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Genome wide association study

Jesse Mez, Jaeyoon Chung, Gyungah Jun, Joshua Kriegel, Alexandra P Bourlas, Richard Sherva, Mark W Logue, Lisa L Barnes, David A Bennett, Joseph D Buxbaum, Goldie S Byrd, Paul K Crane, Nilüfer Ertekin-Taner, Denis Evans, M Daniele Fallin, Tatiana Foroud, Alison Goate, Neill R Graff-Radford, Kathleen S Hall, M Ilyas Kamboh, Walter A Kukull, Eric B Larson, Jennifer J Manly, Jonathan L Haines, Richard Mayeux, Margaret A Pericak-Vance, Gerard D Schellenberg, Kathryn L Lunetta, Lindsay A Farrer
INTRODUCTION: African Americans' (AAs) late-onset Alzheimer's disease (LOAD) genetic risk profile is incompletely understood. Including clinical covariates in genetic analyses using informed conditioning might improve study power. METHODS: We conducted a genome-wide association study (GWAS) in AAs employing informed conditioning in 1825 LOAD cases and 3784 cognitively normal controls. We derived a posterior liability conditioned on age, sex, diabetes status, current smoking status, educational attainment, and affection status, with parameters informed by external prevalence information...
October 19, 2016: Alzheimer's & Dementia: the Journal of the Alzheimer's Association
Riin Tamm, Reedik Mägi, Roman Tremmel, Stefan Winter, Evelin Mihailov, Alenka Smid, Anja Möricke, Kathrin Klein, Martin Schrappe, Martin Stanulla, Richard Houlston, Richard Weinshilboum, Irena Mlinarič Raščan, Andres Metspalu, Lili Milani, Matthias Schwab, Elke Schaeffeler
Thiopurine-related hematotoxicity in paediatric acute lymphoblastic leukemia (ALL) and inflammatory bowel diseases has been linked to genetically defined variability in thiopurine S-methyltransferase (TPMT) activity. While gene testing of TPMT is being clinically implemented, it is unclear if additional genetic variation influences TPMT activity with consequences for thiopurine-related toxicity. To examine this possibility, we performed a genome-wide association study (GWAS) of red blood cell TPMT activity in 844 Estonian individuals and 245 paediatric ALL-cases...
October 22, 2016: Clinical Pharmacology and Therapeutics
Guoqin Yu, Steve Phillips, Mitchell H Gail, James J Goedert, Michael Humphrys, Jacques Ravel, Yanfang Ren, Neil E Caporaso
BACKGROUND: The human microbiota is postulated to affect cancer risk, but collecting microbiota specimens with prospective follow-up for diseases will take time. Buccal cell samples have been obtained from mouthwash for the study of human genomic DNA in many cohort studies. Here we evaluate the feasibility of using buccal cell samples to examine associations of human microbiota and disease risk. METHODS: We obtained buccal cells from mouthwash in 41 healthy participants using a protocol that is widely employed to obtain buccal cells for the study of human DNA...
October 21, 2016: Cancer Epidemiology, Biomarkers & Prevention
Laura M G Meems, Hasan Mahmud, Hendrik Buikema, Jorg Tost, Sven Michel, Janny Takens, Rikst N Verkaik-Schakel, Inge Vreeswijk-Baudoin, Irene V Mateo-Leach, Torsten Plosch, Rudolf A de Boer
Vitamin D deficiency is one of the most common nutritional deficiencies worldwide. Maternal vitamin D deficiency is associated with increased susceptibility to hypertension in offspring but the reasons for this remain unknown. The aim of this study was to determine if parental vitamin D deficiency leads to altered DNA methylation in offspring that may relate to hypertension. Male and female Sprague-Dawley rats were fed a standard or vitamin D depleted diet. After 10 weeks, non-sibling rats were mated. The conceived pups received standard chow...
October 21, 2016: American Journal of Physiology. Heart and Circulatory Physiology
Paola G Ferrario, Inke R König
Genome-wide association studies are moving to genome-wide interaction studies, as the genetic background of many diseases appears to be more complex than previously supposed. Thus, many statistical approaches have been proposed to detect gene-gene (GxG) interactions, among them numerous information theory-based methods, inspired by the concept of entropy. These are suggested as particularly powerful and, because of their nonlinearity, as better able to capture nonlinear relationships between genetic variants and/or variables...
October 21, 2016: Briefings in Bioinformatics
Ryo Nakao, Keita Matsuno, Yongjin Qiu, Junki Maruyama, Nao Eguchi, Naganori Nao, Masahiro Kajihara, Kentaro Yoshii, Hirofumi Sawa, Ayato Takada, Chihiro Sugimoto
Ticks harbour various microorganisms, some of which act as pathogens of humans and animals. The recent advancement of genome sequencing technologies revealed that a wide range of previously unrecognised microorganisms exist in ticks. Continuous cell lines established from ticks could play a key role in the isolation of such microorganisms; however, tick cells themselves have been known to harbour symbiotic microorganisms. The present study aimed to characterise putative RNA viral sequences detected in the culture supernatant of one of the most frequently used tick cell lines, ISE6, which was derived from embryos of the blacklegged tick Ixodes scapularis...
October 15, 2016: Ticks and Tick-borne Diseases
Franziska Hopfner, Dietrich Haubenberger, Wendy R Galpern, Katrina Gwinn, Ashlee Van't Veer, Samantha White, Kailash Bhatia, Charles H Adler, David Eidelberg, William Ondo, Glenn T Stebbins, Caroline M Tanner, Rick C Helmich, Fred A Lenz, Roy V Sillitoe, David Vaillancourt, Jerrold L Vitek, Elan D Louis, Holly A Shill, Matthew P Frosch, Tatiana Foroud, Gregor Kuhlenbäumer, Andrew Singleton, Claudia M Testa, Mark Hallett, Rodger Elble, Günther Deuschl
Essential tremor (ET) is a common cause of significant disability, but its etiologies and pathogenesis are poorly understood. Research has been hampered by the variable definition of ET and by non-standardized research approaches. The National Institute of Neurological Disorders and Stroke (USA) invited experts in ET and related fields to discuss current knowledge, controversies, and gaps in our understanding of ET and to develop recommendations for future research. Discussion focused on phenomenology and phenotypes, therapies and clinical trials, pathophysiology, pathology, and genetics...
October 4, 2016: Parkinsonism & related Disorders
Yanping Wang, Jin Li, Thomas F Kolon, Alicia Olivant Fisher, T Ernesto Figueroa, Ahmad H BaniHani, Jennifer A Hagerty, Ricardo Gonzalez, Paul H Noh, Rosetta M Chiavacci, Kisha R Harden, Debra J Abrams, Deborah Stabley, Cecilia E Kim, Katia Sol-Church, Hakon Hakonarson, Marcella Devoto, Julia Spencer Barthold
BACKGROUND: Copy number variation (CNV) is a potential contributing factor to many genetic diseases. Here we investigated the potential association of CNV with nonsyndromic cryptorchidism, the most common male congenital genitourinary defect, in a Caucasian population. METHODS: Genome wide genotyping were performed in 559 cases and 1772 controls (Group 1) using Illumina HumanHap550 v1, HumanHap550 v3 or Human610-Quad platforms and in 353 cases and 1149 controls (Group 2) using the Illumina Human OmniExpress 12v1 or Human OmniExpress 12v1-1...
October 21, 2016: BMC Urology
Lei Shi, Wenfa Zhang, Fagui Zou, Lihua Mei, Gang Wu, Yong Teng
BACKGROUND: Hepatocellular carcinoma (HCC) has very high prevalence and associated-mortality. However, targeted therapies that are currently used in clinical practice for HCC have certain limitations, in part because of the lack of reliable and clinically applicable biomarkers that can be used for diagnosis and prognosis assessments and for the surveillance of treatment effectiveness. METHODS: Meta-analysis was used to analyze the integrated microarray data for global identification of a set of robust biomarkers for HCC...
October 21, 2016: BMC Cancer
Hongwu Wang, Kun Li, Xiaojiao Hu, Zhifang Liu, Yujin Wu, Changling Huang
BACKGROUND: Plant digestibility of silage maize (Zea mays L.) has a large influence on nutrition intake for animal feeding. Improving forage quality will enhance the utilization efficiency and feeding value of forage maize. Dissecting the genetic basis of forage quality will improve our understanding of the complex nature of cell wall biosynthesis and degradation, which is also helpful for breeding good quality silage maize. RESULTS: Acid detergent fiber (ADF), neutral detergent fiber (NDF) and in vitro dry matter digestibility (IVDMD) of stalk were evaluated in a diverse maize population, which is comprised of 368 inbred lines and planted across seven environments...
October 21, 2016: BMC Plant Biology
Chunwen Tan, Wangxiong Hu, Yanqin Huang, Jiaojiao Zhou, Shu Zheng
BACKGROUND: Recent genome-wide association studies (GWAS) identified eighteen single-nucleotide polymorphisms (SNPs) to be significantly associated with the risk of colorectal cancer (CRC). However, overall results of the following replications are inconsistent and little is known about whether these associations also exit in colorectal adenomas (CRA). METHODS: The SNP genotyping was performed using a Sequenom MassARRAY to investigate the association of these eighteen SNPs with colorectal neoplasm in a case-control study consisted of 1049 colorectal cancers, 283 adenomas, and 1030 controls...
October 19, 2016: Oncotarget
Si Chen, Xiaoting Wen, Jing Li, Yuan Li, Liubing Li, Xinping Tian, Hui Yuan, Fengchun Zhang, Yongzhe Li
Takayasu arteritis (TA) is a chronic large-vessel vasculitis of unclear pathogenesis. A recent genome-wide association study (GWAS) has revealed that the FCGR2A/FCGR3A, EEFSEC, RPS9/LILRB3, RIPPLY2 and MLX genes confer susceptibility to TA. We investigated the linkage between presumptive TA-related genes (FCGR2A/FCGR3A, EEFSEC, RPS9/LILRB3, RIPPLY2 and MLX) and TA in the Han Chinese population. We performed a large case-control multi-center study of 412 Han Chinese TA patients and 597 ethnically matched healthy controls...
October 18, 2016: Oncotarget
Malik Nassan, Qingqin Li, Paul E Croarkin, Wenan Chen, Colin L Colby, Marin Veldic, Susan L McElroy, Gregory D Jenkins, Euijung Ryu, Julie M Cunningham, Marion Leboyer, Mark A Frye, Joanna M Biernacka
BACKGROUND: Although multiple genes have been implicated in bipolar disorder (BD), they explain only a small proportion of its heritability. Identifying additional BD risk variants may be impaired by phenotypic heterogeneity, which is usually not taken into account in genome-wide association studies (GWAS). BD with early age at onset is a more homogeneous familial form of the disorder associated with greater symptom severity. METHODS: We conducted a GWAS of early-onset BD (onset of mania/hypomania ≤19 years old) in a discovery sample of 419 cases and 1034 controls and a replication sample of 181 cases and 777 controls...
September 30, 2016: Journal of Affective Disorders
Chloe Y Y Cheung, Elaine Y L Hui, Chi-Ho Lee, Kelvin H M Kwok, Rita A Gangwani, Kenneth K W Li, Jeffrey C W Chan, Yu-Cho Woo, Wing-Sun Chow, Michele M A Yuen, Rachel L C Wong, Carol H Y Fong, Aimin Xu, David S H Wong, Pak-Chung Sham, Karen S L Lam
Purpose: Diabetic retinopathy (DR) is a common microvascular complication of type 2 diabetes (T2DM). Genome-wide association studies (GWAS) had identified novel DR-susceptibility genetic variants in various populations. We examined the associations of these DR-associated single nucleotide polymorphisms (SNPs) with severe DR in a Chinese T2DM cohort. Methods: Cross-sectional case-control studies on sight-threatening DR (STDR) and proliferative DR (PDR) were performed...
October 1, 2016: Investigative Ophthalmology & Visual Science
Ishfaq A Sheikh, Ejaz Ahmad, Mohammad S Jamal, Mohd Rehan, Mourad Assidi, Iftikhar A Tayubi, Samera F AlBasri, Osama S Bajouh, Rola F Turki, Adel M Abuzenadah, Ghazi A Damanhouri, Mohd A Beg, Mohammed Al-Qahtani
BACKGROUND: Preterm birth (PTB), birth at <37 weeks of gestation, is a significant global public health problem. World-wide, about 15 million babies are born preterm each year resulting in more than a million deaths of children. Preterm neonates are more prone to problems and need intensive care hospitalization. Health issues may persist through early adulthood and even be carried on to the next generation. Majority (70 %) of PTBs are spontaneous with about a half without any apparent cause and the other half associated with a number of risk factors...
October 17, 2016: BMC Genomics
Sajjad Karim, Hend Fakhri NourEldin, Heba Abusamra, Nada Salem, Elham Alhathli, Joel Dudley, Max Sanderford, Laura B Scheinfeldt, Sudhir Kumar
BACKGROUND: Genome-wide association studies (GWAS) have become a mainstay of biological research concerned with discovering genetic variation linked to phenotypic traits and diseases. Both discrete and continuous traits can be analyzed in GWAS to discover associations between single nucleotide polymorphisms (SNPs) and traits of interest. Associations are typically determined by estimating the significance of the statistical relationship between genetic loci and the given trait. However, the prioritization of bona fide, reproducible genetic associations from GWAS results remains a central challenge in identifying genomic loci underlying common complex diseases...
October 17, 2016: BMC Genomics
Mamdooh Abdullah Gari, Mohammed AlKaff, Haneen S Alsehli, Ashraf Dallol, Abdullah Gari, Muhammad Abu-Elmagd, Roaa Kadam, Mohammed F Abuzinadah, Mazin Gari, Adel M Abuzenadah, Kalamegam Gauthaman, Heba Alkhatabi, Mohammed M Abbas
BACKGROUND: Osteoarthritis (OA) is a progressive joint disease characterized by gradual degradation of extracellular matrix (ECM) components in the cartilage and bone. The ECM of cartilage is a highly specified structure that is mainly composed of type II collagen and provides tensile strength to the tissue via aggrecan and proteoglycans. However, changes in the ECM composition and structure can lead to loss of collagen type II and network integrity. Several risk factors have been correlated with OA including age, genetic predisposition, hereditary factors, obesity, mechanical injuries, and joint trauma...
October 10, 2016: BMC Medical Genetics
Juan L Reig-Valiente, Juan Viruel, Ester Sales, Luis Marqués, Javier Terol, Marta Gut, Sophia Derdak, Manuel Talón, Concha Domingo
BACKGROUND: After its domestication, rice cultivation expanded from tropical regions towards northern latitudes with temperate climate in a progressive process to overcome limiting photoperiod and temperature conditions. This process has originated a wide range of diversity that can be regarded as a valuable resource for crop improvement. In general, current rice breeding programs have to deal with a lack of both germplasm accessions specifically adapted to local agro-environmental conditions and adapted donors carrying desired agronomical traits...
December 2016: Rice
Guiyou Liu, Fang Zhang, Yang Hu, Yongshuai Jiang, Zhongying Gong, Shoufeng Liu, Xiuju Chen, Qinghua Jiang, Junwei Hao
A recent genome-wide association study reported a significant association between rs9828519 (G) and nonresponsiveness to interferon-beta (IFN-β) treatment and dysregulation of SLC9A9 expression in multiple sclerosis (MS) cases. We hypothesize that disease-relevant tissues are necessary to detect the effects of rs9828519-tagged SNPs on SLC9A9 expression. Here, we investigated whether SLC9A9 expression is regulated by rs9828519-tagged SNPs in human brain tissue. We used HaploReg to identify the proxy SNPs of the rs9828519 variant based on linkage disequilibrium information from the 1000 Genomes Project...
October 20, 2016: Molecular Neurobiology
Shouchun Yan, Ridong Xia, Tianbo Jin, Hui Ren, Hua Yang, Jing Li, Mengdan Yan, Yuanyuan Zhu, Mingwei Chen
RTEL1 (regulator of telomere elongation helicase 1; OMIM 608833) gene polymorphisms were linked to lung cancer (LC) susceptibility in a cancer genome-wide association study (GWAS) Here, we assessed whether seven previously reported RTEL1 polymorphisms influenced LC risk in Han Chinese population. All study samples (554 LC cases and 696 cancer-free controls) were collected from the Affiliated Hospital of Xizang Minzu University in China. We assessed associations between SNPs and LC risk using various several genetic models (codominant, dominant, recessive, overdominant, and additive)...
September 28, 2016: Oncotarget
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