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https://www.readbyqxmd.com/read/28335481/genetic-variants-contributing-to-colistin-cytotoxicity-identification-of-tgif1-and-hoxd10-using-a-population-genomics-approach
#1
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/28335003/identification-of-genetic-variants-affecting-vitamin-d-receptor-binding-and-associations-with-autoimmune-disease
#2
Giuseppe Gallone, Wilfried Haerty, Giulio Disanto, Sreeram V Ramagopalan, Chris P Ponting, Antonio J Berlanga-Taylor
Large numbers of statistically significant associations between sentinel SNPs and case-control status have been replicated by genome-wide association studies. Nevertheless, few underlying molecular mechanisms of complex disease are currently known. We investigated whether variation in binding of a transcription factor, the vitamin D receptor (VDR) whose activating ligand vitamin D has been proposed as a modifiable factor in multiple disorders, could explain any of these associations. VDR modifies gene expression by binding DNA as a heterodimer with the Retinoid X receptor (RXR)...
March 9, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28328801/influence-of-polymorphisms-in-the-wnt-%C3%AE-catenin-pathway-genes-on-hepatocellular-carcinoma-risk-in-a-chinese-han-population
#3
Qing-Min Li, Feng-Qin Zhang, Ya-Feng Li, Qing-Jie Xian, Yan-Qiang Zhang, Peng Li
The Wnt/β-catenin pathway plays a vital role in initiating and sustaining hepatocellular carcinoma (HCC). However, few studies have investigated polymorphisms in the Wnt/β-catenin signaling pathway genes in the Chinese Han population. The aim of the present retrospective study was to investigate the correlations between polymorphisms of the Wnt/β-catenin signaling pathway genes (CTNNB1 and WNT2) and HCC susceptibility, development, and progression.Twenty tagging single nucleotide polymorphisms were chosen from HapMap data and genotyped in 320 patients with HCC, 320 chronic hepatitis B virus (HBV)-infected patients without HCC (N-HCC, including 95 liver cirrhosis, 164 chronic hepatitis B, and 61 asymptomatic HBV carriers), and 320 healthy controls...
March 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28242483/classical-rather-than-genetic-risk-factors-account-for-high-cardiovascular-disease-prevalence-in-lithuania-a-cross-sectional-population-study
#4
Neringa Burokienė, Ingrida Domarkienė, Laima Ambrozaitytė, Ingrida Uktverytė, Raimonda Meškienė, Dovilė Karčiauskaitė, Vytautas Kasiulevičius, Virginijus Šapoka, Vaidutis Kučinskas, Zita Aušrelė Kučinskienė
PURPOSE: Cardiovascular disease (CVD) mortality accounts for 54% of all deaths in Lithuania, making it the highest among all of the European Union countries. We evaluated the prevalence of several CVD risk factors, including lifestyle, blood biochemistry and genetic predisposition to determine the reasons behind significantly increased CVD prevalence in Lithuania. MATERIALS AND METHODS: In total 435 volunteers of Lithuanian ethnicity and stable geographic settlement for 3 generations, had their anthropometric, biochemical and behavioural risk factors measured...
February 24, 2017: Advances in Medical Sciences
https://www.readbyqxmd.com/read/28238281/new-multilocus-linkage-disequilibrium-measure-for-tag-snp-selection
#5
Bo Liao, Xiangjun Wang, Wen Zhu, Xiong Li, Lijun Cai, Haowen Chen
Numerous approaches have been proposed for selecting an optimal tag single-nucleotide polymorphism (SNP) set. Most of these approaches are based on linkage disequilibrium (LD). Classical LD measures, such as D' and r(2), are frequently used to quantify the relationship between two marker (pairwise) linkage disequilibria. Despite of their successful use in many applications, these measures cannot be used to measure the LD between multiple-marker. These LD measures need information about the frequencies of alleles collected from haplotype dataset...
February 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28231061/role-of-treatment-modifying-mthfr677c-t-and-1298a-c-polymorphisms-in-metformin-treated-puerto-rican-patients-with-type-2-diabetes-mellitus-and-peripheral-neuropathy
#6
Francisco J Jiménez-Ramírez, Liza M Castro, Clarymar Ortiz, Jennifer Concepción, Jessicca Y Renta, Raúl H Morales-Borges, Jorge R Miranda-Massari, Jorge Duconge
BACKGROUND: The study was conducted to investigate potential association between MTHFR genotypes and diabetic peripheral neuropathy (DPN) in Puerto Ricans with type-2 diabetes mellitus (T2DM) treated with metformin. The prevalence of major MTHFR polymorphisms in this cohort was also ascertained. METHODS: DNAs from 89 metformin-treated patients with T2DM and DPN were genotyped using the PCR-based RFLP assay for MTHFR677C>T and 1298A>C polymorphisms. Frequency distributions of these variants in the study cohort were compared to those reported for three reference populations (HapMap project) and controls (400 newborn specimens)...
March 1, 2017: Drug Metabolism and Personalized Therapy
https://www.readbyqxmd.com/read/28225073/high-mutation-rates-explain-low-population-genetic-divergence-at-copy-number-variable-loci-in-homo-sapiens
#7
Xin-Sheng Hu, Francis C Yeh, Yang Hu, Li-Ting Deng, Richard A Ennos, Xiaoyang Chen
Copy-number-variable (CNV) loci differ from single nucleotide polymorphic (SNP) sites in size, mutation rate, and mechanisms of maintenance in natural populations. It is therefore hypothesized that population genetic divergence at CNV loci will differ from that found at SNP sites. Here, we test this hypothesis by analysing 856 CNV loci from the genomes of 1184 healthy individuals from 11 HapMap populations with a wide range of ancestry. The results show that population genetic divergence at the CNV loci is generally more than three times lower than at genome-wide SNP sites...
February 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28198814/inference-of-multiple-wave-population-admixture-by-modeling-decay-of-linkage-disequilibrium-with-polynomial-functions
#8
Y Zhou, K Yuan, Y Yu, X Ni, P Xie, E P Xing, S Xu
To infer the histories of population admixture, one important challenge with methods based on the admixture linkage disequilibrium (ALD) is to remove the effect of source LD (SLD), which is directly inherited from source populations. In previous methods, only the decay curve of weighted LD between pairs of sites whose genetic distance were larger than a certain starting distance was fitted by single or multiple exponential functions, for the inference of recent single- or multiple-wave admixture. However, the effect of SLD has not been well defined and no tool has been developed to estimate the effect of SLD on weighted LD decay...
February 15, 2017: Heredity
https://www.readbyqxmd.com/read/28183281/assessing-the-risk-for-suicide-in-schizophrenia-according-to-migration-ethnicity-and-geographical-ancestry
#9
Nuwan C Hettige, Ali Bani-Fatemi, James L Kennedy, Vincenzo De Luca
BACKGROUND: Suicide is a leading cause of mortality among those afflicted by schizophrenia. Previous studies demonstrated that the stressors associated with immigration may lead to an onset of schizophrenia and suicide separately in susceptible individuals. However, no studies have shown whether immigration may lead to suicidal behaviour for individuals with schizophrenia. Our study proposes that an individual's geographical ancestry, ethnicity or migration status may be predictive of suicide risk in schizophrenia...
February 9, 2017: BMC Psychiatry
https://www.readbyqxmd.com/read/28181496/haplotype-based-case-control-study-of-the-receptor-calcitonin-activity-modifying-protein-ramp-1-gene-in-essential-hypertension
#10
T Nakayama, T Nakazato, H Naruse, Z Fu, Z Wang, M Soma, T Hoshino, M Shimodaira, N Aoi
The adrenomedullin receptor is a complex molecule that comprises the calcitonin-receptor-like receptor (CRLR) and the receptor-activity-modifying protein (RAMP). RAMP1 is a vasodilation factor, and RAMP1-deficient mice (RAMP1(-/-)) exhibit inflammatory responses with a significant transient increase in serum calcitonin-gene-related peptide levels and proinflammatory cytokines when compared with RAMP1(+/+) mice. The purpose of the present study was to investigate the relationships between essential hypertension (EH) and RAMP1 gene single-nucleotide polymorphisms (SNPs) or haplotypes in a Japanese population via a case-control study...
February 9, 2017: Journal of Human Hypertension
https://www.readbyqxmd.com/read/28154511/effects-of-single-nucleotide-polymorphism-marker-density-on-haplotype-block-partition
#11
Sun Ah Kim, Yun Joo Yoo
Many researchers have found that one of the most important characteristics of the structure of linkage disequilibrium is that the human genome can be divided into non-overlapping block partitions in which only a small number of haplotypes are observed. The location and distribution of haplotype blocks can be seen as a population property influenced by population genetic events such as selection, mutation, recombination and population structure. In this study, we investigate the effects of the density of markers relative to the full set of all polymorphisms in the region on the results of haplotype partitioning for five popular haplotype block partition methods: three methods in Haploview (confidence interval, four gamete test, and solid spine), MIG++ implemented in PLINK 1...
December 2016: Genomics & Informatics
https://www.readbyqxmd.com/read/28135296/genome-wide-association-of-copy-number-polymorphisms-and-kidney-function
#12
Man Li, Jacob Carey, Stephen Cristiano, Katalin Susztak, Josef Coresh, Eric Boerwinkle, Wen Hong L Kao, Terri H Beaty, Anna Köttgen, Robert B Scharpf
Genome-wide association studies (GWAS) using single nucleotide polymorphisms (SNPs) have identified more than 50 loci associated with estimated glomerular filtration rate (eGFR), a measure of kidney function. However, significant SNPs account for a small proportion of eGFR variability. Other forms of genetic variation have not been comprehensively evaluated for association with eGFR. In this study, we assess whether changes in germline DNA copy number are associated with GFR estimated from serum creatinine, eGFRcrea...
2017: PloS One
https://www.readbyqxmd.com/read/28120839/signatures-of-human-european-palaeolithic-expansion-shown-by-resequencing-of-non-recombining-x-chromosome-segments
#13
Pierpaolo Maisano Delser, Rita Neumann, Stéphane Ballereau, Pille Hallast, Chiara Batini, Daniel Zadik, Mark A Jobling
Human genetic diversity in Europe has been extensively studied using uniparentally inherited sequences (mitochondrial DNA (mtDNA) and the Y chromosome), which reveal very different patterns indicating sex-specific demographic histories. The X chromosome, haploid in males and inherited twice as often from mothers as from fathers, could provide insights into past female behaviours, but has not been extensively investigated. Here, we use HapMap single-nucleotide polymorphism data to identify genome-wide segments of the X chromosome in which recombination is historically absent and mutations are likely to be the only source of genetic variation, referring to these as phylogeographically informative haplotypes on autosomes and X chromosome (PHAXs)...
January 25, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28117334/a-systematic-snp-selection-approach-to-identify-mechanisms-underlying-disease-aetiology-linking-height-to-post-menopausal-breast-and-colorectal-cancer-risk
#14
Rachel J J Elands, Colinda C J M Simons, Mona Riemenschneider, Aaron Isaacs, Leo J Schouten, Bas A Verhage, Kristel Van Steen, Roger W L Godschalk, Piet A van den Brandt, Monika Stoll, Matty P Weijenberg
Data from GWAS suggest that SNPs associated with complex diseases or traits tend to co-segregate in regions of low recombination, harbouring functionally linked gene clusters. This phenomenon allows for selecting a limited number of SNPs from GWAS repositories for large-scale studies investigating shared mechanisms between diseases. For example, we were interested in shared mechanisms between adult-attained height and post-menopausal breast cancer (BC) and colorectal cancer (CRC) risk, because height is a risk factor for these cancers, though likely not a causal factor...
January 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28107422/comparison-of-hapmap-and-1000-genomes-reference-panels-in-a-large-scale-genome-wide-association-study
#15
Paul S de Vries, Maria Sabater-Lleal, Daniel I Chasman, Stella Trompet, Tarunveer S Ahluwalia, Alexander Teumer, Marcus E Kleber, Ming-Huei Chen, Jie Jin Wang, John R Attia, Riccardo E Marioni, Maristella Steri, Lu-Chen Weng, Rene Pool, Vera Grossmann, Jennifer A Brody, Cristina Venturini, Toshiko Tanaka, Lynda M Rose, Christopher Oldmeadow, Johanna Mazur, Saonli Basu, Mattias Frånberg, Qiong Yang, Symen Ligthart, Jouke J Hottenga, Ann Rumley, Antonella Mulas, Anton J M de Craen, Anne Grotevendt, Kent D Taylor, Graciela E Delgado, Annette Kifley, Lorna M Lopez, Tina L Berentzen, Massimo Mangino, Stefania Bandinelli, Alanna C Morrison, Anders Hamsten, Geoffrey Tofler, Moniek P M de Maat, Harmen H M Draisma, Gordon D Lowe, Magdalena Zoledziewska, Naveed Sattar, Karl J Lackner, Uwe Völker, Barbara McKnight, Jie Huang, Elizabeth G Holliday, Mark A McEvoy, John M Starr, Pirro G Hysi, Dena G Hernandez, Weihua Guan, Fernando Rivadeneira, Wendy L McArdle, P Eline Slagboom, Tanja Zeller, Bruce M Psaty, André G Uitterlinden, Eco J C de Geus, David J Stott, Harald Binder, Albert Hofman, Oscar H Franco, Jerome I Rotter, Luigi Ferrucci, Tim D Spector, Ian J Deary, Winfried März, Andreas Greinacher, Philipp S Wild, Francesco Cucca, Dorret I Boomsma, Hugh Watkins, Weihong Tang, Paul M Ridker, Jan W Jukema, Rodney J Scott, Paul Mitchell, Torben Hansen, Christopher J O'Donnell, Nicholas L Smith, David P Strachan, Abbas Dehghan
An increasing number of genome-wide association (GWA) studies are now using the higher resolution 1000 Genomes Project reference panel (1000G) for imputation, with the expectation that 1000G imputation will lead to the discovery of additional associated loci when compared to HapMap imputation. In order to assess the improvement of 1000G over HapMap imputation in identifying associated loci, we compared the results of GWA studies of circulating fibrinogen based on the two reference panels. Using both HapMap and 1000G imputation we performed a meta-analysis of 22 studies comprising the same 91,953 individuals...
2017: PloS One
https://www.readbyqxmd.com/read/28092654/promoter-polymorphism-of-toll-like-receptor-4-is-associated-with-a-decreased-risk-of-coronary-artery-disease-a-case-control-study-in-the-chinese-han-population
#16
Dandan Sun, Liping Sun, Qian Xu, Honghu Wang, Jun Yang, Yuan Yuan
BACKGROUND Coronary artery disease (CAD) is considered a chronic inflammatory disease of the blood vessels. Toll-like receptor 4 (TLR4) is a transmembrane receptor involved in inflammatory reactions. The aim of this study was to determine the association between polymorphisms in the promoter region and 3'-untranslated region (3'-UTR) of TLR4, and the associated CAD risk. MATERIAL AND METHODS This study enrolled 424 participants with CAD and 424 controls without CAD. The polymorphisms in the promoter region and 3'-UTR of TLR4 were identified from the HapMap database, including rs10116253, rs10983755, and rs11536889...
January 16, 2017: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/28090804/choline-acetyltransferase-may-contribute-to-the-risk-of-tourette-syndrome-combination-of-family-based-analysis-and-case-control-study
#17
Xiuling Yang, Wenmiao Liu, Mingji Yi, Ru Zhang, Yinglei Xu, Zuzhou Huang, Shiguo Liu, Tang Li
OBJECTIVES: Twin and family analyses have revealed a genetic contribution to Tourette syndrome and postmortem studies have raised the intriguing possibility of a reduction in cholinergic interneuronsin TS patients. METHODS: We selected five tag SNPs (rs100824791, rs12264845, rs1880676, rs3793790 and rs3793798) of Choline Acetyltransferase (CHAT) from the Han Chinese population Hapmap database. Genotyping was conducted on 401 TS nuclear family trios and 405 control subjects...
January 16, 2017: World Journal of Biological Psychiatry
https://www.readbyqxmd.com/read/28073353/discovery-of-large-genomic-inversions-using-long-range-information
#18
Marzieh Eslami Rasekh, Giorgia Chiatante, Mattia Miroballo, Joyce Tang, Mario Ventura, Chris T Amemiya, Evan E Eichler, Francesca Antonacci, Can Alkan
BACKGROUND: Although many algorithms are now available that aim to characterize different classes of structural variation, discovery of balanced rearrangements such as inversions remains an open problem. This is mainly due to the fact that breakpoints of such events typically lie within segmental duplications or common repeats, which reduces the mappability of short reads. The algorithms developed within the 1000 Genomes Project to identify inversions are limited to relatively short inversions, and there are currently no available algorithms to discover large inversions using high throughput sequencing technologies...
January 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28065468/the-genetic-architecture-of-gene-expression-in-peripheral-blood
#19
Luke R Lloyd-Jones, Alexander Holloway, Allan McRae, Jian Yang, Kerrin Small, Jing Zhao, Biao Zeng, Andrew Bakshi, Andres Metspalu, Manolis Dermitzakis, Greg Gibson, Tim Spector, Grant Montgomery, Tonu Esko, Peter M Visscher, Joseph E Powell
We analyzed the mRNA levels for 36,778 transcript expression traits (probes) from 2,765 individuals to comprehensively investigate the genetic architecture and degree of missing heritability for gene expression in peripheral blood. We identified 11,204 cis and 3,791 trans independent expression quantitative trait loci (eQTL) by using linear mixed models to perform genome-wide association analyses. Furthermore, using information on both closely and distantly related individuals, heritability was estimated for all expression traits...
February 2, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28039329/a-genome-wide-interaction-analysis-of-tricyclic-tetracyclic-antidepressants-and-rr-and-qt-intervals-a-pharmacogenomics-study-from-the-cohorts-for-heart-and-aging-research-in-genomic-epidemiology-charge-consortium
#20
Raymond Noordam, Colleen M Sitlani, Christy L Avery, James D Stewart, Stephanie M Gogarten, Kerri L Wiggins, Stella Trompet, Helen R Warren, Fangui Sun, Daniel S Evans, Xiaohui Li, Jin Li, Albert V Smith, Joshua C Bis, Jennifer A Brody, Evan L Busch, Mark J Caulfield, Yii-Der I Chen, Steven R Cummings, L Adrienne Cupples, Qing Duan, Oscar H Franco, Rául Méndez-Giráldez, Tamara B Harris, Susan R Heckbert, Diana van Heemst, Albert Hofman, James S Floyd, Jan A Kors, Lenore J Launer, Yun Li, Ruifang Li-Gao, Leslie A Lange, Henry J Lin, Renée de Mutsert, Melanie D Napier, Christopher Newton-Cheh, Neil Poulter, Alexander P Reiner, Kenneth M Rice, Jeffrey Roach, Carlos J Rodriguez, Frits R Rosendaal, Naveed Sattar, Peter Sever, Amanda A Seyerle, P Eline Slagboom, Elsayed Z Soliman, Nona Sotoodehnia, David J Stott, Til Stürmer, Kent D Taylor, Timothy A Thornton, André G Uitterlinden, Kirk C Wilhelmsen, James G Wilson, Vilmundur Gudnason, J Wouter Jukema, Cathy C Laurie, Yongmei Liu, Dennis O Mook-Kanamori, Patricia B Munroe, Jerome I Rotter, Ramachandran S Vasan, Bruce M Psaty, Bruno H Stricker, Eric A Whitsel
BACKGROUND: Increased heart rate and a prolonged QT interval are important risk factors for cardiovascular morbidity and mortality, and can be influenced by the use of various medications, including tricyclic/tetracyclic antidepressants (TCAs). We aim to identify genetic loci that modify the association between TCA use and RR and QT intervals. METHODS AND RESULTS: We conducted race/ethnic-specific genome-wide interaction analyses (with HapMap phase II imputed reference panel imputation) of TCAs and resting RR and QT intervals in cohorts of European (n=45 706; n=1417 TCA users), African (n=10 235; n=296 TCA users) and Hispanic/Latino (n=13 808; n=147 TCA users) ancestry, adjusted for clinical covariates...
December 30, 2016: Journal of Medical Genetics
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