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Prediction snp

Xu Chen, Stefan Gustafsson, Thomas Whitington, Yan Borné, Erik Lorentzen, Jitong Sun, Peter Almgren, Jun Su, Robert Karlsson, Jie Song, Yi Lu, Yiqiang Zhan, Sara Hägg, Per Svensson, Karin E Smedby, Susan L Slager, Erik Ingelsson, Cecilia M Lindgren, Andrew P Morris, Olle Melander, Thomas Karlsson, Ulf de Faire, Kenneth Caidahl, Gunnar Engström, Lars Lind, Mikael C I Karlsson, Nancy L Pedersen, Johan Frostegård, Patrik K E Magnusson
Phosphorylcholine (PC) is an epitope on oxidized low-density lipoprotein (oxLDL), apoptotic cells and several pathogens like Streptococcus pneumoniae. Immunoglobulin M against PC (IgM anti-PC) has the ability to inhibit uptake of oxLDL by macrophages and increase clearance of apoptotic cells. From our genome-wide association studies (GWAS) in four European-ancestry cohorts, six SNPs in 11q24.1 were discovered (in 3002 individuals) and replicated (in 646 individuals) to be associated with serum level of IgM anti-PC (the leading SNP rs35923643-G, combined beta=0...
March 14, 2018: Human Molecular Genetics
Germano Orrù, Mauro Giovanni Carta, Alessia Bramanti
Background: Several studies have shown that the Single Nucleotide Polymorphism (SNP) in the CACAN1C gene, rs1006737, is related to different mood disorder illnesses, such as bipolar disorder and schizophrenia. Current day molecular procedures for allele detection of this gene can be very expensive and time consuming. Hence, a sensitive and specific molecular procedure for detecting these mutations in a large number of subjects is desirable, especially for research groups who have no complex laboratory equipment...
2018: Clinical Practice and Epidemiology in Mental Health: CP & EMH
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
Evangelia Elenis, Alkistis Skalkidou, Agneta Skoog-Svanberg, Gunilla Sydsjö, Anneli Stavreus-Evers, Helena Åkerud
BACKGROUND: Preeclampsia and gestational hypertensive disorders are thought to occur due to endothelial cell dysfunction and abnormal placentation, triggered by angiogenesis-related factors yet undetermined. The aim of this study was to investigate whether a genetic polymorphism (SNP) of Histidine-rich glycoprotein (HRG), HRG C633T SNP, is associated with gestational hypertensive disorders. METHODS: It was performed a nested case-control study from the BASIC Cohort of Uppsala University Hospital comprising 92 women diagnosed with gestational hypertensive disorders without other comorbidities and 200 women with full term uncomplicated pregnancies, all genotyped regarding HRG C633T SNP...
March 14, 2018: BMC Medical Genetics
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
Ewelina Gowin, Bogna Świątek-Kościelna, Ewelina Kałużna, Ewa Strauss, Jacek Wysocki, Jerzy Nowak, Michał Michalak, Danuta Januszkiewicz-Lewandowska
The aim of this study is to describe the prevalence of single single-nucleotide polymorphisms (SNPs) as well as their combinations in genes encoding proteins involved in the immune response in children with bacterial meningitis. The prospective study group consisted of 39 children with bacterial meningitis and 49 family members surveyed between 2012 and 2016. Eleven SNPs in five genes involved in immune response were analysed. The mean number of minor frequency alleles (MAF) of studied SNPs was lowest in the control group and highest in patients with pneumococcal meningitis...
January 1, 2018: Innate Immunity
Masoud Tajamolian, Parisa Kolahdouz, Parvaneh Nikpour, Seyed Khalil Forouzannia, Mohammad Hasan Sheikhha, Ehsan Farashahi Yazd
Background: Familial hypercholesterolemia (FH) is a disorder that is inherited by autosomal dominant pattern. The main cause of FH disease is the occurrence of mutations in low-density lipoprotein receptor (LDLR) gene sequence, as well as apolipoprotein B and proprotein convertase subtilisin/kexin type 9 genes, located in the next ranks, respectively. Materials and Methods: Forty-five unrelated Iranian patients with FH were screened using a high-resolution melting (HRM) method for exon 9 along with intron/exon boundaries of LDLR gene...
2018: Advanced Biomedical Research
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
Daisuke Ogawa, Eiji Yamamoto, Toshikazu Ohtani, Noriko Kanno, Hiroshi Tsunematsu, Yasunori Nonoue, Masahiro Yano, Toshio Yamamoto, Jun-Ichi Yonemaru
Multi-parent advanced generation inter-cross (MAGIC) lines have broader genetic variation than bi-parental recombinant inbred lines. Genome-wide association study (GWAS) using high number of DNA polymorphisms such as single-nucleotide polymorphisms (SNPs) is a popular tool for allele mining in MAGIC populations, in which the associations of phenotypes with SNPs are investigated; however, the effects of haplotypes from multiple founders on phenotypes are not considered. Here, we describe an improved method of allele mining using the newly developed Japan-MAGIC (JAM) population, which is derived from eight high-yielding rice cultivars in Japan...
March 12, 2018: Scientific Reports
William Manley, Michael P Moreau, Marco Azaro, Stephen K Siecinski, Gillian Davis, Steven Buyske, Veronica Vieland, Anne S Bassett, Linda Brzustowicz
Despite much progress, few genetic findings for schizophrenia have been assessed by functional validation experiments at the molecular level. We previously reported evidence for genetic linkage of broadly defined schizophrenia to chromosome 17q25 in a sample of 24 multiplex families. 2,002 SNPs under this linkage peak were analyzed for evidence of linkage disequilibrium using the posterior probability of linkage (PPL) framework. SNP rs1060120 produced the strongest evidence for association, with a PPLD|L score of 0...
2018: PloS One
Zixiang Wen, Ruijuan Tan, Shichen Zhang, Paul J Collins, Jiazheng Yuan, Wenyan Du, Cuihua Gu, Shujun Ou, Qijian Song, Yong-Qiang Charles An, John F Boyse, Martin I Chilvers, Dechun Wang
White mold of soybean, caused by Sclerotinia sclerotiorum (Lib.) de Bary, is a necrotrophic fungus capable of infecting a wide range of plants. To dissect the genetic architecture of resistance to white mold, a high-density customized single nucleotide polymorphism (SNP) array (52,041 SNPs) was used to genotype two soybean diversity panels. Combined with resistance variation data observed in the field and greenhouse environments, genome-wide association studies (GWAS) were conducted to identify quantitative trait loci (QTL) controlling resistance against white mold...
March 12, 2018: Plant Biotechnology Journal
Camille Ribeyre, Federico Carlini, Céline René, François Jordier, Christophe Picard, Jacques Chiaroni, Laurent Abi-Rached, Philippe Gouret, Grégory Marin, Nicolas Molinari, Pascal Chanez, Julien Paganini, Delphine Gras, Julie Di Cristofaro
Human leukocyte antigen (HLA)-G, a HLA class Ib molecule, interacts with receptors on lymphocytes such as T cells, B cells, and natural killer cells to influence immune responses. Unlike classical HLA molecules, HLA-G expression is not found on all somatic cells, but restricted to tissue sites, including human bronchial epithelium cells (HBEC). Individual variation in HLA-G expression is linked to its genetic polymorphism and has been associated with many pathological situations such as asthma, which is characterized by epithelium abnormalities and inflammatory cell activation...
2018: Frontiers in Immunology
Varun Warrier, Roberto Toro, Bhismadev Chakrabarti, Anders D Børglum, Jakob Grove, David A Hinds, Thomas Bourgeron, Simon Baron-Cohen
Empathy is the ability to recognize and respond to the emotional states of other individuals. It is an important psychological process that facilitates navigating social interactions and maintaining relationships, which are important for well-being. Several psychological studies have identified difficulties in both self-report and performance-based measures of empathy in a range of psychiatric conditions. To date, no study has systematically investigated the genetic architecture of empathy using genome-wide association studies (GWAS)...
March 12, 2018: Translational Psychiatry
Kathleen E Hupfeld, David E Vaillancourt, Rachael D Seidler
Mobility and memory declines with aging can limit independence. Several single-nucleotide polymorphisms have been associated with cognitive performance, but studies investigating motor function are scant. We examined 4 single-nucleotide polymorphisms involved in dopaminergic metabolism: BDNF (Val66Met), DRD3 (Ser9Gly), DBH (C>T), and COMT (Val158Met) for their relationship to motor and cognitive function in healthy older adults (n = 4605 and n = 7331) who participated in the U.S. Health and Retirement Study...
February 10, 2018: Neurobiology of Aging
Mansi Desai, J B Chauhan
Methylenetetrahydrofolate reductase (MTHFR) is a key enzyme involved in folate metabolism and plays a central role in DNA methylation and biosynthesis. MTHFR mutations may alter the cellular folate supply which in turn affects nucleic acid synthesis, DNA methylation and chromosomal damage. The identification of number of SNPs in the human genome growing nowadays and hence, the evaluation of functional & structural consequences of these SNPs is very laborious by means of experimental analysis. Therefore, in the present study, recently developed various computational algorithms have been used which can predict the functional and structural consequences of the SNPs...
February 27, 2018: Computational Biology and Chemistry
Xiaoyun Lei, Dejian Yuan, Zuobin Zhu, Shi Huang
Lung cancer is the leading cause of cancer deaths in both men and women in the US. While most sporadic lung cancer cases are related to environmental factors such as smoking, genetic susceptibility may also play an important role and a number of lung cancer associated single-nucleotide polymorphisms (SNPs) have been identified although many remain to be found. The collective effects of genome-wide minor alleles of common SNPs, or the minor allele content (MAC) in an individual, have been linked with quantitative variations of complex traits and diseases...
March 10, 2018: Heredity
Romain Madelaine, James H Notwell, Gemini Skariah, Caroline Halluin, Charles C Chen, Gill Bejerano, Philippe Mourrain
Thousands of human disease-associated single nucleotide polymorphisms (SNPs) lie in the non-coding genome, but only a handful have been demonstrated to affect gene expression and human biology. We computationally identified risk-associated SNPs in deeply conserved non-exonic elements (CNEs) potentially contributing to 45 human diseases. We further demonstrated that human CNE1/rs17421627 associated with retinal vasculature defects showed transcriptional activity in the zebrafish retina, while introducing the risk-associated allele completely abolished CNE1 enhancer activity...
March 6, 2018: Nucleic Acids Research
Lucía Trilla-Fuertes, Angelo Gámez-Pozo, Jorge M Arevalillo, Mariana Díaz-Almirón, Guillermo Prado-Vázquez, Andrea Zapater-Moros, Hilario Navarro, Rosa Aras-López, Irene Dapía, Rocío López-Vacas, Paolo Nanni, Sara Llorente-Armijo, Pedro Arias, Alberto M Borobia, Paloma Maín, Jaime Feliú, Enrique Espinosa, Juan Ángel Fresno Vara
Metabolic reprogramming is a hallmark of cancer. It has been described that breast cancer subtypes present metabolism differences and this fact enables the possibility of using metabolic inhibitors as targeted drugs in specific scenarios. In this study, breast cancer cell lines were treated with metformin and rapamycin, showing a heterogeneous response to treatment and leading to cell cycle disruption. The genetic causes and molecular effects of this differential response were characterized by means of SNP genotyping and mass spectrometry-based proteomics...
February 9, 2018: Oncotarget
Yongle Li, Pradeep Ruperao, Jacqueline Batley, David Edwards, Tanveer Khan, Timothy D Colmer, Jiayin Pang, Kadambot H M Siddique, Tim Sutton
Drought tolerance is a complex trait that involves numerous genes. Identifying key causal genes or linked molecular markers can facilitate the fast development of drought tolerant varieties. Using a whole-genome resequencing approach, we sequenced 132 chickpea varieties and advanced breeding lines and found more than 144,000 single nucleotide polymorphisms (SNPs). We measured 13 yield and yield-related traits in three drought-prone environments of Western Australia. The genotypic effects were significant for all traits, and many traits showed highly significant correlations, ranging from 0...
2018: Frontiers in Plant Science
Andrés J Cortés, Matthew W Blair
Drought will reduce global crop production by >10% in 2050 substantially worsening global malnutrition. Breeding for resistance to drought will require accessing crop genetic diversity found in the wild accessions from the driest high stress ecosystems. Genome-environment associations (GEA) in crop wild relatives reveal natural adaptation, and therefore can be used to identify adaptive variation. We explored this approach in the food crop Phaseolus vulgaris L., characterizing 86 geo-referenced wild accessions using genotyping by sequencing (GBS) to discover single nucleotide polymorphisms (SNPs)...
2018: Frontiers in Plant Science
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