166 results match your criteria genotyped 386


Development of genomic predictions for Angus cattle in Brazil incorporating genotypes from related American sires.

J Anim Sci 2022 Jan 14. Epub 2022 Jan 14.

Department of Animal and Dairy Science, University of Georgia, 30602, Athens, GA, USA.

Genomic prediction has become the new standard for genetic improvement programs, and currently, there is a desire to implement this technology for the evaluation of Angus cattle in Brazil. Thus, the main objective of this study was to assess the feasibility of evaluating young Brazilian Angus (BA) bulls and heifers for 12 routinely recorded traits using single-step genomic BLUP (ssGBLUP) with and without genotypes from American Angus (AA) sires. The second objective was to obtain estimates of effective population size (Ne) and linkage disequilibrium (LD) in the Brazilian Angus population. Read More

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January 2022

The role of 25-hydroxyvitamin-D3 and vitamin D receptor gene in human periodontal ligament fibroblasts as response to orthodontic compressive strain: an in vitro study.

BMC Oral Health 2021 08 6;21(1):386. Epub 2021 Aug 6.

Department of Orthodontics, University of Regensburg, Franz-Josef-Strauss-Allee 11, 93053, Regensburg, Germany.

Background: This study aimed to investigate, if different physiological concentrations of vitamin D (25(OH)D) and single nucleotide polymorphisms in vitamin D receptor (VDR) gene have an impact on gene expression in human periodontal ligament (hPDL) fibroblasts induced by simulated orthodontic compressive strain.

Methods: A pool of hPDL fibroblasts was treated in absence or presence of 25(OH)D in 3 different concentrations (10, 40 and 60 ng/ml). In order to evaluate the role of single nucleotide polymorphisms in the VDR gene, hPDL fibroblasts from 9 patients were used and treated in absence or presence of 40 ng/ml 25(OH)D. Read More

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Landscape barriers to pollen and seed flow in the dioecious tropical tree Astronium fraxinifolium in Brazilian savannah.

PLoS One 2021 2;16(8):e0255275. Epub 2021 Aug 2.

Instituto de Biotecnologia/ UNESP, Botucatu, São Paulo, Brazil.

Gene flow studies provide information on gene exchange between populations, which is essential for developing genetic conservation strategies. Such analyses enable a better understanding of the life history and seed and pollen dispersal mechanisms of plant species. In this study, we investigate pollen and seed flow in a regenerant population of the pioneer species Astronium fraxinifolium in an area degraded during the construction of a hydroelectric dam. Read More

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November 2021

A genome-wide association study of the longitudinal course of executive functions.

Transl Psychiatry 2021 07 10;11(1):386. Epub 2021 Jul 10.

AMEOS Clinical Center Hildesheim, Hildesheim, 31135, Germany.

Executive functions are metacognitive capabilities that control and coordinate mental processes. In the transdiagnostic PsyCourse Study, comprising patients of the affective-to-psychotic spectrum and controls, we investigated the genetic basis of the time course of two core executive subfunctions: set-shifting (Trail Making Test, part B (TMT-B)) and updating (Verbal Digit Span backwards) in 1338 genotyped individuals. Time course was assessed with four measurement points, each 6 months apart. Read More

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BAFF, APRIL and BAFFR on the pathogenesis of Immunoglobulin-A vasculitis.

Sci Rep 2021 06 1;11(1):11510. Epub 2021 Jun 1.

Research Group on Genetic Epidemiology and Atherosclerosis in Systemic Diseases and in Metabolic Bone Diseases of the Musculoskeletal System, IDIVAL, Division of Rheumatology, Hospital Universitario Marqués de Valdecilla, Avenida Cardenal Herrera Oria s/n, 39011, Santander, Spain.

BAFF, APRIL and BAFF-R are key proteins involved in the development of B-lymphocytes and autoimmunity. Additionally, BAFF, APRIL and BAFFR polymorphisms were associated with immune-mediated conditions, being BAFF GCTGT>A a shared insertion-deletion genetic variant for several autoimmune diseases. Accordingly, we assessed whether BAFF, APRIL and BAFFR represent novel genetic risk factors for Immunoglobulin-A vasculitis (IgAV), a predominantly B-lymphocyte inflammatory condition. Read More

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Four species associated with two mass-occurring populations.

J Nematol 2020 30;52. Epub 2020 Nov 30.

Sugadaira Research Station, Mountain Science Center, University of Tsukuba, 1278-294 Sugadairakogen, Ueda, Nagano 386-2204, Japan.

Phoretic nematodes associated with two mass-occurring populations of the millipede were examined, focusing on spp. The nematodes that propagated on dissected millipedes were genotyped using the D2-D3 expansion segments of the 28S ribosomal RNA gene. Four spp. Read More

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November 2020

Gene Polymorphisms in Healthy Individuals with Family History of Premature Coronary Artery Disease.

Dis Markers 2021 29;2021:8832478. Epub 2021 Jan 29.

Department of Medical and Molecular Biology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, Katowice 40-055, Poland.

Aim: The gene encoding the vitamin D receptor () is considered in many studies to be a good candidate responsible for susceptibility to several diseases such as coronary artery disease (CAD). Epidemiological data show that cardiovascular disease is one of the major health problems in Polish society. Basic studies show that genetic factors play a significant role in the pathogenesis of CAD. Read More

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October 2021

Exploration of a Resequenced Tomato Core Collection for Phenotypic and Genotypic Variation in Plant Growth and Fruit Quality Traits.

Genes (Basel) 2020 10 29;11(11). Epub 2020 Oct 29.

Plant Breeding, Wageningen University & Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands.

A tomato core collection consisting of 122 gene bank accessions, including landraces, old cultivars, and wild relatives, was explored for variation in several plant growth, yield and fruit quality traits. The resequenced accessions were also genotyped with respect to a number of mutations or variations in key genes known to underlie these traits. The yield-related traits fruit number and fruit weight were much higher in cultivated varieties when compared to wild accessions, while, in wild tomato accessions, Brix was higher than in cultivated varieties. Read More

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October 2020

Survival analyses in Holstein cows considering direct disease diagnoses and specific SNP marker effects.

J Dairy Sci 2020 Sep 16;103(9):8257-8273. Epub 2020 Jul 16.

Institute of Animal Breeding and Genetics, Justus-Liebig-University of Giessen, 35390 Giessen, Germany. Electronic address:

The aim of the present study was to infer influences of health disorders and of specific SNP markers on longevity in Holstein cows via survival analyses. Longevity was defined as the length of productive life (LPL), reflecting the interval from first calving until the culling or censoring date. In this regard, we considered longevity records from 129,386 Holstein cows from 57 large-scale herds, with calving dates in first parity between January 2004 and December 2017 (30. Read More

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September 2020

The European Union summary report on surveillance for the presence of transmissible spongiform encephalopathies (TSE) in 2018.

Authors:

EFSA J 2019 Dec 3;17(12):e05925. Epub 2019 Dec 3.

This report presents the results of surveillance on transmissible spongiform encephalopathies (TSE) in bovine animals, sheep, goats, cervids and other species, and genotyping in sheep, carried out in 2018 by 28 Member States (MS) according to legislation, and by Iceland, North Macedonia, Norway and Switzerland (non-MS). In total, 1,181,934 cattle were tested by MS, a 10% decrease from 2017 and 20,402 by the four non-MS. One case of classical bovine spongiform encephalopathy (BSE) was reported in 2018 by the UK, born after the enforcement of the total feed ban. Read More

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December 2019

[Study on the correlation between prognosis of patients with chronic hepatitis B under interferon treatment and polymorphism of both calcitonin gene related peptide and receptor activity modifying protein 1].

Zhonghua Liu Xing Bing Xue Za Zhi 2020 Jun;41(6):924-928

Department of Epidemiology and Statistics, Hebei Medical University, Shijiazhuang 050017, China.

To analyze the association of two single-nucleotide polymorphisms (SNP) [Calcitonin gene related peptide (CGRP) rs155209 and receptor activity modifying protein 1 (RAMP1) rs3754701] and the prognosis of chronic hepatitis B patients who were under interferon therapy. A total of 317 patients and their anticoagulant blood samples were collected in this study. The SNPs in the CGRP and region RAMP1 were genotyped using matrix-assisted laser desorption/ionization time of flight mass spectrometry. Read More

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Study of the Association Between microRNA (miR-25T>C, miR-32C>A, miR-125C>T, and miR-222G>T) Polymorphisms and the Risk of Recurrent Pregnancy Loss in Korean Women.

Genes (Basel) 2020 03 26;11(4). Epub 2020 Mar 26.

Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Korea.

Recurrent pregnancy loss (RPL), which is defined as two pregnancy losses that occur before 20 weeks of gestation, is relatively common, occurring in approximately 1-5% of women. The underlying cause is often unclear, although numerous factors may contribute to RPL, including environmental and immunological factors, blood coagulation disorders, and genetics. In particular, single nucleotide variants have been associated with RPL, including those found in microRNAs (miRNAs). Read More

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Association between variant alleles of major histocompatibility complex class II regulatory genes and nasopharyngeal carcinoma susceptibility.

Eur J Cancer Prev 2020 11;29(6):531-537

Nanjing Medical University, Nanjing.

Major histocompatibility complex (MHC) class II regulatory genes play a paramount role in immune response that can exert a predominant influence on clinical outcome of Epstein-Barr virus infection consistently assumed as the main pathogenetic factor for nasopharyngeal carcinoma. To elucidate the relationship between allelic variants of MHC class II regulatory genes and susceptibility to nasopharyngeal carcinoma, a total of 28 polymorphic loci at MHC class II regulatory genes, involving CIITA, CREB1, RFX family genes (RFX5, RFXAP, and RFXANK), and NFY family genes (NFYA, NFYB, and NFYC), were genotyped by multiplex SNaPshot minisequencing in 137 patients with nasopharyngeal carcinoma and 107 healthy controls from the southern Chinese population. Allelic analysis disclosed that rs7404873, rs6498121, rs6498126, and rs56074043 shared correlations with nasopharyngeal carcinoma (Ptrend < 0. Read More

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November 2020

Interactions between macro-nutrients' intake, FTO and IRX3 gene expression, and FTO genotype in obese and overweight male adolescents.

Adipocyte 2019 12;8(1):386-391

Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA.

This study is the first to identify the effects of FTO genotype on the interactions between the level of macro-nutrients intake and the expression level of fat mass and obesity associated (FTO) and homeobox transcription factor iriquois-3 (IRX3) genes This longitudinal study was carried out on 84 overweight and obese adolescent boys in Tehran, Iran. The rs9930506 SNP in was genotyped at baseline and the level of and expression in PBMCs and macro-nutrients' intake were assessed at baseline and after 18 weeks of the intervention. The results identified that the higher carbohydrates intake significantly up-regulated the FTO gene (P = 0. Read More

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December 2019

Economic optimization of full-sib test group size and genotyping effort in a breeding program for Atlantic salmon.

Genet Sel Evol 2019 Sep 3;51(1):49. Epub 2019 Sep 3.

Wageningen University & Research, Animal Breeding and Genomics, P.O. Box 338, 6708 PB, Wageningen, The Netherlands.

Background: Breeding companies may want to maximize the rate of genetic gain from their breeding program within a limited budget. In salmon breeding programs, full-sibs of selection candidates are subjected to performance tests for traits that cannot be recorded on selection candidates. While marginal gains in the aggregate genotype from phenotyping and genotyping more full-sibs per candidate decrease, costs increase linearly, which suggests that there is an optimum in the allocation of the budget among these activities. Read More

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September 2019

Genetic Variation Underpinning ADHD Risk in a Caribbean Community.

Cells 2019 08 16;8(8). Epub 2019 Aug 16.

División de Ingenierías, Universidad del Norte, Barranquilla 081007, Colombia.

Attention Deficit Hyperactivity Disorder (ADHD) is a highly heritable and prevalent neurodevelopmental disorder that frequently persists into adulthood. Strong evidence from genetic studies indicates that single nucleotide polymorphisms (SNPs) harboured in the (), , , , and genes are associated with ADHD. We genotyped 26 SNPs harboured in genes previously reported to be associated with ADHD and evaluated their potential association in 386 individuals belonging to 113 nuclear families from a Caribbean community in Barranquilla, Colombia, using family-based association tests. Read More

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Assessment of sire contribution and breed-of-origin of alleles in a three-way crossbred broiler dataset.

Poult Sci 2019 Dec;98(12):6270-6280

Cobb-Vantress Inc., Siloam Springs, AR 72761-1030.

Broiler breeding programs rely on crossbreeding. With genomic selection, widespread use of crossbred performance in breeding programs comes within reach. Commercial crossbreds, however, may have unknown pedigrees and their genomes may include DNA from 2 to 4 different breeds. Read More

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December 2019

Source and Relevance of the BK Polyomavirus Genotype for Infection After Kidney Transplantation.

Open Forum Infect Dis 2019 Mar 19;6(3):ofz078. Epub 2019 Feb 19.

Department of Medical Microbiology, Leiden University Medical Center, the Netherlands.

Background: BK polyomavirus (BKPyV)-associated nephropathy (BKPyVAN) is a major threat for kidney transplant recipients (KTRs). The role of specific BKPyV genotypes/serotypes in development of BKPyVAN is poorly understood. Pretransplantation serotyping of kidney donors and recipients and posttransplantation genotyping of viremic recipients, could reveal the clinical relevance of specific BKPyV variants. Read More

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A Sex-Stratified Genome-Wide Association Study of Tuberculosis Using a Multi-Ethnic Genotyping Array.

Front Genet 2018 18;9:678. Epub 2019 Jan 18.

DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.

Tuberculosis (TB), caused by , is a complex disease with a known human genetic component. Males seem to be more affected than females and in most countries the TB notification rate is twice as high in males than in females. While socio-economic status, behavior and sex hormones influence the male bias they do not fully account for it. Read More

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January 2019

Identification of TEX101-associated Proteins Through Proteomic Measurement of Human Spermatozoa Homozygous for the Missense Variant rs35033974.

Mol Cell Proteomics 2019 02 14;18(2):338-351. Epub 2018 Nov 14.

Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada;; Department of Pathology and Laboratory Medicine,; Department of Clinical Biochemistry, University Health Network, Toronto, Canada. Electronic address:

TEX101 is a germ-cell-specific protein and a validated biomarker of male infertility. Mouse TEX101 was found essential for male fertility and was suggested to function as a cell surface chaperone involved in maturation of proteins required for sperm migration and sperm-oocyte interaction. However, the precise functional role of human TEX101 is not known and cannot be studied due to the lack of human germ cell lines. Read More

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February 2019

Genetic diversity of the msp-1, msp-2, and glurp genes of Plasmodium falciparum isolates in Northwest Ethiopia.

Malar J 2018 Oct 25;17(1):386. Epub 2018 Oct 25.

Menzies School of Health Research and Charles Darwin University, Darwin, Australia.

Background: Determination of the genetic diversity of malaria parasites can inform the intensity of transmission and identify potential deficiencies in malaria control programmes. This study was conducted to characterize the genetic diversity and allele frequencies of Plasmodium falciparum in Northwest Ethiopia along the Eritrea and Sudan border.

Methods: A total of 90 isolates from patients presenting to the local health centre with uncomplicated P. Read More

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October 2018

Effects of Klotho polymorphisms on Preeclampsia risk in a case-control study.

Pregnancy Hypertens 2018 Jul 23;13:95-99. Epub 2018 Apr 23.

Internal Medicine-Cardiovascular Department, The Affiliated Hospital of Qingdao University, Qingdao, China. Electronic address:

Preeclampsia (PE) is a serious disorder of human pregnancy and always is accompanied with multi-organ disorder, which severely threatens the health of both the mothers and the offspring. The oxidative stress and genetic factors involves in the development of PE. The Klotho encodes Klotho protein that is capable of increasing resistance to oxidative stress. Read More

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Functional miRNA variants affect lung cancer susceptibility and platinum-based chemotherapy response.

J Thorac Dis 2018 Jun;10(6):3329-3340

Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410008, China.

Background: Platinum-based chemotherapy is widely used as the first-line treatment of lung cancer. MicroRNAs have an important role in lung carcinogenesis and progression. Single-nucleotide polymorphisms (SNPs) in miRNA involved in miRNA biogenesis and structural alteration may affect miRNA expression. Read More

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Associations between loneliness and personality are mostly driven by a genetic association with Neuroticism.

J Pers 2019 04 2;87(2):386-397. Epub 2018 Aug 2.

Department of Psychology, University of Chicago, Chicago, Illinois, USA.

Objective: Loneliness is an aversive response to a discrepancy between desired and actual social relationships and correlates with personality. We investigate the relationship of loneliness and personality in twin family and molecular genetic data.

Method: Phenotypic correlations between loneliness and the Big Five personality traits were estimated in 29,625 adults, and in a group with genome-wide genotype data (N = 4,222), genetic correlations were obtained. Read More

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Association between the XPG gene rs2094258 polymorphism and risk of gastric cancer.

J Clin Lab Anal 2018 Oct 7;32(8):e22564. Epub 2018 May 7.

General Surgery Department, Tongde Hospital of Zhejiang Province, Hangzhou, China.

Background: Xeroderma pigmentosum group G (XPG) plays an important role in maintaining the stability and integrity of genomic DNA. Previous studies demonstrate some XPG gene polymorphisms are associated with susceptibility to gastric cancer (GC).

Methods: The association between XPG rs2094258 polymorphism and GC risk was investigated first by a hospital-based case-control study involving 386 patients and 439 controls and then by a meta-analysis. Read More

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October 2018

An ultra-dense integrated linkage map for hexaploid chrysanthemum enables multi-allelic QTL analysis.

Theor Appl Genet 2017 Dec 29;130(12):2527-2541. Epub 2017 Aug 29.

Plant Breeding, Wageningen University and Research, P.O. Box 386, 6708 PB, Wageningen, The Netherlands.

Key Message: We constructed the first integrated genetic linkage map in a polysomic hexaploid. This enabled us to estimate inheritance of parental haplotypes in the offspring and detect multi-allelic QTL. Construction and use of linkage maps are challenging in hexaploids with polysomic inheritance. Read More

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December 2017

Development and characterization of microsatellite markers for diploid populations of the wind-pollinated herb Mercurialis annua.

BMC Res Notes 2017 Aug 10;10(1):386. Epub 2017 Aug 10.

Department of Ecology and Evolution, Biophore Building, University of Lausanne, 1015, Lausanne, Switzerland.

Objective: Mercurialis annua is a wind-pollinated annual plant that has long been used as a model for the study of ploidy and sexual-systems evolution. However, no molecular markers are yet available for genetic studies of its diploid populations. Here, we develop and characterize a set of eight polymorphic microsatellite markers for diploid dioecious M. Read More

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Conclusive evidence for hexasomic inheritance in chrysanthemum based on analysis of a 183 k SNP array.

BMC Genomics 2017 08 7;18(1):585. Epub 2017 Aug 7.

Plant Breeding, Wageningen University and Research, P.O. Box 386, 6708 PB, Wageningen, the Netherlands.

Background: Cultivated chrysanthemum is an outcrossing hexaploid (2n = 6× = 54) with a disputed mode of inheritance. In this paper, we present a single nucleotide polymorphism (SNP) selection pipeline that was used to design an Affymetrix Axiom array with 183 k SNPs from RNA sequencing data (1). With this array, we genotyped four bi-parental populations (with sizes of 405, 53, 76 and 37 offspring plants respectively), and a cultivar panel of 63 genotypes. Read More

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Blood lead levels, iron metabolism gene polymorphisms and homocysteine: a gene-environment interaction study.

Occup Environ Med 2017 12 3;74(12):899-904. Epub 2017 Aug 3.

Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, South Korea.

Objectives: Homocysteine has been causally associated with various adverse health outcomes. Evidence supporting the relationship between lead and homocysteine levels has been accumulating, but most prior studies have not focused on the interaction with genetic polymorphisms.

Methods: From a community-based prospective cohort, we analysed 386 participants (aged 41-71 years) with information regarding blood lead and plasma homocysteine levels. Read More

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December 2017