A Case of 22Q11 Deletion Syndrome
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase -
Analysis of the Indacaterol-Regulated Transcriptome in Human Airway
Supplemental material to this article can be found at: http://jpet.aspetjournals.org/content/suppl/2018/04/13/jpet.118.249292.DC1 1521-0103/366/1/220–236$35.00 https://doi.org/10.1124/jpet.118.249292 THE JOURNAL OF PHARMACOLOGY AND EXPERIMENTAL THERAPEUTICS J Pharmacol Exp Ther 366:220–236, July 2018 Copyright ª 2018 by The American Society for Pharmacology and Experimental Therapeutics Analysis of the Indacaterol-Regulated Transcriptome in Human Airway Epithelial Cells Implicates Gene Expression Changes in the s Adverse and Therapeutic Effects of b2-Adrenoceptor Agonists Dong Yan, Omar Hamed, Taruna Joshi,1 Mahmoud M. Mostafa, Kyla C. Jamieson, Radhika Joshi, Robert Newton, and Mark A. Giembycz Departments of Physiology and Pharmacology (D.Y., O.H., T.J., K.C.J., R.J., M.A.G.) and Cell Biology and Anatomy (M.M.M., R.N.), Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada Received March 22, 2018; accepted April 11, 2018 Downloaded from ABSTRACT The contribution of gene expression changes to the adverse and activity, and positive regulation of neutrophil chemotaxis. The therapeutic effects of b2-adrenoceptor agonists in asthma was general enriched GO term extracellular space was also associ- investigated using human airway epithelial cells as a therapeu- ated with indacaterol-induced genes, and many of those, in- tically relevant target. Operational model-fitting established that cluding CRISPLD2, DMBT1, GAS1, and SOCS3, have putative jpet.aspetjournals.org the long-acting b2-adrenoceptor agonists (LABA) indacaterol, anti-inflammatory, antibacterial, and/or antiviral activity. Numer- salmeterol, formoterol, and picumeterol were full agonists on ous indacaterol-regulated genes were also induced or repressed BEAS-2B cells transfected with a cAMP-response element in BEAS-2B cells and human primary bronchial epithelial cells by reporter but differed in efficacy (indacaterol $ formoterol . -
Downloaded Per Proteome Cohort Via the Web- Site Links of Table 1, Also Providing Information on the Deposited Spectral Datasets
www.nature.com/scientificreports OPEN Assessment of a complete and classifed platelet proteome from genome‑wide transcripts of human platelets and megakaryocytes covering platelet functions Jingnan Huang1,2*, Frauke Swieringa1,2,9, Fiorella A. Solari2,9, Isabella Provenzale1, Luigi Grassi3, Ilaria De Simone1, Constance C. F. M. J. Baaten1,4, Rachel Cavill5, Albert Sickmann2,6,7,9, Mattia Frontini3,8,9 & Johan W. M. Heemskerk1,9* Novel platelet and megakaryocyte transcriptome analysis allows prediction of the full or theoretical proteome of a representative human platelet. Here, we integrated the established platelet proteomes from six cohorts of healthy subjects, encompassing 5.2 k proteins, with two novel genome‑wide transcriptomes (57.8 k mRNAs). For 14.8 k protein‑coding transcripts, we assigned the proteins to 21 UniProt‑based classes, based on their preferential intracellular localization and presumed function. This classifed transcriptome‑proteome profle of platelets revealed: (i) Absence of 37.2 k genome‑ wide transcripts. (ii) High quantitative similarity of platelet and megakaryocyte transcriptomes (R = 0.75) for 14.8 k protein‑coding genes, but not for 3.8 k RNA genes or 1.9 k pseudogenes (R = 0.43–0.54), suggesting redistribution of mRNAs upon platelet shedding from megakaryocytes. (iii) Copy numbers of 3.5 k proteins that were restricted in size by the corresponding transcript levels (iv) Near complete coverage of identifed proteins in the relevant transcriptome (log2fpkm > 0.20) except for plasma‑derived secretory proteins, pointing to adhesion and uptake of such proteins. (v) Underrepresentation in the identifed proteome of nuclear‑related, membrane and signaling proteins, as well proteins with low‑level transcripts. -
Wiki-Pi: a Web-Server of Annotated Human Protein- Protein Interactions to Aid in Discovery of Protein Function
Wiki-Pi: A Web-Server of Annotated Human Protein- Protein Interactions to Aid in Discovery of Protein Function Naoki Orii1,2, Madhavi K. Ganapathiraju1* 1 Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America, 2 Language Technologies Institute, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America Abstract Protein-protein interactions (PPIs) are the basis of biological functions. Knowledge of the interactions of a protein can help understand its molecular function and its association with different biological processes and pathways. Several publicly available databases provide comprehensive information about individual proteins, such as their sequence, structure, and function. There also exist databases that are built exclusively to provide PPIs by curating them from published literature. The information provided in these web resources is protein-centric, and not PPI-centric. The PPIs are typically provided as lists of interactions of a given gene with links to interacting partners; they do not present a comprehensive view of the nature of both the proteins involved in the interactions. A web database that allows search and retrieval based on biomedical characteristics of PPIs is lacking, and is needed. We present Wiki-Pi (read Wiki-p), a web-based interface to a database of human PPIs, which allows users to retrieve interactions by their biomedical attributes such as their association to diseases, pathways, drugs and biological functions. Each retrieved PPI is shown with annotations of both of the participant proteins side-by-side, creating a basis to hypothesize the biological function facilitated by the interaction. Conceptually, it is a search engine for PPIs analogous to PubMed for scientific literature. -
Promoterless Transposon Mutagenesis Drives Solid Cancers Via Tumor Suppressor Inactivation
bioRxiv preprint doi: https://doi.org/10.1101/2020.08.17.254565; this version posted August 17, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Promoterless Transposon Mutagenesis Drives Solid Cancers via Tumor Suppressor Inactivation 2 Aziz Aiderus1, Ana M. Contreras-Sandoval1, Amanda L. Meshey1, Justin Y. Newberg1,2, Jerrold M. Ward3, 3 Deborah Swing4, Neal G. Copeland2,3,4, Nancy A. Jenkins2,3,4, Karen M. Mann1,2,3,4,5,6,7, and Michael B. 4 Mann1,2,3,4,6,7,8,9 5 1Department of Molecular Oncology, Moffitt Cancer Center & Research Institute, Tampa, FL, USA 6 2Cancer Research Program, Houston Methodist Research Institute, Houston, Texas, USA 7 3Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 8 Singapore, Republic of Singapore 9 4Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, 10 Maryland, USA 11 5Departments of Gastrointestinal Oncology & Malignant Hematology, Moffitt Cancer Center & Research 12 Institute, Tampa, FL, USA 13 6Cancer Biology and Evolution Program, Moffitt Cancer Center & Research Institute, Tampa, FL, USA 14 7Department of Oncologic Sciences, Morsani College of Medicine, University of South Florida, Tampa, FL, 15 USA. 16 8Donald A. Adam Melanoma and Skin Cancer Research Center of Excellence, Moffitt Cancer Center, Tampa, 17 FL, USA 18 9Department of Cutaneous Oncology, Moffitt Cancer Center & Research Institute, Tampa, FL, USA 19 These authors contributed equally: Aziz Aiderus, Ana M. -
Novel and De Novo Mutations in Pediatric Refractory Epilepsy Jing Liu1,2, Lili Tong1,2, Shuangshuang Song3, Yue Niu1,2, Jun Li1,2, Xiu Wu1,2, Jie Zhang4, Clement C
Liu et al. Molecular Brain (2018) 11:48 https://doi.org/10.1186/s13041-018-0392-5 RESEARCH Open Access Novel and de novo mutations in pediatric refractory epilepsy Jing Liu1,2, Lili Tong1,2, Shuangshuang Song3, Yue Niu1,2, Jun Li1,2, Xiu Wu1,2, Jie Zhang4, Clement C. Zai5, Fang Luo4, Jian Wu4, Haiyin Li5, Albert H. C. Wong5, Ruopeng Sun1,2, Fang Liu2,5 and Baomin Li1,2* Abstract Pediatric refractory epilepsy is a broad phenotypic spectrum with great genetic heterogeneity. Next-generation sequencing (NGS) combined with Sanger sequencing could help to understand the genetic diversity and underlying disease mechanisms in pediatric epilepsy. Here, we report sequencing results from a cohort of 172 refractory epilepsy patients aged 0–14 years. The pathogenicity of identified variants was evaluated in accordance with the American College of Medical Genetics and Genomics (ACMG) criteria. We identified 43 pathogenic or likely pathogenic variants in 40 patients (23.3%). Among these variants, 74.4% mutations (32/43) were de novo and 60.5% mutations (26/43) were novel. Patients with onset age of seizures ≤12 months had higher yields of deleterious variants compared to those with onset age of seizures > 12 months (P = 0.006). Variants in ion channel genes accounted for the greatest functional gene category (55.8%), with SCN1A coming first (16/43). 81.25% (13/16) of SCN1A mutations were de novo and 68.8% (11/16) were novel in Dravet syndrome. Pathogenic or likely pathogenic variants were found in the KCNQ2, STXBP1, SCN2A genes in Ohtahara syndrome. Novel deleterious variants were also found in West syndrome, Doose syndrome and glucose transporter type 1 deficiency syndrome patients. -
UQ722401 OA.Pdf
ARTICLE DOI: 10.1038/s41467-018-03371-0 OPEN Integrative analysis of omics summary data reveals putative mechanisms underlying complex traits Yang Wu1, Jian Zeng 1, Futao Zhang1, Zhihong Zhu1, Ting Qi1, Zhili Zheng1,2, Luke R. Lloyd-Jones1, Riccardo E. Marioni3,4, Nicholas G. Martin5, Grant W. Montgomery 1, Ian J. Deary4, Naomi R. Wray 1,6, Peter M. Visscher 1,6, Allan F. McRae1 & Jian Yang 1,6 The identification of genes and regulatory elements underlying the associations discovered 1234567890():,; by GWAS is essential to understanding the aetiology of complex traits (including diseases). Here, we demonstrate an analytical paradigm of prioritizing genes and regulatory elements at GWAS loci for follow-up functional studies. We perform an integrative analysis that uses summary-level SNP data from multi-omics studies to detect DNA methylation (DNAm) sites associated with gene expression and phenotype through shared genetic effects (i.e., pleio- tropy). We identify pleiotropic associations between 7858 DNAm sites and 2733 genes. These DNAm sites are enriched in enhancers and promoters, and >40% of them are mapped to distal genes. Further pleiotropic association analyses, which link both the methylome and transcriptome to 12 complex traits, identify 149 DNAm sites and 66 genes, indicating a plausible mechanism whereby the effect of a genetic variant on phenotype is mediated by genetic regulation of transcription through DNAm. 1 Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia. 2 The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China. 3 Medical Genetics Section, Centre for Genomics and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK. -
The 2Q37-Deletion Syndrome: an Update of the Clinical Spectrum Including Overweight, Brachydactyly and Behavioural Features in 14 New Patients
European Journal of Human Genetics (2013) 21, 602–612 & 2013 Macmillan Publishers Limited All rights reserved 1018-4813/13 www.nature.com/ejhg ARTICLE The 2q37-deletion syndrome: an update of the clinical spectrum including overweight, brachydactyly and behavioural features in 14 new patients Camille Leroy1,2,3, Emilie Landais1,2,4, Sylvain Briault5, Albert David6, Olivier Tassy7, Nicolas Gruchy8, Bruno Delobel9, Marie-Jose´ Gre´goire10, Bruno Leheup3,11, Laurence Taine12, Didier Lacombe12, Marie-Ange Delrue12, Annick Toutain13, Agathe Paubel13, Francine Mugneret14, Christel Thauvin-Robinet3,15, Ste´phanie Arpin13, Cedric Le Caignec6, Philippe Jonveaux3,10, Myle`ne Beri10, Nathalie Leporrier8, Jacques Motte16, Caroline Fiquet17,18, Olivier Brichet16, Monique Mozelle-Nivoix1,3, Pascal Sabouraud16, Nathalie Golovkine19, Nathalie Bednarek20, Dominique Gaillard1,2,3 and Martine Doco-Fenzy*,1,2,3,18 The 2q37 locus is one of the most commonly deleted subtelomeric regions. Such a deletion has been identified in 4100 patients by telomeric fluorescence in situ hybridization (FISH) analysis and, less frequently, by array-based comparative genomic hybridization (array-CGH). A recognizable ‘2q37-deletion syndrome’ or Albright’s hereditary osteodystrophy-like syndrome has been previously described. To better map the deletion and further refine this deletional syndrome, we formed a collaboration with the Association of French Language Cytogeneticists to collect 14 new intellectually deficient patients with a distal or interstitial 2q37 deletion characterized by FISH and array-CGH. Patients exhibited facial dysmorphism (13/14) and brachydactyly (10/14), associated with behavioural problems, autism or autism spectrum disorders of varying severity and overweight or obesity. The deletions in these 14 new patients measured from 2.6 to 8.8 Mb. -
Supplemental Figures 04 12 2017
Jung et al. 1 SUPPLEMENTAL FIGURES 2 3 Supplemental Figure 1. Clinical relevance of natural product methyltransferases (NPMTs) in brain disorders. (A) 4 Table summarizing characteristics of 11 NPMTs using data derived from the TCGA GBM and Rembrandt datasets for 5 relative expression levels and survival. In addition, published studies of the 11 NPMTs are summarized. (B) The 1 Jung et al. 6 expression levels of 10 NPMTs in glioblastoma versus non‐tumor brain are displayed in a heatmap, ranked by 7 significance and expression levels. *, p<0.05; **, p<0.01; ***, p<0.001. 8 2 Jung et al. 9 10 Supplemental Figure 2. Anatomical distribution of methyltransferase and metabolic signatures within 11 glioblastomas. The Ivy GAP dataset was downloaded and interrogated by histological structure for NNMT, NAMPT, 12 DNMT mRNA expression and selected gene expression signatures. The results are displayed on a heatmap. The 13 sample size of each histological region as indicated on the figure. 14 3 Jung et al. 15 16 Supplemental Figure 3. Altered expression of nicotinamide and nicotinate metabolism‐related enzymes in 17 glioblastoma. (A) Heatmap (fold change of expression) of whole 25 enzymes in the KEGG nicotinate and 18 nicotinamide metabolism gene set were analyzed in indicated glioblastoma expression datasets with Oncomine. 4 Jung et al. 19 Color bar intensity indicates percentile of fold change in glioblastoma relative to normal brain. (B) Nicotinamide and 20 nicotinate and methionine salvage pathways are displayed with the relative expression levels in glioblastoma 21 specimens in the TCGA GBM dataset indicated. 22 5 Jung et al. 23 24 Supplementary Figure 4. -
Supporting Online Material For
www.sciencemag.org/cgi/content/full/319/5863/620/DC1 Supporting Online Material for Cancer Proliferation Gene Discovery Through Functional Genomics Michael R. Schlabach, Ji Luo, Nicole L. Solimini, Guang Hu, Qikai Xu, Mamie Z. Li, Zhenming Zhao, Agata Smogorzewska, Mathew E. Sowa, Xiaolu L. Ang, Thomas F. Westbrook, Anthony C. Liang, Kenneth Chang, Jennifer A. Hackett, J. Wade Harper, Gregory J. Hannon, Stephen J. Elledge* *To whom correspondence should be addressed. E-mail: [email protected] Published 1 February 2008, Science 319, 620 (2008) DOI: 10.1126/science.1149200 This PDF file includes: Materials and Methods SOM Text Figs. S1 to S3 Tables S1 to S6 References Schlabach et al. SUPPLEMENTAL ONLINE MATERIALS SUPPLEMENTAL MATERIALS AND METHODS Cell culture and virus production HCT116 (S1) and DLD-1 colon cancer cells were gifts from Dr. Todd Waldman and Dr. Bert Vogelstein. Both HCT116 cells and DLD-1 cells were maintained in McCoy’s 5A media with 10% FBS. HCC1954 breast cancer cells were from American Type Culture Collection (ATCC) and were mantained in RPMI-1640 media with 10% FBS. HMECs taken from a reduction mammoplasty were immortalized with human telomerase and maintained in MEGM media (Lonza). Mouse CCE ES cells were from StemCell Technology (S2, S3), and were maintained in Knockout DMEM (Invitrogen) with 15% ES serum (Hyclone), 1% non-essential amino acids, 2 mM Glutamine (Invitrogen), 0.1 mM b-ME, 1000 U ESGRO (Chemicon). Retroviruses were produced by transfecting 293T cells with MSCV-PM-shRNA, pCG- gag/pol, and pVSV-G plasmids using TransIT-293 (Mirus) per manufacturer’s instructions. -
Human Genome Meeting 2016 Houston, TX, USA
Human Genomics 2016, Volume 10 Suppl 1 DOI 10.1186/s40246-016-0063-5 MEETING ABSTRACTS Open Access Human genome meeting 2016 Houston, TX, USA. 28 February - 2 March 2016 Published: 26 May 2016 O1 O2 The metabolomics approach to autism: identification of Phenome-wide association study for smoking- and drinking- biomarkers for early detection of autism spectrum disorder associated genes in 26,394 American women with African, Asian, A. K. Srivastava1, Y. Wang2, R. Huang3, C. Skinner1, T. Thompson3, European, and Hispanic descents L. Pollard3, T. Wood3, F. Luo2, R. Stevenson1 R. Polimanti1, J. Gelernter1,2,3 1JCSRI, Greenwood Genetic Center, Greenwood, SC, USA; 2School of 1Department Psychiatry, Yale Sch Med and VA CT Healthcare Center, Computing, Clemson University, Clemson, SC, USA; 3Biochemical West Haven, CT, USA; 2Department Genetics, Yale Sch Med and VA CT Genetics Laboratory, Greenwood Genetic Center, Greenwood, SC, USA Healthcare Center, West Haven, CT, USA; 3Department Neurobiology, Correspondence: A. K. Srivastava – JCSRI, Greenwood Genetic Center, Yale Sch Med and VA CT Healthcare Center, West Haven, CT, USA Greenwood, SC, USA Correspondence: R. Polimanti – Dept Psychiatry, Yale Sch Med and VA Human Genomics 2016, 10(Suppl 1):O1 CT Healthcare Center, West Haven, CT, USA Human Genomics 2016, 10(Suppl 1):O2 Objectives From the first description by Leo Kanner [1], autism has been an en- Objectives igmatic neurobehavioral phenomenon. The new genetic/genomic To uncover novel traits associated with nicotine and alcohol use gen- technologies of the past decade have not been as productive as ori- etics, we performed a phenome-wide association study in a large ginally anticipated in unveiling the mysteries of autism. -
Meta-Analysis of Genome-Wide Association Studies Identifies Six New Loci for Serum Calcium Concentrations
Meta-Analysis of Genome-Wide Association Studies Identifies Six New Loci for Serum Calcium Concentrations The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation O'Seaghdha, C. M., H. Wu, Q. Yang, K. Kapur, I. Guessous, A. M. Zuber, A. Köttgen, et al. 2013. “Meta-Analysis of Genome- Wide Association Studies Identifies Six New Loci for Serum Calcium Concentrations.” PLoS Genetics 9 (9): e1003796. doi:10.1371/journal.pgen.1003796. http://dx.doi.org/10.1371/ journal.pgen.1003796. Published Version doi:10.1371/journal.pgen.1003796 Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:11877086 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA Meta-Analysis of Genome-Wide Association Studies Identifies Six New Loci for Serum Calcium Concentrations Conall M. O’Seaghdha1,2", Hongsheng Wu1,3,4, Qiong Yang1,3, Karen Kapur5, Idris Guessous6,7,8" , Annie Mercier Zuber9, Anna Ko¨ ttgen10,11", Candice Stoudmann9, Alexander Teumer12, Zolta´n Kutalik5,13, Massimo Mangino14, Abbas Dehghan15, Weihua Zhang16,17, Gudny Eiriksdottir18, Guo Li19, Toshiko Tanaka20, Laura Portas21, Lorna M. Lopez22, Caroline Hayward23, Kurt Lohman24, Koichi Matsuda25, Sandosh Padmanabhan26, Dmitri Firsov9, Rossella Sorice27, Sheila Ulivi28, A. Catharina Brockhaus29,30, Marcus E. Kleber31,32, Anubha Mahajan33, Florian D. Ernst12, Vilmundur Gudnason18,34, Lenore J. Launer35, Aurelien Mace5,13, Eric Boerwinckle36, Dan E.