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https://www.readbyqxmd.com/read/28092654/promoter-polymorphism-of-toll-like-receptor-4-is-associated-with-a-decreased-risk-of-coronary-artery-disease-a-case-control-study-in-the-chinese-han-population
#1
Dandan Sun, Liping Sun, Qian Xu, Honghu Wang, Jun Yang, Yuan Yuan
BACKGROUND Coronary artery disease (CAD) is considered a chronic inflammatory disease of the blood vessels. Toll-like receptor 4 (TLR4) is a transmembrane receptor involved in inflammatory reactions. The aim of this study was to determine the association between polymorphisms in the promoter region and 3'-untranslated region (3'-UTR) of TLR4, and the associated CAD risk. MATERIAL AND METHODS This study enrolled 424 participants with CAD and 424 controls without CAD. The polymorphisms in the promoter region and 3'-UTR of TLR4 were identified from the HapMap database, including rs10116253, rs10983755, and rs11536889...
January 16, 2017: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/28090804/choline-acetyltransferase-may-contribute-to-the-risk-of-tourette-syndrome-combination-of-family-based-analysis-and-case-control-study
#2
Xiuling Yang, Wenmiao Liu, Mingji Yi, Ru Zhang, Yinglei Xu, Zuzhou Huang, Shiguo Liu, Tang Li
OBJECTIVES: Twin and family analyses have revealed a genetic contribution to Tourette syndrome and postmortem studies have raised the intriguing possibility of a reduction in cholinergic interneuronsin TS patients. METHODS: We selected five tag SNPs (rs100824791, rs12264845, rs1880676, rs3793790 and rs3793798) of Choline Acetyltransferase (CHAT) from the Han Chinese population Hapmap database. Genotyping was conducted on 401 TS nuclear family trios and 405 control subjects...
January 16, 2017: World Journal of Biological Psychiatry
https://www.readbyqxmd.com/read/28073353/discovery-of-large-genomic-inversions-using-long-range-information
#3
Marzieh Eslami Rasekh, Giorgia Chiatante, Mattia Miroballo, Joyce Tang, Mario Ventura, Chris T Amemiya, Evan E Eichler, Francesca Antonacci, Can Alkan
BACKGROUND: Although many algorithms are now available that aim to characterize different classes of structural variation, discovery of balanced rearrangements such as inversions remains an open problem. This is mainly due to the fact that breakpoints of such events typically lie within segmental duplications or common repeats, which reduces the mappability of short reads. The algorithms developed within the 1000 Genomes Project to identify inversions are limited to relatively short inversions, and there are currently no available algorithms to discover large inversions using high throughput sequencing technologies...
January 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28065468/the-genetic-architecture-of-gene-expression-in-peripheral-blood
#4
Luke R Lloyd-Jones, Alexander Holloway, Allan McRae, Jian Yang, Kerrin Small, Biao Zeng, Andrew Bakshi, Andres Metspalu, Manolis Dermitzakis, Greg Gibson, Tim Spector, Grant Montgomery, Tonu Esko, Peter M Visscher, Joseph E Powell
We analyzed the mRNA levels for 36,778 transcript expression traits (probes) from 2,765 individuals to comprehensively investigate the genetic architecture and degree of missing heritability for gene expression in peripheral blood. We identified 11,204 cis and 3,791 trans independent expression quantitative trait loci (eQTL) by using linear mixed models to perform genome-wide association analyses. Furthermore, using information on both closely and distantly related individuals, heritability was estimated for all expression traits...
December 24, 2016: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28039329/a-genome-wide-interaction-analysis-of-tricyclic-tetracyclic-antidepressants-and-rr-and-qt-intervals-a-pharmacogenomics-study-from-the-cohorts-for-heart-and-aging-research-in-genomic-epidemiology-charge-consortium
#5
Raymond Noordam, Colleen M Sitlani, Christy L Avery, James D Stewart, Stephanie M Gogarten, Kerri L Wiggins, Stella Trompet, Helen R Warren, Fangui Sun, Daniel S Evans, Xiaohui Li, Jin Li, Albert V Smith, Joshua C Bis, Jennifer A Brody, Evan L Busch, Mark J Caulfield, Yii-Der I Chen, Steven R Cummings, L Adrienne Cupples, Qing Duan, Oscar H Franco, Rául Méndez-Giráldez, Tamara B Harris, Susan R Heckbert, Diana van Heemst, Albert Hofman, James S Floyd, Jan A Kors, Lenore J Launer, Yun Li, Ruifang Li-Gao, Leslie A Lange, Henry J Lin, Renée de Mutsert, Melanie D Napier, Christopher Newton-Cheh, Neil Poulter, Alexander P Reiner, Kenneth M Rice, Jeffrey Roach, Carlos J Rodriguez, Frits R Rosendaal, Naveed Sattar, Peter Sever, Amanda A Seyerle, P Eline Slagboom, Elsayed Z Soliman, Nona Sotoodehnia, David J Stott, Til Stürmer, Kent D Taylor, Timothy A Thornton, André G Uitterlinden, Kirk C Wilhelmsen, James G Wilson, Vilmundur Gudnason, J Wouter Jukema, Cathy C Laurie, Yongmei Liu, Dennis O Mook-Kanamori, Patricia B Munroe, Jerome I Rotter, Ramachandran S Vasan, Bruce M Psaty, Bruno H Stricker, Eric A Whitsel
BACKGROUND: Increased heart rate and a prolonged QT interval are important risk factors for cardiovascular morbidity and mortality, and can be influenced by the use of various medications, including tricyclic/tetracyclic antidepressants (TCAs). We aim to identify genetic loci that modify the association between TCA use and RR and QT intervals. METHODS AND RESULTS: We conducted race/ethnic-specific genome-wide interaction analyses (with HapMap phase II imputed reference panel imputation) of TCAs and resting RR and QT intervals in cohorts of European (n=45 706; n=1417 TCA users), African (n=10 235; n=296 TCA users) and Hispanic/Latino (n=13 808; n=147 TCA users) ancestry, adjusted for clinical covariates...
December 30, 2016: Journal of Medical Genetics
https://www.readbyqxmd.com/read/28035032/using-genotype-array-data-to-compare-multi-and-single-sample-variant-calls-and-improve-variant-call-sets-from-deep-coverage-whole-genome-sequencing-data
#6
Suyash S Shringarpure, Rasika A Mathias, Ryan D Hernandez, Timothy D O'Connor, Zachary A Szpiech, Raul Torres, Francisco M De La Vega, Carlos D Bustamante, Kathleen C Barnes, Margaret A Taub
MOTIVATION: Variant calling from next-generation sequencing (NGS) data is susceptible to false positive calls due to sequencing, mapping and other errors. To better distinguish true from false positive calls, we present a method that uses genotype array data from the sequenced samples, rather than public data such as HapMap or dbSNP, to train an accurate classifier using Random Forests. We demonstrate our method on a set of variant calls obtained from 642 African-ancestry genomes from the Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA), sequenced to high depth (30X)...
December 29, 2016: Bioinformatics
https://www.readbyqxmd.com/read/28009992/identification-of-a-synonymous-variant-in-trim59-gene-for-gastric-cancer-risk-in-a-chinese-population
#7
Dakui Luo, Younan Wang, Xiangkun Huan, Chi Huang, Chao Yang, Hao Fan, Zekuan Xu, Li Yang
Tripartite motif 59 (TRIM59) is a novel oncogenic driver in gastric cancer (GC) that is implicated in disease progression as well as dismal survival. Genetic variants in peculiar gene are likely candidates for conferring hereditary susceptibility. The role of TRIM59 polymorphism in predicting the risk of malignant diseases and its relevance to TRIM59 expression have not been discussed. Using a HapMap tagSNPs approach, we screened three tag TRIM59 single nucleotide polymorphisms (SNPs) (rs1141023G>A, rs7629A>G, rs11706810T>C) which were genotyped in 602 GC patients and 868 healthy controls...
December 21, 2016: Oncotarget
https://www.readbyqxmd.com/read/27992465/discovering-genome-wide-tag-snps-based-on-the-mutual-information-of-the-variants
#8
Abdulkadir Elmas, Tai-Hsien Ou Yang, Xiaodong Wang, Dimitris Anastassiou
Exploring linkage disequilibrium (LD) patterns among the single nucleotide polymorphism (SNP) sites can improve the accuracy and cost-effectiveness of genomic association studies, whereby representative (tag) SNPs are identified to sufficiently represent the genomic diversity in populations. There has been considerable amount of effort in developing efficient algorithms to select tag SNPs from the growing large-scale data sets. Methods using the classical pairwise-LD and multi-locus LD measures have been proposed that aim to reduce the computational complexity and to increase the accuracy, respectively...
2016: PloS One
https://www.readbyqxmd.com/read/27951431/developmental-validation-of-a-custom-panel-including-273-snps-for-forensic-application-using-ion-torrent-pgm
#9
Suhua Zhang, Yingnan Bian, Anqi Chen, Hancheng Zheng, Yuzhen Gao, Yiping Hou, Chengtao Li
Utilizing massively parallel sequencing (MPS) technology for SNP testing in forensic genetics is becoming attractive because of the shortcomings of STR markers, such as their high mutation rates and disadvantages associated with the current PCR-CE method as well as its limitations regarding multiplex capabilities. MPS offers the potential to genotype hundreds to thousands of SNPs from multiple samples in a single experimental run. In this study, we designed a customized SNP panel that includes 273 forensically relevant identity SNPs chosen from SNPforID, IISNP, and the HapMap database as well as previously related studies and evaluated the levels of genotyping precision, sequence coverage, sensitivity and SNP performance using the Ion Torrent PGM...
December 7, 2016: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/27903959/genome-wide-haplotype-association-study-identify-the-fgfr2-gene-as-a-risk-gene-for-acute-myeloid-leukemia
#10
Hongchao Lv, Mingming Zhang, Zhenwei Shang, Jin Li, Shanshan Zhang, Duan Lian, Ruijie Zhang
Acute myeloid leukemia (AML) is a cancer of the myeloid line of blood cells, and generally considered to be caused by environment and genetic factors. In this study, we combined a genome-wide haplotype association study (GWHAS) and gene prioritization strategy to mine AML-related genetic affect factors and understand its pathogenesis. A total of 175 AML patients were downloaded from the public GEO database (GSE32462) and 218 matched Caucasian controls were from the HapMap Project. We first identified the linkage disequilibrium (LD) blocks and performed a GWHAS to scan AML-related haplotypes...
November 26, 2016: Oncotarget
https://www.readbyqxmd.com/read/27885705/multiple-linear-combination-mlc-regression-tests-for-common-variants-adapted-to-linkage-disequilibrium-structure
#11
Yun Joo Yoo, Lei Sun, Julia G Poirier, Andrew D Paterson, Shelley B Bull
By jointly analyzing multiple variants within a gene, instead of one at a time, gene-based multiple regression can improve power, robustness, and interpretation in genetic association analysis. We investigate multiple linear combination (MLC) test statistics for analysis of common variants under realistic trait models with linkage disequilibrium (LD) based on HapMap Asian haplotypes. MLC is a directional test that exploits LD structure in a gene to construct clusters of closely correlated variants recoded such that the majority of pairwise correlations are positive...
November 25, 2016: Genetic Epidemiology
https://www.readbyqxmd.com/read/27831922/the-association-between-single-nucleotide-polymorphisms-of-the-apelin-gene-and-diabetes-mellitus-in-a-chinese-population
#12
Hui Zheng, Xiaofang Fan, Xuesong Li, Yu Zhang, Yujuan Fan, Ning Zhang, Yuping Song, Fengdong Ren, Chunfang Shen, Jiayi Shen, Jialin Yang
BACKGROUND: The objective of the study was to analyze the association of apelin gene (APLN) single nucleotide polymorphisms (SNPs) and type 2 diabetes mellitus (T2DM). METHODS: A total of 1966 subjects were enrolled in this study, including 168 cases (first batch), 330 cases (second batch), and 1468 nondiabetic controls. The SNPs in the HapMap-HCB of APLN were detected using Sequenom MassARRAY SNP technology and included rs2281068, rs3115757, rs2235309, and rs2235310...
December 1, 2016: Journal of Pediatric Endocrinology & Metabolism: JPEM
https://www.readbyqxmd.com/read/27809781/pse-hmm-genome-wide-cnv-detection-from-ngs-data-using-an-hmm-with-position-specific-emission-probabilities
#13
Seyed Amir Malekpour, Hamid Pezeshk, Mehdi Sadeghi
BACKGROUND: Copy Number Variation (CNV) is envisaged to be a major source of large structural variations in the human genome. In recent years, many studies apply Next Generation Sequencing (NGS) data for the CNV detection. However, still there is a necessity to invent more accurate computational tools. RESULTS: In this study, mate pair NGS data are used for the CNV detection in a Hidden Markov Model (HMM). The proposed HMM has position specific emission probabilities, i...
November 3, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27797945/population-stratification-and-underrepresentation-of-indian-subcontinent-genetic-diversity-in-the-1000-genomes-project-dataset
#14
Dhriti Sengupta, Ananyo Choudhury, Analabha Basu, Michèle Ramsay
Genomic variation in Indian populations is of great interest due to the diversity of ancestral components, social stratification, endogamy and complex admixture patterns. With an expanding population of 1.2 billion, India is also a treasure trove to catalogue innocuous as well as clinically relevant rare mutations. Recent studies have revealed four dominant ancestries in populations from mainland India: Ancestral North-Indian (ANI), Ancestral South-Indian (ASI), Ancestral Tibeto-Burman (ATB) and Ancestral Austro-Asiatic (AAA)...
December 31, 2016: Genome Biology and Evolution
https://www.readbyqxmd.com/read/27766935/analysis-of-optimal-alignments-unfolds-aligners-bias-in-existing-variant-profiles
#15
Quang Tran, Shanshan Gao, Vinhthuy Phan
Efforts such as International HapMap Project and 1000 Genomes Project resulted in a catalog of millions of single nucleotides and insertion/deletion (INDEL) variants of the human population. Viewed as a reference of existing variants, this resource commonly serves as a gold standard for studying and developing methods to detect genetic variants. Our analysis revealed that this reference contained thousands of INDELs that were constructed in a biased manner. This bias occurred at the level of aligning short reads to reference genomes to detect variants...
October 6, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27766139/methodology-for-single-nucleotide-polymorphism-selection-in-promoter-regions-for-clinical-use-an-example-of-its-applicability
#16
Herlander Marques, José Freitas, Rui Medeiros, Adhemar Longatto-Filho
Genetic variability in humans can explain many differences in disease risk factors. Polymorphism-related studies focus mainly on the single nucleotide polymorphisms (SNPs) of coding regions of the genes. SNPs on DNA binding motifs of the promoter region have been less explored. On a recent study of SNPs in patients with non-Hodgkin lymphomas we faced the problem of SNP selection from promoter regions and developed a practical methodology for clinical studies. The process consists in identifying SNPs in the coding and promoter regions of the antigen-processing system using the 'dbSNP' database...
2016: International Journal of Molecular Epidemiology and Genetics
https://www.readbyqxmd.com/read/27765809/discovering-snps-regulating-human-gene-expression-using-allele-specific-expression-from-rna-seq-data
#17
Eun Yong Kang, Lisa Martin, Serghei Mangul, Warin Isvilanonda, Jennifer Zou, Eyal Ben-David, Buhm Han, Aldons J Lusis, Sagiv Shifman, Eleazar Eskin
The study of the genetics of gene expression is of considerable importance to understanding the nature of common, complex diseases. The most widely applied approach to identifying relationships between genetic variation and gene expression is the expression quantitative trait loci (eQTL) approach. Here we increase the computational power of eQTL with an alternative and complementary approach based on analyzing allele specific expression (ASE). We design a novel analytical method to identify cis-acting regulatory variants based on genome sequencing and measurements of ASE from RNA-seq data...
October 7, 2016: Genetics
https://www.readbyqxmd.com/read/27760738/the-framework-for-population-epigenetic-study
#18
Linna Zhao, Di Liu, Jing Xu, Zhaoyang Wang, Yang Chen, Changgui Lei, Ying Li, Guiyou Liu, Yongshuai Jiang
At present, understanding of DNA methylation at the population level is still limited. Here, we first extended the classical framework of population genetics, such as single nucleotide polymorphism allele frequency, linkage disequilibrium (LD), LD block and haplotype, to epigenetics. Then, as an example, we compared the DNA methylation disequilibrium (MD) maps between HapMap CEU (Caucasian residents of European ancestry from Utah) population and YRI (Yoruba people from Ibadan) population (lymphoblastoid cell lines)...
October 19, 2016: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/27706680/association-between-txnrd1-polymorphisms-and-anti-tuberculosis-drug-induced-hepatotoxicity-in-a-prospective-study
#19
G Y Ji, Y Wang, S Q Wu, Q Q Liu, J C Wu, M M Zhang, A J Sandford, J Q He
Anti-tuberculosis drug-induced hepatotoxicity (ATDH) is a serious adverse reaction to anti-tuberculosis (TB) treatment. Thioredoxin reductase 1 (TXNRD1), encoded by the TXNRD1 gene, is an important enzyme involved in oxidant challenge. TXNRD1 plays a key role in regulating cell growth and transformation, and protects cells against oxidative damage. We investigated the association between TXNRD1 polymorphisms and ATDH susceptibility. In this prospective study, 280 newly diagnosed TB patients were followed-up for 3 months after beginning anti-TB therapy...
September 2, 2016: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/27686742/bithionol-blocks-pathogenicity-of-bacterial-toxins-ricin-and-zika-virus
#20
William Leonardi, Leeor Zilbermintz, Luisa W Cheng, Josue Zozaya, Sharon H Tran, Jeffrey H Elliott, Kseniya Polukhina, Robert Manasherob, Amy Li, Xiaoli Chi, Dima Gharaibeh, Tara Kenny, Rouzbeh Zamani, Veronica Soloveva, Andrew D Haddow, Farooq Nasar, Sina Bavari, Michael C Bassik, Stanley N Cohen, Anastasia Levitin, Mikhail Martchenko
Diverse pathogenic agents often utilize overlapping host networks, and hub proteins within these networks represent attractive targets for broad-spectrum drugs. Using bacterial toxins, we describe a new approach for discovering broad-spectrum therapies capable of inhibiting host proteins that mediate multiple pathogenic pathways. This approach can be widely used, as it combines genetic-based target identification with cell survival-based and protein function-based multiplex drug screens, and concurrently discovers therapeutic compounds and their protein targets...
September 30, 2016: Scientific Reports
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