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Single Polymorphism Nucleotide (SNPs)

Clément Niel, Christine Sinoquet, Christian Dina, Ghislain Rocheleau
Motivation: Large scale genome-wide association studies (GWAS) are tools of choice for discovering associations between genotypes and phenotypes. To date, many studies rely on univariate statistical tests for association between the phenotype and each assayed single nucleotide polymorphism (SNP). However, interaction between SNPs, namely epistasis, must be considered when tackling the complexity of underlying biological mechanisms. Epistasis analysis at large scale entails a prohibitive computational burden when addressing the detection of more than two interacting SNPs...
March 14, 2018: Bioinformatics
Sofía I Deperi, Martín E Tagliotti, M Cecilia Bedogni, Norma C Manrique-Carpintero, Joseph Coombs, Ruofang Zhang, David Douches, Marcelo A Huarte
The reported narrow genetic base of cultivated potato (Solanum tuberosum) can be expanded by the introgression of many related species with large genetic diversity. The analysis of the genetic structure of a potato population is important to broaden the genetic base of breeding programs by the identification of different genetic pools. A panel composed by 231 diverse genotypes was characterized using single nucleotide polymorphism (SNP) markers of the Illumina Infinium Potato SNP Array V2 to identify population structure and assess genetic diversity using discriminant analysis of principal components (DAPC) and pedigree analysis...
2018: PloS One
Hirofumi Chiba, Yoichi Kakuta, Yoshitaka Kinouchi, Yosuke Kawai, Kazuhiro Watanabe, Munenori Nagao, Takeo Naito, Motoyuki Onodera, Rintaro Moroi, Masatake Kuroha, Yoshitake Kanazawa, Tomoya Kimura, Hisashi Shiga, Katsuya Endo, Kenichi Negoro, Masao Nagasaki, Michiaki Unno, Tooru Shimosegawa
BACKGROUND: Inflammatory bowel disease (IBD) has an unknown etiology; however, accumulating evidence suggests that IBD is a multifactorial disease influenced by a combination of genetic and environmental factors. The influence of genetic variants on DNA methylation in cis and cis effects on expression have been demonstrated. We hypothesized that IBD susceptibility single-nucleotide polymorphisms (SNPs) regulate susceptibility gene expressions in cis by regulating DNA methylation around SNPs...
2018: PloS One
Laura Tarancon-Diez, Rebeca S De Pablo-Bernal, José Luis Jiménez, Ana I Álvarez-Ríos, Miguel Genebat, Isaac Rosado-Sánchez, María-Ángeles Muñoz-Fernández, Ezequiel Ruiz-Mateos, Manuel Leal
OBJECTIVE: Cardiovascular diseases (CVDs) are one of the main causes of morbimortality in HIV-infected patients on suppressive antiretroviral therapy. The objective of this work was to evaluate the role of single nucleotide polymorphisms (SNPs) in lipopolysaccharide (LPS) Toll-like receptor 4 (TLR4) and CVDs occurrence in HIV-infected patients. Additionally, the functional consequences of carrying these SNPs were analyzed. METHODS: The association of TLR4 SNPs, Asp299Gly/Thr399Ile with CVDs occurrence was analyzed using multivariate logistic regression models...
March 15, 2018: AIDS
Xianhua Wang, Aiguo Ma, Xiuxia Han, Aishan Litifu, Feng Xue
Seven single-nucleotide polymorphism (SNP) sites located in ASAP1 gene have been found associated with tuberculosis (TB) susceptibility by genome-wide association studies in Russia. The case-control study was carried out to test whether these seven SNPs were associated with susceptibility to TB in a Chinese Xinjiang Muslim population. The seven SNPs were genotyped in a case-control design that included 780 Xinjiang Muslim subjects (400 TB patients and 380 controls). Multiplex PCR and direct sequencing were used to detect ASAP1 gene polymorphisms...
April 2018: Experimental and Therapeutic Medicine
Katie M O'Brien, Dale P Sandler, Min Shi, Quaker E Harmon, Jack A Taylor, Clarice R Weinberg
Genetic factors likely influence individuals' concentrations of 25-hydroxyvitamin D [25(OH)D], a biomarker of vitamin D exposure previously linked to reduced risk of several chronic diseases. We conducted a genome-wide association study of serum 25(OH)D (assessed using liquid chromatography-tandem mass spectrometry) and 386,449 single nucleotide polymorphisms (SNPs). Our sample consisted of 1,829 participants randomly selected from the Sister Study, a cohort of women who had a sister with breast cancer but had never had breast cancer themselves...
2018: Frontiers in Genetics
Amr El Noury, Osama Azmy, Jehan Alsharnoubi, Sameh Salama, Ahmed Okasha, Weaam Gouda
OBJECTIVES: Pathophysiological similarity exists between gestational diabetes mellitus (GDM) and type 2 diabetes mellitus with common genetic origin. Genetic liability for GDM in our population is still not researched. The goal was to reveal the genotypic and allele frequency differences of 2 single nucleotide polymorphisms (SNPs) namely, CDKAL1 (rs7754840) and CDKN2A/2B (rs10811661) between GDM pregnancies and normal pregnancies. We assessed them by real time polymerase chain reaction using Taqman® allelic discrimination assays...
March 15, 2018: BMC Research Notes
K Soelberg, A C Nilsson, C Nielsen, S Jarius, M Reindl, B Wildemann, S T Lillevang, N Asgari
BACKGROUND: Optic neuritis (ON) is an inflammatory optic neuropathy, where the genetic and autoimmune dependency remains poorly characterized. OBJECTIVE: To investigate autoimmune and immunogenetic aspects of ON. METHOD: In a prospective population-based cohort 51 patients with ON were included. At follow up 20 patients had progressed to multiple sclerosis (MS-ON). All patients were screened for neuronal and systemic autoantibodies. HLA genotypes and allele and genotype frequencies of the PTPN22 C1858T and the PD-1...
March 7, 2018: Multiple Sclerosis and related Disorders
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
Hui Yu, Xinxin You, Jia Li, Xinhui Zhang, Shuai Zhang, Shoujia Jiang, Xueqiang Lin, Hao-Ran Lin, Zining Meng, Qiong Shi
The orange-spotted grouper, Epinephelus coioides, is one of the most popular fish in China and Southeast Asian countries because of its important economic value. However, molecular mechanism underlying the growth of orange-spotted grouper has never been fully understood. Herein, we performed a genome-wide association study (GWAS) on a natural population of 198 individuals aiming to screen the whole genome of orange-spotted grouper for identification of growth-related loci by restrictionsite associated DNA sequencing...
March 12, 2018: Science China. Life Sciences
Aleksander H Erga, Ingvild Dalen, Anastasia Ushakova, Janete Chung, Charalampos Tzoulis, Ole Bjørn Tysnes, Guido Alves, Kenn Freddy Pedersen, Jodi Maple-Grødem
Introduction: Impulse control disorders (ICDs) are frequent non-motor symptoms in Parkinson's disease (PD), with potential negative effects on the quality of life and social functioning. ICDs are closely associated with dopaminergic therapy, and genetic polymorphisms in several neurotransmitter pathways may increase the risk of addictive behaviors in PD. However, clinical differentiation between patients at risk and patients without risk of ICDs is still troublesome. The aim of this study was to investigate if genetic polymorphisms across several neurotransmitter pathways were associated with ICD status in patients with PD...
2018: Frontiers in Neurology
Roberta Pastorino, Anna Puggina, Robert Carreras-Torres, Pagona Lagiou, Ivana Holcátová, Lorenzo Richiardi, Kristina Kjaerheim, Antonio Agudo, Xavier Castellsagué, Tatiana V Macfarlane, Luigi Barzan, Cristina Canova, Nalin S Thakker, David I Conway, Ariana Znaor, Claire M Healy, Wolfgang Ahrens, David Zaridze, Neonilia Szeszenia-Dabrowska, Jolanta Lissowska, Eleonora Fabianova, Ioan Nicolae Mates, Vladimir Bencko, Lenka Foretova, Vladimir Janout, Paul Brennan, Valérie Gaborieau, James D McKay, Stefania Boccia
With the aim to dissect the effect of adult height on head and neck cancer (HNC), we use the Mendelian randomization (MR) approach to test the association between genetic instruments for height and the risk of HNC. 599 single nucleotide polymorphisms (SNPs) were identified as genetic instruments for height, accounting for 16% of the phenotypic variation. Genetic data concerning HNC cases and controls were obtained from a genome-wide association study. Summary statistics for genetic association were used in complementary MR approaches: the weighted genetic risk score (GRS) and the inverse-variance weighted (IVW)...
March 14, 2018: Scientific Reports
Qingtao Meng, Shenshen Wu, Yajie Wang, Jin Xu, Hao Sun, Runze Lu, Na Gao, Hongbao Yang, Xiaobo Li, Boping Tang, Michael Aschner, Rui Chen
Myeloperoxidase (MPO) promoter single nucleotide polymorphisms (SNPs) rs2243828 (-764T>C) and rs2333227 (G-463A) program malignant phenotypes by regulating MPO transcriptional activity. In this study, we enrolled a total of 1,175 controls and 1,078 colorectal cancer (CRC) patients with comprehensive clinical and survival information to assess whether these SNPs could affect the susceptibility and development of CRC. The MPO rs2333227 TT genotype significantly increased the risk of CRC and decreased the overall survival time of patients...
March 14, 2018: Cancer Research
Ana Huđek, Lucija Škara, Barbara Smolkovič, Snježana Kazazić, Sanda Ravlić, Lucia Nanić, Martina Matovinović Osvatić, Jozo Jelčić, Ivica Rubelj, Višnja Bačun-Družina
Obesity is composed of multifunctional interactions of eating habits, behaviors, microbiota, genetics, and other unknown factors. We hypothesize that correlations occur between the fat mass and obesity-associated single nucleotide polymorphisms (FTO SNPs), the composition of microorganisms in the saliva, and life habits in obese women from Zagreb County. Our results of the analysis of 3 FTO SNPs showed a statistically significant positive correlation among the frequencies of the high-risk genotypes AA rs9939609 (P = ...
February 2018: Nutrition Research
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
Ji Young Lee, Hyun Mi Kim, Mi Ju Kim, Hyun-Hwa Cha, Won Joon Seong
OBJECTIVE: To compare single nucleotide polymorphisms (SNPs) in the 3'-untranslated region (3'UTR) of human leukocyte antigen (HLA)-G in placentas between spontaneous preterm birth and preeclampsia pregnancies. RESULTS: Placental samples matched for gestational age were obtained from 20 cases of spontaneous preterm births and 19 cases of preeclampsia. Genomic deoxyribonucleic acid was extracted from placenta tissue and the 3'UTR region of HLA-G was amplified via polymerase chain reaction...
March 14, 2018: BMC Research Notes
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
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
R W W Brouwer, M C G N van den Hout, C E M Kockx, E Brosens, B Eussen, A de Klein, F Sleutels, W F J van IJcken
Motivation: PCR-based DNA enrichment followed by massively parallel sequencing is a straightforward and cost effective method to sequence genes up to high depth. The full potential of amplicon based sequencing assays is currently not achieved as analysis methods do not take into account the source amplicons of the detected variants. Tracking the source amplicons has the potential to identify systematic biases, enhance variant calling and improve the designs of future assays. Results: We present Nimbus, a software suite for the analysis of amplicon based sequencing data...
March 10, 2018: Bioinformatics
Tamas Jilling, Namasivayam Ambalavanan, C Michael Cotten, Colin A Martin, Akhil Maheshwari, Kurt Schibler, Joshua Levy, Grier P Page
BACKGROUND: Twin studies suggest that genetic factors may account for up to 50% increased risk for necrotizing enterocolitis (NEC), but genome-wide association studies (GWAS) for NEC are lacking. METHODS: Genotyping was done on Illumina BeadChip, followed by analysis using PLINK with logistic regression under an additive model. RESULTS: Among 751 extremely low birth weight (<1000 g, >401 g) neonates, 30 had surgical NEC. 261 single nucleotide polymorphisms (SNPs) showed association with NEC at P<0...
March 14, 2018: Pediatric Research
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