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https://www.readbyqxmd.com/read/29161772/microarray-analysis-of-gene-expression-in-the-cyclooxygenase-cox-knockout-mice-a-connection-to-autism-spectrum-disorder
#1
Ravneet Rai-Bhogal, Eizaaz Ahmad, Hongyan Li, Dorota A Crawford
The cellular and molecular events that take place during brain development play an important role in governing function of the mature brain. Lipid signalling molecules such as prostaglandin E2 (PGE2 ) play an important role in healthy brain development. Abnormalities along the COX/PGE2 signalling pathway due to genetic or environmental causes have been linked to Autism Spectrum Disorders (ASDs). This study aims to evaluate the effect of altered COX/PGE2 signalling on development and function of the prenatal brain using male mice lacking cyclooxygenase-1 and -2 (COX-1(-/-) and COX-2(-/-) ) as potential model systems of ASD...
November 21, 2017: European Journal of Neuroscience
https://www.readbyqxmd.com/read/29161691/failure-to-thrive-in-the-context-of-carney-complex
#2
Amit Tirosh, Adi Auerbach, Belen Bonella, Phaedon D Zavras, Elena Belyavskaya, Charalampos Lyssikatos, Karen Meir, Ram Weiss, Hagit Daum, Maya B Lodish, David Gillis, Constantine A Stratakis
BACKGROUND/AIMS: Carney complex (CNC) is a rare syndrome associated with multiple tumors and several other unique manifestations. We describe the clinical, genetic, and laboratory findings in a cohort of patients with CNC and failure to thrive (FTT). METHODS: A retrospective case series of pediatric patients with CNC presenting with FTT. RESULTS: We describe a patient with infantile Cushing syndrome (CS) who presented with severe FTT and liver disease; the patient was subsequently diagnosed with CNC...
November 21, 2017: Hormone Research in Pædiatrics
https://www.readbyqxmd.com/read/29161666/genetic-variants-and-acute-kidney-injury-a-review-of-the-literature
#3
REVIEW
Daniel B Larach, Milo C Engoren, Ellen M Schmidt, Michael Heung
PURPOSE: Limited data exists on potential genetic contributors to acute kidney injury. This review examines current knowledge of AKI genomics. MATERIALS AND METHODS: 32 studies were selected from PubMed and GWAS Catalog queries for original data studies of human AKI genetics. Hand search of references identified 3 additional manuscripts. RESULTS: 33 of 35 studies were hypothesis-driven investigations of candidate polymorphisms that either did not consistently replicate statistically significant findings, or obtained significant results only in few small-scale studies...
November 13, 2017: Journal of Critical Care
https://www.readbyqxmd.com/read/29161441/contributions-of-function-altering-variants-in-genes-implicated-in-pubertal-timing-and-body-mass-for-self-limited-delayed-puberty
#4
Sasha R Howard, Leonardo Guasti, Ariel Poliandri, Alessia David, Claudia P Cabrera, Michael R Barnes, Karoliina Wehkalampi, Stephen O'Rahilly, Catherine E Aiken, Anthony P Coll, Marcella Ma, Debra Rimmington, Giles S H Yeo, Leo Dunkel
Context: Self-limited delayed puberty (DP) is often associated with delay in physical maturation, but whilst highly heritable the causal genetic factors remain elusive. Genome-wide association studies of the timing of puberty have identified multiple loci for age of menarche (AAM) in females and voice break in males, particularly in pathways controlling energy balance. Objective/Main outcome measures: We aimed to assess the contribution of rare variants in such genes to the phenotype of familial DP...
November 16, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/29161432/modeling-mutant-wild-type-interactions-to-ascertain-pathogenicity-of-prokr2-missense-variants-in-patients-with-isolated-gnrh-deficiency
#5
Kimberly H Cox, Luciana M B Oliveira, Lacey Plummer, Braden Corbin, Thomas Gardella, Ravikumar Balasubramanian, William F Crowley
A major challenge in human genetics is the validation of pathogenicity of heterozygous missense variants. This problem is well-illustrated by PROKR2 variants associated with Isolated GnRH Deficiency (IGD). Homozygous, loss of function variants in PROKR2 were initially implicated in autosomal recessive IGD; however, most IGD-associated PROKR2 variants are heterozygous. Moreover, while IGD patient cohorts are enriched for PROKR2 missense variants similar rare variants are also found in normal individuals. To elucidate the pathogenic mechanisms distinguishing IGD-associated PROKR2 variants from rare variants in controls, we assessed 59 variants using three approaches: (i) in silico prediction, (ii) traditional in vitro functional assays across 3 signaling pathways with mutant-alone transfections, and (iii) modified in vitro assays with mutant and wild-type expression constructs co-transfected to model in vivo heterozygosity...
November 17, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/29161428/arabidopsis-inositol-polyphosphate-multikinase-delays-flowering-time-through-mediating-transcriptional-activation-of-flowering-locus-c
#6
Sihong Sang, Yao Chen, Qiaofeng Yang, Peng Wang
Timely flowering is critical for successful reproduction and seed yield in plants. A diverse range of regulators have been found to control flowering time in response to environmental and endogenous signals. Among these regulators, FLOWERING LOCUS C (FLC) acts as a central repressor of floral transition by blocking the expression of flowering integrator genes. Here, we report that Arabidopsis inositol polyphosphate multikinase (AtIPK2β) functions in flowering time control by mediating transcriptional regulation of FLC at the chromatin level...
November 17, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/29161422/prevalence-and-genetic-variability-of-human-polyomaviruses-6-and-7-in-healthy-skin-among-asymptomatic-individuals
#7
Yumiko Hashida, Tomonori Higuchi, Shigenobu Matsuzaki, Kimiko Nakajima, Shigetoshi Sano, Masanori Daibata
Background: Despite the pathogenetic potential of human polyomavirus 6 (HPyV6) and human polyomavirus 7 (HPyV7), they have been found in the normal skin of healthy individuals. However, little is known about the prevalence, infection levels, and geographical variations of these polyomaviruses in the skin. Methods: Using skin swabs from 470 participants aged 2-98 years, we estimated the prevalence of copy numbers of HPyV6 and HPyV7 with respect to age and ethnicity...
November 17, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/29161321/association-mapping-unveils-favorable-alleles-for-grain-iron-and-zinc-concentrations-in-lentil-lens-culinaris-subsp-culinaris
#8
Akanksha Singh, Vinay Sharma, Harsh Kumar Dikshit, Muraleedhar Aski, Harish Kumar, Nepolean Thirunavukkarasu, Basavanagouda S Patil, Shiv Kumar, Ashutosh Sarker
Lentil is a major cool-season grain legume grown in South Asia, West Asia, and North Africa. Populations in developing countries of these regions have micronutrient deficiencies; therefore, breeding programs should focus more on improving the micronutrient content of food. In the present study, a set of 96 diverse germplasm lines were evaluated at three different locations in India to examine the variation in iron (Fe) and zinc (Zn) concentration and identify simple sequence repeat (SSR) markers that associate with the genetic variation...
2017: PloS One
https://www.readbyqxmd.com/read/29161273/enrichment-of-colorectal-cancer-associations-in-functional-regions-insight-for-using-epigenomics-data-in-the-analysis-of-whole-genome-sequence-imputed-gwas-data
#9
Stephanie A Bien, Paul L Auer, Tabitha A Harrison, Conghui Qu, Charles M Connolly, Peyton G Greenside, Sai Chen, Sonja I Berndt, Stéphane Bézieau, Hyun M Kang, Jeroen Huyghe, Hermann Brenner, Graham Casey, Andrew T Chan, John L Hopper, Barbara L Banbury, Jenny Chang-Claude, Stephen J Chanock, Robert W Haile, Michael Hoffmeister, Christian Fuchsberger, Mark A Jenkins, Suzanne M Leal, Mathieu Lemire, Polly A Newcomb, Steven Gallinger, John D Potter, Robert E Schoen, Martha L Slattery, Joshua D Smith, Loic Le Marchand, Emily White, Brent W Zanke, Goncalo R Abeçasis, Christopher S Carlson, Ulrike Peters, Deborah A Nickerson, Anshul Kundaje, Li Hsu
BACKGROUND: The evaluation of less frequent genetic variants and their effect on complex disease pose new challenges for genomic research. To investigate whether epigenetic data can be used to inform aggregate rare-variant association methods (RVAM), we assessed whether variants more significantly associated with colorectal cancer (CRC) were preferentially located in non-coding regulatory regions, and whether enrichment was specific to colorectal tissues. METHODS: Active regulatory elements (ARE) were mapped using data from 127 tissues and cell-types from NIH Roadmap Epigenomics and Encyclopedia of DNA Elements (ENCODE) projects...
2017: PloS One
https://www.readbyqxmd.com/read/29161261/mrna-processing-in-mutant-zebrafish-lines-generated-by-chemical-and-crispr-mediated-mutagenesis-produces-unexpected-transcripts-that-escape-nonsense-mediated-decay
#10
Jennifer L Anderson, Timothy S Mulligan, Meng-Chieh Shen, Hui Wang, Catherine M Scahill, Frederick J Tan, Shao J Du, Elisabeth M Busch-Nentwich, Steven A Farber
As model organism-based research shifts from forward to reverse genetics approaches, largely due to the ease of genome editing technology, a low frequency of abnormal phenotypes is being observed in lines with mutations predicted to lead to deleterious effects on the encoded protein. In zebrafish, this low frequency is in part explained by compensation by genes of redundant or similar function, often resulting from the additional round of teleost-specific whole genome duplication within vertebrates. Here we offer additional explanations for the low frequency of mutant phenotypes...
November 21, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/29161028/exploring-the-active-centre-of-lsd1-corest-complex-by-molecular-dynamics-simulation-utilizing-its-co-crystallized-cofactor-tetrahydrofolate-as-a-probe
#11
Waleed A A Zalloum, Hiba M Zalloum
Epigenetic targeting of cancer is a recent era to manipulate the gene without destroying the genetic material. Lysine-specific demethylase 1 (LSD1) is one of the enzymes associated with the chromatin for post-translational modifications, where it demethylates lysine amino acid in the chromatin H3 tail. Many studies showed that inhibiting LSD1 could potentially be used to treat cancer epigenetically. LSD1 is associated with its corepressor protein CoREST, and uses tetrahydrofolate as a cofactor to accept CH2 from the demethylation process...
November 21, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/29161012/top-down-proteomics-ready-for-prime-time
#12
Bifan Chen, Kyle A Brown, Ziqing Lin, Ying Ge
In the post-genomics era, the study of proteins is critical for understanding cellular functions at the molecular level.1-5 Beyond the genetic code, the human proteome is greatly diversified by various genetic variations, alternative splicing of RNA transcripts, and post-translational modifi-cations (PTMs).6,7 In 2013, the term "proteoform" was designated to describe "all of the different molecular forms in which the protein product of a single gene can be found",6 clearing up the confusion in nomenclature and joining research efforts to develop methodologies for pro-teoform characterization...
November 21, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29160859/the-role-of-rnf213-4810g-a-and-4950g-a-variants-in-patients-with-moyamoya-disease-in-korea
#13
Young Seok Park, Hui Jeong An, Jung Oh Kim, Won Seop Kim, In Bo Han, Ok Joon Kim, Nam Keun Kim, Dong-Seok Kim
Although a founder variant of RNF213 4810G>A is a major genetic risk factor for moyamoya disease (MMD) in East Asians, the frequency and disease susceptibility of RNF213 variants remain largely unknown. This study investigated the mutation analysis of RNF213 (4448, 4810, 4863, and 4950) between Korean MMD and healthy controls. We performed a polymerase chain reaction-restriction fragment length polymorphism analysis. To identify the association between RNF213 gene polymorphisms and MMD disease, we performed statistical analyses such as multivariable logistic regression and Fisher's exact test...
November 21, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29160764/dna-methylation-profile-in-chronic-myelomonocytic-leukemia-associates-with-distinct-clinical-biological-and-genetic-features
#14
Laura Palomo, Roberto Malinverni, Marta Cabezón, Blanca Xicoy, Montserrat Arnan, Rosa Coll, Helena Pomares, Olga García, Francisco Fuster-Tormo, Javier Grau, Evarist Feliu, Francesc Solé, Marcus Buschbeck, Lurdes Zamora
Chromosomal abnormalities are detected in 20-30% of patients with chronic myelomonocytic leukemia (CMML) and correlate with prognosis. On the mutation level, disruptive alterations are particularly frequent in chromatin regulatory genes. However, little is known about the consequential alterations in the epigenetic marking of the genome. Here, we report the analysis of genomic DNA methylation patterns of 64 CMML patients and 10 healthy controls, using a DNA methylation microarray focused on promoter regions...
November 21, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/29160746/nucleic-acid-therapies-for-cystic-fibrosis
#15
Shruti Sasaki, Shuling Guo
Nucleic acid therapeutics are an established class of drugs that enable specific targeting of a gene of interest. This diverse family of drugs includes antisense oligonucleotides, siRNAs, and mRNA replacement therapies, which can elicit both gene repression and activation, primarily at the RNA level. Recent advances in medicinal chemistry have increased drug potency and enhanced delivery and distribution to a broad array of tissue and cell types. A key advantage of nucleic acid therapeutics is in their application to monogenic diseases...
November 21, 2017: Nucleic Acid Therapeutics
https://www.readbyqxmd.com/read/29160618/deciphering-the-fine-nucleotide-diversity-of-full-hla-class-i-and-class-ii-genes-in-a-well-documented-population-from-sub-saharan-africa
#16
Thomas Goeury, Lisa Creary, Lydie Brunet, Maxime Galan, Maeva Pasquier, Barbara Kervaire, André Langaney, Jean-Marie Tiercy, Marcelo A Fernández-Viña, José Manuel Nunes, Alicia Sanchez-Mazas
With the aim to understand how NGS improves both our assessment of genetic variation within populations and our knowledge on HLA molecular evolution, we sequenced and analysed 8 HLA loci in a well-documented population from sub-Saharan Africa (Mandenka). The results of full-gene NGS-MiSeq sequencing compared to those obtained by traditional typing techniques or limited sequencing strategies showed that segregating sites located outside exon 2 are crucial to describe not only class I, but also class II population diversity...
November 21, 2017: HLA
https://www.readbyqxmd.com/read/29160564/functional-differences-in-transport-properties-of-natural-hkt1-1-variants-influence-shoot-na-exclusion-in-grapevine-rootstocks
#17
Sam W Henderson, Jake D Dunlevy, Yue Wu, Deidre H Blackmore, Rob R Walker, Everard J Edwards, Matthew Gilliham, Amanda R Walker
Under salinity, Vitis spp. rootstocks can mediate salt (NaCl) exclusion from grafted V. vinifera scions enabling higher grapevine yields and production of superior wines with lower salt content. Until now, the genetic and mechanistic elements controlling sodium (Na(+) ) exclusion in grapevine were unknown. Using a cross between two Vitis interspecific hybrid rootstocks, we mapped a dominant quantitative trait locus (QTL) associated with leaf Na(+) exclusion (NaE) under salinity stress. The NaE locus encodes six high-affinity potassium transporters (HKT)...
November 21, 2017: New Phytologist
https://www.readbyqxmd.com/read/29160304/il11-is-a-crucial-determinant-of-cardiovascular-fibrosis
#18
Sebastian Schafer, Sivakumar Viswanathan, Anissa A Widjaja, Wei-Wen Lim, Aida Moreno-Moral, Daniel M DeLaughter, Benjamin Ng, Giannino Patone, Kingsley Chow, Ester Khin, Jessie Tan, Sonia P Chothani, Lei Ye, Owen J L Rackham, Nicole S J Ko, Norliza E Sahib, Chee Jian Pua, Nicole T G Zhen, Chen Xie, Mao Wang, Henrike Maatz, Shiqi Lim, Kathrin Saar, Susanne Blachut, Enrico Petretto, Sabine Schmidt, Tracy Putoczki, Nuno Guimarães-Camboa, Hiroko Wakimoto, Sebastiaan van Heesch, Kristmundur Sigmundsson, See L Lim, Jia L Soon, Victor T T Chao, Yeow L Chua, Teing E Tan, Sylvia M Evans, Yee J Loh, Muhammad H Jamal, Kim K Ong, Kim C Chua, Boon-Hean Ong, Mathew J Chakaramakkil, Jonathan G Seidman, Christine E Seidman, Norbert Hubner, Kenny Y K Sin, Stuart A Cook
Fibrosis is a final common pathology in cardiovascular disease(1). In the heart, fibrosis causes mechanical and electrical dysfunction(1,2) and in the kidney, it predicts the onset of renal failure(3). Transforming growth factor β1 (TGFB1) is the principal pro-fibrotic factor(4,5) but its inhibition is associated with side effects due to its pleiotropic roles(6,7). We hypothesised that downstream effectors of TGFB1 in fibroblasts could be attractive therapeutic targets and lack upstream toxicities. Using integrated imaging-genomics analyses of primary human fibroblasts, we found that Interleukin 11 (IL11) upregulation is the dominant transcriptional response to TGFB1 exposure and required for its profibrotic effect...
November 13, 2017: Nature
https://www.readbyqxmd.com/read/29160301/new-insights-into-the-pharmacogenomics-of-antidepressant-response-from-the-gendep-and-star-d-studies-rare-variant-analysis-and-high-density-imputation
#19
C Fabbri, K E Tansey, R H Perlis, J Hauser, N Henigsberg, W Maier, O Mors, A Placentino, M Rietschel, D Souery, G Breen, C Curtis, L Sang-Hyuk, S Newhouse, H Patel, M Guipponi, N Perroud, G Bondolfi, M O'Donovan, G Lewis, J M Biernacka, R M Weinshilboum, A Farmer, K J Aitchison, I Craig, P McGuffin, R Uher, C M Lewis
Genome-wide association studies have generally failed to identify polymorphisms associated with antidepressant response. Possible reasons include limited coverage of genetic variants that this study tried to address by exome genotyping and dense imputation. A meta-analysis of Genome-Based Therapeutic Drugs for Depression (GENDEP) and Sequenced Treatment Alternatives to Relieve Depression (STAR*D) studies was performed at the single-nucleotide polymorphism (SNP), gene and pathway levels. Coverage of genetic variants was increased compared with previous studies by adding exome genotypes to previously available genome-wide data and using the Haplotype Reference Consortium panel for imputation...
November 21, 2017: Pharmacogenomics Journal
https://www.readbyqxmd.com/read/29160300/genome-wide-association-study-identifies-the-common-variants-in-cyp3a4-and-cyp3a5-responsible-for-variation-in-tacrolimus-trough-concentration-in-caucasian-kidney-transplant-recipients
#20
W S Oetting, B Wu, D P Schladt, W Guan, R P Remmel, R B Mannon, A J Matas, A K Israni, P A Jacobson
The immunosuppressant tacrolimus (TAC) is metabolized by both cytochrome P450 3A4 (CYP3A4) and CYP3A5 enzymes. It is common for European Americans (EA) to carry two CYP3A5 loss-of-function (LoF) variants that profoundly reduces TAC metabolism. Despite having two LoF alleles, there is still considerable variability in TAC troughs and identifying additional variants in genes outside of the CYP3A5 gene could provide insight into this variability. We analyzed TAC trough concentrations in 1345 adult EA recipients with two CYP3A5 LoF alleles in a genome-wide association study...
November 21, 2017: Pharmacogenomics Journal
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