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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
#1
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
#2
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
#3
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...
January 11, 2018: Gene
https://www.readbyqxmd.com/read/29300887/construction-of-the-third-generation-zea-mays-haplotype-map
#4
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 1,218 maize lines, covering pre-domestication and domesticated Zea mays varieties across the world. Results: A new computational pipeline was set up to process over 12 trillion bp of sequencing data and a set of population genetics filters were applied to identify over 83 million variant sites...
December 30, 2017: GigaScience
https://www.readbyqxmd.com/read/29233455/genetic-variation-of-cytochrome-p450-in-uyghur-chinese-population
#5
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...
March 6, 2017: 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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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