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Julian Hecker, Xin Xu, F William Townes, Heide Loehlein Fier, Chris Corcoran, Nan Laird, Christoph Lange
For family-based association studies, Horvath et al. proposed an algorithm for the association analysis between haplotypes and arbitrary phenotypes when the phase of the haplotypes is unknown, that is, genotype data is given. Their approach to haplotype analysis maintains the original features of the TDT/FBAT-approach, that is, complete robustness against genetic confounding and misspecification of the phenotype. The algorithm has been implemented in the FBAT and PBAT software package and has been used in numerous substantive manuscripts...
November 21, 2017: Genetic Epidemiology
So Young Yang, Soon Ae Kim, Gang Min Hur, Mira Park, Jong-Eun Park, Hee Jeong Yoo
BACKGROUND: Arginine vasopressin has been shown to affect social and emotional behaviors, which is mediated by the arginine vasopressin receptor (AVPR1A). Genetic polymorphisms in the AVPR1A promoter region have been identified to be associated with susceptibility to social deficits in autism spectrum disorder (ASD). We hypothesize that alleles of polymorphisms in the promoter region of AVPR1A may differentially interact with certain transcriptional factors, which in turn affect quantitative traits, such as sociality, in children with autism...
2017: Molecular Autism
Shuo Wang, Jieyun Song, Yide Yang, Nitesh V Chawla, Jun Ma, Haijun Wang
BACKGROUND: Recent studies indicated that eating behaviors are under genetic influence, and the melanocortin 4 receptor (MC4R) gene polymorphisms can affect the total energy intake and the consumption of fat, protein and carbohydrates. Our study aims at investigating the association of the MC4R polymorphism with appetite and food intake among Chinese children. METHODS: A family-based association study was conducted among 151 Chinese trios whose offsprings were overweight/obese children aged 9-15 years...
2017: PloS One
William A de Glanville, Raquel Conde-Álvarez, Ignacio Moriyón, John Njeru, Ramón Díaz, Elizabeth A J Cook, Matilda Morin, Barend M de C Bronsvoort, Lian F Thomas, Samuel Kariuki, Eric M Fèvre
Human brucellosis is considered to be an important but typically under-diagnosed cause of febrile illness in many low and middle-income countries. In Kenya, and throughout East Africa, laboratory diagnosis for the disease is based primarily on the febrile antigen Brucella agglutination test (FBAT), yet few studies of the diagnostic accuracy of this test exist. Assessment of the performance of the FBAT is essential for its appropriate clinical use, as well as for evaluating surveillance data reported by public health systems...
April 2017: PLoS Neglected Tropical Diseases
Marcus Sokolowski, Jerzy Wasserman, Danuta Wasserman
Suicidal behavior (SB) has a complex etiology involving genes and environment. One of the genetic components in SB could be copy number variations (CNVs), as CNVs are implicated in neurodevelopmental disorders. However, a recently published genome-wide and case-control study did not observe any significant role of CNVs in SB. Here we complemented these initial observations by instead using a family-based trio-sample that is robust to control biases, having severe suicide attempt (SA) in offspring as main outcome (n = 660 trios)...
2016: PloS One
Sunday M Francis, Soo-Jeong Kim, Emily Kistner-Griffin, Stephen Guter, Edwin H Cook, Suma Jacob
Background: There are limited treatments available for autism spectrum disorder (ASD). Studies have reported significant associations between the receptor genes of oxytocin (OT) and vasopressin (AVP) and ASD diagnosis, as well as ASD-related phenotypes. Researchers have also found the manipulation of these systems affects social and repetitive behaviors, core characteristics of ASD. Consequently, research involving the oxytocin/vasopressin pathways as intervention targets has increased. Therefore, further examination into the relationship between these neuropeptides and ASD was undertaken...
2016: Frontiers in Neuroscience
Whitney E Melroy-Greif, Csaba Vadasz, Helen M Kamens, Matthew B McQueen, Robin P Corley, Michael C Stallings, Christian J Hopfer, Kenneth S Krauter, Sandra A Brown, John K Hewitt, Marissa A Ehringer
Recent work using a mouse model has identified the glutamate metabotropic receptor 7 (Grm7) gene as a strong candidate gene for alcohol consumption. Although there has been some work examining the effect of human glutamate metabotropic receptor 7 (GRM7) polymorphisms on human substance use disorders, the majority of the work has focused on other psychiatric disorders such as ADHD, major depressive disorder, schizophrenia, bipolar disorder, panic disorder, and autism spectrum disorders. The current study aimed to evaluate evidence for association between GRM7 and alcohol behaviors in humans using a single nucleotide polymorphism (SNP) approach, as well as a gene-based approach...
September 2016: Alcohol
Dan Holmberg, Karin Ruikka, Petter Lindgren, Mats Eliasson, Sofia Mayans
BACKGROUND: T1D and AITD are autoimmune disorders commonly occurring in the same family and even in the same individual. The genetic contribution to these disorders is complex making uncovering of susceptibility genes very challenging. The general aim of this study was to identify loci and genes contributing to T1D/AITD susceptibility. Our strategy was to perform linkage and association studies in the relatively genetically homogenous population of northern Sweden. We performed a GWLS to find genomic regions linked to T1D/AITD in families from northern Sweden and we performed an association study in the families to test for association between T1D/AITD and variants in previously published candidate genes as well as a novel candidate gene, CD247...
October 4, 2016: BMC Medical Genetics
W Xu, W T Han, Y P Lu, W H Feng, M Dai
The aim of this study was to determine the association between two SNPs (rs2235371 and rs2013162) in the interferon regulatory factor 6 (IRF6) gene and non-syndromic cleft palate (NSCP) in northeast China. We genotyped these two SNPs in 104 NSCP cases, as well as in 178 parents and 300 controls. Case-control and case-parent analyses were performed using χ2 tests and family-based association tests (FBAT). Results indicated that there were significant differences in both genotypic and allelic distributions between patients and controls at rs2235371 and rs2013162 in the IRF6 gene...
September 2, 2016: Genetics and Molecular Research: GMR
Ke-Sheng Wang, Xuefeng Liu, Changchun Xie, Ying Liu, Chun Xu
Non-parametric methods such as Wilcoxon test have the advantages of no assumptions for the underlying survival distributions. Alzheimer's disease (AD) is a chronic neurodegenerative disease while the ectopic P-granules autophagy protein 5 homolog (EPG5 gene) is highly expressed in human brain and may implicate in the pathogenesis of neurodegenerative disorders. The present study explored the associations of 26 single-nucleotide polymorphisms (SNPs) in the EPG5 gene with the age at onset (AAO) of AD using a family-based association test (FBAT)-Wilcoxon statistic in a family-based study...
December 2016: Journal of Molecular Neuroscience: MN
Sandra Hernández, Beatriz Camarena, Laura González, Alejandro Caballero, Griselda Flores, Alejandro Aguilar
OBJECTIVE: To explore the association of three polymorphisms of the serotonin receptor 1Dβ gene (HTR1B) in the etiology of eating disorders and their relationship with clinical characteristics. METHODS: We analyzed the G861C, A-161T, and A1180G polymorphisms of the HTR1B gene through a family-based association test (FBAT) in 245 nuclear families. The sample was stratified into anorexia nervosa (AN) spectrum and bulimia nervosa (BN) spectrum. In addition, we performed a quantitative FBAT analysis of anxiety severity, depression severity, and Yale-Brown-Cornell Eating Disorders Scale (YBC-EDS) in the AN and BN-spectrum groups...
July 2016: Revista Brasileira de Psiquiatria
Monika Stoll, Frank Rühle, Anika Witten, Andrei Barysenka, Astrid Arning, Christina Strauss, Ulrike Nowak-Göttl
BACKGROUND: Recently, we reported a gene network of ADAMTS (A Disintegrin-like and Metalloprotease with Thrombospondin motifs) genes as central component of the genetic risk contributing to pediatric stroke. ADAMTS13 is a prime example for such a key component as it cleaves von Willebrand factor multimers, reduces platelet adhesion and aggregation, and downregulates thrombus formation and inflammation. METHODS AND RESULTS: We characterized the genetic architecture of ADAMTS13 through targeted next-generation sequencing of 48 affected children and their unaffected siblings and identified in total 241 variants (single nucleotide polymorphisms or insertions/deletions) in the ADAMTS13 gene...
August 2016: Circulation. Cardiovascular Genetics
Sunday M Francis, Emily Kistner-Griffin, Zhongyu Yan, Stephen Guter, Edwin H Cook, Suma Jacob
BACKGROUND: There has been increasing interest in oxytocin (peptide: OT, gene: OXT) as a treatment pathway for neurodevelopmental disorders such as Autism Spectrum Disorder (ASD). Neurodevelopmental disorders affect functional, social, and intellectual abilities. With advances in molecular biology, research has connected multiple gene regions to the clinical presentation of ASD. Studies have also shown that the neuropeptide hormones OT and arginine vasopressin (AVP) influence mammalian social and territorial behaviors and may have treatment potential for neurodevelopmental disorders...
2016: Frontiers in Neuroscience
Varsha Dhankani, David L Gibbs, Theo Knijnenburg, Roger Kramer, Joseph Vockley, John Niederhuber, Ilya Shmulevich, Brady Bernard
Most currently available family based association tests are designed to account only for nuclear families with complete genotypes for parents as well as offspring. Due to the availability of increasingly less expensive generation of whole genome sequencing information, genetic studies are able to collect data for more families and from large family cohorts with the goal of improving statistical power. However, due to missing genotypes, many families are not included in the family based association tests, negating the benefits of large scale sequencing data...
2016: Frontiers in Genetics
Fang-yu Lin, Zhu Huang, Ning Lu, Wei Chen, Hui Fang, Wei Han
Functional studies have suggested the important role of early growth response 1 (EGR1) and Laminin α2-chain (LAMA2) in human eye development. Genetic studies have reported a significant association of the single nucleotide polymorphism (SNP) in the LAMA2 gene with myopia. This study aimed to evaluate the association of the tagging SNPs (tSNPs) in the EGR1 and LAMA2 genes with high myopia in two independent Han Chinese populations. Four tSNPs (rs11743810 in the EGR1 gene; rs2571575, rs9321170, and rs1889891 in the LAMA2 gene) were selected, according to the HapMap database (http://hapmap...
March 2016: Journal of Zhejiang University. Science. B
Lawrence Shih-Hsin Wu, Chau-Shoun Lee, Tzu-Ya Weng, Kathy Hsiao-Tsz Wang, Andrew Tai-Ann Cheng
BACKGROUND: The roles of GABA, serotonin, dopamine, and alcohol metabolism pathways in alcohol dependence (AD) are evident from animal models and human studies. Aims of this study were to investigate associations between genes in the 4 pathways and AD. METHODS: Male subjects from 2 independent samples of Taiwanese Han descent, a family sample of 179 trios and a case-control sample of 262 AD cases and 273 normal controls, were included in this study. The Schedules for Clinical Assessment in Neuropsychiatry was used for phenotype assessment of AD...
February 2016: Alcoholism, Clinical and Experimental Research
Marie-Hélène Dizier, Rachel Nadif, Patricia Margaritte-Jeannin, Sheila J Barton, Chloé Sarnowski, Valérie Gagné-Ouellet, Myriam Brossard, Nolwenn Lavielle, Jocelyne Just, Mark Lathrop, John W Holloway, Catherine Laprise, Emmanuelle Bouzigon, Florence Demenais
A previous genome-wide linkage scan of bronchial hyperresponsiveness (BHR) in the French Epidemiological study on the Genetics and Environment of Asthma (EGEA) families, performed in the presence of a gene×early-life environmental tobacco smoke (ETS) exposure interaction, showed the strongest interaction in the 17p11 region where linkage was detected only among unexposed siblings. Our goal was to conduct fine-scale mapping of 17p11 to identify single nucleotide polymorphisms (SNPs) interacting with ETS that influence BHR...
April 2016: European Respiratory Journal: Official Journal of the European Society for Clinical Respiratory Physiology
Yiqun Wu, Shuai Li, Kuo Liu, Xun Tang, Kai Fang, Na Li, Jin Li, Tao Wu, Dafang Chen, Yonghua Hu
OBJECTIVE: To investigate the association between polymorphism of leukotriene A4 hydrolase (LTA4H) gene among ischemic stroke patients and the related subtypes in the discordant sib pairs. METHODS: Families including ischemic stroke patients and their siblings were recruited. Four single nucleotide polymorphisms (SNPs) of LTA4H as rs2072512, rs2540489, rs2540500 and rs6538697 were selected. Generalized estimating equation (GEE) was used to adjust for in-family correlation in the analysis of discordant sib pairs...
August 2015: Zhonghua Liu Xing Bing Xue za Zhi, Zhonghua Liuxingbingxue Zazhi
Tanushree Haldar, Saurabh Ghosh
Clinical end-point traits are usually governed by quantitative precursors. Hence, there is active research interest in developing statistical methods for association mapping of quantitative traits. Unlike population-based tests for association, family-based tests for transmission disequilibrium are protected against population stratification. In this study, we propose a logistic regression model to test the association for quantitative traits based on a trio design. We show that the method can be viewed as a direct extension of the classical transmission diequilibrium test for binary traits to quantitative traits...
December 2015: Journal of Genetics
Jinfeng Tian, Yuan Wei, Liang Wang, Jinzhen Guo, Qian Zhou, Wenli Zhu
OBJECTIVE: To explore the relationship between polymorphism of interferon regulatory factor 6 (IRF6) gene rs642961 locus and nonsyndromic cleft lip with or without cleft palate (NSCL ± P). METHODS: There were 88 NSCL ± P nuclear families and 116 healthy people as control recruited from Chinese northern area. The polymorphism of IRF6 rs642961 locus was detected by tetra-primer amplification refractory mutation system-polymerase chain reaction (tetra-primer ARMS-PCR)...
July 2015: Wei Sheng Yan Jiu, Journal of Hygiene Research
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