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https://www.readbyqxmd.com/read/29675042/genetic-variability-in-eif2-%C3%AE-gene-is-associated-with-islet-%C3%AE-cell-function-in-the-development-of-diabetes-in-a-chinese-han-population
#1
Nan Gu, Xiaowei Ma, Jianwei Zhang, Mengmeng Jin, Nan Feng, Ruifen Deng, Ge Bai, Hong Zhang, Xiaohui Guo
Aims: Protein kinase-like endoplasmic reticulum kinase (PERK)/eukaryotic translation initiation factor 2 alpha ( eIF2α ) pathway mutations lead to failure of β -cell function. The aim of this article was to assess the association between eIF2α and the risk of glucose metabolism abnormalities. Methods: Two eIF2α SNPs (rs9840992 T>C and rs13072593 A>G) were selected based on CHB data from HapMap, and 1466 unrelated nondiabetes individuals were genotyped...
2018: International Journal of Endocrinology
https://www.readbyqxmd.com/read/29674479/regionally-clustered-abcc8-polymorphisms-in-a-prospective-cohort-predict-cerebral-oedema-and-outcome-in-severe-traumatic-brain-injury
#2
Ruchira Menka Jha, Theresa A Koleck, Ava M Puccio, David O Okonkwo, Seo-Young Park, Benjamin E Zusman, Robert S B Clark, Lori A Shutter, Jessica S Wallisch, Philip E Empey, Patrick M Kochanek, Yvette P Conley
OBJECTIVE: ABCC8 encodes sulfonylurea receptor 1, a key regulatory protein of cerebral oedema in many neurological disorders including traumatic brain injury (TBI). Sulfonylurea-receptor-1 inhibition has been promising in ameliorating cerebral oedema in clinical trials. We evaluated whether ABCC8 tag single-nucleotide polymorphisms predicted oedema and outcome in TBI. METHODS: DNA was extracted from 485 prospectively enrolled patients with severe TBI. 410 were analysed after quality control...
April 19, 2018: Journal of Neurology, Neurosurgery, and Psychiatry
https://www.readbyqxmd.com/read/29615764/genome-wide-screen-for-universal-individual-identification-snps-based-on-the-hapmap-and-1000-genomes-databases
#3
Erwen Huang, Changhui Liu, Jingjing Zheng, Xiaolong Han, Weian Du, Yuanjian Huang, Chengshi Li, Xiaoguang Wang, Dayue Tong, Xueling Ou, Hongyu Sun, Zhaoshu Zeng, Chao Liu
Differences among SNP panels for individual identification in SNP-selecting and populations led to few common SNPs, compromising their universal applicability. To screen all universal SNPs, we performed a genome-wide SNP mining in multiple populations based on HapMap and 1000Genomes databases. SNPs with high minor allele frequencies (MAF) in 37 populations were selected. With MAF from ≥0.35 to ≥0.43, the number of selected SNPs decreased from 2769 to 0. A total of 117 SNPs with MAF ≥0.39 have no linkage disequilibrium with each other in every population...
April 3, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29551892/type-2-diabetes-mellitus-distribution-of-genetic-markers-in-kazakh-population
#4
Nurgul Sikhayeva, Yerkebulan Talzhanov, Aisha Iskakova, Jarkyn Dzharmukhanov, Raushan Nugmanova, Elena Zholdybaeva, Erlan Ramanculov
Background: Ethnic differences exist in the frequencies of genetic variations that contribute to the risk of common disease. This study aimed to analyse the distribution of several genes, previously associated with susceptibility to type 2 diabetes and obesity-related phenotypes, in a Kazakh population. Methods: A total of 966 individuals belonging to the Kazakh ethnicity were recruited from an outpatient clinic. We genotyped 41 common single nucleotide polymorphisms (SNPs) previously associated with type 2 diabetes in other ethnic groups and 31 of these were in Hardy-Weinberg equilibrium...
2018: Clinical Interventions in Aging
https://www.readbyqxmd.com/read/29507384/mseq-cnv-accurate-detection-of-copy-number-variation-from-sequencing-of-multiple-samples
#5
Seyed Amir Malekpour, Hamid Pezeshk, Mehdi Sadeghi
Currently a few tools are capable of detecting genome-wide Copy Number Variations (CNVs) based on sequencing of multiple samples. Although aberrations in mate pair insertion sizes provide additional hints for the CNV detection based on multiple samples, the majority of the current tools rely only on the depth of coverage. Here, we propose a new algorithm (MSeq-CNV) which allows detecting common CNVs across multiple samples. MSeq-CNV applies a mixture density for modeling aberrations in depth of coverage and abnormalities in the mate pair insertion sizes...
March 5, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29439659/validation-of-genotype-imputation-in-southeast-asian-populations-and-the-effect-of-single-nucleotide-polymorphism-annotation-on-imputation-outcome
#6
Worachart Lert-Itthiporn, Bhoom Suktitipat, Harald Grove, Anavaj Sakuntabhai, Prida Malasit, Nattaya Tangthawornchaikul, Fumihiko Matsuda, Prapat Suriyaphol
BACKGROUND: Imputation involves the inference of untyped single nucleotide polymorphisms (SNPs) in genome-wide association studies. The haplotypic reference of choice for imputation in Southeast Asian populations is unclear. Moreover, the influence of SNP annotation on imputation results has not been examined. METHODS: This study was divided into two parts. In the first part, we applied imputation to genotyped SNPs from Southeast Asian populations from the Pan-Asian SNP database...
February 13, 2018: BMC Medical Genetics
https://www.readbyqxmd.com/read/29389922/novel-findings-with-reassessment-of-exome-data-implications-for-validation-testing-and-interpretation-of-genomic-data
#7
Kristin McDonald Gibson, Addie Nesbitt, Kajia Cao, Zhenming Yu, Elizabeth Denenberg, Elizabeth DeChene, Qiaoning Guan, Elizabeth Bhoj, Xiangdong Zhou, Bo Zhang, Chao Wu, Holly Dubbs, Alisha Wilkens, Livija Medne, Emma Bedoukian, Peter S White, Jeffrey Pennington, Minjie Lou, Laura Conlin, Dimitri Monos, Mahdi Sarmady, Eric Marsh, Elaine Zackai, Nancy Spinner, Ian Krantz, Matt Deardorff, Avni Santani
PurposeThe objective of this study was to assess the ability of our laboratory's exome-sequencing test to detect known and novel sequence variants and identify the critical factors influencing the interpretation of a clinical exome test.MethodsWe developed a two-tiered validation strategy: (i) a method-based approach that assessed the ability of our exome test to detect known variants using a reference HapMap sample, and (ii) an interpretation-based approach that assessed our relative ability to identify and interpret disease-causing variants, by analyzing and comparing the results of 19 randomly selected patients previously tested by external laboratories...
October 12, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29337087/genetic-polymorphisms-of-pharmacogenomic-vip-variants-in-the-yi-population-from-china
#8
Mengdan Yan, Dianzhen Li, Guige Zhao, Jing Li, Fanglin Niu, Bin Li, Peng Chen, Tianbo Jin
INTRODUCTION: Drug response and target therapeutic dosage are different among individuals. The variability is largely genetically determined. With the development of pharmacogenetics and pharmacogenomics, widespread research have provided us a wealth of information on drug-related genetic polymorphisms, and the very important pharmacogenetic (VIP) variants have been identified for the major populations around the world whereas less is known regarding minorities in China, including the Yi ethnic group...
March 30, 2018: Gene
https://www.readbyqxmd.com/read/29300887/construction-of-the-third-generation-zea-mays-haplotype-map
#9
Robert Bukowski, Xiaosen Guo, Yanli Lu, Cheng Zou, Bing He, Zhengqin Rong, Bo Wang, Dawen Xu, Bicheng Yang, Chuanxiao Xie, Longjiang Fan, Shibin Gao, Xun Xu, Gengyun Zhang, Yingrui Li, Yinping Jiao, John F Doebley, Jeffrey Ross-Ibarra, Anne Lorant, Vince Buffalo, M Cinta Romay, Edward S Buckler, Doreen Ware, Jinsheng Lai, Qi Sun, Yunbi Xu
Background: Characterization of genetic variations in maize has been challenging, mainly due to deterioration of collinearity between individual genomes in the species. An international consortium of maize research groups combined resources to develop the maize haplotype version 3 (HapMap 3), built from whole-genome sequencing data from 1218 maize lines, covering predomestication and domesticated Zea mays varieties across the world. Results: A new computational pipeline was set up to process more than 12 trillion bp of sequencing data, and a set of population genetics filters was applied to identify more than 83 million variant sites...
April 1, 2018: GigaScience
https://www.readbyqxmd.com/read/29233455/genetic-variation-of-cytochrome-p450-in-uyghur-chinese-population
#10
Guangzhao Qi, Duolu Li, Xiaojian Zhang
Interindividual and interethnic variability of drug responses could be attributed to the differences of genetic polymorphisms in the drug metabolizing enzymes and transporters genes among the populations. Here we reviewed the studies of genetic variations in Uyghur Chinese of fifteen CYP450 genes including CYP1A1, CYP1A2, CYP2A6, CYP2B6, CYP2C8, CYP2C9, CYP2C19, CYP2D6, CYP2E1, CYP2J2, CYP2W1, CYP3A4, CYP3A5, CYP4A11, and CYP17A1, which totally covered 277 variants. We also collected the data of 277 variants covered in our study in two extensive population sequencing projects, the International HapMap Project (Hap-Map) and the 1000 Genomes Project and compared them with the data of Uyghur Chinese...
February 2018: Drug Metabolism and Pharmacokinetics
https://www.readbyqxmd.com/read/29212900/genome-wide-gene-potassium-interaction-analyses-on-blood-pressure-the-gensalt-study-genetic-epidemiology-network-of-salt-sensitivity
#11
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
#12
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
#13
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
#14
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/retracted-influence-of-genetic-variants-of-idh1-idh2-tet2-and-dnmt3a-on-cytarabine-cytotoxicity-in-different-populations
#15
Y Wang, J K Lamba
'Influence of genetic variants of IDH1, IDH2, TET2 and DNMT3A on cytarabine cytotoxicity in different populations' by Y. Wang & J. K. Lamba1 The above article from the Journal of Clinical Pharmacy and Therapeutics, published online on 21 November 2017 in Wiley Online Library (wileyonlinelibrary.com), has been retracted following discussions with the authors, the Journal Editors and John Wiley & Sons Ltd. The Retraction has been agreed as this paper was submitted under the joint names of Yan Wang, Jatinder K...
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
#16
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
#17
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
#18
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
#19
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
#20
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
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