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genetic polymorphism

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
Pascal Fleurkens, Agnes van Minnen, Eni S Becker, Iris van Oostrom, Anne Speckens, Mike Rinck, Janna N Vrijsen
Depression risk genes in combination with childhood events have been associated with biased processing as an intermediate phenotype for depression. The aim of the present conceptual replication study was to investigate the role of biased automatic approach-avoidance tendencies as a candidate intermediate phenotype for depression, in the context of genes (5-HTTLPR polymorphism) and childhood trauma. A naturalistic remitted depressed patients sample (N = 209) performed an Approach-Avoidance Task (AAT) with facial expressions (angry, sad, happy and neutral)...
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
D Liao, H Yu, L Han, C Zhong, X Ran, D Wang, L Mo
PURPOSE: Evidences showed that paraoxonase 1 (PON1) gene polymorphism has an impact on women's susceptibility to polycystic ovarian syndrome (PCOS) by influencing the expression and activity of PON1. However, the effects of three PON1 polymorphisms (- 108 C>T, L55M and Q192R) on the incidence of PCOS have generated inconsistent results. Here, we conducted a meta-analysis to investigate the association between PON1 polymorphisms and PCOS risk. METHODS: All eligible trials were identified via systematic searches of multiple literature databases...
March 15, 2018: Journal of Endocrinological Investigation
Daohua Shi, Tiancheng Xie, Jie Deng, Peiguang Niu, Weizhen Wu
PURPOSE: We intend to investigate the association between tacrolimus-induced new-onset diabetes after transplantation (NODAT) and polymorphisms of CYP3A4, CYP3A5, ATP-binding cassette transporter sub-family C member 8 (ABCC8), and glucokinase (GCK) in renal transplant recipients. METHODS: Polymorphisms of CYP3A4 *18B, CYP3A5 *3, ABCC8 T-3C, and GCK G-30A were genotyped in 169 renal transplant recipients. Trough concentrations of tacrolimus were detected by an ELISA kit...
March 15, 2018: European Journal of Clinical Pharmacology
Carolina Ribeiro, Rosa Quinta, Ana Raposo, Ana Valentim, José Albuquerque, Manuela Grazina
Objective: Prospective observational study to analyze CYP2D6 pharmacogenetics in 55 Portuguese adult parturients undergoing elective cesarean section and to investigate the association between CYP2D6 alleles and pain score. Methods: DNA was extracted from peripheral blood by standard methods. Genetic analysis included allelic discrimination (CYP2D6*1, *2, *3, *4, *5, *6, *10, *17, and *41) and copy number determination with TaqMan probes by real-time polymerase chain reaction (PCR)...
March 12, 2018: Pain Medicine: the Official Journal of the American Academy of Pain Medicine
Lu Xie, Wei Guo, Yi Yang, Tao Ji, Jie Xu
5,10-Methylenetrahydrofolate reductase (MTHFR), a key enzyme for folate metabolism, catalyses the irreversible conversion of 5,10-methylenetetrahydrofolate to 5-methyltetrahydrofolate, which is located at the end of the short arm (1p36.3). Two common non-synonymous variants, the C677T (Ala222Val) and A1298C (Glu429Ala), were mainly described with decreased enzymatic activity and an alteration of intracellular folate distribution. Osteosarcomas are currently treated with high dose of methotrexate (MTX). The decreased enzyme activity of MTHFR theoretically could increase the drug action of MTX and at the same time increase toxic and side effect...
February 20, 2018: Oncotarget
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
Zi-Ru Chen, Lu Kuang, Yi-Qun Gao, Ya-Ling Wang, David E Salt, Dai-Yin Chao
Zinc (Zn) is an essential element for plant growth and development, and Zn derived from crop plants in the diet is also important for human health. Here, we report that genetic variation in Heavy Metal-ATPase 4 ( HMA4 ) controls natural variation in leaf Zn content. Investigation of the natural variation in leaf Zn content in a world-wide collection of 349 Arabidopsis thaliana wild collected accessions identified two accessions, Van-0 and Fab-2, which accumulate significantly lower Zn when compared with Col-0...
2018: Frontiers in Plant Science
Yun-Yan Zhang, En Shi, Zhao-Ping Yang, Qi-Fang Geng, Ying-Xiong Qiu, Zhong-Sheng Wang
Parrotia subaequalis is an endangered palaeoendemic tree from disjunct montane sites in eastern China. Due to the lack of effective genomic resources, the genetic diversity and population structure of this endangered species are not clearly understood. In this study, we conducted paired-end shotgun sequencing (2 × 125 bp) of genomic DNA for two individuals of P. subaequalis on the Illumina HiSeq platform. Based on the resulting sequences, we have successfully assembled the complete chloroplast genome of P...
2018: Frontiers in Plant Science
Jeffrey Hsu, Shamone Gore-Panter, Gregory Tchou, Laurie Castel, Beth Lovano, Christine S Moravec, Gosta B Pettersson, Eric E Roselli, A Marc Gillinov, Kenneth R McCurry, Nicholas G Smedira, John Barnard, David R Van Wagoner, Mina K Chung, Jonathan D Smith
BACKGROUND: Genome-wide association studies have identified 23 loci for atrial fibrillation (AF), but the mechanisms responsible for these associations, as well as the causal genes and genetic variants, remain undefined. METHODS: To identify the effect of common genetic variants on gene expression that might explain the mechanisms linking genome-wide association loci with AF risk, we performed RNA sequencing of left atrial appendages from a biracial cohort of 265 subjects...
March 2018: Circ Genom Precis Med
Zhen-Jian Zhuo, Wei Liu, Jiao Zhang, Jinhong Zhu, Ruizhong Zhang, Jue Tang, Tianyou Yang, Yan Zou, Jing He, Huimin Xia
Variations in nucleotide excision repair pathway genes may predispose to initiation of cancers. However, polymorphisms of ERCC1/XPF genes and neuroblastoma risk have not been investigated before. To evaluate the relevance of polymorphisms of ERCC1/XPF genes in influencing neuroblastoma susceptibility, we genotyped four polymorphisms in ERCC1/XPF genes using a Chinese population of 393 cases and 812 controls. The results showed that ERCC1 rs2298881 and rs11615 predisposed to enhanced neuroblastoma risk [CA vs...
March 7, 2018: EBioMedicine
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
Hanaa Hardi, Rahma Melki, Zouhour Boughaleb, Tijani El Harroudi, Souria Aissaoui, Noureddine Boukhatem
BACKGROUND: Genetic determinants of breast cancer (BC) remained largely unknown in the majority of Moroccan patients. The purpose of this study was to explore the association of ERCC2 and MTHFR polymorphisms with genetic susceptibility to breast cancer in Moroccan population. METHODS: We genotyped ERCC2 polymorphisms (rs1799793 (G934A) and rs13181 (A2251C)) and MTHFR polymorphisms (rs1801133 (C677T) and rs1801131 (A1298C)) using TaqMan SNP Genotyping Assays. Genotypes were compared in 151 BC cases and 156 population-matched controls...
March 15, 2018: BMC Cancer
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
Aleksandra Augusciak-Duma, Joanna Witecka, Aleksander L Sieron, Magdalena Janeczko, Jacek J Pietrzyk, Karolina Ochman, Anna Galicka, Maria K Borszewska-Kornacka, Jacek Pilch, Elzbieta Jakubowska-Pietkiewicz
Although over 85% of osteogenesis imperfecta (OI) cases are associated with mutations in the procollagen type I genes (COL1A1 or COL1A2), no hot spots for the mutations were associated with particular clinical phenotypes. Eight patients that were studied here, diagnosed with OI by clinical standards, are from the Polish population with no ethnic background indicated. Previously unpublished mutations were found in six out of those eight patients. Genotypes for polymorphisms (Sp1 - rs1800012 and PvuII - rs412777), linked to bone formation and metabolism were determined...
March 15, 2018: Acta Biochimica Polonica
Krzysztof Karpowicz, Katarzyna Krych, Małgorzata Karpowicz, Witold Nowak, Piotr Gronek
The map of candidate genes that can potentially affect physical fitness becomes larger every year, and they are associated with such aspects as respiratory and cardiovascular stability; body build and composition - especially muscle mass and strength; carbohydrate and lipid metabolism; response to training; and exercise intolerance.The aim of this study was to analyze the relationship between the CA repeat polymorphism of the P1 promoter of the IGF1 gene and the structure of motor skills in the two groups of Polish young athletes in 2011-2013...
March 15, 2018: Acta Biochimica Polonica
ChengLin Zhong, SiChen Li, JingJing Li, FengPeng Li, MingXia Ran, LingYun Qiu, DiYan Li, Qing Zhu, Yan Wang, HuaDong Yin, Gang Shu, Chaowu Yang, XiaoLing Zhao
Peroxisome proliferator activated receptor-alpha (PPARα) and Egl nine homolog 3 (EGLN3) play critical roles in facilitating the adaptation to a hypoxic environment. However, the relationship between EGLN3 and PPARα variants and hypoxic adaptation remains poorly understood in Tibetan chickens. To better understand the effects of genetic variation, we sequenced exons of PPARα and EGLN3 in 138 Lowland chickens (LC) from 7 breeds that were located in Emei, Miyi, Shimian, Wanyuan, Pengxian, and Muchuan in the Sichuan province, and Wenchang in the Hainan province (altitudes for these locations are below 1800 meters)...
2018: PloS One
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
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