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Genome wide association studies

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https://www.readbyqxmd.com/read/29055159/genomics-of-natural-populations-evolutionary-forces-that-establish-and-maintain-gene-arrangements-in-drosophila-pseudoobscura
#1
Zachary L Fuller, Gwilym D Haynes, Stephen Richards, Stephen W Schaeffer
The evolution of complex traits in heterogeneous environments may shape the order of genes within chromosomes. Drosophila pseudoobscura has a rich gene arrangement polymorphism that allows one to test evolutionary genetic hypotheses about how chromosomal inversions are established in populations. D. pseudoobscura has >30 gene arrangements on a single chromosome that were generated through a series of overlapping inversion mutations with > 10 inversions with appreciable frequencies and wide geographic distributions...
October 21, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29055111/genetic-based-dissection-of-arsenic-accumulation-in-maize-using-a-genome-wide-association-analysis-method
#2
Zhan Zhao, Huaisheng Zhang, Zhongjun Fu, Hao Chen, Yanan Lin, Pengshuai Yan, Weihua Li, Huiling Xie, Zhanyong Guo, Xuehai Zhang, Jihua Tang
Understanding the mechanism of arsenic (As) accumulation in plants is important in reducing As's toxicity to plants and its potential risks to human health. Here, we performed a genome-wide association study to dissect the genetic basis of the As contents of different maize tissues in Xixian, which was irrigated with As-rich surface water, and Changge using an association population consisting of 230 representative inbred maize lines. Phenotypic data revealed a wide normal distribution and high repeatability for the As contents in maize tissues...
October 21, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/29054864/heterogeneous-patterns-of-genetic-diversity-and-differentiation-in-european-and-siberian-chiffchaff-phylloscopus-collybita-abietinus-p-tristis
#3
Venkat Talla, Faheema Kalsoom, Daria Shipilina, Irina Marova, Niclas Backström
Identification of candidate genes for trait variation in diverging lineages and characterization of mechanistic underpinnings of genome differentiation are key steps towards understanding the processes underlying the formation of new species. Hybrid zones provide a valuable resource for such investigations since they allow for studying how genomes evolve as species exchange genetic material and for associating particular genetic regions with phenotypic traits of interest. Here we use whole-genome resequencing of both allopatric and hybridising populations of the European (Phylloscopus collybita abietinus) and the Siberian chiffchaff (P...
October 20, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29054677/expression-of-the-ppm1f-gene-is-regulated-by-stress-and-associated-with-anxiety-and-depression
#4
Aliza P Wingo, Eric R Velasco, Antonio Florido, Adriana Lori, Dennis C Choi, Tanja Jovanovic, Kerry J Ressler, Raül Andero
BACKGROUND: Molecular mechanisms underlying psychological sequelae of exposure to stressful experiences, such as posttraumatic stress disorder (PTSD) and depression, are not well understood. METHODS: Using convergent evidence from animal and human transcriptomic and genomic studies, we aimed to identify genetic mechanisms underlying depression and anxiety after traumatic experiences. RESULTS: From a transcriptome-wide analysis in mice, we found the Ppm1f gene to be differentially expressed in the amygdala and medial prefrontal cortex (mPFC) a week after immobilization stress...
August 30, 2017: Biological Psychiatry
https://www.readbyqxmd.com/read/29054604/susceptibility-loci-associated-cutaneous-squamous-cell-carcinoma-invasiveness
#5
Wei Wang, Eric Jorgenson, Alice S Whittemore, Maryam M Asgari
Genome-wide association studies (GWAS) have identified genetic loci associated with cutaneous squamous cell carcinoma (cSCC) risk, but single nucleotide polymorphisms (SNP) associations with cSCC invasiveness have not been investigated. We examined associations between cSCC invasiveness and 23 reported SNPs among 67,833 non-Hispanic white subjects. Additionally, we performed a genome-wide scan and identified one SNP with significantly different frequencies in 5,724 subjects with at least one invasive tumor and 1,943 subjects with in-situ tumors only...
October 17, 2017: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/29054568/genetic-epidemiology-of-ovarian-cancer-and-prospects-for-polygenic-risk-prediction
#6
REVIEW
Michelle R Jones, Daniella Kamara, Beth Y Karlan, Paul D P Pharoah, Simon A Gayther
Epithelial ovarian cancer (EOC) is a heterogeneous disease with a major heritable component. The different histotypes of invasive disease - high grade serous, clear cell, endometrioid and mucinous - are associated with different underlying genetic susceptibility and epidemiological and lifestyle risk factors, all of which contribute to the different biology and clinical characteristics of each histotype. A combination of familial and population based sequencing studies, and genome wide association studies (GWAS) have identified a range of genetic susceptibility alleles for EOC comprising rare but highly penetrant genes (e...
October 17, 2017: Gynecologic Oncology
https://www.readbyqxmd.com/read/29054530/a-molecular-morphometric-approach-to-diabetic%C3%A2-kidney-disease-can-link-structure-to%C3%A2-function-and-outcome
#7
Viji Nair, Claudiu V Komorowsky, E Jennifer Weil, Berne Yee, Jeffrey Hodgin, Jennifer L Harder, Bradley Godfrey, Wenjun Ju, Carine M Boustany-Kari, Margrit Schwarz, Kevin V Lemley, Peter J Nelson, Robert G Nelson, Matthias Kretzler
Diabetic kidney disease is the leading cause of kidney failure. However, studies of molecular mechanisms of early kidney damage are lacking. Here we examined for possible linkage between transcriptional regulation and quantitative structural damage in early diabetic kidney disease in Pima Indians with type 2 diabetes. Tissue obtained from protocol kidney biopsies underwent genome-wide compartment-specific gene expression profiling and quantitative morphometric analysis. The ultrastructural lesion most strongly associated with transcriptional regulation was cortical interstitial fractional volume (VvInt), an index of tubule-interstitial damage...
October 18, 2017: Kidney International
https://www.readbyqxmd.com/read/29053852/genome-wide-scan-and-analysis-of-positive-selective-signatures-in-dwarf-brown-egg-layers-and-silky-fowl-chickens
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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