubMed  Google Scholar 

Flynn ED et al (2022) Transcription factor regulation of eQTL activity across individuals and tissues. PLoS Genet 18(1):e1009719

Article  CAS  PubMed  PubMed Central  Google Scholar 

Folkersen L et al (2017) Mapping of 79 loci for 83 plasma protein biomarkers in cardiovascular disease. PLoS Genet 13(4):e1006706

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