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Statistical genetics

Laurel Fogarty, Joe Yuichiro Wakano, Marcus W Feldman, Kenichi Aoki
The forces driving cultural accumulation in human populations, both modern and ancient, are hotly debated. Did genetic, demographic, or cognitive features of behaviorally modern humans (as opposed to, say, early modern humans or Neanderthals) allow culture to accumulate to its current, unprecedented levels of complexity? Theoretical explanations for patterns of accumulation often invoke demographic factors such as population size or density, whereas statistical analyses of variation in cultural complexity often point to the importance of environmental factors such as food stability, in determining cultural complexity...
October 25, 2016: Human Nature: An Interdisciplinary Biosocial Perspective
Can Cai, Rong Xiao, Nicholas Van Halm-Lutterodt, Jie Zhen, Xiaochen Huang, Yao Xu, Shuying Chen, Linhong Yuan
BACKGROUND/AIM: Studies have indicated a relationship between either gene polymorphism or in vivo B vitamins' nutritional status with cognition in the elderly. However, the combined effects of MTHFR and SLC19A1gene polymorphism with serum folate and vitamin B12 levels on cognition in Chinese adult population remain unclear. METHODS: Demographic information of 426 Chinese adults aged from 55 to 90 were collected by a well designed self-administered questionnaire...
October 24, 2016: Nutrients
B Knegt, T Potter, N A Pearson, Y Sato, H Staudacher, B C J Schimmel, E T Kiers, M Egas
When two related species interbreed, their hybrid offspring frequently suffer from reduced fitness. The genetics of hybrid incompatibility are described by the Bateson-Dobzhansky-Muller (BDM) model, where fitness is reduced by epistatic interactions between alleles of heterospecific origin. Unfortunately, most empirical evidence for the BDM model comes from a few well-studied model organisms, restricting our genetic understanding of hybrid incompatibilities to limited taxa. These systems are predominantly diploid and incompatibility is often complete, which complicates the detection of recessive allelic interactions and excludes the possibility to study viable or intermediate stages...
October 26, 2016: Heredity
Martina Landini, Ivan Merelli, M Elisabetta Raggi, Nadia Galluccio, Francesca Ciceri, Arianna Bonfanti, Serena Camposeo, Angelo Massagli, Laura Villa, Erika Salvi, Daniele Cusi, Massimo Molteni, Luciano Milanesi, Anna Marabotti, Alessandra Mezzelani
Since involved in synaptic transmission and located on X-chromosome, neuroligins 3 and 4X have been studied as good positional and functional candidate genes for autism spectrum disorder pathogenesis, although contradictory results have been reported. Here, we performed a case-control study to assess the association between noncoding genetic variants in NLGN3 and NLGN4X genes and autism, in an Italian cohort of 202 autistic children analyzed by high-resolution melting. The results were first compared with data from 379 European healthy controls (1000 Genomes Project) and then with those from 1061 Italian controls genotyped by Illumina single nucleotide polymorphism (SNP) array 1M-duo...
October 22, 2016: International Journal of Molecular Sciences
Carlos Iribarren, Meng Lu, Eric Jorgenson, Manuel Martinez, Carla Lluís-Ganella, Isaac Subirana, Eduardo Salas, Roberto Elosua
BACKGROUND: -We evaluated whether including multi-locus genetic risk scores (GRS's) into the Framingham Risk Equation improves the predictive capacity, discrimination and reclassification of asymptomatic individuals with respect to coronary heart disease (CHD) risk. METHODS AND RESULTS: -We performed a cohort study among 51,954 European-ancestry members of a Northern California integrated health care system (67% female; mean age 59) free of CHD at baseline (2007-08)...
October 25, 2016: Circulation. Cardiovascular Genetics
Anna M Dahlin, Carl Wibom, Soma Ghasimi, Thomas Brännström, Ulrika Andersson, Beatrice Melin
Genome-wide association studies and candidate gene studies have identified several genetic variants that increase glioma risk. The majority of these variants are non-coding and the mechanisms behind the increased risk in carriers are not known. In this study, we hypothesize that some of the established glioma risk variants induce aberrant DNA methylation in the developing tumor, either locally (gene-specific) or globally (genome-wide). In a pilot data set including 77 glioma patients, we used Illumina beadchip technology to analyze genetic variants in blood and DNA methylation in matched tumor samples...
2016: PloS One
A R Docherty, A Moscati, R Peterson, A C Edwards, D E Adkins, S A Bacanu, T B Bigdeli, B T Webb, J Flint, K S Kendler
Biometrical genetic studies suggest that the personality dimensions, including neuroticism, are moderately heritable (~0.4 to 0.6). Quantitative analyses that aggregate the effects of many common variants have recently further informed genetic research on European samples. However, there has been limited research to date on non-European populations. This study examined the personality dimensions in a large sample of Han Chinese descent (N=10 064) from the China, Oxford, and VCU Experimental Research on Genetic Epidemiology study, aimed at identifying genetic risk factors for recurrent major depression among a rigorously ascertained cohort...
October 25, 2016: Translational Psychiatry
María Belén Cerliani, Walter Pavicic, Juan Antonio Gili, Graciela Klein, Silvia Saba, Silvina Richard
AIM: To analyze the association between oncohematological diseases and GSTT1/GSTM1/CYP1A1 polymorphisms, dietary habits and smoking, in an argentine hospital-based case-control study. METHODS: This hospital-based case-control study involved 125 patients with oncohematological diseases and 310 control subjects. A questionnaire was used to obtain sociodemographic data and information about habits. Blood samples were collected, and DNA was extracted using salting out methods...
October 10, 2016: World Journal of Clinical Oncology
John E Pool, Dylan T Braun, Justin B Lack
Drosophila melanogaster originated in tropical Africa before expanding into strikingly different temperate climates in Eurasia and beyond. Here, we find elevated cold tolerance in three distinct geographic regions: beyond the well-studied non-African case, we show that populations from the highlands of Ethiopia and South Africa have significantly increased cold tolerance as well. We observe greater cold tolerance in outbred versus inbred flies, but only in populations with higher inversion frequencies. Each cold-adapted population shows lower inversion frequencies than a closely-related warm-adapted population, suggesting that inversion frequencies may decrease with altitude in addition to latitude...
October 24, 2016: Molecular Biology and Evolution
Annie Gravel, Isabelle Dubuc, Angela Brooks-Wilson, Kristan J Aronson, Jacques Simard, Hector Velasquez-Garcia, John J Spinelli, Louis Flamand
Background Inherited chromosomally-integrated human herpesvirus 6 (iciHHV-6) is a condition observed in approximately 1% of the population. Whether such a genetic alteration predisposes to cancer development in currently unknown. Two studies were conducted to determine whether iciHHV-6 is associated with cancer development. Methods First, a screen of 19,597 people from the province of Quebec was conducted. A replication test, using data from a population-based case-control study of 1090 women with incident breast cancer and 1053 controls from British Columbia and Ontario was conducted...
October 24, 2016: Cancer Epidemiology, Biomarkers & Prevention
Natalie S Ryan, Jennifer M Nicholas, Philip S J Weston, Yuying Liang, Tammaryn Lashley, Rita Guerreiro, Gary Adamson, Janna Kenny, Jon Beck, Lucia Chavez-Gutierrez, Bart de Strooper, Tamas Revesz, Janice Holton, Simon Mead, Martin N Rossor, Nick C Fox
BACKGROUND: The causes of phenotypic heterogeneity in familial Alzheimer's disease with autosomal dominant inheritance are not well understood. We aimed to characterise clinical phenotypes and genetic associations with APP and PSEN1 mutations in symptomatic autosomal dominant familial Alzheimer's disease (ADAD). METHODS: We retrospectively analysed genotypic and phenotypic data (age at symptom onset, initial cognitive or behavioural symptoms, and presence of myoclonus, seizures, pyramidal signs, extrapyramidal signs, and cerebellar signs) from all individuals with ADAD due to APP or PSEN1 mutations seen at the Dementia Research Centre in London, UK...
October 21, 2016: Lancet Neurology
Amy B Wilfert, Katherine R Chao, Madhurima Kaushal, Sanjay Jain, Sebastian Zöllner, David R Adams, Donald F Conrad
Standard techniques from genetic epidemiology are ill-suited to formally assess the significance of variants identified from a single case. We developed a statistical inference framework for identifying unusual functional variation from a single exome or genome, what we refer to as the 'n-of-one' problem. Using this approach we assessed our ability to identify the causal genotypes in over 5 million simulated cases of Mendelian disease, identifying 39% of disease genotypes as the most damaging unit in a typical exome background...
October 24, 2016: Nature Genetics
Jinhu Huang, Jiale Ma, Kexin Shang, Xiao Hu, Yuan Liang, Daiwei Li, Zuowei Wu, Lei Dai, Li Chen, Liping Wang
Streptococcus suis is a previously neglected, newly emerging multidrug-resistant zoonotic pathogen. Mobile genetic elements (MGEs) play a key role in intra- and interspecies horizontal transfer of antimicrobial resistance (AMR) determinants. Although, previous studies showed the presence of several MGEs, a comprehensive analysis of AMR-associated mobilome as well as their interaction and evolution has not been performed. In this study, we presented the AMR-associated mobilome and their insertion hotspots in S...
2016: Frontiers in Cellular and Infection Microbiology
Filip Bielejec, Guy Baele, Allen G Rodrigo, Marc A Suchard, Philippe Lemey
Various factors determine the rate at which mutations are generated and fixed in viral genomes. Viral evolutionary rates may vary over the course of a single persistent infection and can reflect changes in replication rates and selective dynamics. Dedicated statistical inference approaches are required to understand how the complex interplay of these processes shapes the genetic diversity and divergence in viral populations. Although evolutionary models accommodating a high degree of complexity can now be formalized, adequately informing these models by potentially sparse data, and assessing the association of the resulting estimates with external predictors, remains a major challenge...
July 2016: Virus Evolution
Anatoliy I Yashin, Konstantin G Arbeev, Deqing Wu, Liubov Arbeeva, Alexander Kulminski, Irina Kulminskaya, Igor Akushevich, Svetlana V Ukraintseva
BACKGROUND AND OBJECTIVE: To clarify mechanisms of genetic regulation of human aging and longevity traits, a number of genome-wide association studies (GWAS) of these traits have been performed. However, the results of these analyses did not meet expectations of the researchers. Most detected genetic associations have not reached a genome-wide level of statistical significance, and suffered from the lack of replication in the studies of independent populations. The reasons for slow progress in this research area include low efficiency of statistical methods used in data analyses, genetic heterogeneity of aging and longevity related traits, possibility of pleiotropic (e...
2016: North American Actuarial Journal: NAAJ
Monica Dalva, Khadija El Jellas, Solrun J Steine, Bente B Johansson, Monika Ringdal, Janniche Torsvik, Heike Immervoll, Dag Hoem, Felix Laemmerhirt, Peter Simon, Markus M Lerch, Stefan Johansson, Pål R Njølstad, Frank U Weiss, Karianne Fjeld, Anders Molven
BACKGROUND/OBJECTIVES: We have recently described copy number variants (CNVs) of the human carboxyl-ester lipase (CEL) gene, including a recombined deletion allele (CEL-HYB) that is a genetic risk factor for chronic pancreatitis. Associations with pancreatic disease have also been reported for the variable number of tandem repeat (VNTR) region located in CEL exon 11. Here, we examined if CEL CNVs and VNTR length polymorphisms affect the risk for developing pancreatic cancer. METHODS: CEL CNVs and VNTR were genotyped in a German family with non-alcoholic chronic pancreatitis and pancreatic cancer, in 265 German and 197 Norwegian patients diagnosed with pancreatic adenocarcinoma, and in 882 controls...
October 11, 2016: Pancreatology: Official Journal of the International Association of Pancreatology (IAP) ... [et Al.]
Kimberley M Kendall, Elliott Rees, Valentina Escott-Price, Mark Einon, Rhys Thomas, Jonathan Hewitt, Michael C O'Donovan, Michael J Owen, James T R Walters, George Kirov
BACKGROUND: The UK Biobank is a unique resource for biomedical research, with extensive phenotypic and genetic data on half a million adults from the general population. We aimed to examine the effect of neurodevelopmental copy number variants (CNVs) on the cognitive performance of participants. METHODS: We used Affymetrix Power Tools and PennCNV-Affy software to analyze Affymetrix microarrays of the first 152,728 genotyped individuals. We annotated a list of 93 CNVs and compared their frequencies with control datasets...
August 18, 2016: Biological Psychiatry
Yousef Sakieh, Abdolrassoul Salmanmahiny, Seyed Hamed Mirkarimi
Continuous surface of urbanization suitability, as an input to many urban growth models (UGM), has a significant role on a proper calibration process. The present study evaluates and compares the simulation success of the Cellular Automata-Markov Chain (CA-MC) model through multiple methods. For this, a series of mapping algorithms are applied ranging from empirical methods such as multi-criteria evaluation (MCE) to statistical algorithms without spatially explicit suitability mapping rules such as logistic regression (LR) and multi-layer perceptron (MLP) neural network and finally statistical and spatially explicit rule-based methods such as SLEUTH-Genetic Algorithm (SLEUTH-GA) model...
November 2016: Environmental Monitoring and Assessment
Oscar Heredia Díaz, José Luis Aldaba Meza, Baltazar M Baltazar, Germán Bojórquez Bojórquez, Luciano Castro Espinoza, José Luis Corrales Madrid, Juan Manuel de la Fuente Martínez, Héctor Abel Durán Pompa, José Alonso Escobedo, Armando Espinoza Banda, José Antonio Garzón Tiznado, Juvencio González García, José Luis Guzmán Rodríguez, Jesús Ignacio Madueño Martínez, José Luis Martínez Carrillo, Chen Meng, Francisco Javier Quiñones Pando, Enrique Rosales Robles, Ignacio Ruiz Hernández, José Elías Treviño Ramírez, Hugo Raúl Uribe Montes, Francisco Zavala García
Environmental risk assessment (ERA) of genetically modified (GM) crops is a process to evaluate whether the biotechnology trait(s) in a GM crop may result in increased pest potential or harm to the environment. In this analysis, two GM insect-resistant (IR) herbicide-tolerant maize hybrids (MON-89Ø34-3 × MON-88Ø17-3 and MON-89Ø34-3 × MON-ØØ6Ø3-6) and one herbicide-tolerant GM hybrid (MON-ØØ6Ø3-6) were compared with conventional maize hybrids of similar genetic backgrounds. Two sets of studies, Experimental Phase and Pilot Phase, were conducted across five ecological regions (ecoregions) in Mexico during 2009-2013, and data were subject to meta-analysis...
October 22, 2016: Transgenic Research
Kalin Vidinov, Dragomira Nikolova
In recent years, there are numerous reports indicating the presence of familial papillary carcinoma. Unfortunately, no genetic defect can be linked directly to the disease. In this study, we set the goal to make a retrospective analysis of the cases with papillary carcinoma in the Department of Endocrine Surgery for the past 10 years, to compare the characteristics of sporadic and familial forms of the disease and to find families with hereditary papillary carcinoma. The study included 810 patients treated for thyroid cancer in the Department of Endocrine Surgery, USBALE "Acad...
October 22, 2016: Endocrine Pathology
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