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Dragana Mijac, Irena Vukovic-Petrovic, Vera Mijac, Vladimir Perovic, Natasa Milic, Srdjan Djuranovic, Daniela Bojic, Dragan Popovic, Djordje Culafic, Miodrag Krstic, Goran Jankovic, Vera Pravica, Milos Markovic
BACKGROUND: Inflammatory bowel disease (IBD) is a chronic disease of unknown etiology in which genetic factors contribute to development of disease. Single nucleotide polymorphisms (SNPs) in multidrug resistance 1 (MDR1) gene encoding transporter P-glycoprotein have been associated with IBD, but their role in disease susceptibility remains unclear. Therefore, the aim of this study was to investigate the association of three MDR1 polymorphisms, C1236T (rs1128503), G2677T/A (rs2032582) and C3435T (rs1045642), with Serbian IBD patients...
2018: PloS One
Jessada Thutkawkorapin, Hovsep Mahdessian, Tom Barber, Simone Picelli, Susanna von Holst, Johanna Lundin, Laura Valle, Vinaykumar Kontham, Tao Liu, Daniel Nilsson, Xiang Jiao, Annika Lindblom
Highly penetrant cancer syndromes account for less than 5% of all cases with familial colorectal cancer (CRC), and other genetic contribution explains the majority of the genetic contribution to CRC. A CRC susceptibility locus on chromosome 9q has been suggested. In this study, families where risk of CRC was linked to the region, were used to search for predisposing mutations in all genes in the region. No disease-causing mutation was found. Next, haplotype association studies were performed in the region, comparing Swedish CRC cases (2664) and controls (4782)...
February 16, 2018: Oncotarget
D P Berry, A O'Brien, J O'Donovan, N McHugh, E Wall, S Randles, K McDermott, R E O'Connor, M A Patil, J Ho, A Kennedy, N Byrne, D C Purfield
Early detection of karyotype abnormalities, including aneuploidy, could aid producers in identifying animals which, for example, would not be suitable candidate parents. Genome-wide genetic marker data in the form of single nucleotide polymorphisms (SNPs) are now being routinely generated on animals. The objective of the present study was to describe the statistics that could be generated from the allele intensity values from such SNP data to diagnose karyotype abnormalities; of particular interest was whether detection of aneuploidy was possible with both commonly used genotyping platforms in agricultural species, namely the Applied BiosystemsTM AxiomTM and the Illumina platform...
March 15, 2018: Animal: An International Journal of Animal Bioscience
Linden Disney-Hogg, Alex J Cornish, Amit Sud, Philip J Law, Ben Kinnersley, Daniel I Jacobs, Quinn T Ostrom, Karim Labreche, Jeanette E Eckel-Passow, Georgina N Armstrong, Elizabeth B Claus, Dora Il'yasova, Joellen Schildkraut, Jill S Barnholtz-Sloan, Sara H Olson, Jonine L Bernstein, Rose K Lai, Minouk J Schoemaker, Matthias Simon, Per Hoffmann, Markus M Nöthen, Karl-Heinz Jöckel, Stephen Chanock, Preetha Rajaraman, Christoffer Johansen, Robert B Jenkins, Beatrice S Melin, Margaret R Wrensch, Marc Sanson, Melissa L Bondy, Richard S Houlston
BACKGROUND: An inverse relationship between allergies with glioma risk has been reported in several but not all epidemiological observational studies. We performed an analysis of genetic variants associated with atopy to assess the relationship with glioma risk using Mendelian randomisation (MR), an approach unaffected by biases from temporal variability and reverse causation that might have affected earlier investigations. METHODS: Two-sample MR was undertaken using genome-wide association study data...
March 15, 2018: BMC Medicine
Li Zheng, Gui-Min Zhang, Yan-Peng Dong, Yi-Fan Wen, Dong Dong, Chu-Zhao Lei, Xing-Lei Qi, Hong Chen, Li-Jun Huo, Yong-Zhen Huang
As a member of MYLK family, MYLK4 gene may play a vital role in muscle development. In this study, one novel single-nucleotide polymorphism (SNP) was identified the bovine MYLK4 by sequencing pooled DNA samples (pool-Seq) and forced polymerase chain reaction-restriction fragment length polymorphism (forced PCR-RFLP) methods. Overall, we reported one mutation (SNP1) in the intron 10 region within the bovine MYLK4 gene in 559 individuals representing five main cattle breeds from China (Nanyang, NY; Qinchuan; Jiaxian, JX; Pinan cattle; and Caidamu cattle, CDM)...
March 14, 2018: Animal Biotechnology
Marius Jacob, Kim Ohl, Tannaz Goodarzi, Sigrid Harendza, Thomas Eggermann, Christina Fitzner, Ralf-Dieter Hilgers, Anna Bolte, Jürgen Floege, Thomas Rauen, Klaus Tenbrock
BACKGROUND/AIMS: IgA nephropathy (IgAN) is the most common form of primary glomerulonephritis and still constitutes one of the most important causes of end-stage renal disease. Abnormal T cell responses may play a role in IgAN pathogenesis. Co-stimulatory molecules such as cytotoxic T lymphocyte-associated antigen 4 (CTLA-4) are important for naive T cells to initiate and terminate immune responses. Single nucleotide polymorphisms (SNPs) in the CTLA4 gene locus are associated with several autoimmune diseases...
March 8, 2018: Kidney & Blood Pressure Research
Sellappan Selvaraju, Sivashanmugam Parthipan, Lakshminarayana Somashekar, B Krishnan Binsila, Atul P Kolte, Arunachalam Arangasamy, Janivara Parameshwaraiah Ravindra, Stephen A Krawetz
With artificial insemination (AI) and other precision dependent assisted reproductive technologies (ART) being followed in large scale in human and animal reproduction, assessing semen quality and fertilizability is under continuous scrutiny. Various tests have been developed to predict semen quality, but so far no single, highly reliable test is available. In this regard, transcriptomic profiling of spermatozoa assumes significance as it carries the information about spermatogenesis, sperm function, and paternal roles in post-fertilization events...
March 14, 2018: Systems Biology in Reproductive Medicine
Øystein A Haaland, Rolv T Lie, Julia Romanowska, Miriam Gjerdevik, Håkon K Gjessing, Astanand Jugessur
Background: It is widely accepted that cleft lip with or without cleft palate (CL/P) results from the complex interplay between multiple genetic and environmental factors. However, a robust investigation of these gene-environment (GxE) interactions at a genome-wide level is still lacking for isolated CL/P. Materials and Methods: We used our R-package Haplin to perform a genome-wide search for GxE effects in isolated CL/P. From a previously published GWAS, genotypes and information on maternal periconceptional cigarette smoking, alcohol intake, and vitamin use were available on 1908 isolated CL/P triads of predominantly European or Asian ancestry...
2018: Frontiers in Genetics
Giorgia Acquaviva, Michela Visani, Dario de Biase, Gianluca Marucci, Enrico Franceschi, Alicia Tosoni, Alba A Brandes, Kerry J Rhoden, Annalisa Pession, Giovanni Tallini
IDH mutational status is required for proper diagnosis according to the WHO criteria revised in 2016. The single nucleotide polymorphism (SNP) rs11554137 (IDH1105GGT ) at codon 105 of IDH1 has been reported in patients with several tumor types, including those with glioma. The aim of this study is to investigate the prevalence of IDH1105GGT in a cohort of brain tumors, and its association with clinicopathologic features and IDH1 and IDH2 missense mutations. Exon 4 of IDH1 and IDH2 was analyzed in a series of brain tumors classified according to current WHO criteria...
March 13, 2018: Scientific Reports
Sarah E Kleinstein, Patrick R Shea, Andrew S Allen, David M Koelle, Anna Wald, David B Goldstein
Herpes simplex virus type 2 (HSV-2) is an incurable viral infection with severity ranging from asymptomatic to frequent recurrences. The viral shedding rate has been shown as a reproducible HSV-2 severity end point that correlates with lesion rates. We used a genome-wide association study (GWAS) to investigate the role of common human genetic variation in HSV-2 severity. We performed a GWAS on 223 HSV-2-positive participants of European ancestry. Severity was measured by viral shedding rate, as defined by the percent of days PCR+ for HSV-2 DNA over at least 30 days...
February 28, 2018: Genes and Immunity
Yu-Lin Li, Shi-Jie Gao, Hong Xu, Yang Liu, Hai-Liang Li, Xing-Yu Chen, Guang-Zhi Ning, Shi-Qing Feng
BACKGROUND: Adolescent idiopathic scoliosis (AIS) is the most common structural deformity of the spine. Genetics constitute largely to AIS, and the rs11190870 polymorphism has the potential for use in public health and clinical settings as a predictor of AIS risk. The aim of the present meta-analysis was to provide exhaustive evidence to evaluate the association of rs11190870 with the susceptibility and severity of adolescent idiopathic scoliosis (AIS) in multiple ethnic groups and different genders...
March 10, 2018: International Journal of Surgery
X Ma, P H Li, M X Zhu, L C He, S P Sui, S Gao, G S Su, N S Ding, Y Huang, Z Q Lu, X G Huang, R H Huang
Litter size has a great impact on the profit of swine producers. Uterine development is an important determinant of reproduction efficiency and could hence affect litter size. Chinese Erhualian pig is one of the most prolific breeds in the world, even though large phenotypic variation in litter size was observed within Erhualian sows. To dissect the genetic basis of the phenotypic variation, we herein conducted genome-wide association studies for total number born and number born alive (NBA) of Erhualian sows...
March 14, 2018: Animal: An International Journal of Animal Bioscience
Stuart K Kim, John P A Ioannidis, Marwa A Ahmed, Andrew L Avins, John P Kleimeyer, Michael Fredericson, Jason L Dragoo
Plantar fascial disorder is comprised of plantar fasciitis and plantar fibromatosis. Plantar fasciitis is the most common cause of heel pain, especially for athletes involved in running and jumping sports. Plantar fibromatosis is a rare fibrous hyperproliferation of the deep connective tissue of the foot. To identify genetic loci associated with plantar fascial disorders, a genome-wide association screen was performed using publically available data from the Research Program in Genes, Environment and Health including 21,624 cases of plantar fascial disorders and 80,879 controls...
March 13, 2018: International Journal of Sports Medicine
Jenni Hällfors, Teemu Palviainen, Ida Surakka, Richa Gupta, Jadwiga Buchwald, Anu Raevuori, Samuli Ripatti, Tellervo Korhonen, Pekka Jousilahti, Pamela A F Madden, Jaakko Kaprio, Anu Loukola
The heritability of nicotine dependence based on family studies is substantial. Nevertheless, knowledge of the underlying genetic architecture remains meager. Our aim was to identify novel genetic variants responsible for interindividual differences in smoking behavior. We performed a genome-wide association study on 1715 ever smokers ascertained from the population-based Finnish Twin Cohort enriched for heavy smoking. Data imputation used the 1000 Genomes Phase I reference panel together with a whole genome sequence-based Finnish reference panel...
March 13, 2018: Addiction Biology
Wilawan Thongda, Honggang Zhao, Dongdong Zhang, Lauren N Jescovitch, Ming Liu, Ximing Guo, Meagan Schrandt, Sean P Powers, Eric Peatman
Culture of the eastern oyster (Crassostrea virginica) is rapidly expanding. Combined with their continuing role as an environmental sentinel species and ecological model, this trend necessitates improved molecular tools for breeding and selection, as well as population assessment and genetic conservation. Here, we describe the development and validation of two panels of 58 single nucleotide polymorphism markers (SNPs) for the species. Population analyses revealed three distinct populations, based on FST values and STRUCTURE, among wild oysters sampled from Delaware Bay (1), northwest Florida (2), Alabama (2), Louisiana (2), and the Texas Gulf Coast (3), consistent with previous microsatellite and mtDNA analyses...
March 13, 2018: Marine Biotechnology
Renata G M Dos Santos, Fernanda C A Pepicelli, Nilce C Batista, Cristina V de Carvalho, Maria A T Bortolini, Rodrigo A Castro
INTRODUCTION AND HYPOTHESIS: We verified the presence of single nucleotide polymorphisms (SNP) rs2236479 of the collagen 18 (COL18A1) and rs2862296 of the lysyl oxidase-like 4 (LOXL-4) genes and the association with pelvic organ prolapse (POP) in Brazilian women and determined risk factors for POP development. METHODS: We assessed 532 postmenopausal women divided into POP (stages III and IV) and control (stages 0 and I) groups by examination and peripheral blood sample collection...
March 12, 2018: International Urogynecology Journal
Matteo Vecellio, Adrian Cortes, Amity R Roberts, Jonathan Ellis, Carla Jayne Cohen, Julian C Knight, Matthew A Brown, Paul Bowness, Bryan Paul Wordsworth
Objectives: To explore the functions of RUNX3 single nucleotide polymorphisms (SNPs) associated with ankylosing spondylitis (AS). Methods: Individual SNP associations were evaluated in 4230 UK cases. Their effects on transcription factor (TF) binding, transcription regulation, chromatin modifications, gene expression and gene interactions were tested by database interrogation, luciferase reporter assays, electrophoretic mobility gel shifts, chromatin immunoprecipitation and real-time PCR...
2018: RMD Open
Z Hashemizadeh, S A Malek-Hosseini, P Badiee
Background: Patients with hepatic diseases are treated with numerous drugs metabolized by cytochrome P450. Objective: To evaluate the frequencies of CYP2C19 variant alleles (*2, *3, and *17), genotypes, and phenotypes, and the relationship between the frequency of these alleles and the underlying hepatic diseases among patients with advanced liver diseases who were candidates for liver transplantation. Methods: The Study was conducted on 120 patients suffering from various hepatic disorders, candidates for liver transplantation, and 52 healthy volunteers...
2018: International Journal of Organ Transplantation Medicine
Joeri J Meijsen, Archie Campbell, Caroline Hayward, David J Porteous, Ian J Deary, Riccardo E Marioni, Kristin K Nicodemus
Lower performances in cognitive ability in individuals with Major Depressive Disorder (MDD) have been observed on multiple occasions. Understanding cognitive performance in MDD could provide a wider insight in the aetiology of MDD as a whole. Using a large, well characterised cohort (N = 7012), we tested for: differences in cognitive performance by MDD status and a gene (single SNP or polygenic score) by MDD interaction effect on cognitive performance. Linear regression was used to assess the association between cognitive performance and MDD status in a case-control, single-episode-recurrent MDD and control-recurrent MDD study design...
March 13, 2018: Translational Psychiatry
Sirui Zhou, Ziv Gan-Or, Amirthagowri Ambalavanan, Dongbing Lai, Pingxing Xie, Cynthia V Bourassa, Stephanie Strong, Jay P Ross, Alexandre Dionne-Laporte, Dan Spiegelman, Nicolas Dupré, Tatiana M Foroud, Lan Xiong, Patrick A Dion, Guy A Rouleau
Intracranial Aneurysm (IA) is a common disease with a worldwide prevalence of 1-3%. In the French-Canadian (FC) population, where there is an important founder effect, the incidence of IA is higher and is frequently seen in families. In this study, we genotyped a cohort of 257 mostly familial FC IA patients and 1,992 FC controls using the Illumina NeuroX SNP-chip. The most strongly associated loci were tested in 34 Inuit IA families and in 32 FC IA patients and 106 FC controls that had been exome sequenced (WES)...
March 12, 2018: Scientific Reports
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