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https://www.readbyqxmd.com/read/28698882/excnvss-a-noise-robust-method-for-copy-number-variation-detection-in-whole-exome-sequencing-data
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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-hscrp-level-and-crp-genetic-polymorphisms-are-associated-with-abdominal-aortic-aneurysm
#8
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, correlation analysis between them were performed in 155 unrelated participants with AAA and 310 non-AAA controls...
May 23, 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
#9
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
https://www.readbyqxmd.com/read/28536599/a-pragmatic-test-for-detecting-association-between-a-dichotomous-trait-and-the-genotypes-of-affected-families-controls-and-independent-cases
#10
Meng Wang, William C L Stewart
The efficient analysis of hybrid designs [e.g., affected families, controls, and (optionally) independent cases] is attractive because it should have increased power to detect associations between genetic variants and disease. However, the computational complexity of such an analysis is not trivial, especially when the data contain pedigrees of arbitrary size and structure. To address this concern, we developed a pragmatic test of association that summarizes all of the available evidence in certain hybrid designs, irrespective of pedigree size or structure...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28512992/association-of-cd8-t-cells-with-bone-erosion-in-patients-with-rheumatoid-arthritis
#11
Young Bin Joo, Youngho Park, Kwangwoo Kim, So-Young Bang, Sang-Cheol Bae, Hye-Soon Lee
AIM: Bone erosion is a major problem worsening quality of rheumatoid arthritis (RA) patients' lives. However, causal factors responsible for bone erosion in RA have remained unclear. We aimed to examine genetic variants conferring bone erosion in RA using a Korean genome-wide association study (GWAS) and to search for possible biological mechanisms underlying the development of bone erosion. METHOD: We obtained genome-wide single nucleotide polymorphism (SNP) data for 711 Korean RA patients using Illumina HapMap 550v3/660W arrays...
May 16, 2017: International Journal of Rheumatic Diseases
https://www.readbyqxmd.com/read/28499414/hlascan-genotyping-of-the-hla-region-using-next-generation-sequencing-data
#12
Sojeong Ka, Sunho Lee, Jonghee Hong, Yangrae Cho, Joohon Sung, Han-Na Kim, Hyung-Lae Kim, Jongsun Jung
BACKGROUND: Several recent studies showed that next-generation sequencing (NGS)-based human leukocyte antigen (HLA) typing is a feasible and promising technique for variant calling of highly polymorphic regions. To date, however, no method with sufficient read depth has completely solved the allele phasing issue. In this study, we developed a new method (HLAscan) for HLA genotyping using NGS data. RESULTS: HLAscan performs alignment of reads to HLA sequences from the international ImMunoGeneTics project/human leukocyte antigen (IMGT/HLA) database...
May 12, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28471380/a-genetic-population-isolate-in-the-netherlands-showing-extensive-haplotype-sharing-and-long-regions-of-homozygosity
#13
Metten Somers, Loes M Olde Loohuis, Maartje F Aukes, Bogdan Pasaniuc, Kees C L de Visser, René S Kahn, Iris E Sommer, Roel A Ophoff
Genetic isolated populations have features that may facilitate genetic analyses and can be leveraged to improve power of mapping genes to complex traits. Our aim was to test the extent to which a population with a former history of geographic isolation and religious endogamy, and currently with one of the highest fertility rates in The Netherlands, shows signs of genetic isolation. For this purpose, genome-wide genotype data was collected of 72 unrelated individuals from this population as well as in a sample of 104 random control subjects from The Netherlands...
May 4, 2017: Genes
https://www.readbyqxmd.com/read/28459102/the-novel-asic2-locus-is-associated-with-severe-gingival-inflammation
#14
Shaoping Zhang, Kimon Divaris, Kevin Moss, Ning Yu, Silvana Barros, Julie Marchesan, Thiago Morelli, Cary Agler, Steven J Kim, Di Wu, Kari E North, James Beck, Steven Offenbacher
An increasing body of evidence suggests a significant genetic regulation of inflammatory response mechanisms; however, little is known regarding the genetic determinants of severe gingival inflammation (GI). We conducted a genome-wide association study of severe GI among 4077 European American adults, participants in the Dental Atherosclerosis Risk In Communities cohort. The severe GI trait was defined dichotomously using the 90(th) percentile of gingival index ≥2 extent score. Genotyping was performed with the Affymetrix 6...
July 2016: JDR Clinical and Translational Research
https://www.readbyqxmd.com/read/28452372/1000-genomes-based-meta-analysis-identifies-10-novel-loci-for-kidney-function
#15
Mathias Gorski, Peter J van der Most, Alexander Teumer, Audrey Y Chu, Man Li, Vladan Mijatovic, Ilja M Nolte, Massimiliano Cocca, Daniel Taliun, Felicia Gomez, Yong Li, Bamidele Tayo, Adrienne Tin, Mary F Feitosa, Thor Aspelund, John Attia, Reiner Biffar, Murielle Bochud, Eric Boerwinkle, Ingrid Borecki, Erwin P Bottinger, Ming-Huei Chen, Vincent Chouraki, Marina Ciullo, Josef Coresh, Marilyn C Cornelis, Gary C Curhan, Adamo Pio d'Adamo, Abbas Dehghan, Laura Dengler, Jingzhong Ding, Gudny Eiriksdottir, Karlhans Endlich, Stefan Enroth, Tõnu Esko, Oscar H Franco, Paolo Gasparini, Christian Gieger, Giorgia Girotto, Omri Gottesman, Vilmundur Gudnason, Ulf Gyllensten, Stephen J Hancock, Tamara B Harris, Catherine Helmer, Simon Höllerer, Edith Hofer, Albert Hofman, Elizabeth G Holliday, Georg Homuth, Frank B Hu, Cornelia Huth, Nina Hutri-Kähönen, Shih-Jen Hwang, Medea Imboden, Åsa Johansson, Mika Kähönen, Wolfgang König, Holly Kramer, Bernhard K Krämer, Ashish Kumar, Zoltan Kutalik, Jean-Charles Lambert, Lenore J Launer, Terho Lehtimäki, Martin de Borst, Gerjan Navis, Morris Swertz, Yongmei Liu, Kurt Lohman, Ruth J F Loos, Yingchang Lu, Leo-Pekka Lyytikäinen, Mark A McEvoy, Christa Meisinger, Thomas Meitinger, Andres Metspalu, Marie Metzger, Evelin Mihailov, Paul Mitchell, Matthias Nauck, Albertine J Oldehinkel, Matthias Olden, Brenda Wjh Penninx, Giorgio Pistis, Peter P Pramstaller, Nicole Probst-Hensch, Olli T Raitakari, Rainer Rettig, Paul M Ridker, Fernando Rivadeneira, Antonietta Robino, Sylvia E Rosas, Douglas Ruderfer, Daniela Ruggiero, Yasaman Saba, Cinzia Sala, Helena Schmidt, Reinhold Schmidt, Rodney J Scott, Sanaz Sedaghat, Albert V Smith, Rossella Sorice, Benedicte Stengel, Sylvia Stracke, Konstantin Strauch, Daniela Toniolo, Andre G Uitterlinden, Sheila Ulivi, Jorma S Viikari, Uwe Völker, Peter Vollenweider, Henry Völzke, Dragana Vuckovic, Melanie Waldenberger, Jie Jin Wang, Qiong Yang, Daniel I Chasman, Gerard Tromp, Harold Snieder, Iris M Heid, Caroline S Fox, Anna Köttgen, Cristian Pattaro, Carsten A Böger, Christian Fuchsberger
HapMap imputed genome-wide association studies (GWAS) have revealed >50 loci at which common variants with minor allele frequency >5% are associated with kidney function. GWAS using more complete reference sets for imputation, such as those from The 1000 Genomes project, promise to identify novel loci that have been missed by previous efforts. To investigate the value of such a more complete variant catalog, we conducted a GWAS meta-analysis of kidney function based on the estimated glomerular filtration rate (eGFR) in 110,517 European ancestry participants using 1000 Genomes imputed data...
April 28, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28445522/revealing-phenotype-associated-functional-differences-by-genome-wide-scan-of-ancient-haplotype-blocks
#16
Ritsuko Onuki, Rui Yamaguchi, Tetsuo Shibuya, Minoru Kanehisa, Susumu Goto
Genome-wide scans for positive selection have become important for genomic medicine, and many studies aim to find genomic regions affected by positive selection that are associated with risk allele variations among populations. Most such studies are designed to detect recent positive selection. However, we hypothesize that ancient positive selection is also important for adaptation to pathogens, and has affected current immune-mediated common diseases. Based on this hypothesis, we developed a novel linkage disequilibrium-based pipeline, which aims to detect regions associated with ancient positive selection across populations from single nucleotide polymorphism (SNP) data...
2017: PloS One
https://www.readbyqxmd.com/read/28444966/correlation-between-genetic-polymorphisms-within-the-mapk1-hif-1-ho-1-signaling-pathway-and-risk-or-prognosis-of-perimenopausal-coronary-artery-disease
#17
Nan Guo, Nan Zhang, Liqiu Yan, Xufen Cao, Jiawang Wang, Yunfei Wang
BACKGROUND: Mitogen-activated protein kinase-1 (MAPK1), as well as its downstream factors of hypoxia-inducible factor-1 (HIF-1) and heme oxygenase-1 (HO-1), have been documented to be involved in modulating development of coronary artery disease (CAD). HYPOTHESIS: Genetic mutations within the MAPK1/HIF-1/HO-1 signaling pathway could alter the risk of perimenopausal CAD in Chinese patients. METHODS: Peripheral blood samples were gathered from 589 CAD patients and 860 healthy controls, and 12 potential single-nucleotide polymorphisms (SNPs) were obtained from HapMap database and previously published studies...
April 26, 2017: Clinical Cardiology
https://www.readbyqxmd.com/read/28442506/genome-wide-association-studies-of-chemotherapeutic-toxicities-genomics-of-inequality
#18
REVIEW
Brandon Mapes, Omar El Charif, Shereen Al-Sawwaf, M Eileen Dolan
With an estimated global population of cancer survivors exceeding 32 million and growing, there is a heightened awareness of the long-term toxicities resulting from cancer treatments and their impact on quality of life. Unexplained heterogeneity in the persistence and development of toxicities, as well as an incomplete understanding of their mechanisms, have generated a growing need for the identification of predictive pharmacogenomic markers. Early studies addressing this need used a candidate gene approach; however, over the last decade, unbiased and comprehensive genome-wide association studies (GWAS) have provided markers of phenotypic risk and potential targets to explore the mechanistic and regulatory pathways of biological functions associated with chemotherapeutic toxicity...
April 25, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28436941/insr-gene-polymorphisms-correlate-with-sensitivity-to-platinum-based-chemotherapy-and-prognosis-in-patients-with-epithelial-ovarian-cancer
#19
J-L Hu, X-L Hu, Q Han, A-Y Guo, C-J Wang, Y-Y Wen, S-D Cang
This study aimed to investigate the correlation between INSR gene polymorphisms on platinum-based chemotherapy sensitivity and prognosis in epithelial ovarian cancer (EOC). A total of 339 EOC patients receiving postoperative chemotherapy were recruited for the study. Tag single-nucleotide polymorphism of INSR gene was screened from HapMap combined with available literature. Frequency distribution of genotypes and alleles in INSR gene was sequenced by ABI3100-Avant. Compared with CC+GC genotype, INSR rs2252673 GG genotype and rs3745546 CC genotype showed less platinum-based chemotherapy sensitivity in EOC patients (odds ratio (OR)=0...
July 2017: Gene Therapy
https://www.readbyqxmd.com/read/28430825/discovery-and-fine-mapping-of-adiposity-loci-using-high-density-imputation-of-genome-wide-association-studies-in-individuals-of-african-ancestry-african-ancestry-anthropometry-genetics-consortium
#20
Maggie C Y Ng, Mariaelisa Graff, Yingchang Lu, Anne E Justice, Poorva Mudgal, Ching-Ti Liu, Kristin Young, Lisa R Yanek, Mary F Feitosa, Mary K Wojczynski, Kristin Rand, Jennifer A Brody, Brian E Cade, Latchezar Dimitrov, Qing Duan, Xiuqing Guo, Leslie A Lange, Michael A Nalls, Hayrettin Okut, Salman M Tajuddin, Bamidele O Tayo, Sailaja Vedantam, Jonathan P Bradfield, Guanjie Chen, Wei-Min Chen, Alessandra Chesi, Marguerite R Irvin, Badri Padhukasahasram, Jennifer A Smith, Wei Zheng, Matthew A Allison, Christine B Ambrosone, Elisa V Bandera, Traci M Bartz, Sonja I Berndt, Leslie Bernstein, William J Blot, Erwin P Bottinger, John Carpten, Stephen J Chanock, Yii-Der Ida Chen, David V Conti, Richard S Cooper, Myriam Fornage, Barry I Freedman, Melissa Garcia, Phyllis J Goodman, Yu-Han H Hsu, Jennifer Hu, Chad D Huff, Sue A Ingles, Esther M John, Rick Kittles, Eric Klein, Jin Li, Barbara McKnight, Uma Nayak, Barbara Nemesure, Adesola Ogunniyi, Andrew Olshan, Michael F Press, Rebecca Rohde, Benjamin A Rybicki, Babatunde Salako, Maureen Sanderson, Yaming Shao, David S Siscovick, Janet L Stanford, Victoria L Stevens, Alex Stram, Sara S Strom, Dhananjay Vaidya, John S Witte, Jie Yao, Xiaofeng Zhu, Regina G Ziegler, Alan B Zonderman, Adebowale Adeyemo, Stefan Ambs, Mary Cushman, Jessica D Faul, Hakon Hakonarson, Albert M Levin, Katherine L Nathanson, Erin B Ware, David R Weir, Wei Zhao, Degui Zhi, Donna K Arnett, Struan F A Grant, Sharon L R Kardia, Olufunmilayo I Oloapde, D C Rao, Charles N Rotimi, Michele M Sale, L Keoki Williams, Babette S Zemel, Diane M Becker, Ingrid B Borecki, Michele K Evans, Tamara B Harris, Joel N Hirschhorn, Yun Li, Sanjay R Patel, Bruce M Psaty, Jerome I Rotter, James G Wilson, Donald W Bowden, L Adrienne Cupples, Christopher A Haiman, Ruth J F Loos, Kari E North
Genome-wide association studies (GWAS) have identified >300 loci associated with measures of adiposity including body mass index (BMI) and waist-to-hip ratio (adjusted for BMI, WHRadjBMI), but few have been identified through screening of the African ancestry genomes. We performed large scale meta-analyses and replications in up to 52,895 individuals for BMI and up to 23,095 individuals for WHRadjBMI from the African Ancestry Anthropometry Genetics Consortium (AAAGC) using 1000 Genomes phase 1 imputed GWAS to improve coverage of both common and low frequency variants in the low linkage disequilibrium African ancestry genomes...
April 2017: PLoS Genetics
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