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https://www.readbyqxmd.com/read/28918587/genome-wide-association-studies-of-albuminuria-towards-genetic-stratification-in-diabetes
#1
REVIEW
Cristian Pattaro
Genome-wide association studies (GWAS) have been very successful in unraveling the polygenic structure of several complex diseases and traits. In the case of albuminuria, despite the large sample size achieved by some studies, results look sparse with a limited number of loci reported so far. This review searched for GWAS studies of albumin excretion, albuminuria, and proteinuria. The resulting picture sets elements of uniqueness for albuminuria GWAS with respect to other complex traits. So far, very few loci associated with albuminuria have been validated by means of genome-wide significant evidence or formal replication...
September 16, 2017: Journal of Nephrology
https://www.readbyqxmd.com/read/28917824/parkinson-s-disease-susceptibility-variants-and-severity-of-lewy-body-pathology
#2
Michael G Heckman, Koji Kasanuki, Nancy N Diehl, Shunsuke Koga, Alexandra Soto, Melissa E Murray, Dennis W Dickson, Owen A Ross
INTRODUCTION: Meta-analyses of genome-wide association studies (GWAS) have established common genetic risk factors for clinical Parkinson's disease (PD); however, associations between these risk factors and quantitative neuropathologic markers of disease severity have not been well-studied. This study evaluated associations of nominated variants from the most recent PD GWAS meta-analysis with Lewy body disease (LBD) subtype (brainstem, transitional, or diffuse) and pathologic burden of LB pathology as measured by LB counts in five cortical regions in a series of LBD cases...
September 11, 2017: Parkinsonism & related Disorders
https://www.readbyqxmd.com/read/28915899/association-between-polymorphisms-of-tas2r16-and-susceptibility-to-colorectal-cancer
#3
Jonathan Barontini, Marco Antinucci, Sergio Tofanelli, Maurizio Cammalleri, Massimo Dal Monte, Federica Gemignani, Pavel Vodicka, Roberto Marangoni, Ludmila Vodickova, Juozas Kupcinskas, Veronika Vymetalkova, Asta Forsti, Federico Canzian, Angelika Stein, Victor Moreno, Nicola Mastrodonato, Francesca Tavano, Anna Panza, Roberto Barale, Stefano Landi, Daniele Campa
BACKGROUND: Genetics plays an important role in the susceptibility to sporadic colorectal cancer (CRC). In the last 10 years genome-wide association studies (GWAS) have identified over 40 independent low penetrance polymorphic variants. However, these loci only explain around 1‑4% of CRC heritability, highlighting the dire need of identifying novel risk loci. In this study, we focused our attention on the genetic variability of the TAS2R16 gene, encoding for one of the bitter taste receptors that selectively binds to salicin, a natural antipyretic that resembles aspirin...
September 15, 2017: BMC Gastroenterology
https://www.readbyqxmd.com/read/28915626/hdl-cholesterol-concentration-in-pregnant-chinese-han-women-of-late-second-trimester-associated-with-genetic-variants-in-cetp-abca1-apoc3-and-galnt2
#4
Mingxuan Cui, Wei Li, Liangkun Ma, Fan Ping, Juntao Liu, Xueyan Wu, Jiangfeng Mao, Xi Wang, Min Nie
OBJECTIVE: To investigate whether HDL-C level in pregnant Chinese Han women of late second trimester correlated with loci in high-density lipoprotein-cholesterol (HDL-C)-related genes found in genome-wide association studies (GWAS). METHODS: Seven single-nucleotide polymorphisms (rs3764261 in CETP, rs1532085 in LIPC, rs7241918 in LIPG, rs1883025 in ABCA1, rs4225 in APOC3, rs1059611 in LPL, and rs16851339 in GALNT2) were genotyped using the Sequenom MassArray system for 1,884 pregnant women...
August 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28915562/detecting-the-genetic-link-between-alzheimer-s-disease-and-obesity-using-bioinformatics-analysis-of-gwas-data
#5
Qi-Shuai Zhuang, Hao Zheng, Xiao-Dan Gu, Liang Shen, Hong-Fang Ji
Alzheimer's disease (AD) represents the major form of dementia in the elderly. In recent years, accumulating evidence indicate that obesity may act as a risk factor for AD, while the genetic link between the two conditions remains unclear. This bioinformatics analysis aimed to detect the genetic link between AD and obesity on single nucleotide polymorphisms (SNPs), gene, and pathway levels based on genome-wide association studies data. A total of 31 SNPs were found to be shared by AD and obesity, which were linked to 7 genes...
August 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28915241/the-relative-contribution-of-dna-methylation-and-genetic-variants-on-protein-biomarkers-for-human-diseases
#6
Muhammad Ahsan, Weronica E Ek, Mathias Rask-Andersen, Torgny Karlsson, Allan Lind-Thomsen, Stefan Enroth, Ulf Gyllensten, Åsa Johansson
Associations between epigenetic alterations and disease status have been identified for many diseases. However, there is no strong evidence that epigenetic alterations are directly causal for disease pathogenesis. In this study, we combined SNP and DNA methylation data with measurements of protein biomarkers for cancer, inflammation or cardiovascular disease, to investigate the relative contribution of genetic and epigenetic variation on biomarker levels. A total of 121 protein biomarkers were measured and analyzed in relation to DNA methylation at 470,000 genomic positions and to over 10 million SNPs...
September 15, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28911207/trans-ethnic-meta-regression-of-genome-wide-association-studies-accounting-for-ancestry-increases-power-for-discovery-and-improves-fine-mapping-resolution
#7
Reedik Mägi, Momoko Horikoshi, Tamar Sofer, Anubha Mahajan, Hidetoshi Kitajima, Nora Franceschini, Mark I McCarthy, Andrew P Morris
Trans-ethnic meta-analysis of genome-wide association studies (GWAS) across diverse populations can increase power to detect complex trait loci when the underlying causal variants are shared between ancestry groups. However, heterogeneity in allelic effects between GWAS at these loci can occur that is correlated with ancestry. Here, a novel approach is presented to detect SNP association and quantify the extent of heterogeneity in allelic effects that is correlated with ancestry. We employ trans-ethnic meta-regression to model allelic effects as a function of axes of genetic variation, derived from a matrix of mean pairwise allele frequency differences between GWAS, and implemented in the MR-MEGA software...
September 15, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28911201/gene-expression-profiling-of-puberty-associated-genes-reveals-abundant-tissue-and-sex-specific-changes-across-postnatal-development
#8
Huayun Hou, Liis Uusküla-Reimand, Maisam Makarem, Christina Corre, Shems Saleh, Ariane Metcalf, Anna Goldenberg, Mark R Palmert, And Michael D Wilson
The timing of human puberty is highly variable, sexually dimorphic, and associated with adverse health outcomes. Over 20 genes carrying rare mutations have been identified in known pubertal disorders, many of which encode critical components of the hypothalamic-pituitary-gonadal (HPG) axis. Recent genome-wide association studies (GWAS) have identified more than 100 candidate genes at loci associated with age at menarche or voice breaking in males. We know little about the spatial, temporal or postnatal expression patterns of the majority of these puberty-associated genes...
September 15, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28905228/genetic-susceptibility-in-childhood-acute-lymphoblastic-leukemia
#9
REVIEW
Angela Gutierrez-Camino, Idoia Martin-Guerrero, Africa García-Orad
Acute lymphoblastic leukemia (ALL) is the most common childhood malignancy and a leading cause of death due to disease in children. The genetic basis of ALL susceptibility has been supported by its association with certain congenital disorders and, more recently, by several genome-wide association studies (GWAS). These GWAS identified common variants in ARID5B, IKZF1, CEBPE, CDKN2A, PIP4K2A, LHPP and ELK3 influencing ALL risk. However, the risk variants of these SNPs were not validated in all populations, suggesting that some of the loci could be population specific...
September 13, 2017: Medical Oncology
https://www.readbyqxmd.com/read/28904015/sasquatch-predicting-the-impact-of-regulatory-snps-on-transcription-factor-binding-from-cell-and-tissue-specific-dnase-footprints
#10
Ron Schwessinger, Maria C Suciu, Simon J McGowan, Jelena Telenius, Stephen Taylor, Doug R Higgs, Jim R Hughes
In the era of genome-wide association studies (GWAS) and personalized medicine, predicting the impact of single nucleotide polymorphisms (SNPs) in regulatory elements is an important goal. Current approaches to determine the potential of regulatory SNPs depend on inadequate knowledge of cell-specific DNA binding motifs. Here, we present Sasquatch, a new computational approach that uses DNase footprint data to estimate and visualize the effects of noncoding variants on transcription factor binding. Sasquatch performs a comprehensive k-mer-based analysis of DNase footprints to determine any k-mer's potential for protein binding in a specific cell type and how this may be changed by sequence variants...
September 13, 2017: Genome Research
https://www.readbyqxmd.com/read/28903908/advances-in-genome-wide-association-studies-for-important-traits-in-sheep-and-goats
#11
Tong-Yu Zhang, Cai-Ye Zhu, Li-Xin Du, Fu-Ping Zhao
Genome-wide association study (GWAS), an effective strategy to identify genetic variants associated with complex traits, has been used to study candidate genes of economical traits in animals. With the recent completion of sheep and goat genomes, single nucleotide polymorphism (SNP) chips of different densities are developed and commercialized. All these advances have enlarged the collection of molecular markers and also shed new light on the genetics of traits of interest in sheep and goats. In this review, we focus on the adoption of GWAS for important traits in sheep and goats, such as horn types, wool, dairy, growth and meat, reproduction and disease types, etc...
June 20, 2017: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/28903898/current-status-of-pathway-analysis-in-genome-wide-association-study
#12
Yu-Yan Wang, Zi-Xing Wang, Yao-da Hu, Lei Wang, Ning Li, Biao Zhang, Wei Han, Jing-Mei Jiang
Since the first publication in 2005, the genome-wide association study (GWAS) strategy has contributed significantly to the understanding of the mechanisms of human genetic diseases. Integrations of statistical methods and systematic biology are important means to explore the GWAS data. Pathway analysis establishes the importance of genetic variants from GWAS and provides insights into their biological significance. It is conducive in correlating the genetic variants, which have only small but interactive changes, to their importance in the biological pathways...
August 20, 2017: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/28902846/downregulation-of-microrna-145-may-contribute-to-liver-fibrosis-in-biliary-atresia-by-targeting-add3
#13
Yongqin Ye, Zhihan Li, Qi Feng, Zimin Chen, Zhouguang Wu, Jianyao Wang, Xiaoshuo Ye, Dahao Zhang, Lei Liu, Wei Gao, Lihui Zhang, Bin Wang
BACKGROUND AND OBJECTIVES: Biliary atresia (BA) is a pediatric liver disease characterized by fibro-obliteration and obstruction of the extrahepatic biliary system, that invariably leads to cirrhosis and even death, if left untreated for extended time. However, its pathology and etiology still remained unknown. In this study, we tested the expression of adducin 3 (ADD3), the gene identified as a susceptibility gene in BA by GWAS, and uncovered its upstream regulatory microRNA in the pathogenesis of BA...
2017: PloS One
https://www.readbyqxmd.com/read/28902444/genomewide-association-studies-of-suicide-attempts-in-us-soldiers
#14
Murray B Stein, Erin B Ware, Colter Mitchell, Chia-Yen Chen, Susan Borja, Tianxi Cai, Catherine L Dempsey, Carol S Fullerton, Joel Gelernter, Steven G Heeringa, Sonia Jain, Ronald C Kessler, James A Naifeh, Matthew K Nock, Stephan Ripke, Xiaoying Sun, Jean C Beckham, Nathan A Kimbrel, Robert J Ursano, Jordan W Smoller
Suicide is a global public health problem with particular resonance for the US military. Genetic risk factors for suicidality are of interest as indicators of susceptibility and potential targets for intervention. We utilized population-based nonclinical cohorts of US military personnel (discovery: N = 473 cases and N = 9778 control subjects; replication: N = 135 cases and N = 6879 control subjects) and a clinical case-control sample of recent suicide attempters (N = 51 cases and N = 112 control subjects) to conduct GWAS of suicide attempts (SA)...
September 13, 2017: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
https://www.readbyqxmd.com/read/28900105/a-genome-wide-association-study-identifies-a-novel-susceptibility-locus-for-the-immunogenicity-of-polyethylene-glycol
#15
Chia-Jung Chang, Chien-Hsiun Chen, Bing-Mae Chen, Yu-Cheng Su, Ying-Ting Chen, Michael S Hershfield, Ming-Ta Michael Lee, Tian-Lu Cheng, Yuan-Tsong Chen, Steve R Roffler, Jer-Yuarn Wu
Conjugation of polyethylene glycol (PEG) to therapeutic molecules can improve bioavailability and therapeutic efficacy. However, some healthy individuals have pre-existing anti-PEG antibodies and certain patients develop anti-PEG antibody during treatment with PEGylated medicines, suggesting that genetics might play a role in PEG immunogenicity. Here we perform genome-wide association studies for anti-PEG IgM and IgG responses in Han Chinese with 177 and 140 individuals, defined as positive for anti-PEG IgM and IgG responses, respectively, and with 492 subjects without either anti-PEG IgM or IgG as controls...
September 12, 2017: Nature Communications
https://www.readbyqxmd.com/read/28899997/improving-disease-prediction-by-incorporating-family-disease-history-in-risk-prediction-models-with-large-scale-genetic-data
#16
Jungsoo Gim, Wonji Kim, Soo Heon Kwak, Hosik Choi, Changyi Park, Kyong Soo Park, Sunghoon Kwon, Taesung Park, Sungho Won
Despite the many successes of genome-wide association studies (GWAS), the known susceptibility variants identified by GWAS have modest effect sizes, leading to notable skepticism about the effectiveness of building a risk prediction model from large-scale genetic data. However, in contrast to genetic variants, the family history of diseases has been largely accepted as an important risk factor in clinical diagnosis and risk prediction. Nevertheless, the complicated structures of the family history of diseases have limited their application in clinical practice...
September 12, 2017: Genetics
https://www.readbyqxmd.com/read/28898263/genome-wide-analysis-of-parent-of-origin-interaction-effects-with-environmental-exposure-pooxe-an-application-to-european-and-asian-cleft-palate-trios
#17
Øystein A Haaland, Astanand Jugessur, Miriam Gjerdevik, Julia Romanowska, Min Shi, Terri H Beaty, Mary L Marazita, Jeffrey C Murray, Allen J Wilcox, Rolv T Lie, Håkon K Gjessing
Cleft palate only is a common birth defect with high heritability. Only a small fraction of this heritability is explained by the genetic variants identified so far, underscoring the need to investigate other disease mechanisms, such as gene-environment (GxE) interactions and parent-of-origin (PoO) effects. Furthermore, PoO effects may vary across exposure levels (PoOxE effects). Such variation is the focus of this study. We upgraded the R-package Haplin to enable direct tests of PoOxE effects at the genome-wide level...
2017: PloS One
https://www.readbyqxmd.com/read/28898252/impact-of-common-genetic-determinants-of-hemoglobin-a1c-on-type-2-diabetes-risk-and-diagnosis-in-ancestrally-diverse-populations-a-transethnic-genome-wide-meta-analysis
#18
Eleanor Wheeler, Aaron Leong, Ching-Ti Liu, Marie-France Hivert, Rona J Strawbridge, Clara Podmore, Man Li, Jie Yao, Xueling Sim, Jaeyoung Hong, Audrey Y Chu, Weihua Zhang, Xu Wang, Peng Chen, Nisa M Maruthur, Bianca C Porneala, Stephen J Sharp, Yucheng Jia, Edmond K Kabagambe, Li-Ching Chang, Wei-Min Chen, Cathy E Elks, Daniel S Evans, Qiao Fan, Franco Giulianini, Min Jin Go, Jouke-Jan Hottenga, Yao Hu, Anne U Jackson, Stavroula Kanoni, Young Jin Kim, Marcus E Kleber, Claes Ladenvall, Cecile Lecoeur, Sing-Hui Lim, Yingchang Lu, Anubha Mahajan, Carola Marzi, Mike A Nalls, Pau Navarro, Ilja M Nolte, Lynda M Rose, Denis V Rybin, Serena Sanna, Yuan Shi, Daniel O Stram, Fumihiko Takeuchi, Shu Pei Tan, Peter J van der Most, Jana V Van Vliet-Ostaptchouk, Andrew Wong, Loic Yengo, Wanting Zhao, Anuj Goel, Maria Teresa Martinez Larrad, Dörte Radke, Perttu Salo, Toshiko Tanaka, Erik P A van Iperen, Goncalo Abecasis, Saima Afaq, Behrooz Z Alizadeh, Alain G Bertoni, Amelie Bonnefond, Yvonne Böttcher, Erwin P Bottinger, Harry Campbell, Olga D Carlson, Chien-Hsiun Chen, Yoon Shin Cho, W Timothy Garvey, Christian Gieger, Mark O Goodarzi, Harald Grallert, Anders Hamsten, Catharina A Hartman, Christian Herder, Chao Agnes Hsiung, Jie Huang, Michiya Igase, Masato Isono, Tomohiro Katsuya, Chiea-Chuen Khor, Wieland Kiess, Katsuhiko Kohara, Peter Kovacs, Juyoung Lee, Wen-Jane Lee, Benjamin Lehne, Huaixing Li, Jianjun Liu, Stephane Lobbens, Jian'an Luan, Valeriya Lyssenko, Thomas Meitinger, Tetsuro Miki, Iva Miljkovic, Sanghoon Moon, Antonella Mulas, Gabriele Müller, Martina Müller-Nurasyid, Ramaiah Nagaraja, Matthias Nauck, James S Pankow, Ozren Polasek, Inga Prokopenko, Paula S Ramos, Laura Rasmussen-Torvik, Wolfgang Rathmann, Stephen S Rich, Neil R Robertson, Michael Roden, Ronan Roussel, Igor Rudan, Robert A Scott, William R Scott, Bengt Sennblad, David S Siscovick, Konstantin Strauch, Liang Sun, Morris Swertz, Salman M Tajuddin, Kent D Taylor, Yik-Ying Teo, Yih Chung Tham, Anke Tönjes, Nicholas J Wareham, Gonneke Willemsen, Tom Wilsgaard, Aroon D Hingorani, Josephine Egan, Luigi Ferrucci, G Kees Hovingh, Antti Jula, Mika Kivimaki, Meena Kumari, Inger Njølstad, Colin N A Palmer, Manuel Serrano Ríos, Michael Stumvoll, Hugh Watkins, Tin Aung, Matthias Blüher, Michael Boehnke, Dorret I Boomsma, Stefan R Bornstein, John C Chambers, Daniel I Chasman, Yii-Der Ida Chen, Yduan-Tsong Chen, Ching-Yu Cheng, Francesco Cucca, Eco J C de Geus, Panos Deloukas, Michele K Evans, Myriam Fornage, Yechiel Friedlander, Philippe Froguel, Leif Groop, Myron D Gross, Tamara B Harris, Caroline Hayward, Chew-Kiat Heng, Erik Ingelsson, Norihiro Kato, Bong-Jo Kim, Woon-Puay Koh, Jaspal S Kooner, Antje Körner, Diana Kuh, Johanna Kuusisto, Markku Laakso, Xu Lin, Yongmei Liu, Ruth J F Loos, Patrik K E Magnusson, Winfried März, Mark I McCarthy, Albertine J Oldehinkel, Ken K Ong, Nancy L Pedersen, Mark A Pereira, Annette Peters, Paul M Ridker, Charumathi Sabanayagam, Michele Sale, Danish Saleheen, Juha Saltevo, Peter Eh Schwarz, Wayne H H Sheu, Harold Snieder, Timothy D Spector, Yasuharu Tabara, Jaakko Tuomilehto, Rob M van Dam, James G Wilson, James F Wilson, Bruce H R Wolffenbuttel, Tien Yin Wong, Jer-Yuarn Wu, Jian-Min Yuan, Alan B Zonderman, Nicole Soranzo, Xiuqing Guo, David J Roberts, Jose C Florez, Robert Sladek, Josée Dupuis, Andrew P Morris, E-Shyong Tai, Elizabeth Selvin, Jerome I Rotter, Claudia Langenberg, Inês Barroso, James B Meigs
BACKGROUND: Glycated hemoglobin (HbA1c) is used to diagnose type 2 diabetes (T2D) and assess glycemic control in patients with diabetes. Previous genome-wide association studies (GWAS) have identified 18 HbA1c-associated genetic variants. These variants proved to be classifiable by their likely biological action as erythrocytic (also associated with erythrocyte traits) or glycemic (associated with other glucose-related traits). In this study, we tested the hypotheses that, in a very large scale GWAS, we would identify more genetic variants associated with HbA1c and that HbA1c variants implicated in erythrocytic biology would affect the diagnostic accuracy of HbA1c...
September 2017: PLoS Medicine
https://www.readbyqxmd.com/read/28893853/a-powerful-framework-for-integrating-eqtl-and-gwas-summary-data
#19
Zhiyuan Xu, Chong Wu, Peng Wei, Wei Pan
Two new gene-based association analysis methods, called PrediXcan and TWAS for GWAS individual-level and summary data respectively, were recently proposed to integrate GWAS with eQTL data, alleviating two common problems in GWAS by boosting statistical power and facilitating biological interpretation of GWAS discoveries. Based on a novel reformulation of PrediXcan and TWAS, we propose a more powerful gene-based association test to integrate single set or multiple sets of eQTL data with GWAS individual-level data or summary statistics...
September 11, 2017: Genetics
https://www.readbyqxmd.com/read/28892062/genome-wide-association-study-identifies-112-new-loci-for-body-mass-index-in-the-japanese-population
#20
Masato Akiyama, Yukinori Okada, Masahiro Kanai, Atsushi Takahashi, Yukihide Momozawa, Masashi Ikeda, Nakao Iwata, Shiro Ikegawa, Makoto Hirata, Koichi Matsuda, Motoki Iwasaki, Taiki Yamaji, Norie Sawada, Tsuyoshi Hachiya, Kozo Tanno, Atsushi Shimizu, Atsushi Hozawa, Naoko Minegishi, Shoichiro Tsugane, Masayuki Yamamoto, Michiaki Kubo, Yoichiro Kamatani
Obesity is a risk factor for a wide variety of health problems. In a genome-wide association study (GWAS) of body mass index (BMI) in Japanese people (n = 173,430), we found 85 loci significantly associated with obesity (P < 5.0 × 10(-8)), of which 51 were previously unknown. We conducted trans-ancestral meta-analyses by integrating these results with the results from a GWAS of Europeans and identified 61 additional new loci. In total, this study identifies 112 novel loci, doubling the number of previously known BMI-associated loci...
September 11, 2017: Nature Genetics
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