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Genome wide association study

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https://www.readbyqxmd.com/read/29053852/genome-wide-scan-and-analysis-of-positive-selective-signatures-in-dwarf-brown-egg-layers-and-silky-fowl-chickens
#1
Mengmeng Zhang, Liu Yang, Zhencheng Su, Muzhen Zhu, Wenting Li, Keliang Wu, Xuemei Deng
Chinese domestic chickens have been routinely subjected to artificial selection for the production of meats and eggs. Selection results in distinctive signatures in the genome that can reveal the genes underlying phenotypes of interest to breeders. In this study, we used the Chicken60K SNP chip to analyze DNA from Dwarf Brown-egg Layers (DB, n = 203) and Silky Fowls (SF, n = 181) and then examined the relative extended haplotype homozygosity (REHH) and fixation index (FST) to detect selection signatures. Since population structure analysis showed that SF was stratified into 2 subpopulations (SF1 and SF2), we removed the 20 SF1 chickens, and the remaining individuals (DB and SF2) were scanned for genome-wide selection signatures...
October 5, 2017: Poultry Science
https://www.readbyqxmd.com/read/29053721/xx-disorder-of-sex-development-is-associated-with-an-insertion-on-chromosome-9-and-downregulation-of-rspo1-in-dogs-canis-lupus-familiaris
#2
Vicki N Meyers-Wallen, Adam R Boyko, Charles G Danko, Jennifer K Grenier, Jason G Mezey, Jessica J Hayward, Laura M Shannon, Chuan Gao, Afrah Shafquat, Edward J Rice, Shashikant Pujar, Stefanie Eggers, Thomas Ohnesorg, Andrew H Sinclair
Remarkable progress has been achieved in understanding the mechanisms controlling sex determination, yet the cause for many Disorders of Sex Development (DSD) remains unknown. Of particular interest is a rare XX DSD subtype in which individuals are negative for SRY, the testis determining factor on the Y chromosome, yet develop testes or ovotestes, and both of these phenotypes occur in the same family. This is a naturally occurring disorder in humans (Homo sapiens) and dogs (C. familiaris). Phenotypes in the canine XX DSD model are strikingly similar to those of the human XX DSD subtype...
2017: PloS One
https://www.readbyqxmd.com/read/29053696/3-end-sequencing-library-preparation-with-a-seq2
#3
Georges Martin, Ralf Schmidt, Andreas J Gruber, Souvik Ghosh, Walter Keller, Mihaela Zavolan
Studies in the last decade have revealed a complex and dynamic variety of pre-mRNA cleavage and polyadenylation reactions. mRNAs with long 3' untranslated regions (UTRs) are generated in differentiated cells whereas proliferating cells preferentially express transcripts with short 3'UTRs. We describe the A-seq protocol, now at its second version, which was developed to map polyadenylation sites genome-wide and study the regulation of pre-mRNA 3' end processing. Also this current protocol takes advantage of the polyadenylate (poly(A)) tails that are added during the biogenesis of most mammalian mRNAs to enrich for fully processed mRNAs...
October 10, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29053637/progress-in-genetic-studies-of-tourette-s-syndrome
#4
REVIEW
Yanjie Qi, Yi Zheng, Zhanjiang Li, Lan Xiong
Tourette's Syndrome (TS) is a complex disorder characterized by repetitive, sudden, and involuntary movements or vocalizations, called tics. Tics usually appear in childhood, and their severity varies over time. In addition to frequent tics, people with TS are at risk for associated problems including attention deficit hyperactivity disorder (ADHD), obsessive-compulsive disorder (OCD), anxiety, depression, and problems with sleep. TS occurs in most populations and ethnic groups worldwide, and it is more common in males than in females...
October 20, 2017: Brain Sciences
https://www.readbyqxmd.com/read/29052958/whole-genome-re-sequencing-reveals-evolutionary-patterns-of-sacred-lotus-nelumbo-nucifera
#5
Longyu Huang, Mei Yang, Ling Li, Hui Li, Dong Yang, Tao Shi, Pingfang Yang
Sacred lotus (Nelumbo nucifera or lotus) is an important aquatic plant in horticulture and ecosystem. As a foundation for exploring genomic variationand evolution among different germplasms, we re-sequenced 19 individuals from three cultivated temperate lotus subgroups (rhizome lotus, seed lotus and flower lotus),one wild temperate lotus subgroup (wild lotus), one tropical lotus group (Thai lotus) and outgroup (Nelumbo lutea). Through genetic diversity and polymorphism analysis by non-missing SNP sites widely distributed in the whole genome, weconfirmed that wild lotus and Thai lotus exhibited greater differentiation with a higher genomic diversity compared to cultivated lotus...
October 20, 2017: Journal of Integrative Plant Biology
https://www.readbyqxmd.com/read/29052934/the-contribution-of-alternative-splicing-to-genetic-risk-for-psychiatric-disorders
#6
REVIEW
Emma Reble, Aidan Dineen, Cathy L Barr
A genetic contribution to psychiatric disorders has clearly been established and genome-wide association studies now provide the location of risk genes and genetic variants associated with risk. However, the mechanism by which these genes and variants contribute to psychiatric disorders is mostly undetermined. This is in part because non-synonymous protein coding changes cannot explain the majority of variants associated with complex genetic traits. Based on this, it is predicted that these variants are causing gene expression changes, including changes to alternative splicing...
October 20, 2017: Genes, Brain, and Behavior
https://www.readbyqxmd.com/read/29052247/meta-analysis-approaches-to-combine-multiple-gene-set-enrichment-studies
#7
Wentao Lu, Xinlei Wang, Xiaowei Zhan, Adi Gazdar
In the field of gene set enrichment analysis (GSEA), meta-analysis has been used to integrate information from multiple studies to present a reliable summarization of the expanding volume of individual biomedical research, as well as improve the power of detecting essential gene sets involved in complex human diseases. However, existing methods, Meta-Analysis for Pathway Enrichment (MAPE), may be subject to power loss because of (1) using gross summary statistics for combining end results from component studies and (2) using enrichment scores whose distributions depend on the set sizes...
October 19, 2017: Statistics in Medicine
https://www.readbyqxmd.com/read/29052219/pharmacogenomic-discovery-to-function-and-mechanism-breast-cancer-as-a-case-study
#8
Liewei Wang, James Ingle, Richard Weinshilboum
Biomedical research is undergoing rapid change, with the development of a series of analytical omics techniques that are capable of generating Biomedical Big Data. These developments provide an unprecedented opportunity to gain novel insight into disease pathophysiology and mechanisms of drug action and response-but they also present significant challenges. Pharmacogenomics is a discipline within Clinical Pharmacology that has been at the forefront in defining, taking advantage of and dealing with the opportunities and challenges of this aspect of the Post-Genome Project world...
October 20, 2017: Clinical Pharmacology and Therapeutics
https://www.readbyqxmd.com/read/29052057/characterization-of-the-genomic-sequence-of-a-novel-cress-dna-virus-identified-in-eurasian-jay-garrulus-glandarius
#9
Eszter Kaszab, Szilvia Marton, Barbara Forró, Krisztina Bali, György Lengyel, Krisztián Bányai, Enikő Fehér
Circular replication associated protein (Rep)-encoding ssDNA (CRESS DNA) viruses have diverse genomic architecture and are widely distributed in different ecosystems. In this study we characterized the complete genomic sequence of a novel circovirus-like virus, Garrulus glandarius associated circular virus-1 (GgaCV-1). The genome size (1971 nt) and other features (the nonanucleotide, rolling circle replication motif and SF3 helicase motif) are also reminiscent of circoviruses. Similar genomes with uni-directionally localized and overlapping rep and cap genes are typical of type V CRESS DNA viruses that were identified in invertebrates and environmental samples of aquatic ecosystems...
October 19, 2017: Archives of Virology
https://www.readbyqxmd.com/read/29051980/genomic-analysis-of-bacillus-sp-strain-b25-a-biocontrol-agent-of-maize-pathogen-fusarium-verticillioides
#10
Nadia R Douriet-Gámez, Ignacio E Maldonado-Mendoza, Enrique Ibarra-Laclette, Jochen Blom, Carlos L Calderón-Vázquez
Bacillus sp. B25 is an effective biocontrol agent against the maize pathogenic fungus Fusarium verticillioides (Fv). Previous in vitro assays have shown that B25 has protease, glucanase, and chitinase activities and siderophores production; however, specific mechanisms by which B25 controls Fv are still unknown. To determine the genetic traits involved in biocontrol, B25 genome was sequenced and analyzed. B25 genome is composed of 5,113,413 bp and 5251 coding genes. A multilocus phylogenetic analysis (MLPA) suggests that B25 is closely related to the Bacillus cereus group and a high percentage (70-75%) of the genetic information is conserved between B25 and related strains, which include most of the genes associated to fungal antagonism...
October 19, 2017: Current Microbiology
https://www.readbyqxmd.com/read/29051922/hidden-heritability-due-to-heterogeneity-across-seven-populations
#11
Felix C Tropf, S Hong Lee, Renske M Verweij, Gert Stulp, Peter J van der Most, Ronald de Vlaming, Andrew Bakshi, Daniel A Briley, Charles Rahal, Robert Hellpap, Anastasia Nyman, Tõnu Esko, Andres Metspalu, Sarah E Medland, Nicholas G Martin, Nicola Barban, Harold Snieder, Matthew R Robinson, Melinda C Mills
Meta-analyses of genome-wide association studies (GWAS), which dominate genetic discovery are based on data from diverse historical time periods and populations. Genetic scores derived from GWAS explain only a fraction of the heritability estimates obtained from whole-genome studies on single populations, known as the 'hidden heritability' puzzle. Using seven sampling populations (N=35,062), we test whether hidden heritability is attributed to heterogeneity across sampling populations and time, showing that estimates are substantially smaller from across compared to within populations...
October 2017: Nature Human Behaviour
https://www.readbyqxmd.com/read/29051702/finding-the-sources-of-missing-heritability-within-rare-variants-through-simulation
#12
Baishali Bandyopadhyay, Veda Chanda, Yupeng Wang
Thousands of genome-wide association studies (GWAS) have been conducted to identify the genetic variants associated with complex disorders. However, only a small proportion of phenotypic variances can be explained by the reported variants. Moreover, many GWAS failed to identify genetic variants associated with disorders displaying hereditary features. The "missing heritability" problem can be partly explained by rare variants. We simulated a causality scenario that gestational ages, a quantitative trait that can distinguish preterm (<37 weeks) and term births, were significantly correlated with the rare variant aggregations at 1000 single-nucleotide polymorphism loci...
2017: Bioinformatics and Biology Insights
https://www.readbyqxmd.com/read/29051540/genome-wide-association-study-identifies-the-serpinb-gene-cluster-as-a-susceptibility-locus-for-food-allergy
#13
Ingo Marenholz, Sarah Grosche, Birgit Kalb, Franz Rüschendorf, Katharina Blümchen, Rupert Schlags, Neda Harandi, Mareike Price, Gesine Hansen, Jürgen Seidenberg, Holger Röblitz, Songül Yürek, Sebastian Tschirner, Xiumei Hong, Xiaobin Wang, Georg Homuth, Carsten O Schmidt, Markus M Nöthen, Norbert Hübner, Bodo Niggemann, Kirsten Beyer, Young-Ae Lee
Genetic factors and mechanisms underlying food allergy are largely unknown. Due to heterogeneity of symptoms a reliable diagnosis is often difficult to make. Here, we report a genome-wide association study on food allergy diagnosed by oral food challenge in 497 cases and 2387 controls. We identify five loci at genome-wide significance, the clade B serpin (SERPINB) gene cluster at 18q21.3, the cytokine gene cluster at 5q31.1, the filaggrin gene, the C11orf30/LRRC32 locus, and the human leukocyte antigen (HLA) region...
October 20, 2017: Nature Communications
https://www.readbyqxmd.com/read/29051501/branched-chain-amino-acids-and-alzheimer-s-disease-a-mendelian-randomization-analysis
#14
Susanna C Larsson, Hugh S Markus
We conducted a two-sample Mendelian randomization study to test the hypothesis that raised plasma levels of the branched-chain amino acids isoleucine, leucine, and valine are associated with Alzheimer's disease (AD). From a genome-wide association study of 16,596 individuals of European ancestry, we obtained summary statistics for four independent single nucleotide polymorphisms (SNPs) associated with isoleucine levels and one SNP associated with both leucine and valine levels at genome-wide significance. Summary statistics of the associations of the five SNPs with AD were obtained from the International Genomics of Alzheimer's Project (17,008 AD cases and 37,154 controls)...
October 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29050696/pharmacogenomics-in-acute-lymphoblastic-leukemia
#15
REVIEW
Shawn H R Lee, Jun J Yang
Pharmacogenomics is a fast-growing field of personalized medicine using a patient's genomic profile to determine drug disposition or response to drug therapy, in order to develop safer and more effective pharmacotherapy. Childhood acute lymphoblastic leukemia (ALL), being the most common malignancy in childhood, which is treated with uniform and standardized clinical trials, is remarkably poised for pharmacogenomic studies. In the last decade, unbiased genome-wide association studies have identified multiple germline risk factors that strongly modify host response to drug therapy...
September 2017: Best Practice & Research. Clinical Haematology
https://www.readbyqxmd.com/read/29050564/a-missense-variant-in-plec-increases-risk%C3%A2-of-atrial-fibrillation
#16
Rosa B Thorolfsdottir, Gardar Sveinbjornsson, Patrick Sulem, Anna Helgadottir, Solveig Gretarsdottir, Stefania Benonisdottir, Audur Magnusdottir, Olafur B Davidsson, Sridharan Rajamani, Dan M Roden, Dawood Darbar, Terje R Pedersen, Marc S Sabatine, Ingileif Jonsdottir, David O Arnar, Unnur Thorsteinsdottir, Daniel F Gudbjartsson, Hilma Holm, Kari Stefansson
BACKGROUND: Genome-wide association studies (GWAS) have yielded variants at >30 loci that associate with atrial fibrillation (AF), including rare coding mutations in the sarcomere genes MYH6 and MYL4. OBJECTIVES: The aim of this study was to search for novel AF associations and in doing so gain insights into the mechanisms whereby variants affect AF risk, using electrocardiogram (ECG) measurements. METHODS: The authors performed a GWAS of 14,255 AF cases and 374,939 controls, using whole-genome sequence data from the Icelandic population, and tested novel signals in 2,002 non-Icelandic cases and 12,324 controls...
October 24, 2017: Journal of the American College of Cardiology
https://www.readbyqxmd.com/read/29050555/natural-variation-in-human-clocks
#17
Malcolm von Schantz
Our own species has a diurnal activity pattern and an average circadian period of 24.2h. Exact determination of circadian period requires expensive and intrusive protocols, and investigators are therefore using chronotype questionnaires as a proxy quantitative measure. Both measures show a normal distribution suggestive of a polygenic trait. The genetic components of the 24-h feedback loop that generates circadian rhythms within our cells have been mapped in detail, identifying a number of candidate genes which have been investigated for genetic polymorphisms relating to the phenotypic variance...
2017: Advances in Genetics
https://www.readbyqxmd.com/read/29050331/a-glo10-score-for-the-prediction-of-prognosis-in-high-grade-gliomas
#18
Feng Chen, Peng Peng, Yi Zhou, Zhen-Yu Yang, Hai-Quan Zhang, Xiang-Sheng Ao, Da-Quan Zhou, Chun-Xiang Xiang
Gliomas are the most common lethal brain tumours and remain great heterogeneity in terms of histopathology and clinical outcomes. Among them, glioblastomas are the most aggressive tumours that lead to a median of less than one-year survival in patients. Despite the little improvement of in diagnosis and treatments for last decades, there is an urgent need for prognostic markers to distinguish high- and low-risk patients before treatment.Here, we generated a list of genes associated with glioblastoma progressions and then performed a comprehensive statistical modelling strategy to derive a 10-gene (GLO10) score from genome wide expression profiles of a large glioblastoma cohort (n=844)...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29050246/nrf2-regulated-metabolic-gene-signature-as-a-prognostic-biomarker-in-non-small-cell-lung-cancer
#19
Akhileshwar Namani, Qin Qin Cui, Yihe Wu, Hongyan Wang, Xiu Jun Wang, Xiuwen Tang
Mutations in Kelch-like ECH-associated protein 1 (KEAP1) cause the aberrant activation of nuclear factor erythroid-derived 2-like 2 (NRF2), which leads to oncogenesis and drug resistance in lung cancer cells. Our study was designed to identify the genes involved in lung cancer progression targeted by NRF2. A series of microarray experiments in normal and cancer cells, as well as in animal models, have revealed regulatory genes downstream of NRF2 that are involved in wide variety of pathways. Specifically, we carried out individual and combinatorial microarray analysis of KEAP1 overexpression and NRF2 siRNA-knockdown in a KEAP1 mutant-A549 non-small cell lung cancer (NSCLC) cell line...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29049906/interaction-between-compound-genetic-risk-for-schizophrenia-and-high-birth-weight-contributes-to-social-anhedonia-and-schizophrenia-in-women
#20
Johanna Liuhanen, Jaana Suvisaari, Eero Kajantie, Jouko Miettunen, Antti-Pekka Sarin, Marjo-Riitta Järvelin, Jouko Lönnqvist, Juha Veijola, Tiina Paunio
Schizophrenia is a highly heritable disease, but despite extensive study, its genetic background remains unresolved. The lack of environmental measures in genetic studies may offer some explanation. In recent Finnish studies, high birth weight was found to increase the risk for familial schizophrenia. We examined the interaction between a polygenic risk score for schizophrenia and high birth weight on social anhedonia and schizophrenia in a general population birth cohort. The study sample included 4223 participants from the 1966 Northern Finland Birth Cohort...
October 9, 2017: Psychiatry Research
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