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https://www.readbyqxmd.com/read/28103232/a-model-of-compound-heterozygous-loss-of-function-alleles-is-broadly-consistent-with-observations-from-complex-disease-gwas-datasets
#1
Jaleal S Sanjak, Anthony D Long, Kevin R Thornton
The genetic component of complex disease risk in humans remains largely unexplained. A corollary is that the allelic spectrum of genetic variants contributing to complex disease risk is unknown. Theoretical models that relate population genetic processes to the maintenance of genetic variation for quantitative traits may suggest profitable avenues for future experimental design. Here we use forward simulation to model a genomic region evolving under a balance between recurrent deleterious mutation and Gaussian stabilizing selection...
January 19, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28102009/detection-of-equine-herpesvirus-ehv-1-2-4-and-5-in-ethiopian-equids-with-and-without-respiratory-problems-and-genetic-characterization-of-ehv-2-and-ehv-5-strains
#2
H Negussie, D Gizaw, L Tesfaw, Y Li, K Oguma, H Sentsui, T S Tessema, H J Nauwynck
Infections with equine herpesviruses (EHVs) are widespread in equine populations worldwide. Whereas both EHV-1 and EHV-4 produce well-documented respiratory syndromes in equids, the contribution of EHV-2 and EHV-5 to disease of the respiratory tract is still enigmatic. This study describes the detection and genetic characterization of EHVs from equids with and without clinical respiratory disease. Virus-specific PCRs were used to detect EHV-1, -2, -4 and -5. From the total of 160 equids with respiratory disease, EHV-5 was detected at the highest prevalence (23...
January 18, 2017: Transboundary and Emerging Diseases
https://www.readbyqxmd.com/read/28101894/sleep-quality-and-body-mass-index-a-co-twin-study
#3
Juan J Madrid-Valero, José M Martínez-Selva, Juan R Ordoñana
There is a consistent relationship between body mass index and sleep quality. However, the directionality and possible confounding factors of this relationship are unclear. Our aim is to confirm the association between sleep quality and body mass index, independent of possible genetic confounding, as well as to provide some indirect inferences about the directionality of this association. The co-twin study design was used to analyse the body mass index-sleep relationship in a sample of 2150 twins. We selected two parallel sub-samples of twins discordant for body mass index (n = 430 pairs), or discordant for sleep quality (n = 316 pairs)...
January 19, 2017: Journal of Sleep Research
https://www.readbyqxmd.com/read/28101829/autism-spectrum-disorders%C3%A2-diagnosis-and-management
#4
REVIEW
Sharmila Banerjee Mukherjee
Autism Spectrum Disorder (ASD) is a neuro-developmental disorder commonly seen in children. It is characterized by age inappropriate, impaired social communication and the presence of stereotypic behavior. This disorder is hypothesized to result from cerebral dysfunction arising from a complex interaction between genetic, epigenetic and environmental factors. ASD should be suspected in children failing ASD specific screening tests, in the presence of red flags in social, language and/or play domains, in children with developmental or language delay, abnormal behavior, poor school performance or in those who are at high risk...
January 19, 2017: Indian Journal of Pediatrics
https://www.readbyqxmd.com/read/28100790/genome-wide-analysis-in-brazilians-reveals-highly-differentiated-native-american-genome-regions
#5
Josyf C Mychaleckyj, Alexandre Havt, Uma Nayak, Relana Pinkerton, Emily Farber, Patrick Concannon, Aldo A Lima, Richard L Guerrant
Despite its population, geographic size, and emerging economic importance, disproportionately little genome-scale research exists into genetic factors that predispose Brazilians to disease, or the population genetics of risk. After identification of suitable proxy populations and careful analysis of tri-continental admixture in 1,538 North-Eastern Brazilians to estimate individual ancestry and ancestral allele frequencies, we computed 400,000 genome-wide locus-specific branch length (LSBL) Fst statistics of Brazilian Amerindian ancestry compared to European and African; and a similar set of differentiation statistics for their Amerindian component compared to the closest Asian 1000 Genomes population (surprisingly, Bengalis in Bangladesh)...
January 18, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28100587/efficient-estimation-of-realized-kinship-from-snp-genotypes
#6
Bowen Wang, Serge Sverdlov, Elizabeth Thompson
Realized kinship is a key statistic in analyses of genetic data involving relatedness of individuals or structure of populations. There are several estimators of kinship that make use of dense single nucleotide polymorphism (SNP) genotypes. We introduce a class of estimators of which some existing estimators are special cases. Within this class, we derive properties of the estimators and determine an optimal estimator. Additionally, we introduce an alternative marker weighting that takes allelic associations (LD: linkage disequilibrium) into account, and apply this weighting to several estimators...
January 18, 2017: Genetics
https://www.readbyqxmd.com/read/28099998/a-generalized-levene-s-scale-test-for-variance-heterogeneity-in-the-presence-of-sample-correlation-and-group-uncertainty
#7
David Soave, Lei Sun
We generalize Levene's test for variance (scale) heterogeneity between k groups for more complex data, when there are sample correlation and group membership uncertainty. Following a two-stage regression framework, we show that least absolute deviation regression must be used in the stage 1 analysis to ensure a correct asymptotic χk-12/(k-1) distribution of the generalized scale (gS) test statistic. We then show that the proposed gS test is independent of the generalized location test, under the joint null hypothesis of no mean and no variance heterogeneity...
January 18, 2017: Biometrics
https://www.readbyqxmd.com/read/28099933/loss-of-maternal-chromosome-11-is-a-signature-event-in-sdhaf2-sdhd-and-vhl-related-paragangliomas-but-less-significant-in-sdhb-related-paragangliomas
#8
Attje S Hoekstra, Erik F Hensen, Ekaterina S Jordanova, Esther Korpershoek, Anouk Na van der Horst-Schrivers, Cees Cornelisse, Eleonora Pm Corssmit, Frederik J Hes, Jeroen C Jansen, Henricus Pm Kunst, Henri Jlm Timmers, Adrian Bateman, Diana Eccles, Judith Vmg Bovée, Peter Devilee, Jean-Pierre Bayley
Germline mutations in the succinate dehydrogenase (SDHA, SDHB, SDHC, SDHD, SDHAF2) or Von Hippel-Lindau (VHL) genes cause hereditary paraganglioma/pheochromocytoma. While SDHB (1p36) and VHL (3p25) are associated with autosomal dominant disease, SDHD (11q23) and SDHAF2 (11q13) show a remarkable parent-of-origin effect whereby tumor formation is almost completely dependent on paternal transmission of the mutant allele. Loss of the entire maternal copy of chromosome 11 occurs frequently in SDHD-linked tumors, and has been suggested to be the basis for this typical inheritance pattern...
January 14, 2017: Oncotarget
https://www.readbyqxmd.com/read/28099159/reducing-false-arrhythmia-alarm-rates-using-robust-heart-rate-estimation-and-cost-sensitive-support-vector-machines
#9
Qiang Zhang, Xianxiang Chen, Zhen Fang, Qingyuan Zhan, Ting Yang, Shanhong Xia
To lessen the rate of false critical arrhythmia alarms, we used robust heart rate estimation and cost-sensitive support vector machines. The PhysioNet MIMIC II database and the 2015 PhysioNet/CinC Challenge public database were used as the training dataset; the 2015 Challenge hidden dataset was for testing. Each record had an alarm labeled with asystole, extreme bradycardia, extreme tachycardia, ventricular tachycardia or ventricular flutter/fibrillation. Before alarm onsets, 300 s multimodal data was provided, including electrocardiogram, arterial blood pressure and/or photoplethysmogram...
January 18, 2017: Physiological Measurement
https://www.readbyqxmd.com/read/28098150/a-survey-of-sub-saharan-gene-flow-into-the-mediterranean-at-risk-loci-for-coronary-artery-disease
#10
Miguel M Álvarez-Álvarez, Daniela Zanetti, Robert Carreras-Torres, Pedro Moral, Georgios Athanasiadis
This study tries to find detectable signals of gene flow of Sub-Saharan origin into the Mediterranean in four genomic regions previously associated with coronary artery disease. A total of 366 single-nucleotide polymorphisms were genotyped in 772 individuals from 10 Mediterranean countries. Population structure analyses were performed, in which a noticeable Sub-Saharan component was found in the studied samples. The overall percentage of this Sub-Saharan component presents differences between the two Mediterranean coasts...
January 18, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28097409/genetic-and-epigenetic-intra-tumour-heterogeneity-in-colorectal-cancer
#11
Huw Geraint Jones, Gareth Jenkins, Namor Williams, Paul Griffiths, Phil Chambers, John Beynon, Dean Harris
INTRODUCTION: Colorectal cancer (CRC) is a highly heterogeneous disease, with pathologically similar cancers having completely different responses to treatment and patient survival. Intra-tumour heterogeneity (defined as distinct morphological and phenotypic differences) has recently been demonstrated to be an important factor in the development and behaviour of cancer cells and can be used to determine response to anticancer therapy. METHOD: Patients with resected CRC had DNA extracted from eight defined tumour areas which were analysed for two genetic mutations (BRAF and KRAS) and one epigenetic trait (CpG island methylator phenotype/CIMP)...
January 17, 2017: World Journal of Surgery
https://www.readbyqxmd.com/read/28097204/genomics-implicates-adaptive-and-innate-immunity-in-alzheimer-s-and-parkinson-s-diseases
#12
Sarah A Gagliano, Jennie G Pouget, John Hardy, Jo Knight, Michael R Barnes, Mina Ryten, Michael E Weale
OBJECTIVES: We assessed the current genetic evidence for the involvement of various cell types and tissue types in the etiology of neurodegenerative diseases, especially in relation to the neuroinflammatory hypothesis of neurodegenerative diseases. METHODS: We obtained large-scale genome-wide association study (GWAS) summary statistics from Parkinson's disease (PD), Alzheimer's disease (AD), and amyotrophic lateral sclerosis (ALS). We used multiple sclerosis (MS), an autoimmune disease of the central nervous system, as a positive control...
December 2016: Annals of Clinical and Translational Neurology
https://www.readbyqxmd.com/read/28097054/hydrogel-scaffolds-promote-neural-gene-expression-and-structural-reorganization-in-human-astrocyte-cultures
#13
V Bleu Knight, Elba E Serrano
Biomaterial scaffolds have the potential to enhance neuronal development and regeneration. Understanding the genetic responses of astrocytes and neurons to biomaterials could facilitate the development of synthetic environments that enable the specification of neural tissue organization with engineered scaffolds. In this study, we used high throughput transcriptomic and imaging methods to determine the impact of a hydrogel, PuraMatrix™, on human glial cells in vitro. Parallel studies were undertaken with cells grown in a monolayer environment on tissue culture polystyrene...
2017: PeerJ
https://www.readbyqxmd.com/read/28096933/the-association-of-male-pattern-baldness-and-risk-of-cancer-and-high-grade-disease-among-men-presenting-for-prostate-biopsy
#14
Ghazi Al Edwan, Bimal Bhindi, David Margel, Karen Chadwick, Antonio Finelli, Alexandre Zlotta, John Trachtenberg, Neil Fleshner
INTRODUCTION: Androgens have been implicated in both male pattern baldness (MPB) and prostate cancer (PCa). We set out to prospectively determine if men with independently assessed MPB are at higher risk for PCa at biopsy and determine if any grade associations exist. METHODS: We prospectively enrolled 394 eligible patients presenting for prostate biopsy and independently determined their MPB pattern using the validated modified Norwood classification system (0: no balding; 1: frontal balding; 2: mild vertex balding; 3: moderate vertex balding; 4: sever vertex balding)...
November 2016: Canadian Urological Association Journal, Journal de L'Association des Urologues du Canada
https://www.readbyqxmd.com/read/28096879/association-between-mitofusin-2-gene-polymorphisms-and-late-onset-alzheimer-s-disease-in-the-korean-population
#15
Young Jong Kim, Jin Kyung Park, Won Sub Kang, Su Kang Kim, Changsu Han, Hae Ri Na, Hae Jeong Park, Jong Woo Kim, Young Youl Kim, Moon Ho Park, Jong-Woo Paik
OBJECTIVE: Mitochondrial dysfunction is a prominent and early feature of Alzheimer's disease (AD). The morphologic changes observed in the AD brain could be caused by a failure of mitochondrial fusion mechanisms. The aim of this study was to investigate whether genetic polymorphisms of two genes involved in mitochondrial fusion mechanisms, optic atrophy 1 (OPA1) and mitofusin 2 (MFN2), were associated with AD in the Korean population by analyzing genotypes and allele frequencies. METHODS: One coding single nucleotide polymorphism (SNP) in the MFN2, rs1042837, and two coding SNPs in the OPA1, rs7624750 and rs9851685, were compared between 165 patients with AD (83 men and 82 women, mean age 72...
January 2017: Psychiatry Investigation
https://www.readbyqxmd.com/read/28096648/identification-of-genetic-and-epigenetic-variants-associated-with-breast-cancer-prognosis-by-integrative-bioinformatics-analysis
#16
Arunima Shilpi, Yingtao Bi, Segun Jung, Samir K Patra, Ramana V Davuluri
INTRODUCTION: Breast cancer being a multifaceted disease constitutes a wide spectrum of histological and molecular variability in tumors. However, the task for the identification of these variances is complicated by the interplay between inherited genetic and epigenetic aberrations. Therefore, this study provides an extrapolate outlook to the sinister partnership between DNA methylation and single-nucleotide polymorphisms (SNPs) in relevance to the identification of prognostic markers in breast cancer...
2017: Cancer Informatics
https://www.readbyqxmd.com/read/28096624/genetic-variability-and-discrimination-of-low-doses-of-toxocara-spp-from-public-areas-soil-inferred-by-loop-mediated-isothermal-amplification-assay-as-a-field-friendly-molecular-tool
#17
Maryam Ozlati, Adel Spotin, Abbas Shahbazi, Mahmoud Mahami-Oskouei, Teimour Hazratian, Mohammad Adibpor, Ehsan Ahmadpour, Afsaneh Dolatkhah, Paria Khoshakhlagh
ABSTRACT: Aim: One of the main diagnostic problems of conventional polymerase chain reaction (PCR) is indiscrimination of low parasitic loads in soil samples. The aim of this study is to determine the genetic diversity and identification of Toxocara spp. from public areas soil inferred by loop-mediated isothermal amplification (LAMP) assay. MATERIALS AND METHODS: A total of 180 soil samples were collected from various streets and public parks of northwest Iran. The DNA of recovered Toxocara eggs were extracted and amplified by PCR and LAMP following ZnSO4 flotation technique...
December 2016: Veterinary World
https://www.readbyqxmd.com/read/28095909/prevalence-and-genetic-characterization-of-cryptosporidium-species-and-giardia-duodenalis-in-lambs-in-oromia-special-zone-central-ethiopia
#18
Teklu Wegayehu, Md Robiul Karim, Junqiang Li, Haileeyesus Adamu, Berhanu Erko, Longxian Zhang, Getachew Tilahun
BACKGROUND: Cryptosporidium and Giardia duodenalis are gastro-intestinal parasites that infect human and animals worldwide. Both parasites share a broad host range and are believed to be zoonosis. The aim of this study was to identify the species of Cryptosporidium and assemblages of G. duodenalis in lambs and to elucidate their role in zoonotic transmission. RESULTS: A total of 389 fecal samples were collected from lambs and screened by microscopy and nested PCR targeting the small-subunit ribosomal RNA for Cryptosporidium; and the small-subunit ribosomal RNA, triose phosphate isomerase, β-giardin, and glutamate dehydrogenase genes for G...
January 17, 2017: BMC Veterinary Research
https://www.readbyqxmd.com/read/28095416/meta-gwas-accuracy-and-power-metagap-calculator-shows-that-hiding-heritability-is-partially-due-to-imperfect-genetic-correlations-across-studies
#19
Ronald de Vlaming, Aysu Okbay, Cornelius A Rietveld, Magnus Johannesson, Patrik K E Magnusson, André G Uitterlinden, Frank J A van Rooij, Albert Hofman, Patrick J F Groenen, A Roy Thurik, Philipp D Koellinger
Large-scale genome-wide association results are typically obtained from a fixed-effects meta-analysis of GWAS summary statistics from multiple studies spanning different regions and/or time periods. This approach averages the estimated effects of genetic variants across studies. In case genetic effects are heterogeneous across studies, the statistical power of a GWAS and the predictive accuracy of polygenic scores are attenuated, contributing to the so-called 'missing heritability'. Here, we describe the online Meta-GWAS Accuracy and Power (MetaGAP) calculator (available at www...
January 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28095286/the-relations-between-polycyclic-aromatic-hydrocarbons-exposure-and-1-ohp-levels-as-a-biomarker-of-the-exposure
#20
Zuzana Klöslová, Marek Drímal, Karol Balog, Kvetoslava Koppová, Jarmila Dubajová
BACKGROUND: Polycyclic aromatic hydrocarbons (PAHs) are the products of incomplete combustion or pyrolysis of various organic materials. Their ubiquity in the environment leads to measurable levels of exposure. However, the exposure varies strongly between different regions in Europe. Some PAHs with four or more rings are suspected to be human carcinogens. Therefore, the occupational and/or environmental exposure to PAHs may cause a significant health risk. The aim of investigation is to evaluate current levels of PAH exposure in defined groups of workers...
December 2016: Central European Journal of Public Health
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