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Expression quantitative trait loci

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https://www.readbyqxmd.com/read/28934397/a-modifier-of-huntington-s-disease-onset-at-the-mlh1-locus
#1
Jong-Min Lee, Michael J Chao, Denise Harold, Kawther Abu Elneel, Tammy Gillis, Peter Holmans, Lesley Jones, Michael Orth, Richard H Myers, Seung Kwak, Vanessa C Wheeler, Marcy E MacDonald, James F Gusella
Huntington's disease (HD) is a dominantly inherited neurodegenerative disease caused by an expanded CAG repeat in HTT. Many clinical characteristics of HD such as age at motor onset are determined largely by the size of HTT CAG repeat. However, emerging evidence strongly supports a role for other genetic factors in modifying the disease pathogenesis driven by mutant huntingtin. A recent genome-wide association analysis to discover genetic modifiers of HD onset age provided initial evidence for modifier loci on chromosomes 8 and 15 and suggestive evidence for a locus on chromosome 3...
October 1, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28931629/selinene-volatiles-are-essential-precursors-for-maize-defense-promoting-fungal-pathogen-resistance
#2
Yezhang Ding, Alisa Huffaker, Tobias G Köllner, Philipp Weckwerth, Christelle A M Robert, Joseph L Spencer, Alexander E Lipka, Eric A Schmelz
To ensure food security, maize (Zea mays) is a model crop for understanding useful traits underlying stress resistance. In contrast to foliar biochemicals, root defenses limiting the spread of disease remain poorly described. To better understand below-ground defenses in the field, we performed root metabolomic profiling and uncovered unexpectedly high levels of the sesquiterpene volatile β-selinene and the corresponding non-volatile antibiotic derivative, β-costic acid. The application of metabolite-based quantitative trait loci (mQTL) mapping using bi-parental populations, genome wide association studies, and near-isogenic lines (NILs) enabled the identification of terpene synthase 21 (ZmTps21) on chromosome 9 as a β-costic acid pathway candidate gene...
September 20, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28929317/risk-alleles-for-iga-nephropathy-associated-snps-conferred-completely-opposite-effects-to-idiopathic-membranous-nephropathy-in-chinese-han
#3
Xiaosong Qin, Chen Wang, Guanting Lu, Mengle Peng, Guixue Cheng, Hongquan Zhu, Yun Cao, Jianhua Liu, Yuzhong Li, Hong Cai, Funing Yang, Yanhong Liu, Xiaoyu Chen, Liubing Li, Nan Wan, Xiaoting Wen, Shijun Li, Ruili Nie, Dongchun Qin, Yongzhe Li, Yong Liu
The coexistence of immunoglobulin A nephropathy (IgAN) and idiopathic membranous nephropathy (IMN) in a few cases suggested that there could be existed a similar mechanism in pathogenesis of these two types of primary glomerulonephritis. In order to verify this hypothesis, a total of 23 reported IgAN-associated SNPs were genotyped in a cohort of 485 IMN patients and 569 healthy controls with Chinese Han origin. After Cochran-Armitage test for trend analysis, seven IgAN-associated SNPs located in the major histocompatibility complex (MHC) region were found to be significantly associated with the susceptibility of IMN, with rs9275596 as the top one (p = 1...
September 19, 2017: Immunologic Research
https://www.readbyqxmd.com/read/28929106/common-expression-quantitative-trait-loci-shared-by-histone-genes
#4
Hanseol Kim, Yujin Suh, Chaeyoung Lee
A genome-wide association study (GWAS) was conducted to examine expression quantitative trait loci (eQTLs) for histone genes. We examined common eQTLs for multiple histone genes in 373 European lymphoblastoid cell lines (LCLs). A linear regression model was employed to identify single-nucleotide polymorphisms (SNPs) associated with expression of the histone genes, and the number of eQTLs was determined by linkage disequilibrium analysis. Additional associations of the identified eQTLs with other genes were also examined...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28922773/crop-model-assisted-phenomics-and-genome-wide-association-study-for-climate-adaptation-of-indica-rice-2-thermal-stress-and-spikelet-sterility
#5
Michael Dingkuhn, Richard Pasco, Julie Mae Pasuquin, Jean Damo, Jean-Christophe Soulié, Louis-Marie Raboin, Julie Dusserre, Abdoulaye Sow, Baboucarr Manneh, Suchit Shrestha, Tobias Kretzschmar
Low night and high day temperatures during sensitive reproductive stages cause spikelet sterility in rice. Phenotyping of tolerance traits in the field is difficult because of temporal interactions with phenology and organ temperature differing from ambient. Physiological models can be used to separate these effects. A 203-accession indica rice diversity panel was phenotyped for sterility in ten environments in Senegal and Madagascar and climate data were recorded. Here we report on sterility responses while a companion study reported on phenology...
July 10, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28922761/rapid-mapping-and-cloning-of-the-virescent-1-gene-in-cotton-by-bulked-segregant-analysis-next-generation-sequencing-and-virus-induced-gene-silencing-strategies
#6
Jiankun Zhu, Jiedan Chen, Fengkai Gao, Chenyu Xu, Huaitong Wu, Kun Chen, Zhanfeng Si, Hu Yan, Tianzhen Zhang
Map-based gene cloning is a vital strategy for the identification of the quantitative trait loci or genes underlying important agronomic traits. The conventional map-based cloning method is powerful but generally time-consuming and labor-intensive. In this context, we introduce an improved bulked segregant analysis method in combination with a virus-induced gene silencing (VIGS) strategy for rapid and reliable gene mapping, identification and functional verification. This method was applied to a multiple recessive marker line of upland cotton, Texas 582 (T582), and identified unique genomic positions harboring mutant loci, showing the reliability and efficacy of this method...
July 10, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28922359/a-first-linkage-map-and-downy-mildew-resistance-qtl-discovery-for-sweet-basil-ocimum-basilicum-facilitated-by-double-digestion-restriction-site-associated-dna-sequencing-ddradseq
#7
Robert Pyne, Josh Honig, Jennifer Vaiciunas, Adolfina Koroch, Christian Wyenandt, Stacy Bonos, James Simon
Limited understanding of sweet basil (Ocimum basilicum L.) genetics and genome structure has reduced efficiency of breeding strategies. This is evidenced by the rapid, worldwide dissemination of basil downy mildew (Peronospora belbahrii) in the absence of resistant cultivars. In an effort to improve available genetic resources, expressed sequence tag simple sequence repeat (EST-SSR) and single nucleotide polymorphism (SNP) markers were developed and used to genotype the MRI x SB22 F2 mapping population, which segregates for response to downy mildew...
2017: PloS One
https://www.readbyqxmd.com/read/28913578/loci-on-chromosomes-1a-and-2a-affect-resistance-to-tan-yellow-spot-in-wheat-populations-not-segregating-for-tsn1
#8
Manisha Shankar, Dorthe Jorgensen, Julian Taylor, Ken J Chalmers, Rebecca Fox, Grant J Hollaway, Stephen M Neate, Mark S McLean, Elysia Vassos, Hossein Golzar, Robert Loughman, Diane E Mather
QTL for tan spot resistance were mapped on wheat chromosomes 1A and 2A. Lines were developed with resistance alleles at these loci and at the tsn1 locus on chromosome 5B. These lines expressed significantly higher resistance than the parent with tsn1 only. Tan spot (syn. yellow spot and yellow leaf spot) caused by Pyrenophora tritici-repentis is an important foliar disease of wheat in Australia. Few resistance genes have been mapped in Australian germplasm and only one, known as tsn1 located on chromosome 5B, is known in Australian breeding programs...
September 14, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28911167/in-utero-exposure-to-a-high-fat-diet-programs-hepatic-hypermethylation-and-gene-dysregulation-and-development-of-metabolic-syndrome-in-male-mice
#9
Yoshinori Seki, Masako Suzuki, Xingyi Guo, Alan Scott Glenn, Patricia M Vuguin, Ariana Fiallo, Quan Du, Yi-An Ko, Yiting Yu, Katalin Susztak, Deyou Zheng, John M Greally, Ellen B Katz, Maureen J Charron
Exposure to a high-fat (HF) diet in utero is associated with increased incidence of cardiovascular disease, diabetes, and metabolic syndrome later in life. However, the molecular basis of this enhanced susceptibility for metabolic disease is poorly understood. Gene expression microarray and genome-wide DNA methylation analyses of mouse liver revealed that exposure to a maternal HF milieu activated genes of immune response, inflammation, and hepatic dysfunction. DNA methylation analysis revealed 3360 differentially methylated loci, most of which (76%) were hypermethylated and distributed preferentially to hotspots on chromosomes 4 [atherosclerosis susceptibility quantitative trait loci (QTLs) 1] and 18 (insulin-dependent susceptibility QTLs 21)...
September 1, 2017: Endocrinology
https://www.readbyqxmd.com/read/28911016/quantifying-rooting-at-depth-in-a-wheat-doubled-haploid-population-with-introgression-from-wild-emmer
#10
Christina K Clarke, Peter J Gregory, Martin Lukac, Amanda J Burridge, Alexandra M Allen, Keith J Edwards, Mike J Gooding
Background and Aims: The genetic basis of increased rooting below the plough layer, post-anthesis in the field, of an elite wheat line (Triticum aestivum 'Shamrock') with recent introgression from wild emmer (T. dicoccoides), is investigated. Shamrock has a non-glaucous canopy phenotype mapped to the short arm of chromosome 2B (2BS), derived from the wild emmer. A secondary aim was to determine whether genetic effects found in the field could have been predicted by other assessment methods...
September 1, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28899996/prediction-and-subtyping-of-hypertension-from-pan-tissue-transcriptomic-and-genetic-analyses
#11
Mahashweta Basu, Mahfuza Sharmin, Avinash Das, Nishanth Ulhas Nair, Kun Wang, Joo Sang Lee, Yen-Pei Christy Chang, Eytan Ruppin, Sridhar Hannenhalli
Hypertension is a complex systemic disease involving transcriptional changes in multiple organs. Here we systematically investigate the pan-tissue transcriptional and genetic landscape of hypertension spanning dozens of tissues in hundreds of individuals. We find that in several tissues previously identified hypertension-linked genes are dysregulated and the gene expression profile is predictive of hypertension. Importantly, many expression quantitative trait loci (eQTL) SNPs associated with the population variance of the dysregulated genes are linked with blood pressure in an independent genome-wide association study, suggesting that the functional effect of hypertension-associated SNPs may be mediated through tissue-specific transcriptional dysregulation...
September 12, 2017: Genetics
https://www.readbyqxmd.com/read/28894906/whole-exome-sequencing-reveals-a-functional-mutation-in-the-gain-domain-of-the-bai2-receptor-underlying-a-forward-mutagenesis-hyperactivity-qtl
#12
David J Speca, James S Trimmer, Andrew S Peterson, Elva Díaz
The identification of novel genes underlying complex mouse behavioral traits remains an important step in understanding normal brain function and its dysfunction in mental health disorders. To identify dominant mutations that influence locomotor activity, we performed a mouse N-ethyl-N-nitrosourea (ENU) forward mutagenesis screen and mapped several loci as quantitative traits. Here we describe the fine-mapping and positional cloning of a hyperactivity locus mapped to the medial portion of mouse chromosome four...
September 12, 2017: Mammalian Genome: Official Journal of the International Mammalian Genome Society
https://www.readbyqxmd.com/read/28892072/neuregulin-signaling-pathway-in-smoking-behavior
#13
R Gupta, B Qaiser, L He, T S Hiekkalinna, A B Zheutlin, S Therman, M Ollikainen, S Ripatti, M Perola, V Salomaa, L Milani, T D Cannon, P A F Madden, T Korhonen, J Kaprio, A Loukola
Understanding molecular processes that link comorbid traits such as addictions and mental disorders can provide novel therapeutic targets. Neuregulin signaling pathway (NSP) has previously been implicated in schizophrenia, a neurodevelopmental disorder with high comorbidity to smoking. Using a Finnish twin family sample, we have previously detected association between nicotine dependence and ERBB4 (a neuregulin receptor), and linkage for smoking initiation at the ERBB4 locus on 2q33. Further, Neuregulin3 has recently been shown to associate with nicotine withdrawal in a behavioral mouse model...
August 22, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28892059/a-meta-analysis-of-genome-wide-association-studies-identifies-17-new-parkinson-s-disease-risk-loci
#14
Diana Chang, Mike A Nalls, Ingileif B Hallgrímsdóttir, Julie Hunkapiller, Marcel van der Brug, Fang Cai, Geoffrey A Kerchner, Gai Ayalon, Baris Bingol, Morgan Sheng, David Hinds, Timothy W Behrens, Andrew B Singleton, Tushar R Bhangale, Robert R Graham
Common variant genome-wide association studies (GWASs) have, to date, identified >24 risk loci for Parkinson's disease (PD). To discover additional loci, we carried out a GWAS comparing 6,476 PD cases with 302,042 controls, followed by a meta-analysis with a recent study of over 13,000 PD cases and 95,000 controls at 9,830 overlapping variants. We then tested 35 loci (P < 1 × 10(-6)) in a replication cohort of 5,851 cases and 5,866 controls. We identified 17 novel risk loci (P < 5 × 10(-8)) in a joint analysis of 26,035 cases and 403,190 controls...
September 11, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28886448/exploring-hepsin-functional-genetic-variation-association-with-disease-specific-protein-expression-in-bipolar-disorder-applications-of-a-proteomic-informed-genomic-approach
#15
Malik Nassan, Yun-Fang Jia, Greg Jenkins, Colin Colby, Scott Feeder, Doo-Sup Choi, Marin Veldic, Susan L McElroy, David J Bond, Richard Weinshilboum, Joanna M Biernacka, Mark A Frye
In a prior discovery study, increased levels of serum Growth Differentiation Factor 15 (GDF15), Hepsin (HPN), and Matrix Metalloproteinase-7 (MMP7) were observed in bipolar depressed patients vs controls. This exploratory post-hoc analysis applied a proteomic-informed genomic research strategy to study the potential functional role of these proteins in bipolar disorder (BP). Utilizing the Genotype-Tissue Expression (GTEx) database to identify cis-acting blood expression quantitative trait loci (cis-eQTLs), five eQTL variants from the HPN gene were analyzed for association with BP cases using genotype data of cases from the discovery study (n = 58) versus healthy controls (n = 777)...
July 4, 2017: Journal of Psychiatric Research
https://www.readbyqxmd.com/read/28885228/genetic-and-transcriptomic-bases-of-intestinal-epithelial-barrier-dysfunction-in-inflammatory-bowel-disease
#16
Maaike Vancamelbeke, Tim Vanuytsel, Ricard Farré, Sare Verstockt, Marc Ferrante, Gert Van Assche, Paul Rutgeerts, Frans Schuit, Séverine Vermeire, Ingrid Arijs, Isabelle Cleynen
BACKGROUND: Intestinal barrier defects are common in patients with inflammatory bowel disease (IBD). To identify which components could underlie these changes, we performed an in-depth analysis of epithelial barrier genes in IBD. METHODS: A set of 128 intestinal barrier genes was selected. Polygenic risk scores were generated based on selected barrier gene variants that were associated with Crohn's disease (CD) or ulcerative colitis (UC) in our study. Gene expression was analyzed using microarray and quantitative reverse transcription polymerase chain reaction...
September 6, 2017: Inflammatory Bowel Diseases
https://www.readbyqxmd.com/read/28883458/genetic-correlations-reveal-the-shared-genetic-architecture-of-transcription-in-human-peripheral-blood
#17
Samuel W Lukowski, Luke R Lloyd-Jones, Alexander Holloway, Holger Kirsten, Gibran Hemani, Jian Yang, Kerrin Small, Jing Zhao, Andres Metspalu, Emmanouil T Dermitzakis, Greg Gibson, Timothy D Spector, Joachim Thiery, Markus Scholz, Grant W Montgomery, Tonu Esko, Peter M Visscher, Joseph E Powell
Transcript co-expression is regulated by a combination of shared genetic and environmental factors. Here, we estimate the proportion of co-expression that is due to shared genetic variance. To do so, we estimated the genetic correlations between each pairwise combination of 2469 transcripts that are highly heritable and expressed in whole blood in 1748 unrelated individuals of European ancestry. We identify 556 pairs with a significant genetic correlation of which 77% are located on different chromosomes, and report 934 expression quantitative trait loci, identified in an independent cohort, with significant effects on both transcripts in a genetically correlated pair...
September 7, 2017: Nature Communications
https://www.readbyqxmd.com/read/28882987/reply-to-hu-et-al-on-the-interpretation-of-gasdermin-b-expression-quantitative-trait-loci-data
#18
Lipika R Pal, Kinlin L Chao, John Moult, Osnat Herzberg
No abstract text is available yet for this article.
September 7, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28881962/applying-meta-analysis-to-genotype-tissue-expression-data-from-multiple-tissues-to-identify-eqtls-and-increase-the-number-of-egenes
#19
Dat Duong, Lisa Gai, Sagi Snir, Eun Yong Kang, Buhm Han, Jae Hoon Sul, Eleazar Eskin
Motivation: There is recent interest in using gene expression data to contextualize findings from traditional genome-wide association studies (GWAS). Conditioned on a tissue, expression quantitative trait loci (eQTLs) are genetic variants associated with gene expression, and eGenes are genes whose expression levels are associated with genetic variants. eQTLs and eGenes provide great supporting evidence for GWAS hits and important insights into the regulatory pathways involved in many diseases...
July 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28878296/genetic-variants-in-ercc1-and-xpc-predict-survival-outcome-of-non-small-cell-lung-cancer-patients-treated-with-platinum-based-therapy
#20
Ruoxin Zhang, Ming Jia, Huijing Xue, Yuan Xu, Mengyun Wang, Meiling Zhu, Menghong Sun, Jianhua Chang, Qingyi Wei
Nucleotide excision repair (NER) plays a vital role in platinum-induced DNA damage during chemotherapy. We hypothesize that regulatory single nucleotide polymorphisms (rSNPs) of the core NER genes modulate clinical outcome of patients with advanced non-small cell lung cancer (NSCLC) treated with platinum-based chemotherapy (PBS). We investigated associations of 25 rSNPs in eight NER genes with progression free survival (PFS) and overall survival (OS) in 710 NSCLC patients. We found that ERCC1 rs3212924 AG/GG and XPC rs2229090 GC/CC genotypes were associated with patients' PFS (HRadj = 1...
September 6, 2017: Scientific Reports
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