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https://www.readbyqxmd.com/read/29212900/genome-wide-gene-potassium-interaction-analyses-on-blood-pressure-the-gensalt-study-genetic-epidemiology-network-of-salt-sensitivity
#1
Changwei Li, Jiang He, Jing Chen, Jinying Zhao, Dongfeng Gu, James E Hixson, Dabeeru C Rao, Cashell E Jaquish, Treva K Rice, Yun Ju Sung, Tanika N Kelly
BACKGROUND: Gene-environmental interaction analysis can identify novel genetic factors for blood pressure (BP). We performed genome-wide analyses to identify genomic loci that interact with potassium to influence BP using single-marker (1 and 2 df joint tests) and gene-based tests among Chinese participants of the GenSalt study (Genetic Epidemiology Network of Salt Sensitivity). METHODS AND RESULTS: Among 1876 GenSalt participants, the average of 3 urine samples was used to estimate potassium excretion...
December 2017: Circulation. Cardiovascular Genetics
https://www.readbyqxmd.com/read/29212447/on-the-impact-of-relatedness-on-snp-association-analysis
#2
Arnd Gross, Anke Tönjes, Markus Scholz
BACKGROUND: When testing for SNP (single nucleotide polymorphism) associations in related individuals, observations are not independent. Simple linear regression assuming independent normally distributed residuals results in an increased type I error and the power of the test is also affected in a more complicate manner. Inflation of type I error is often successfully corrected by genomic control. However, this reduces the power of the test when relatedness is of concern. In the present paper, we derive explicit formulae to investigate how heritability and strength of relatedness contribute to variance inflation of the effect estimate of the linear model...
December 6, 2017: BMC Genetics
https://www.readbyqxmd.com/read/29184566/selection-signatures-in-the-first-exon-of-paralogous-receptor-kinase-genes-from-the-sym2-region-of-the-pisum-sativum-l-genome
#3
Anton S Sulima, Vladimir A Zhukov, Alexey A Afonin, Aleksandr I Zhernakov, Igor A Tikhonovich, Ludmila A Lutova
During the initial step of the symbiosis between legumes (Fabaceae) and nitrogen-fixing bacteria (rhizobia), the bacterial signal molecule known as the Nod factor (nodulation factor) is recognized by plant LysM motif-containing receptor-like kinases (LysM-RLKs). The fifth chromosome of barrel medic (Medicago truncatula Gaertn.) contains a cluster of paralogous LysM-RLK genes, one of which is known to participate in symbiosis. In the syntenic region of the pea (Pisum sativum L.) genome, three genes have been identified: PsK1 and PsSym37, two symbiosis-related LysM-RLK genes with known sequences, and the unsequenced PsSym2 gene which presumably encodes a LysM-RLK and is associated with increased selectivity to certain Nod factors...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29178884/a-new-panel-of-snps-to-assess-thyroid-carcinoma-risk-a-pilot-study-in-a-brazilian-admixture-population
#4
Isabelle C C Dos Santos, Julieta Genre, Diego Marques, Ananília M G da Silva, Jéssica C Dos Santos, Jéssica N G de Araújo, Victor H R Duarte, Angel Carracedo, Maria Torres-Español, Gisele Bastos, Carlos C de Oliveira Ramos, André D Luchessi, Vivian N Silbiger
BACKGROUND: Thyroid cancer is a common malignant disease of the endocrine system with increasing incidence rates over the last few decades. In this study, we sought to analyze the possible association of 45 single nucleotide polymorphisms (SNPs) with thyroid cancer in a population from Rio Grande do Norte, Brazil. METHODS: Based on histological analysis by a pathologist, 80 normal thyroid specimens of tissue adjacent to thyroid tumors were obtained from the biobank at the Laboratory of Pathology of Liga Norte Riograndense Contra o Câncer, Natal, RN...
November 25, 2017: BMC Medical Genetics
https://www.readbyqxmd.com/read/29164635/influence-of-genetic-variants-of-idh1-idh2-tet2-and-dnmt3a-on-cytarabine-cytotoxicity-in-different-populations
#5
Y Wang, J K Lamba
WHAT IS KNOWN AND OBJECTIVE: Cytarabine (ara-C) is the mainstay of treatment for acute myeloid leukaemia. Resistance and toxicity are common reasons for its treatment failure. Genetic variants of susceptibility genes may be involved in resistance and toxicity to ara-C. This study is aimed to explore the association between influence of genetic variants of IDH1, IDH2, TET2 and DNMT3A on cytarabine cytotoxicity in European and/or African populations. METHODS: HapMap cell lines derived from European descent (CEU) and African descent (YRI) were exposed to ara-C at different concentrations (1, 5, 40 and 80 μmol/L)...
November 21, 2017: Journal of Clinical Pharmacy and Therapeutics
https://www.readbyqxmd.com/read/29151966/polymorphisms-of-ccnb1-associated-with-the-clinical-outcomes-of-platinum-based-chemotherapy-in-chinese-nsclc-patients
#6
Di Liu, Wen Xu, Xi Ding, Yang Yang, Bo Su, Ke Fei
As a crucial cell cycle regulator and G2/M phase promotor, CCNB1 played an essential role in progression of chemotherapy related cell death. Platinum-based chemotherapy is still the first-line chemotherapy regimen for most advanced NSCLC patients. We aim to investigate the correlation of CCNB1 polymorphisms to the efficiency of platinum-based chemotherapy in Chinese advanced NSCLC patients. We enrolled 972 patients with advanced NSCLC, and extracted DNA from their peripheral blood for genotyping CCNB1 four tagSNPs which selected from the Hapmap database...
2017: Journal of Cancer
https://www.readbyqxmd.com/read/29151331/polymorphisms-of-cancer-related-genes-and-risk-of-multipleprimary-malignancies-involving-colorectal-cancer
#7
Peiguo Cao, Li Yu, Anshan Wu, Jingjing Li, Ling Liu, Chunlan Liu, Jianda Zhou, Ke Cao, Chengxian Guo
Background/aim: This study aimed to investigate the relationship between single nucleotide polymorphisms (SNPs) of cancer-related genes and the risk of multiple primary malignancies involving colorectal cancer.Materials and methods: We collected tissue samples from 22 multiple primary cancer patients with primary colorectal cancer and performed genotyping assay for 116 SNP loci from 62 genes encoding peptides functioning in various signaling pathways using the DNA MassARRAY system. The chi-square test was used to compare the differences in base frequencies between patients and a control Chinese population from HapMap through the NCBI database...
November 13, 2017: Turkish Journal of Medical Sciences
https://www.readbyqxmd.com/read/29113108/polymorphisms-in-ffar4-gpr120-gene-modulate-insulin-levels-and-sensitivity-after-fish-oil-supplementation
#8
Bastien Vallée Marcotte, Hubert Cormier, Iwona Rudkowska, Simone Lemieux, Patrick Couture, Marie-Claude Vohl
The objective was to test whether FFAR4 single nucleotide polymorphisms (SNPs) are associated with glycemic control-related traits in humans following fish oil supplementation. A total of 210 participants were given 3 g/day of omega-3 (n-3) fatty acids (FA) (1.9-2.2 g of eicosapentaenoic acid (EPA) and 1.1 g of docosahexaenoic acid (DHA)) during six weeks. Biochemical parameters were taken before and after the supplementation. Using the HapMap database and the tagger procedure in Haploview, 12 tagging SNPs in FFAR4 were selected and then genotyped using TaqMan technology...
November 6, 2017: Journal of Personalized Medicine
https://www.readbyqxmd.com/read/29067977/genetic-variations-in-the-dravidian-population-of-south-west-coast-of-india-implications-in-designing-case-control-studies
#9
Anitha D'Cunha, Lekha Pandit, Chaithra Malli
BACKGROUND & OBJECTIVES: Indian data have been largely missing from genome-wide databases that provide information on genetic variations in different populations. This hinders association studies for complex disorders in India. This study was aimed to determine whether the complex genetic structure and endogamy among Indians could potentially influence the design of case-control studies for autoimmune disorders in the south Indian population. METHODS: A total of 12 single nucleotide variations (SNVs) related to genes associated with autoimmune disorders were genotyped in 370 healthy individuals belonging to six different caste groups in southern India...
June 2017: Indian Journal of Medical Research
https://www.readbyqxmd.com/read/29045655/determinants-of-the-efficacy-of-natural-selection-on-coding-and-noncoding-variability-in-two-passerine-species
#10
Pádraic Corcoran, Toni I Gossmann, Henry J Barton, Jon Slate, Kai Zeng
Population genetic theory predicts that selection should be more effective when the effective population size (Ne) is larger, and that the efficacy of selection should correlate positively with recombination rate. Here, we analyzed the genomes of ten great tits and ten zebra finches. Nucleotide diversity at 4-fold degenerate sites indicates that zebra finches have a 2.83-fold larger Ne. We obtained clear evidence that purifying selection is more effective in zebra finches. The proportion of substitutions at 0-fold degenerate sites fixed by positive selection (α) is high in both species (great tit 48%; zebra finch 64%) and is significantly higher in zebra finches...
November 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28984075/association-of-glucocorticoid-receptor-gene-polymorphisms-with-systemic-lupus-erythematosus-in-a-chinese-population
#11
Yang-Fan Chen, Jian-Hua Xu, Yan-Feng Zou, Li Lian, Fen Wang, Shan-Yu Chen, Jing Cai, Mu Li
OBJECTIVES: To identify the association of glucocorticoid receptor (GR) gene polymorphism with systemic lupus erythematosus (SLE). METHODS: A case-control study was carried out, in which 400 Chinese patients with SLE and 400 normal people were enrolled. DNA was extracted using a genomic DNA extraction kit, and tagged single nucleotide polymorphisms (SNPs) were identified by Haploview (4.0) Project from the Chinese HapMap Project. Eighteen tagged SNPs of the GR gene were genotyped by the Multiplex SNaPshot technique...
October 6, 2017: International Journal of Rheumatic Diseases
https://www.readbyqxmd.com/read/28969913/genetic-predisposition-to-bevacizumab-induced-hypertension
#12
Melissa K Frey, Fanny Dao, Narciso Olvera, Jason A Konner, Maura N Dickler, Douglas A Levine
OBJECTIVE: Bevacizumab, a monoclonal antibody to VEGF, has shown efficacy in ovarian, cervical and endometrial cancer in addition to several other solid tumors. Serious side effects include hypertension, proteinuria, bowel perforation, and thrombosis. We tested the hypothesis that genetic variation in hypertension-associated genes is associated with bevacizumab-induced hypertension (BIH). METHODS: Patients with solid tumors treated with bevacizumab in combination with other therapy were identified from six clinical trials...
September 29, 2017: Gynecologic Oncology
https://www.readbyqxmd.com/read/28929400/can-polymorphisms-in-the-fatty-acid-desaturase-fads-gene-cluster-alter-the-effects-of-fish-oil-supplementation-on-plasma-and-erythrocyte-fatty-acid-profiles-an-exploratory-study
#13
Suzanne J Meldrum, Yuchun Li, Guicheng Zhang, Alexandra E M Heaton, Nina D'Vaz, Judith Manz, Eva Reischl, Berthold V Koletzko, Susan L Prescott, Karen Simmer
PURPOSE: The enzymes encoded by fatty acid desaturases (FADS) genes determine the desaturation of long-chain polyunsaturated fatty acids (LCPUFA). We investigated if haplotype and single nucleotide polymorphisms (SNPs) in FADS gene cluster can influence LCPUFA status in infants who received either fish oil or placebo supplementation. METHODS: Children enrolled in the Infant Fish Oil Supplementation Study (IFOS) were randomly allocated to receive either fish oil or placebo from birth to 6 months of age...
September 19, 2017: European Journal of Nutrition
https://www.readbyqxmd.com/read/28902521/identification-of-novel-protein-expression-changes-following-cisplatin-treatment-and-application-to-combination-therapy
#14
Amy L Stark, Ashraf G Madian, Sawyer W Williams, Vincent Chen, Claudia Wing, Ronald J Hause, Lida Anita To, Amy L Gill, Jamie L Myers, Lidija K Gorsic, Mark F Ciaccio, Kevin P White, Richard B Jones, M Eileen Dolan
Determining the effect of chemotherapeutic treatment on changes in protein expression can provide important targets for overcoming resistance. Due to challenges in simultaneously measuring large numbers of proteins, a paucity of data exists on global changes. To overcome these challenges, we utilized microwestern arrays that allowed us to measure the abundance and modification state of hundreds of cell signaling and transcription factor proteins in cells following drug exposure. HapMap lymphoblastoid cell lines (LCLs) were exposed to cisplatin, a chemotherapeutic agent commonly used to treat testicular, head and neck, non-small cell lung, and gynecological cancers...
September 29, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28894026/associations-of-tgfbr1-and-tgfbr2-gene-polymorphisms-with-the-risk-of-hypospadias-a-case-control-study-in-a-chinese-population
#15
Xin-Rui Han, Xin Wen, Shan Wang, Xiao-Wu Hong, Shao-Hua Fan, Juan Zhuang, Yong-Jian Wang, Zi-Feng Zhang, Meng-Qiu Li, Bin Hu, Qun Shan, Chun-Hui Sun, Ya-Xing Bao, Meng Lin, Tan He, Dong-Mei Wu, Jun Lu, Yuan-Lin Zheng
This case-control study investigated the association of transforming growth factor-β (TGF-β) receptor type I and II (TGFBR1 and TGFBR2) gene polymorphisms with the risk of hypospadias in a Chinese population. One hundred and sixty two patients suffering from hypospadias were enrolled as case group and 165 children who underwent circumcision were recruited as control group. Single nucleotide polymorphisms (SNPs) in TGFBR1 and TGFBR2 genes were selected on the basis of genetic data obtained from HapMap. PCR-restriction fragment length polymorphism (PCR-RFLP) was performed to identify TGFBR1 and TGFBR2 gene polymorphisms and analyze genotype distribution and allele frequency...
October 31, 2017: Bioscience Reports
https://www.readbyqxmd.com/read/28871955/-the-polymorphisms-of-il-13-rs848g-t-and-rs1295686a-g-in-guangxi-population-of-china-and-comparative-analysis
#16
Rong Wang, Huatuo Huang, Yulan Lu, Haimei Qin, Junli Wang, Chunfang Wang, Yesheng Wei
Objective To investigate the distribution characteristics of polymorphisms of rs848G/T and rs1295686A/G in the interleukin 13 (IL-13) gene in Guangxi normal people and compare them with those of Europeans, Beijing peoples, Japanese and Africans published in HapMap. Methods The rs848G/T and rs1295686A/G of IL-13 gene in 275 cases of Guangxi people were genotyped by SNaPshot and DNA sequencing. The differences between groups were analyzed statistically. Results Three genotypes, namely GG, GT and TT, were found in rs848G/T with frequency distributions of 38...
August 2017: Xi Bao Yu Fen Zi Mian Yi Xue za Zhi, Chinese Journal of Cellular and Molecular Immunology
https://www.readbyqxmd.com/read/28842783/population-genetics-of-ifitm3-in-portugal-and-central-africa-reveals-a-potential-modifier-of-influenza-severity
#17
Susana David, Vanessa Correia, Liliana Antunes, Ricardo Faria, José Ferrão, Paula Faustino, Baltazar Nunes, Fernando Maltez, João Lavinha, Helena Rebelo de Andrade
Influenza epidemics are a serious global public health and economic problem. The IFITM3 allele (rs12252-C) was suggested as a population-based genetic risk factor for severe influenza virus infection by A(H1N1)pdm09. We analyzed the population genetics of IFITM3 variants in the Portuguese general population (n = 200) and Central Africans (largely Angolan) (n = 148) as well as its association to influenza severity in Portuguese patients (n = 41). Seven SNPs, within the 352 bp IFITM3 amplicon around rs12252, were identified...
August 25, 2017: Immunogenetics
https://www.readbyqxmd.com/read/28821984/nonassociation-of-homocysteine-gene-polymorphisms-with-treatment-outcome-in-south-indian-tamil-rheumatoid-arthritis-patients
#18
Niveditha Muralidharan, Reena Gulati, Durga Prasanna Misra, Vir S Negi
The aim of the study was to look for any association of MTR 2756A>G and MTRR 66A>G gene polymorphisms with clinical phenotype, methotrexate (MTX) treatment response, and MTX-induced adverse events in South Indian Tamil patients with rheumatoid arthritis (RA). A total of 335 patients with RA were investigated. MTR 2756A>G gene polymorphism was analyzed by PCR-RFLP, and MTRR 66A>G SNP was analyzed by TaqMan 5' nuclease assay. The allele frequencies were compared with HapMap groups. MTR 2756G allele was found to be associated with risk of developing RA...
August 18, 2017: Clinical and Experimental Medicine
https://www.readbyqxmd.com/read/28753063/association-between-adrb2-genetic-polymorphisms-and-the-risk-of-chronic-obstructive-pulmonary-disease-a-case-control-study-in-a-chinese-population
#19
Hui Zhao, Xuan Wu, Chun-Ling Dong, Bi-Ying Wang, Jiao Zhao, Xian-E Cao
OBJECTIVE: This study was designed to investigate the association between single nucleotide polymorphisms (SNPs) of the β2-adrenergic receptor (ADRB2) gene and the risk of chronic obstructive pulmonary disease (COPD) in a Chinese population. METHODS: From January 2010 to October 2014, 261 COPD patients were selected as the case group and 239 healthy subjects were selected as the control group. Pulmonary function tests were performed to detect forced vital capacity (FVC), 1-s forced expiratory volume (FEV1), and FEV1/FVC (%)...
August 2017: Genetic Testing and Molecular Biomarkers
https://www.readbyqxmd.com/read/28748955/bayesian-association-scan-reveals-loci-associated-with-human-lifespan-and-linked-biomarkers
#20
Aaron F McDaid, Peter K Joshi, Eleonora Porcu, Andrea Komljenovic, Hao Li, Vincenzo Sorrentino, Maria Litovchenko, Roel P J Bevers, Sina Rüeger, Alexandre Reymond, Murielle Bochud, Bart Deplancke, Robert W Williams, Marc Robinson-Rechavi, Fred Paccaud, Valentin Rousson, Johan Auwerx, James F Wilson, Zoltán Kutalik
The enormous variation in human lifespan is in part due to a myriad of sequence variants, only a few of which have been revealed to date. Since many life-shortening events are related to diseases, we developed a Mendelian randomization-based method combining 58 disease-related GWA studies to derive longevity priors for all HapMap SNPs. A Bayesian association scan, informed by these priors, for parental age of death in the UK Biobank study (n=116,279) revealed 16 independent SNPs with significant Bayes factor at a 5% false discovery rate (FDR)...
July 27, 2017: Nature Communications
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