23 results match your criteria cgat associated

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Genetic association analysis between IL9 and coronary artery disease in a Chinese Han population.

Cytokine 2021 Nov 20;150:155761. Epub 2021 Nov 20.

Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China. Electronic address:

Interleukin-9 (IL-9) plays important role in coronary artery disease (CAD). However, the exact relationship between them is not explored yet. Here, four tag SNPs covering IL9 (rs31563, rs2069868, rs2069870 and rs31564) were selected to conduct case-control association analyses in a total of 3704 individuals from Chinese Han population (1863 CAD vs 1841 control). Read More

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November 2021

Expanding Our Understanding of Nevogenesis: Copy Number Gain of Chromosome 15q in Melanocytic Nevi Is Associated With Distinct Histomorphologic Findings.

Am J Surg Pathol 2021 06;45(6):825-831

Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon.

As the landscape of melanomagenesis becomes better refined through increasingly detailed schema grounded in distinct clinicopathologic-molecular pathways, the stepwise process and variations of molecular nevogenesis have largely remained elusive. Herein, we present a series of 8 melanocytic nevi in patients ranging from 40 to 74 years of age (median: 59.5 y), which demonstrated a reproducible constellation of histomorphologic features as well as a copy number gain of the long arm of chromosome 15 (15q). Read More

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Embryonic progenitor pools generate diversity in fine-scale excitatory cortical subnetworks.

Nat Commun 2019 11 19;10(1):5224. Epub 2019 Nov 19.

Department of Pharmacology, University of Oxford, Mansfield Road, Oxford, OX1 3QT, UK.

The mammalian neocortex is characterized by a variety of neuronal cell types and precise arrangements of synaptic connections, but the processes that generate this diversity are poorly understood. Here we examine how a pool of embryonic progenitor cells consisting of apical intermediate progenitors (aIPs) contribute to diversity within the upper layers of mouse cortex. In utero labeling combined with single-cell RNA-sequencing reveals that aIPs can generate transcriptionally defined glutamatergic cell types, when compared to neighboring neurons born from other embryonic progenitor pools. Read More

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November 2019

Vitamin D Receptor Gene Polymorphism: An Important Predictor of Arthritis Development.

Biomed Res Int 2019 18;2019:8326246. Epub 2019 Mar 18.

Cell and Molecular Biology Lab, Department of Zoology, University of the Punjab, Quaid-i-Azam Campus, Lahore 54590, Pakistan.

Vitamin D is an anti-inflammatory molecule and has a role in prevention of arthritis development. Biologically active form 1, 25(OH)D3 of vitamin D can only exert its action after binding its definite vitamin D receptor encoded by VDR gene. VDR gene polymorphism leads to dysfunctioning of 1, 25(OH)D ultimately disease onset. Read More

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Genomic alterations important for the prognosis in patients with follicular lymphoma treated in SWOG study S0016.

Blood 2019 01 16;133(1):81-93. Epub 2018 Nov 16.

Fred Hutchinson Cancer Research Center, Seattle, WA.

Although recent advances in molecular genetics have enabled improved risk classification of follicular lymphoma (FL) using, for example, the m7-FLIPI score, the impact on treatment has been limited. We aimed to assess the prognostic significance of copy-number aberrations (CNAs) and copy-neutral loss of heterozygosity (cnLOH) identified by chromosome genomic-array testing (CGAT) at FL diagnosis using prospectively collected clinical trial specimens from 255 patients enrolled in the SWOG study S0016. The impact of genomic aberrations was assessed for early progression (progressed or died within 2 years after registration), progression-free survival (PFS), and overall survival (OS). Read More

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January 2019

Missense Mutations of the Pro65 Residue of PCGF2 Cause a Recognizable Syndrome Associated with Craniofacial, Neurological, Cardiovascular, and Skeletal Features.

Am J Hum Genet 2018 11 18;103(5):786-793. Epub 2018 Oct 18.

Institute of Medical Genetics, University Hospital of Wales, Cardiff CF14 4XW, UK; Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK. Electronic address:

PCGF2 encodes the polycomb group ring finger 2 protein, a transcriptional repressor involved in cell proliferation, differentiation, and embryogenesis. PCGF2 is a component of the polycomb repressive complex 1 (PRC1), a multiprotein complex which controls gene silencing through histone modification and chromatin remodelling. We report the phenotypic characterization of 13 patients (11 unrelated individuals and a pair of monozygotic twins) with missense mutations in PCGF2. Read More

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November 2018

Low-Bias RNA Sequencing of the HIV-2 Genome from Blood Plasma.

J Virol 2019 01 10;93(1). Epub 2018 Dec 10.

Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom

Accurate determination of the genetic diversity present in the HIV quasispecies is critical for the development of a preventative vaccine: in particular, little is known about viral genetic diversity for the second type of HIV, HIV-2. A better understanding of HIV-2 biology is relevant to the HIV vaccine field because a substantial proportion of infected people experience long-term viral control, and prior HIV-2 infection has been associated with slower HIV-1 disease progression in coinfected subjects. The majority of traditional and next-generation sequencing methods have relied on target amplification prior to sequencing, introducing biases that may obscure the true signals of diversity in the viral population. Read More

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January 2019

Genomic Response to Vitamin D Supplementation in the Setting of a Randomized, Placebo-Controlled Trial.

EBioMedicine 2018 May 10;31:133-142. Epub 2018 Apr 10.

Wellcome Centre for Human Genetics (WHG), Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK. Electronic address:

Background: Vitamin D deficiency has been associated with multiple diseases, but the causal relevance and underlying processes are not fully understood. Elucidating the mechanisms of action of drug treatments in humans is challenging, but application of functional genomic approaches in randomized trials may afford an opportunity to systematically assess molecular responses.

Methods: In the Biochemical Efficacy and Safety Trial of Vitamin D (BEST-D), a double-blind, placebo-controlled, dose-finding, randomized clinical trial, 305 community-dwelling individuals aged over 65 years were randomly allocated to treatment with vitamin D 4000 IU, 2000 IU or placebo daily for 12 months. Read More

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De novo mutations in GRIN1 cause extensive bilateral polymicrogyria.

Brain 2018 03;141(3):698-712

Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA.

Polymicrogyria is a malformation of cortical development. The aetiology of polymicrogyria remains poorly understood. Using whole-exome sequencing we found de novo heterozygous missense GRIN1 mutations in 2 of 57 parent-offspring trios with polymicrogyria. Read More

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Impact of copy neutral loss of heterozygosity and total genome aberrations on survival in myelodysplastic syndrome.

Mod Pathol 2018 04 15;31(4):569-580. Epub 2017 Dec 15.

Fred Hutchinson Cancer Research Center, Seattle, WA, USA.

Myelodysplastic syndromes (MDS) are a heterogeneous group of diseases with varying genetic aberrations. Half of MDS patients have normal karyotype, obscuring the underlying condition indicating a need for new markers for improved diagnostics and prognosis. We performed a retrospective review of sequential MDS patients who underwent chromosomal genetic array testing (CGAT) between November 2008 and March 2014. Read More

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Identification of genetic variants affecting vitamin D receptor binding and associations with autoimmune disease.

Hum Mol Genet 2017 06;26(11):2164-2176

Wellcome Trust Centre for Human Genetics, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7BN, UK.

Large numbers of statistically significant associations between sentinel SNPs and case-control status have been replicated by genome-wide association studies. Nevertheless, few underlying molecular mechanisms of complex disease are currently known. We investigated whether variation in binding of a transcription factor, the vitamin D receptor (VDR), whose activating ligand vitamin D has been proposed as a modifiable factor in multiple disorders, could explain any of these associations. Read More

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Adult Low-Hypodiploid Acute B-Lymphoblastic Leukemia With IKZF3 Deletion and TP53 Mutation: Comparison With Pediatric Patients.

Am J Clin Pathol 2015 Aug;144(2):263-70

Department of Hematopathology, University of Texas MD Anderson Cancer Center, Houston.

Objectives: Chromosomal ploidy is a major risk stratification tool for acute B-cell lymphoblastic leukemia (B-ALL). Low hypodiploidy and near-haploidy are thought to be confined to pediatric B-ALL and associated with a poor prognosis. Doubling of either a low-hypodiploid or a near-haploid clone results in an apparently high-hyperdiploid karyotype, which is often misclassified for risk. Read More

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De novo point mutations in patients diagnosed with ataxic cerebral palsy.

Brain 2015 Jul 16;138(Pt 7):1817-32. Epub 2015 May 16.

4 Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, UK 16 Department of Clinical Genetics, Churchill Hospital, Oxford University Hospitals NHS Trust, Oxford, OX3 7LJ, UK

Cerebral palsy is a sporadic disorder with multiple likely aetiologies, but frequently considered to be caused by birth asphyxia. Genetic investigations are rarely performed in patients with cerebral palsy and there is little proven evidence of genetic causes. As part of a large project investigating children with ataxia, we identified four patients in our cohort with a diagnosis of ataxic cerebral palsy. Read More

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Mycoplasma CG- and GATC-specific DNA methyltransferases selectively and efficiently methylate the host genome and alter the epigenetic landscape in human cells.

Epigenetics 2015 19;10(4):303-18. Epub 2015 Feb 19.

a Infectious & Inflammatory Disease Center ; Sanford-Burnham Medical Research Institute ; La Jolla , CA USA.

Aberrant DNA methylation is frequently observed in disease, including many cancer types, yet the underlying mechanisms remain unclear. Because germline and somatic mutations in the genes that are responsible for DNA methylation are infrequent in malignancies, additional mechanisms must be considered. Mycoplasmas spp. Read More

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November 2015

Long-term effects of gestational nicotine exposure and food-restriction on gene expression in the striatum of adolescent rats.

PLoS One 2014 19;9(2):e88896. Epub 2014 Feb 19.

Medical Research Council (MRC), Social, Genetic and Developmental Psychiatry (SGDP) centre, Institute of Psychiatry, King's College London, London, United Kingdom.

Gestational exposure to environmental toxins such as nicotine may result in detectable gene expression changes in later life. To investigate the direct toxic effects of prenatal nicotine exposure on later brain development, we have used transcriptomic analysis of striatal samples to identify gene expression differences between adolescent Lister Hooded rats exposed to nicotine in utero and controls. Using an additional group of animals matched for the reduced food intake experienced in the nicotine group, we were also able to assess the impact of imposed food-restriction on gene expression profiles. Read More

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January 2015

Human snRNA genes use polyadenylation factors to promote efficient transcription termination.

Nucleic Acids Res 2014 Jan 4;42(1):264-75. Epub 2013 Oct 4.

Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK and CGAT, MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3PT, UK.

RNA polymerase II transcribes both protein coding and non-coding RNA genes and, in yeast, different mechanisms terminate transcription of the two gene types. Transcription termination of mRNA genes is intricately coupled to cleavage and polyadenylation, whereas transcription of small nucleolar (sno)/small nuclear (sn)RNA genes is terminated by the RNA-binding proteins Nrd1, Nab3 and Sen1. The existence of an Nrd1-like pathway in humans has not yet been demonstrated. Read More

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January 2014

Association between DNA methyltransferases 3B gene polymorphisms and the susceptibility to acute myeloid leukemia in Chinese Han population.

PLoS One 2013 17;8(9):e74626. Epub 2013 Sep 17.

Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, China.

DNMT3B plays a crucial role in the generation of aberrant methylation during carcinogenesis. Polymorphisms in the DNMT3B gene may influence the DNA methylation enzymatic activity of DNMT3B, thereby modulating the susceptibility to AML. Thus, we investigated the association between SNPs in the DNMT3Bgene and their haplotypes with the risk of AML in the Chinese Han population. Read More

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A genome-wide association study implicates the APOE locus in nonpathological cognitive ageing.

Mol Psychiatry 2014 Jan 4;19(1):76-87. Epub 2012 Dec 4.

1] Centre for Cognitive Ageing and Cognitive Epidemiology, The University of Edinburgh, Edinburgh, UK [2] Alzheimer Scotland Dementia Research Centre, The University of Edinburgh, Edinburgh, UK.

Cognitive decline is a feared aspect of growing old. It is a major contributor to lower quality of life and loss of independence in old age. We investigated the genetic contribution to individual differences in nonpathological cognitive ageing in five cohorts of older adults. Read More

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January 2014

PPP1R13L variant associated with prognosis for patients with rectal cancer.

J Cancer Res Clin Oncol 2013 Mar 21;139(3):465-73. Epub 2012 Nov 21.

Department of Oncology and Hematology, Kyungpook National University Medical Center, Kyungpook National University School of Medicine, 807 Hogukno, Buk-Gu, Daegu 702-210, Korea.

Background: ERCC1, CD3EAP, and PPP1R13L polymorphisms in the chromosomal region 19q13.2-3 have already been shown to have a synergistic effect on apoptosis and DNA repair pathways. Therefore, the aim of this study was to investigate the association between such genetic variants and the prognosis of colorectal cancer (CRC) following curative surgery. Read More

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A comparison of the lidocaine patch 5% vs naproxen 500 mg twice daily for the relief of pain associated with carpal tunnel syndrome: a 6-week, randomized, parallel-group study.

MedGenMed 2006 Aug 9;8(3):33. Epub 2006 Aug 9.

Kansas City University of Medicine and Biosciences, Kansas City, Missouri, USA.

Objectives: Carpal tunnel syndrome (CTS) is a common entrapment neuropathy caused by median nerve compression. This pilot clinical trial was designed to compare the safety and effectiveness of the lidocaine patch 5% to that of naproxen 500 mg twice daily for the treatment of neuropathic pain associated with CTS.

Methods: In this 6-week, randomized, parallel-group, open-label, multicenter study, participants from 2 practice sites, aged 18 to 75 years with clinical/electrodiagnostic evidence of CTS, were randomized to receive up to 3 lidocaine 5% patches every 24 hours or naproxen 500 mg twice daily for 6 weeks. Read More

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Idiotypic analysis of anti-GAT antibodies. VIII. Comparison of interstrain and allotype-associated idiotypic specificities.

J Immunol 1981 Jan;126(1):177-82

A guinea pig anti-idiotypic antiserum made against pooled specifically purified A/J anti-GAT antibodies was characterized. This antiserum contains anti-idiotypic antibodies specific to interspecies, interstrain, and allotype-linked idiotypic determinants. These idiotypic determinants are associated with the combining sites of idiotypic antibodies that are induced by GT-related but not GA-related antigenic moieties. Read More

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January 1981

Idiotypic analysis of antibodies against the terpolymer L-glutamic acid60-L-alanine30-L-tyrosine10 (GAT). IV. Induction of CGAT idiotype following immunization with various synthetic polymers containing glutamic acid and tyrosine.

Authors:
S T Ju M E Dorf

Eur J Immunol 1979 Jul;9(7):553-60

The immune responses of all inbred strains of mice specific to the synthetic terpolymer poly(LGlu60LAla30LTyr10), referred to as GAT10, are characterized by the presence of anti-GAT antibodies which share a common (CGAT) idiotype. In this report, we describe the ability of the synthetic polymers, LGlu33LAla33LTyr33, LGlu51-LAla34LTyr15 and poly-L(Tyr, Glu)-DLAla--LLys [(T,G)-A--L] to induce antibodies with CGAT idiotypic specificities. All of these polymers contain "GT"-related determinants. Read More

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Idiotypic analysis of monoclonal antibodies to poly(Glu60Ala30Tyr10).

Proc Natl Acad Sci U S A 1979 Jun;76(6):2942-6

Fifteen hybridoma anti-poly(Glu60Ala30Tyr10) (anti-GAT) antibodies were analyzed for the presence of a common set of idiotypic specificities associated with murine anti-GAT antibodies, termed CGAT idiotype, which are present on the anti-GAT antibodies of all mouse strains. Thirteen of these monoclonal anti-GAT antibodies expressed a major fraction of CGAT idiotypic specificities. However, the remaining fraction of CGAT idiotypic specificities were not detected in individual or pooled hybridoma anti-GAT antibodies. Read More

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