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Expression quantitative trait loci ( eQTLs )

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https://www.readbyqxmd.com/read/28339748/genotype-based-gene-signature-of-glioma-risk
#1
Yen-Tsung Huang, Yi Zhang, Zhijin Wu, Dominique S Michaud
Background.: Glioma accounts for 80% of malignant brain tumors, but its etiologic determinants remain elusive. Despite genetic susceptibility loci identified by genome-wide association study (GWAS), the agnostic approach leaves open the possibility that other susceptibility genes remain to be discovered. Here we conduct a gene-centric integrative GWAS (iGWAS) of glioma risk that combines transcriptomics and genetics. Methods.: We synthesized a brain transcriptomics dataset (n = 354), a GWAS dataset (n = 4203), and an advanced glioma tumor transcriptomic dataset (n = 483) to conduct an iGWAS...
February 22, 2017: Neuro-oncology
https://www.readbyqxmd.com/read/28339471/expression-quantitative-trait-loci-for-pax8-contributes-to-the-prognosis-of-hepatocellular-carcinoma
#2
Shijie Ma, Jianshui Yang, Ci Song, Zijun Ge, Jing Zhou, Guoxin Zhang, Zhibin Hu
Paired-box family member PAX8 encodes a transcription factor that has a role in cell differentiation and cell growth and may participate in the prognosis of hepatocellular carcinoma (HCC). By bioinformatics analysis, we identified several single nucleotide polymorphisms (SNPs) within a newly identified long non-coding RNA (lncRNA) AC016683.6 as expression quantitative trait loci (eQTLs) for PAX8. Hence, we hypothesized that PAX8eQTLs in lncRNA AC016683.6 may influence the HCC prognosis. We then performed a case-only study to assess the association between the two SNPs as well as the prognosis of HCC in 331 HBV-positive HCC patients without surgical treatment...
2017: PloS One
https://www.readbyqxmd.com/read/28335076/fine-mapping-of-chromosome-5p15-33-identifies-novel-lung-cancer-susceptibility-loci-in-han-chinese
#3
Jing Dong, Yang Cheng, Meng Zhu, Yang Wen, Cheng Wang, Yuzhuo Wang, Liguo Geng, Wei Shen, Jia Liu, Zhihua Li, Jiahui Zhang, Hongxia Ma, Juncheng Dai, Guangfu Jin, Zhibin Hu, Hongbing Shen
Genome-wide association studies in European and Asian populations have consistently identified chromosome 5p15.33 as a lung cancer susceptibility region. To investigate further the genetic architecture of common variants in this region, we conducted a two-stage fine-mapping analysis discovered by targeted resequencing of 200 cases and 300 controls individually, and validated in multiethnic lung cancer GWASs with 12,843 cases and 12,639 controls. Two independent variants were identified in approximate conditional analysis with GCTA and consistently validated in lung cancer GWASs in both Asian and European populations...
March 23, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28334830/predicting-the-impact-of-non-coding-variants-on-dna-methylation
#4
Haoyang Zeng, David K Gifford
DNA methylation plays a crucial role in the establishment of tissue-specific gene expression and the regulation of key biological processes. However, our present inability to predict the effect of genome sequence variation on DNA methylation precludes a comprehensive assessment of the consequences of non-coding variation. We introduce CpGenie, a sequence-based framework that learns a regulatory code of DNA methylation using a deep convolutional neural network and uses this network to predict the impact of sequence variation on proximal CpG site DNA methylation...
March 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334234/breast-cancer-risk-associated-variants-at-6q25-1-influence-risk-of-hepatocellular-carcinoma-in-a-chinese-population
#5
Jiaoyuan Li, Ying Wang, Ying Zhu, Yajie Gong, Yang Yang, Jianbo Tian, Yi Zhang, Danyi Zou, Xiating Peng, Juntao Ke, Jing Gong, Rong Zhong, Jiang Chang
The gender disparity observed in the incidence of hepatocellular carcinoma (HCC) suggests an important role of estrogens in HCC pathogenesis. In this study, we conducted a case-control study to investigate whether breast cancer risk-associated single nucleotide polymorphisms (SNPs) located at estrogens loci identified by genome-wide association studies (GWASs) also predispose to HCC in a Chinese population. Three candidate SNPs at 6q25.1 were genotyped in 2,025 HCC cases and 2,032 healthy controls. Differential expression analyses and expression quantitative trait loci (eQTL) analyses were conducted to further explore the role of significant SNPs and genes they reside in...
March 3, 2017: Carcinogenesis
https://www.readbyqxmd.com/read/28334222/qrank-a-novel-quantile-regression-tool-for-eqtl-discovery
#6
Xiaoyu Song, Gen Li, Zhenwei Zhou, Xianling Wang, Iuliana Ionita-Laza, Ying Wei
Motivation: Over the past decade, there has been a remarkable improvement in our understanding of the role of genetic variation in complex human diseases, especially via genome-wide association studies. However, the underlying molecular mechanisms are still poorly characterized, impending the development of therapeutic interventions. Identifying genetic variants that influence the expression level of a gene, i.e. expression quantitative trait loci (eQTLs), can help us understand how genetic variants influence traits at the molecular level...
March 11, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28321907/systematical-analyses-of-variants-in%C3%A2-dnase-i-hypersensitive-sites-identified-two-novel-hepatocellular-carcinoma-susceptibility-loci-among-chinese-population
#7
Tao Jiang, Fangzhi Du, Na Qin, Qun Lu, Juncheng Dai, Hongbing Shen, Zhibin Hu
BACKGROUND AND AIM: Although several variants located at coding and non-coding regions were evaluated by previous studies, the evidence for associations between variants located in DNase I-hypersensitive sites (DHSs) and hepatocellular carcinoma (HCC) risk was still limited. Recent advances using ENCODE data indicated that genetic variants in DHSs played an important role in carcinogenesis. Therefore, systematically investigate the associations between regulatory variants in DHSs and HCC risk should be put on the agenda...
March 20, 2017: Journal of Gastroenterology and Hepatology
https://www.readbyqxmd.com/read/28317323/a-functional-snp-regulated-by-mir-196a-3p-in-the-3-utr-of-fgf2-is-associated-with-bone-mineral-density-in-the-chinese-population
#8
Dong-Li Zhu, Yan Guo, Yan Zhang, Shan-Shan Dong, Wen Xu, Ruo-Han Hao, Xiao-Feng Chen, Han Yan, Shui-Yun Yang, Tie-Lin Yang
Previous studies have identified FGF2 as a susceptibility gene for osteoporosis in Caucasians. Evaluating the genetic associations in different ethnicities is necessary. Moreover, elucidating the functional mechanism for the susceptibility loci is important to offer new targets for therapeutic studies. Here, we genotyped ten SNPs in FGF2 and tested for associations with bone mineral density (BMD) in a discovery sample of 1300 Chinese subjects. Nominally significant results were subjected to replication in another sample of 1039 Chinese subjects...
March 19, 2017: Human Mutation
https://www.readbyqxmd.com/read/28302177/cepip-context-dependent-epigenomic-weighting-for-prioritization-of-regulatory-variants-and-disease-associated-genes
#9
Mulin Jun Li, Miaoxin Li, Zipeng Liu, Bin Yan, Zhicheng Pan, Dandan Huang, Qian Liang, Dingge Ying, Feng Xu, Hongcheng Yao, Panwen Wang, Jean-Pierre A Kocher, Zhengyuan Xia, Pak Chung Sham, Jun S Liu, Junwen Wang
It remains challenging to predict regulatory variants in particular tissues or cell types due to highly context-specific gene regulation. By connecting large-scale epigenomic profiles to expression quantitative trait loci (eQTLs) in a wide range of human tissues/cell types, we identify critical chromatin features that predict variant regulatory potential. We present cepip, a joint likelihood framework, for estimating a variant's regulatory probability in a context-dependent manner. Our method exhibits significant GWAS signal enrichment and is superior to existing cell type-specific methods...
March 16, 2017: Genome Biology
https://www.readbyqxmd.com/read/28289284/the-schizophrenia-risk-gene-znf804a-clinical-associations-biological-mechanisms-and-neuronal-functions
#10
REVIEW
H Chang, X Xiao, M Li
ZNF804A (zinc-finger protein 804A) has been recognized as a schizophrenia risk gene across multiple world populations. Its intronic single-nucleotide polymorphism (SNP) rs1344706 is among one of the strongest susceptibility variants that have achieved genome-wide significance in genome-wide association studies (GWAS) for schizophrenia and has been widely and intensively studied. To elucidate the biological mechanisms underlying the genetic risk conferred by rs1344706, we retrospectively analyzed the progresses in brain gene expression quantitative trait loci (eQTL) analyses, ZNF804A-induced pathway alterations in neural cells and changes in synaptic phenotypes associated with ZNF804A expression...
March 14, 2017: Molecular Psychiatry
https://www.readbyqxmd.com/read/28266165/il33-and-il1rl1-variants-are-associated-with-asthma-and-atopy-in-a-brazilian-population
#11
G A Queiroz, R S Costa, N M Alcantara-Neves, G Nunes de Oliveira Costa, M L Barreto, V L Carneiro, C A Figueiredo
Atopic asthma is a chronic inflammatory disease in airways resulting from genetic and environmental factors, characterized by production of the Th2 cytokines interleukin-4 (IL-4), interleukin-5 (IL-5) and interleukin-13 (IL-13). Interleukin-33 (IL-33) appears to be a potent inducer of Th2 immune response. This occurs when IL-33 binds and activates its receptor, the membrane ST2 (ST2L) in mast cells, dendritic cells, basophils, eosinophils, innate lymphoids and Th2 cells, leading to the release of these cytokines and intensifying allergic inflammation...
April 2017: International Journal of Immunogenetics
https://www.readbyqxmd.com/read/28257690/genetic-regulation-of-adipose-gene-expression-and-cardio-metabolic-traits
#12
Mete Civelek, Ying Wu, Calvin Pan, Chelsea K Raulerson, Arthur Ko, Aiqing He, Charles Tilford, Niyas K Saleem, Alena Stančáková, Laura J Scott, Christian Fuchsberger, Heather M Stringham, Anne U Jackson, Narisu Narisu, Peter S Chines, Kerrin S Small, Johanna Kuusisto, Brian W Parks, Päivi Pajukanta, Todd Kirchgessner, Francis S Collins, Peter S Gargalovic, Michael Boehnke, Markku Laakso, Karen L Mohlke, Aldons J Lusis
Subcutaneous adipose tissue stores excess lipids and maintains energy balance. We performed expression quantitative trait locus (eQTL) analyses by using abdominal subcutaneous adipose tissue of 770 extensively phenotyped participants of the METSIM study. We identified cis-eQTLs for 12,400 genes at a 1% false-discovery rate. Among an approximately 680 known genome-wide association study (GWAS) loci for cardio-metabolic traits, we identified 140 coincident cis-eQTLs at 109 GWAS loci, including 93 eQTLs not previously described...
March 2, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28241135/an-atlas-of-human-long-non-coding-rnas-with-accurate-5-ends
#13
Chung-Chau Hon, Jordan A Ramilowski, Jayson Harshbarger, Nicolas Bertin, Owen J L Rackham, Julian Gough, Elena Denisenko, Sebastian Schmeier, Thomas M Poulsen, Jessica Severin, Marina Lizio, Hideya Kawaji, Takeya Kasukawa, Masayoshi Itoh, A Maxwell Burroughs, Shohei Noma, Sarah Djebali, Tanvir Alam, Yulia A Medvedeva, Alison C Testa, Leonard Lipovich, Chi-Wai Yip, Imad Abugessaisa, Mickaël Mendez, Akira Hasegawa, Dave Tang, Timo Lassmann, Peter Heutink, Magda Babina, Christine A Wells, Soichi Kojima, Yukio Nakamura, Harukazu Suzuki, Carsten O Daub, Michiel J L de Hoon, Erik Arner, Yoshihide Hayashizaki, Piero Carninci, Alistair R R Forrest
Long non-coding RNAs (lncRNAs) are largely heterogeneous and functionally uncharacterized. Here, using FANTOM5 cap analysis of gene expression (CAGE) data, we integrate multiple transcript collections to generate a comprehensive atlas of 27,919 human lncRNA genes with high-confidence 5' ends and expression profiles across 1,829 samples from the major human primary cell types and tissues. Genomic and epigenomic classification of these lncRNAs reveals that most intergenic lncRNAs originate from enhancers rather than from promoters...
March 1, 2017: Nature
https://www.readbyqxmd.com/read/28224684/accurate-eqtl-prioritization-with-an-ensemble-based-framework
#14
Haoyang Zeng, Matthew D Edwards, Yuchun Guo, David K Gifford
We present a novel ensemble-based computational framework, EnsembleExpr, that achieved the best performance in the Fourth Critical Assessment of Genome Interpretation (CAGI4) "eQTL-causal SNPs" challenge for identifying eQTLs and prioritizing their gene expression effects. Expression quantitative trait loci (eQTLs) are genome sequence variants that result in gene expression changes and thus are prime suspects in the search for contributions to the causality of complex traits. When EnsembleExpr is trained on data from massively parallel reporter assays (MPRA) it accurately predicts reporter expression levels from unseen regulatory sequences and identifies sequence variants that exhibit significant changes in reporter expression...
February 21, 2017: Human Mutation
https://www.readbyqxmd.com/read/28220625/predicting-gene-expression-in-massively-parallel-reporter-assays-a-comparative-study
#15
Anat Kreimer, Haoyang Zeng, Matthew D Edwards, Yuchun Guo, Kevin Tian, Sunyoung Shin, Rene Welch, Michael Wainberg, Rahul Mohan, Nicholas A Sinnott-Armstrong, Yue Li, Gökcen Eraslan, Talal Bin Amin, Jonathan Goke, Nikola S Mueller, Manolis Kellis, Anshul Kundaje, Michael A Beer, Sunduz Keles, David K Gifford, Nir Yosef
In many human diseases, associated genetic changes tend to occur within noncoding regions, whose effect might be related to transcriptional control. A central goal in human genetics is to understand the function of such noncoding regions: given a region that is statistically associated with changes in gene expression (expression quantitative trait locus [eQTL]), does it in fact play a regulatory role? And if so, how is this role "coded" in its sequence? These questions were the subject of the Critical Assessment of Genome Interpretation eQTL challenge...
February 21, 2017: Human Mutation
https://www.readbyqxmd.com/read/28219444/a-functional-snp-associated-with-atopic-dermatitis-controls-cell-type-specific-methylation-of-the-vstm1-gene-locus
#16
Dilip Kumar, Kia Joo Puan, Anand Kumar Andiappan, Bernett Lee, Geertje H A Westerlaken, Doreen Haase, Rossella Melchiotti, Zhuang Li, Nurhashikin Yusof, Josephine Lum, Geraldine Koh, Shihui Foo, Joe Yeong, Alexessander Couto Alves, Juha Pekkanen, Liang Dan Sun, Astrid Irwanto, Benjamin P Fairfax, Vivek Naranbhai, John E A Common, Mark Tang, Chin Keh Chuang, Marjo-Riitta Jarvelin, Julian C Knight, Xuejun Zhang, Fook Tim Chew, Shyam Prabhakar, Liu Jianjun, De Yun Wang, Francesca Zolezzi, Michael Poidinger, E Birgitte Lane, Linde Meyaard, Olaf Rötzschke
BACKGROUND: Expression quantitative trait loci (eQTL) databases represent a valuable resource to link disease-associated SNPs to specific candidate genes whose gene expression is significantly modulated by the SNP under investigation. We previously identified signal inhibitory receptor on leukocytes-1 (SIRL-1) as a powerful regulator of human innate immune cell function. While it is constitutively high expressed on neutrophils, on monocytes the SIRL-1 surface expression varies strongly between individuals...
February 20, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28218759/limited-statistical-evidence-for-shared-genetic-effects-of-eqtls-and-autoimmune-disease-associated-loci-in-three-major-immune-cell-types
#17
Sung Chun, Alexandra Casparino, Nikolaos A Patsopoulos, Damien C Croteau-Chonka, Benjamin A Raby, Philip L De Jager, Shamil R Sunyaev, Chris Cotsapas
Most autoimmune-disease-risk effects identified by genome-wide association studies (GWAS) localize to open chromatin with gene-regulatory activity. GWAS loci are also enriched in expression quantitative trait loci (eQTLs), thus suggesting that most risk variants alter gene expression. However, because causal variants are difficult to identify, and cis-eQTLs occur frequently, it remains challenging to identify specific instances of disease-relevant changes to gene regulation. Here, we used a novel joint likelihood framework with higher resolution than that of previous methods to identify loci where autoimmune-disease risk and an eQTL are driven by a single shared genetic effect...
February 20, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28193859/genetic-regulatory-signatures-underlying-islet-gene-expression-and-type-2-diabetes
#18
Arushi Varshney, Laura J Scott, Ryan P Welch, Michael R Erdos, Peter S Chines, Narisu Narisu, Ricardo D'O Albanus, Peter Orchard, Brooke N Wolford, Romy Kursawe, Swarooparani Vadlamudi, Maren E Cannon, John P Didion, John Hensley, Anthony Kirilusha, Lori L Bonnycastle, D Leland Taylor, Richard Watanabe, Karen L Mohlke, Michael Boehnke, Francis S Collins, Stephen C J Parker, Michael L Stitzel
Genome-wide association studies (GWAS) have identified >100 independent SNPs that modulate the risk of type 2 diabetes (T2D) and related traits. However, the pathogenic mechanisms of most of these SNPs remain elusive. Here, we examined genomic, epigenomic, and transcriptomic profiles in human pancreatic islets to understand the links between genetic variation, chromatin landscape, and gene expression in the context of T2D. We first integrated genome and transcriptome variation across 112 islet samples to produce dense cis-expression quantitative trait loci (cis-eQTL) maps...
February 28, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28193307/heritability-and-gwas-studies-for-monocyte-lymphocyte-ratio
#19
Bochao D Lin, Gonneke Willemsen, Iryna O Fedko, Rick Jansen, Brenda Penninx, E de Geus, C Kluft, JoukeJan Hottenga, Dorret I Boomsma
The monocyte-lymphocyte ratio (MLR) is a useful biomarker for disease development, but little is known about the extent to which genetic and environmental factors influence MLR variation. Here, we study the genetic architecture of MLR and determine the influence of demographic and lifestyle factors on MLR in data from a Dutch non-patient twin-family population. Data were obtained in 9,501 individuals from the Netherlands Twin Register. We used regression analyses to determine the effects of age, sex, smoking, and body mass index (BMI) on MLR and its subcomponents...
February 14, 2017: Twin Research and Human Genetics: the Official Journal of the International Society for Twin Studies
https://www.readbyqxmd.com/read/28181565/genetic-susceptibility-variants-for-lung-cancer-replication-study-and-assessment-as-expression-quantitative-trait-loci
#20
Giulia Pintarelli, Chiara Elisabetta Cotroneo, Sara Noci, Matteo Dugo, Antonella Galvan, Simona Delli Carpini, Lorena Citterio, Paolo Manunta, Matteo Incarbone, Davide Tosi, Luigi Santambrogio, Tommaso A Dragani, Francesca Colombo
Many single nucleotide polymorphisms (SNPs) have been associated with lung cancer but lack confirmation and functional characterization. We retested the association of 56 candidate SNPs with lung adenocarcinoma risk and overall survival in a cohort of 823 Italian patients and 779 healthy controls, and assessed their function as expression quantitative trait loci (eQTLs). In the replication study, eight SNPs (rs401681, rs3019885, rs732765, rs2568494, rs16969968, rs6495309, rs11634351, and rs4105144) associated with lung adenocarcinoma risk and three (rs9557635, rs4105144, and rs735482) associated with survival...
February 9, 2017: Scientific Reports
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