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https://www.readbyqxmd.com/read/27903959/genome-wide-haplotype-association-study-identify-the-fgfr2-gene-as-a-risk-gene-for-acute-myeloid-leukemia
#1
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
#2
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
#3
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
#4
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
#5
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)...
October 23, 2016: Genome Biology and Evolution
https://www.readbyqxmd.com/read/27766935/analysis-of-optimal-alignments-unfolds-aligners-bias-in-existing-variant-profiles
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
https://www.readbyqxmd.com/read/27664568/osteomalacia-induced-by-long-term-low-dose-adefovir-dipivoxil-clinical-characteristics-and-genetic-predictors
#12
Zhe Wei, Jin-Wei He, Wen-Zhen Fu, Zhen-Lin Zhang
CONTEXT: Adefovir dipivoxil (ADV) was an important cause of adult-onset hypophosphatemic osteomalacia. However, its clinical characteristics and mechanisms have not been well defined. OBJECTIVE: The objective of the study was to summarize the clinical characteristics of ADV-induced osteomalacia and to explore the association between ADV-associated tubulopathy and polymorphisms in genes encoding drug transporters. DESIGN, SETTING, PATIENTS, AND MAIN OUTCOME MEASURE: Seventy-six affected patients were clinically studied...
September 21, 2016: Bone
https://www.readbyqxmd.com/read/27646535/direct-chromosome-length-haplotyping-by-single-cell-sequencing
#13
David Porubský, Ashley D Sanders, Niek van Wietmarschen, Ester Falconer, Mark Hills, Diana C J Spierings, Marianna R Bevova, Victor Guryev, Peter M Lansdorp
Haplotypes are fundamental to fully characterize the diploid genome of an individual, yet methods to directly chart the unique genetic makeup of each parental chromosome are lacking. Here we introduce single-cell DNA template strand sequencing (Strand-seq) as a novel approach to phasing diploid genomes along the entire length of all chromosomes. We demonstrate this by building a complete haplotype for a HapMap individual (NA12878) at high accuracy (concordance 99.3%), without using generational information or statistical inference...
November 2016: Genome Research
https://www.readbyqxmd.com/read/27602231/a-hapmap-leads-to-a-capsicum-annuum-snp-infinium-array-a-new-tool-for-pepper-breeding
#14
Amanda M Hulse-Kemp, Hamid Ashrafi, Joerg Plieske, Jana Lemm, Kevin Stoffel, Theresa Hill, Hartmut Luerssen, Charit L Pethiyagoda, Cindy T Lawley, Martin W Ganal, Allen Van Deynze
The Capsicum genus (Pepper) is a part of the Solanacae family. It has been important in many cultures worldwide for its key nutritional components and uses as spices, medicines, ornamentals and vegetables. Worldwide population growth is associated with demand for more nutritionally valuable vegetables while contending with decreasing resources and available land. These conditions require increased efficiency in pepper breeding to deal with these imminent challenges. Through resequencing of inbred lines we have completed a valuable haplotype map (HapMap) for the pepper genome based on single-nucleotide polymorphisms (SNP)...
2016: Horticulture Research
https://www.readbyqxmd.com/read/27596337/genomic-ancestry-and-the-social-pathways-leading-to-major-depression-in-adulthood-the-mediating-effect-of-socioeconomic-position-and-discrimination
#15
Christian Loret de Mola, Fernando Pires Hartwig, Helen Gonçalves, Luciana de Avila Quevedo, Ricardo Pinheiro, Denise Petrucci Gigante, Janaína Vieira Dos Santos Motta, Alexandre C Pereira, Fernando C Barros, Bernardo Lessa Horta
BACKGROUND: Evidence suggests that there is an association between ethnicity/skin color and depression; however, many contextual and individual variables, like sense of discrimination and socioeconomic position (SEP), might influence the direction of this association. We assessed the association between African ancestry and major depression among young adults that have been followed-up since birth in a Southern Brazilian city, and the mediating effect of SEP and discrimination. METHODS: In 1982, all hospital deliveries in Pelotas (Southern Brazil) were identified; liveborns were examined and their mothers interviewed (n = 5914)...
2016: BMC Psychiatry
https://www.readbyqxmd.com/read/27586631/short-tandem-repeat-number-estimation-from-paired-end-reads-for-multiple-individuals-by-considering-coalescent-tree
#16
Kaname Kojima, Yosuke Kawai, Naoki Nariai, Takahiro Mimori, Takanori Hasegawa, Masao Nagasaki
BACKGROUND: Two types of approaches are mainly considered for the repeat number estimation in short tandem repeat (STR) regions from high-throughput sequencing data: approaches directly counting repeat patterns included in sequence reads spanning the region and approaches based on detecting the difference between the insert size inferred from aligned paired-end reads and the actual insert size. Although the accuracy of repeat numbers estimated with the former approaches is high, the size of target STR regions is limited to the length of sequence reads...
2016: BMC Genomics
https://www.readbyqxmd.com/read/27580882/a-genetic-variation-associated-with-plasma-erythropoietin-and-a-non-coding-transcript-of-prkar1a-in-sickle-cell-disease
#17
Xu Zhang, Binal N Shah, Wei Zhang, Santosh L Saraf, Galina Miasnikova, Adelina Sergueeva, Tatiana Ammosova, Xiaomei Niu, Mehdi Nouraie, Sergei Nekhai, Oswaldo Castro, Mark T Gladwin, Josef T Prchal, Joe G N Garcia, Roberto F Machado, Victor R Gordeuk
Blood erythropoietin (EPO) increases primarily to hypoxia. In sickle cell anemia (homozygous HBB(E6V); HbSS), plasma EPO is elevated due to hemolytic anemia-related hypoxia. Hydroxyurea treatment reduces hemolysis and anemia by increasing fetal hemoglobin, which leads to lower hypoxic transcriptional responses in blood mononuclear cells but paradoxically further increases EPO. To investigate this apparent hypoxia-independent EPO regulation, we assessed two sickle cell disease (SCD) cohorts for genetic associations with plasma EPO, by prioritizing 237,079 quantitative trait loci for expression level and/or transcript isoform variations of 12,727 genes derived from SCD blood mononuclear cells...
August 30, 2016: Human Molecular Genetics
https://www.readbyqxmd.com/read/27562048/-a-comparative-study-on-characterizations-of-genetic-recombination-hotspots-in-pparg-gene-between-kirgiz-and-uyghur-ethnic-groups-in-xinjiang
#18
Rozi Zohra, M S Song, Nizam Iliham, Mamatyusupu Dolikun
OBJECTIVE: To investigate the characterizations of genetic recombination hotspots and linkage disequilibrium (LD) patterns in peroxisome proliferative activated receptor gamma (PPARG) gene in Kirgiz and Uyghur ethnic groups. METHODS: Blood samples were collected from 100 Kirgiz (50 healthy controls and 50 patients with type 2 diabetes mellitus) residents in Halajun County, Artux City, Kizilsu Kirgiz Autonomous Prefecture, Xinjiang in August 2013, and 50 healthy Uyghur residents in Hotan Prefecture of Xinjiang Uygur Autonomous Region in May 2012...
August 16, 2016: Zhonghua Yi Xue za Zhi [Chinese medical journal]
https://www.readbyqxmd.com/read/27553423/characterisation-of-the-global-transcriptional-response-to-heat-shock-and-the-impact-of-individual-genetic-variation
#19
Peter Humburg, Narelle Maugeri, Wanseon Lee, Bert Mohr, Julian C Knight
BACKGROUND: The heat shock transcriptional response is essential to effective cellular function under stress. This is a highly heritable trait but the nature and extent of inter-individual variation in heat shock response remains unresolved. METHODS: We determined global transcription profiles of the heat shock response for a panel of lymphoblastoid cell lines established from 60 founder individuals in the Yoruba HapMap population. We explore the observed differentially expressed gene sets following heat shock, establishing functional annotations, underlying networks and nodal genes involving heat shock factor 1 recruitment...
2016: Genome Medicine
https://www.readbyqxmd.com/read/27522085/cgdm-collaborative-genomic-data-model-for-molecular-profiling-data-using-nosql
#20
Shicai Wang, Mihaela A Mares, Yi-Ke Guo
MOTIVATION: High-throughput molecular profiling has greatly improved patient stratification and mechanistic understanding of diseases. With the increasing amount of data used in translational medicine studies in recent years, there is a need to improve the performance of data warehouses in terms of data retrieval and statistical processing. Both relational and Key Value models have been used for managing molecular profiling data. Key Value models such as SeqWare have been shown to be particularly advantageous in terms of query processing speed for large datasets...
December 1, 2016: Bioinformatics
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