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https://www.readbyqxmd.com/read/29045655/determinants-of-the-efficacy-of-natural-selection-on-coding-and-noncoding-variability-in-two-passerine-species
#1
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 analysed the genomes of 10 great tits and 10 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...
October 17, 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
#2
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
#3
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
#4
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
#5
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 13, 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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
https://www.readbyqxmd.com/read/28698882/excnvss-a-noise-robust-method-for-copy-number-variation-detection-in-whole-exome-sequencing-data
#12
Jinhwa Kong, Jaemoon Shin, Jungim Won, Keonbae Lee, Unjoo Lee, Jeehee Yoon
Copy number variations (CNVs) are structural variants associated with human diseases. Recent studies verified that disease-related genes are based on the extraction of rare de novo and transmitted CNVs from exome sequencing data. The need for more efficient and accurate methods has increased, which still remains a challenging problem due to coverage biases, as well as the sparse, small-sized, and noncontinuous nature of exome sequencing. In this study, we developed a new CNV detection method, ExCNVSS, based on read coverage depth evaluation and scale-space filtering to resolve these problems...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28688048/susceptibility-background-for-type-2-diabetes-in-eleven-mexican-indigenous-populations-hnf4a-gene-analysis
#13
M A Granados-Silvestre, M G Ortiz-López, J Granados, S Canizales-Quinteros, Rosenda I Peñaloza-Espinosa, C Lechuga, V Acuña-Alonzo, K Sánchez-Pozos, M Menjivar
The genetic risk of developing type 2 diabetes (T2D) increases in parallel with the proportion of Native American ancestry. Mestizo Mexicans have a 70% Native Amerindian genetic background. The T130I polymorphism in the HNF4A gene has been associated with early-onset T2D in mestizo Mexicans. Thus, the aim of the present study was to evaluate the frequency and relationship of the T130I variant in the HNF4A gene with risk factors for developing T2D in eleven indigenous groups from Mexico. In two groups, all exons of the HNF4A gene were directly sequenced; in the remaining the T130I polymorphism was analyzed by restriction fragment length polymorphism...
July 7, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28687963/sparc-gene-variants-predict-clinical-outcome-in-locally-advanced-and-metastatic-pancreatic-cancer-patients
#14
Cristina Arqueros, Juliana Salazar, M J Arranz, Ana Sebio, Josefina Mora, Ivana Sullivan, María Tobeña, Marta Martín-Richard, Agustí Barnadas, Montserrat Baiget, David Páez
Secreted protein acidic and rich in cysteine (SPARC) is a glycoprotein of the extracellular matrix whose expression can be altered in malignant pancreatic cells and in the adjacent stromal fibroblasts. We evaluated the possible role of SPARC gene variants as prognostic markers for locally advanced and metastatic pancreatic cancer. We analyzed eight tagging single-nucleotide polymorphisms (TagSNPs) in the SPARC gene in 74 patients with pancreatic ductal adenocarcinoma treated with chemotherapy alone or combined with radiotherapy...
August 2017: Medical Oncology
https://www.readbyqxmd.com/read/28632032/plasminogen-activator-inhibitor-type-1-tag-single-nucleotide-polymorphisms-in-patients-with-diabetes-mellitus-type-2-and-diabetic-retinopathy
#15
Vasileios Siokas, Efthimios Dardiotis, Thomas Sokolakis, Maria Kotoula, Sophia V Tachmitzi, Dimitrios Z Chatzoulis, Pavlina Almpanidou, Ioannis Stefanidis, Georgios M Hadjigeorgiou, Evangelia E Tsironi
BACKGROUND: There is accumulating evidence for genetic susceptibility to the development of diabetic retinopathy (DR). The role of plasminogen activator inhibitor-1 (PAI-1) in DR risk remains controversial. OBJECTIVE: The present study was designed to investigate possible influence of PAI-1 gene region polymorphisms on the risk of DR and on the risk of developing DR early vs late in the course of type 2 diabetes mellitus (T2DM). METHODS: A total of 138 patients with DR, 107 patients with T2DM without DR, and 315 healthy controls were recruited...
February 28, 2017: Current Eye Research
https://www.readbyqxmd.com/read/28588705/galnt14-genotype-is-associated-with-perineural-invasion-lymph-node-metastasis-and-overall-survival-in-resected-cholangiocarcinoma
#16
Kung-Hao Liang, Ta-Sen Yeh, Ren-Chin Wu, Chun-Nan Yeh, Chau-Ting Yeh
Cholangiocarcinoma is a rare, sporadic and aggressive type of cancer. The genetic basis of cholangiocarcinoma remains poorly understood. The present study investigated the prognostic role of the N-acetylgalactosaminyltransferase 14 (GALNT14)-rs9679162 genotype, an effective therapeutic response predictor for hepatocellular carcinoma in patients with cholangiocarcinoma receiving surgical resection. A cohort of patients with intrahepatic or perihilar cholangiocarcinoma (n=112) were retrospectively recruited. Of these patients, 31...
June 2017: Oncology Letters
https://www.readbyqxmd.com/read/28580392/a-genome-wide-association-study-meta-analysis-of-clinical-fracture-in-10-012-african-american-women
#17
Kira C Taylor, Daniel S Evans, Digna R Velez Edwards, Todd L Edwards, Tamar Sofer, Guo Li, Youfang Liu, Nora Franceschini, Rebecca D Jackson, Ayush Giri, Macarius Donneyong, Bruce Psaty, Jerome I Rotter, Andrea Z LaCroix, Joanne M Jordan, John A Robbins, Beth Lewis, Marcia L Stefanick, Yongmei Liu, Melissa Garcia, Tamara Harris, Jane A Cauley, Kari E North
BACKGROUND: Osteoporosis is a major public health problem associated with excess disability and mortality. It is estimated that 50-70% of the variation in osteoporotic fracture risk is attributable to genetic factors. The purpose of this hypothesis-generating study was to identify possible genetic determinants of fracture among African American (AA) women in a GWAS meta-analysis. METHODS: Data on clinical fractures (all fractures except fingers, toes, face, skull or sternum) were analyzed among AA female participants in the Women's Health Initiative (WHI) (N = 8155), Cardiovascular Health Study (CHS) (N = 504), BioVU (N = 704), Health ABC (N = 651), and the Johnston County Osteoarthritis Project (JoCoOA) (N = 291)...
December 2016: Bone Reports
https://www.readbyqxmd.com/read/28555039/fads-gene-polymorphisms-fatty-acid-desaturase-activities-and-hdl-c-in-type-2-diabetes
#18
Meng-Chuan Huang, Wen-Tsan Chang, Hsin-Yu Chang, Hsin-Fang Chung, Fang-Pei Chen, Ya-Fang Huang, Chih-Cheng Hsu, Shang-Jyh Hwang
Polyunsaturated fatty acids (PUFA) correlate with risk of dyslipidemia and cardiovascular diseases. Fatty acid desaturase (FADS) single nucleotide polymorphisms (SNPs) modulate circulating PUFA concentrations. This study examined influence of FADS1 and FADS2 genetic variants on desaturase activities and blood lipid concentrations in type 2 diabetes patients, and further assessed their interrelationships. Selected SNPs (FADS1: rs174547, rs174548, rs174550; FADS2: rs174575, rs174576, rs174583, rs498793 and rs2727270) were genotyped in 820 type 2 diabetes patients and compared with those reported in the HapMap...
May 28, 2017: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/28549956/serum-high-sensitive-c-reactive-protein-level-and-crp-genetic-polymorphisms-are-associated-with-abdominal-aortic-aneurysm
#19
Zuo Shangwei, Wei Yingqi, Xiong Jiang, Wu Zhongyin, Juan Juan, Chen Dafang, Hu Yonghua, Guo Wei
BACKGROUND: Abdominal aortic aneurysm (AAA) development involves an inflammatory process with a potential genetic background. C-reactive protein (CRP) is an acute phase protein and was elevated in patients with AAA. The aim of this study was to investigate the association among serum high-sensitive CRP (hsCRP) concentration, its CRP genetic polymorphisms, and AAA. METHODS: Serum hsCRP concentrations and abdominal aorta diameters were measured, and correlation analysis between them was performed in 155 unrelated participants with AAA and 310 non-AAA controls...
May 24, 2017: Annals of Vascular Surgery
https://www.readbyqxmd.com/read/28546950/genetic-polymorphisms-of-multidrug-and-toxin-extrusion-proteins-mate1-and-mate2-in-south-indian-population
#20
Gerard Marshall Raj, Jayanthi Mathaiyan, Mukta Wyawahare, Katiboina Srinivasa Rao, Rekha Priyadarshini
Introduction: Drug transporters are key determinants of pharmacokinetic and pharmacodynamic profiles of certain drugs. SLC47A1 (MATE1) and SLC47A2 (MATE2) are major efflux transporters involved in the hepatic and renal excretion of many cationic drugs including metformin. Our study was proposed to determine the normative frequencies of the single nucleotide polymorphisms (SNPs) rs2289669 and rs12943590 in the SLC47A1 and SLC47A2 genes, respectively, in South Indian population and also to compare those with those of the HapMap populations...
2017: BioImpacts: BI
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