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https://www.readbyqxmd.com/read/28344342/disease-genomics-transitioning-from-association-to-causation-with-eqtls
#1
Dorothy Clyde
No abstract text is available yet for this article.
March 27, 2017: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/28343628/functional-architectures-of-local-and-distal-regulation-of-gene-expression-in-multiple-human-tissues
#2
Xuanyao Liu, Hilary K Finucane, Alexander Gusev, Gaurav Bhatia, Steven Gazal, Luke O'Connor, Brendan Bulik-Sullivan, Fred A Wright, Patrick F Sullivan, Benjamin M Neale, Alkes L Price
Genetic variants that modulate gene expression levels play an important role in the etiology of human diseases and complex traits. Although large-scale eQTL mapping studies routinely identify many local eQTLs, the molecular mechanisms by which genetic variants regulate expression remain unclear, particularly for distal eQTLs, which these studies are not well powered to detect. Here, we leveraged all variants (not just those that pass stringent significance thresholds) to analyze the functional architecture of local and distal regulation of gene expression in 15 human tissues by employing an extension of stratified LD-score regression that produces robust results in simulations...
March 18, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28339748/genotype-based-gene-signature-of-glioma-risk
#3
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
#4
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/28335481/genetic-variants-contributing-to-colistin-cytotoxicity-identification-of-tgif1-and-hoxd10-using-a-population-genomics-approach
#5
Michael T Eadon, Ronald J Hause, Amy L Stark, Ying-Hua Cheng, Heather E Wheeler, Kimberly S Burgess, Eric A Benson, Patrick N Cunningham, Robert L Bacallao, Pierre C Dagher, Todd C Skaar, M Eileen Dolan
Colistin sulfate (polymixin E) is an antibiotic prescribed with increasing frequency for severe Gram-negative bacterial infections. As nephrotoxicity is a common side effect, the discovery of pharmacogenomic markers associated with toxicity would benefit the utility of this drug. Our objective was to identify genetic markers of colistin cytotoxicity that were also associated with expression of key proteins using an unbiased, whole genome approach and further evaluate the functional significance in renal cell lines...
March 18, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28335076/fine-mapping-of-chromosome-5p15-33-identifies-novel-lung-cancer-susceptibility-loci-in-han-chinese
#6
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/28334899/association-analyses-of-east-asian-individuals-and-trans-ancestry-analyses-with-european-individuals-reveal-new-loci-associated-with-cholesterol-and-triglyceride-levels
#7
Cassandra N Spracklen, Peng Chen, Young Jin Kim, Xu Wang, Hui Cai, Shengxu Li, Jirong Long, Ying Wu, Ya Xing Wang, Fumihiko Takeuchi, Jer-Yuarn Wu, Keum-Ji Jung, Cheng Hu, Koichi Akiyama, Yonghong Zhang, Sanghoon Moon, Todd A Johnson, Huaixing Li, Rajkumar Dorajoo, Meian He, Maren E Cannon, Tamara S Roman, Elias Salfati, Keng-Hung Lin, Xiuqing Guo, Wayne H H Sheu, Devin Absher, Linda S Adair, Themistocles L Assimes, Tin Aung, Qiuyin Cai, Li-Ching Chang, Chien-Hsiun Chen, Li-Hsin Chien, Lee-Ming Chuang, Shu-Chun Chuang, Shufa Du, Qiao Fan, Cathy S J Fann, Alan B Feranil, Yechiel Friedlander, Penny Gordon-Larsen, Dongfeng Gu, Lixuan Gui, Zhirong Guo, Chew-Kiat Heng, James Hixson, Xuhong Hou, Chao Agnes Hsiung, Yao Hu, Mi Yeong Hwang, Chii-Min Hwu, Masato Isono, Jyh-Ming Jimmy Juang, Chiea-Chuen Khor, Yun Kyoung Kim, Woon-Puay Koh, Michiaki Kubo, I-Te Lee, Sun-Ju Lee, Wen-Jane Lee, Kae-Woei Liang, Blanche Lim, Sing-Hui Lim, Jianjun Liu, Toru Nabika, Wen-Harn Pan, Hao Peng, Thomas Quertermous, Charumathi Sabanayagam, Kevin Sandow, Jinxiu Shi, Liang Sun, Pok Chien Tan, Shu-Pei Tan, Kent D Taylor, Yik-Ying Teo, Sue-Anne Toh, Tatsuhiko Tsunoda, Rob M van Dam, Aili Wang, Feijie Wang, Jie Wang, Wen Bin Wei, Yong-Bing Xiang, Jie Yao, Jian-Min Yuan, Rong Zhang, Wanting Zhao, Yii-Der Ida Chen, Stephen S Rich, Jerome I Rotter, Tzung-Dau Wang, Tangchun Wu, Xu Lin, Bok-Ghee Han, Toshihiro Tanaka, Yoon Shin Cho, Tomohiro Katsuya, Weiping Jia, Sun-Ha Jee, Yuan-Tsong Chen, Norihiro Kato, Jost B Jonas, Ching-Yu Cheng, Xiao-Ou Shu, Jiang He, Wei Zheng, Tien-Yin Wong, Wei Huang, Bong-Jo Kim, E-Shyong Tai, Karen L Mohlke, Xueling Sim
Large-scale meta-analyses of genome-wide association studies (GWAS) have identified >175 loci associated with fasting cholesterol levels, including total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), and triglycerides (TG). With differences in linkage disequilibrium (LD) structure and allele frequencies between ancestry groups, studies in additional large samples may detect new associations. We conducted staged GWAS meta-analyses in up to 69,414 East Asian individuals from 24 studies with participants from Japan, the Philippines, Korea, China, Singapore, and Taiwan...
February 21, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28334860/genetic-regulation-of-gene-expression-in-the-epileptic-human-hippocampus
#8
Nasir Mirza, Richard Appleton, Sasha Burn, Daniel du Plessis, Roderick Duncan, Jibril Osman Farah, Bjarke Feenstra, Anders Hviid, Vivek Josan, Rajiv Mohanraj, Arif Shukralla, Graeme J Sills, Anthony G Marson, Munir Pirmohamed
Epilepsy is a serious and common neurological disorder. Expression quantitative loci (eQTL) analysis is a vital aid for the identification and interpretation of disease-risk loci. Many eQTLs operate in a tissue- and condition-specific manner. We have performed the first genome-wide cis-eQTL analysis of human hippocampal tissue to include not only normal (n = 22) but also epileptic (n = 22) samples. We demonstrate that disease-associated variants from an epilepsy GWAS meta-analysis and a febrile seizures (FS) GWAS are significantly more enriched with epilepsy-eQTLs than with normal hippocampal eQTLs from two larger independent published studies...
March 3, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28334830/predicting-the-impact-of-non-coding-variants-on-dna-methylation
#9
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
#10
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
#11
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/28332274/time-course-expression-qtl-atlas-of-the-global-transcriptional-response-of-wheat-to-fusarium-graminearum
#12
Mina Samad-Zamini, Wolfgang Schweiger, Thomas Nussbaumer, Klaus F X Mayer, Hermann Buerstmayr
Fusarium head blight is a devastating disease of small grain cereals such as bread wheat (Triticum aestivum). The pathogen switches from a biotrophic to a nectrotrophic lifestyle in course of disease development forcing its host to adapt its defence strategies. Using a genetical genomics approach we illustrate genome-wide reconfigurations of genetic control over transcript abundances between two decisive time points after inoculation with the causative pathogen Fusarium graminearum. Whole transcriptome measurements have been recorded for 163 lines of a wheat doubled haploid population segregating for several resistance genes yielding 15 552 at 30 hours and 15 888 eQTL at 50 hours after inoculation...
March 23, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28322319/functional-confirmation-of-plag1-as-the-candidate-causative-gene-underlying-major-pleiotropic-effects-on-body-weight-and-milk-characteristics
#13
Tania Fink, Kathryn Tiplady, Thomas Lopdell, Thomas Johnson, Russell G Snell, Richard J Spelman, Stephen R Davis, Mathew D Littlejohn
A major pleiotropic quantitative trait locus (QTL) located at ~25 Mbp on bovine chromosome 14 affects a myriad of growth and developmental traits in Bos taurus and indicus breeds. These QTL have been attributed to two functional variants in the bidirectional promoter of PLAG1 and CHCHD7. Although PLAG1 is a good candidate for mediating these effects, its role remains uncertain given that these variants are also associated with expression of five additional genes at the broader locus. In the current study, we conducted expression QTL (eQTL) mapping of this region using a large, high depth mammary RNAseq dataset representing 375 lactating cows...
March 21, 2017: Scientific Reports
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
#14
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
#15
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
#16
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/28301596/screening-for-interaction-effects-in-gene-expression-data
#17
Peter J Castaldi, Michael H Cho, Liming Liang, Edwin K Silverman, Craig P Hersh, Kenneth Rice, Hugues Aschard
Expression quantitative trait (eQTL) studies are a powerful tool for identifying genetic variants that affect levels of messenger RNA. Since gene expression is controlled by a complex network of gene-regulating factors, one way to identify these factors is to search for interaction effects between genetic variants and mRNA levels of transcription factors (TFs) and their respective target genes. However, identification of interaction effects in gene expression data pose a variety of methodological challenges, and it has become clear that such analyses should be conducted and interpreted with caution...
2017: PloS One
https://www.readbyqxmd.com/read/28289284/the-schizophrenia-risk-gene-znf804a-clinical-associations-biological-mechanisms-and-neuronal-functions
#18
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/28285768/dynamic-role-of-trans-regulation-of-gene-expression-in-relation-to-complex-traits
#19
Chen Yao, Roby Joehanes, Andrew D Johnson, Tianxiao Huan, Chunyu Liu, Jane E Freedman, Peter J Munson, David E Hill, Marc Vidal, Daniel Levy
Identifying causal genetic variants and understanding their mechanisms of effect on traits remains a challenge in genome-wide association studies (GWASs). In particular, how genetic variants (i.e., trans-eQTLs) affect expression of remote genes (i.e., trans-eGenes) remains unknown. We hypothesized that some trans-eQTLs regulate expression of distant genes by altering the expression of nearby genes (cis-eGenes). Using published GWAS datasets with 39,165 single-nucleotide polymorphisms (SNPs) associated with 1,960 traits, we explored whole blood gene expression associations of trait-associated SNPs in 5,257 individuals from the Framingham Heart Study...
March 8, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28285767/large-scale-trans-eqtls-affect-hundreds-of-transcripts-and-mediate-patterns-of-transcriptional-co-regulation
#20
Boel Brynedal, JinMyung Choi, Towfique Raj, Robert Bjornson, Barbara E Stranger, Benjamin M Neale, Benjamin F Voight, Chris Cotsapas
Efforts to decipher the causal relationships between differences in gene regulation and corresponding differences in phenotype have been stymied by several basic technical challenges. Although detecting local, cis-eQTLs is now routine, trans-eQTLs, which are distant from the genes of origin, are far more difficult to find because millions of SNPs must currently be compared to thousands of transcripts. Here, we demonstrate an alternative approach: we looked for SNPs associated with the expression of many genes simultaneously and found that hundreds of trans-eQTLs each affect hundreds of transcripts in lymphoblastoid cell lines across three African populations...
March 1, 2017: American Journal of Human Genetics
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