A Multi-Strategy Sequencing Workflow In
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Genetic Heterogeneity of Usher Syndrome Type II
J7Med Genet 1996;33:753-757 753 Genetic heterogeneity of Usher syndrome type II in a Dutch population J Med Genet: first published as 10.1136/jmg.33.9.753 on 1 September 1996. Downloaded from S Pieke-Dahl, A van Aarem, A Dobin, C W R J Cremers, W J Kimberling Abstract In 1959, Hallgren' laid the foundation for the The Usher syndromes are a group ofauto- clinical definition of US in a study of 172 US somal recessive disorders characterised patients from Sweden. Hallgren' showed sig- by retinitis pigmentosa (RP) with con- nificant phenotypic heterogeneity of US by genital, stable (non-progressive) sen- describing two clinically distinct forms, Usher sorineural hearing loss. Profound deaf- syndrome type I and Usher syndrome type II. ness, RP, and no vestibular responses are Profound congenital deafness, RP, and absent features of Usher type I, whereas moder- vestibular responses was defined as Usher I, ate to severe hearing loss and RP with while those exhibiting a congenital moderate to normal vestibular function describe severe hearing loss, RP, and no associated ves- Usher type II. The gene responsible for tibular problems was defined as Usher II.2 3 most cases ofUsher II, USH2a, is on chro- Although the existence of a type of US with mosome 1q41; at least one other Usher II progressive hearing loss had been proposed,4 gene (as yet unlinked) is known to exist. there was no firm genetic evidence for a Usher III presents with a progressive separate Usher III phenotype until a group of hearing loss that can mimic the audiomet- Finnish families with a phenotype of progres- ric profile seen in Usher II. -
The USH2A C.2299Delg Mutation: Dating Its Common Origin in a Southern European Population
European Journal of Human Genetics (2010) 18, 788–793 & 2010 Macmillan Publishers Limited All rights reserved 1018-4813/10 www.nature.com/ejhg ARTICLE The USH2A c.2299delG mutation: dating its common origin in a Southern European population Elena Aller1,2, Lise Larrieu3, Teresa Jaijo1,2, David Baux3, Carmen Espino´s2, Fernando Gonza´lez-Candelas4,5,6, Carmen Na´jera7, Francesc Palau2,8, Mireille Claustres3,9,10, Anne-Franc¸oise Roux3,9 and Jose´ M Milla´n*,1,2 Usher syndrome type II is the most common form of Usher syndrome. USH2A is the main responsible gene of the three known to be disease causing. It encodes two isoforms of the protein usherin. This protein is part of an interactome that has an essential role in the development and function of inner ear hair cells and photoreceptors. The gene contains 72 exons spanning over a region of 800 kb. Although numerous mutations have been described, the c.2299delG mutation is the most prevalent in several populations. Its ancestral origin was previously suggested after the identification of a common core haplotype restricted to 250 kb in the 5¢ region that encodes the short usherin isoform. By extending the haplotype analysis over the 800 kb region of the USH2A gene with a total of 14 intragenic single nucleotide polymorphisms, we have been able to define 10 different c.2299delG haplotypes, showing high variability but preserving the previously described core haplotype. An exhaustive c.2299delG/control haplotype study suggests that the major source of variability in the USH2A gene is recombination. Furthermore, we have evidenced twice the amount of recombination hotspots located in the 500 kb region that covers the 3¢ end of the gene, explaining the higher variability observed in this region when compared with the 250 kb of the 5¢ region. -
Cited1 (NM 001276466) Mouse Tagged ORF Clone Product Data
OriGene Technologies, Inc. 9620 Medical Center Drive, Ste 200 Rockville, MD 20850, US Phone: +1-888-267-4436 [email protected] EU: [email protected] CN: [email protected] Product datasheet for MR228487 Cited1 (NM_001276466) Mouse Tagged ORF Clone Product data: Product Type: Expression Plasmids Product Name: Cited1 (NM_001276466) Mouse Tagged ORF Clone Tag: Myc-DDK Symbol: Cited1 Synonyms: AI316840; AU019144; Msg1 Vector: pCMV6-Entry (PS100001) E. coli Selection: Kanamycin (25 ug/mL) Cell Selection: Neomycin ORF Nucleotide >MR228487 representing NM_001276466 Sequence: Red=Cloning site Blue=ORF Green=Tags(s) TTTTGTAATACGACTCACTATAGGGCGGCCGGGAATTCGTCGACTGGATCCGGTACCGAGGAGATCTGCC GCCGCGATCGCC ATGCCAACTATGTCGAGGCCTGCACTTGATGTCAAGGGTGGCACCACCTCTGGGAAGGAGGATGCCAACC AGGAGATGAACTCTCTGGCCTACTCCAACCTTGGAGTGAAGGATCGCAAGGCAGTGACTGTCCTGCACTA CCCCGGGGTCACCGCAAATGGAGCCAAAGCCAACGGAGTTCCCACTAGCTCCTCTGGATCGACATCTCCA ATAGGCTCTCCTACTGCCACCCCTTCTTCCAAACCCCCATCCTTCAACCTGCATCCTACCCCTCACCTGA TGGCCAGCATGCAGCTTCAGAAGCTTAATAGCCAGTACCAAGGGGCTGCGGCTACTGCTGCTGCTGCCCT CACTGGTGCAGGCCTACCAGGGGAGGAAGAGCCCATGCAAAACTGGGTCACCGCCCCTCTGGTAGTGGGA GGGTCTCCGGGATCTGTCTCTCCTCCTGCTGGTGCCCAGAGCCCTGCTCTCATTGATTCTGACCCGGTGG ATGAGGAGGTGCTGATGTCTCTGGTGGTTGAATTGGGGCTAGACCGAGCCAATGAGCTTCCCGAGCTGTG GCTGGGGCAGAATGAGTTTGATTTCACTGCAGATTTTCCCTCTGGCTGC ACGCGTACGCGGCCGCTCGAGCAGAAACTCATCTCAGAAGAGGATCTGGCAGCAAATGATATCCTGGATT ACAAGGATGACGACGATAAGGTTTAA Protein Sequence: >MR228487 representing NM_001276466 Red=Cloning site Green=Tags(s) MPTMSRPALDVKGGTTSGKEDANQEMNSLAYSNLGVKDRKAVTVLHYPGVTANGAKANGVPTSSSGSTSP -
Common MFRP Sequence Variants Are Not Associated with Moderate to High Hyperopia, Isolated Microphthalmia, and High Myopia
Molecular Vision 2008; 14:387-393 <http://www.molvis.org/molvis/v14/a47> © 2008 Molecular Vision Received 12 December 2007 | Accepted 6 February 2008 | Published 4 March 2008 Common MFRP sequence variants are not associated with moderate to high hyperopia, isolated microphthalmia, and high myopia Ravikanth Metlapally,1,2 Yi-Ju Li,2 Khanh-Nhat Tran-Viet,2 Anuradha Bulusu,2 Tristan R. White,2 Jaclyn Ellis, 2 Daniel Kao,2 Terri L. Young1,2 1Duke University Eye Center, Durham, NC; 2Duke University Center for Human Genetics, Durham, NC Purpose: The membrane-type frizzled-related protein (MFRP) gene is selectively expressed in the retinal pigment epithelium and ciliary body, and mutations of this gene cause nanophthalmos. The MFRP gene may not be essential for retinal function but has been hypothesized to play a role in ocular axial length regulation. The involvement of the MFRP gene in moderate to high hyperopic, isolated microphthalmic/anophthalmic, and high myopic patients was tested in two phases: a mutation screening/sequence variant discovery phase and a genetic association study phase. Methods: Eleven hyperopic, ten microphthalmic/anophthalmic, and seven non-syndromic high-grade myopic patients of varying ages and 11 control subjects participated in the mutation screening phase. Sixteen primer pairs were designed to amplify the 13 exons of the MFRP gene including intron/exon boundaries. Polymerase chain reactions were performed, and amplified products were sequenced using standard techniques. Normal and affected individual DNA sequences were compared alongside the known reference sequence (UCSC genome browser) for the MFRP gene. The genetic association study included 146 multiplex non-syndromic high-grade myopia families. -
Supplementary Table 1: Adhesion Genes Data Set
Supplementary Table 1: Adhesion genes data set PROBE Entrez Gene ID Celera Gene ID Gene_Symbol Gene_Name 160832 1 hCG201364.3 A1BG alpha-1-B glycoprotein 223658 1 hCG201364.3 A1BG alpha-1-B glycoprotein 212988 102 hCG40040.3 ADAM10 ADAM metallopeptidase domain 10 133411 4185 hCG28232.2 ADAM11 ADAM metallopeptidase domain 11 110695 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 195222 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 165344 8751 hCG20021.3 ADAM15 ADAM metallopeptidase domain 15 (metargidin) 189065 6868 null ADAM17 ADAM metallopeptidase domain 17 (tumor necrosis factor, alpha, converting enzyme) 108119 8728 hCG15398.4 ADAM19 ADAM metallopeptidase domain 19 (meltrin beta) 117763 8748 hCG20675.3 ADAM20 ADAM metallopeptidase domain 20 126448 8747 hCG1785634.2 ADAM21 ADAM metallopeptidase domain 21 208981 8747 hCG1785634.2|hCG2042897 ADAM21 ADAM metallopeptidase domain 21 180903 53616 hCG17212.4 ADAM22 ADAM metallopeptidase domain 22 177272 8745 hCG1811623.1 ADAM23 ADAM metallopeptidase domain 23 102384 10863 hCG1818505.1 ADAM28 ADAM metallopeptidase domain 28 119968 11086 hCG1786734.2 ADAM29 ADAM metallopeptidase domain 29 205542 11085 hCG1997196.1 ADAM30 ADAM metallopeptidase domain 30 148417 80332 hCG39255.4 ADAM33 ADAM metallopeptidase domain 33 140492 8756 hCG1789002.2 ADAM7 ADAM metallopeptidase domain 7 122603 101 hCG1816947.1 ADAM8 ADAM metallopeptidase domain 8 183965 8754 hCG1996391 ADAM9 ADAM metallopeptidase domain 9 (meltrin gamma) 129974 27299 hCG15447.3 ADAMDEC1 ADAM-like, -
Mutation Screening of the USH2A Gene in Retinitis Pigmentosa and USHER Patients in a Han Chinese Population
Eye (2018) 32:1608–1614 https://doi.org/10.1038/s41433-018-0130-3 ARTICLE Mutation screening of the USH2A gene in retinitis pigmentosa and USHER patients in a Han Chinese population 1,2,3 1 1 1 4 1,2,3 Lulin Huang ● Yao Mao ● Jiyun Yang ● Yuanfeng Li ● Yang Li ● Zhenglin Yang Received: 12 October 2016 / Revised: 1 January 2018 / Accepted: 25 April 2018 / Published online: 13 June 2018 © The Author(s) 2018. This article is published with open access Abstract Objectives USH2A encodes for usherin, a basement membrane protein in the inner ear and retina. USH2A can cause retinitis pigmentosa (RP) with or without hearing loss. The aim of this study was to detect USH2A mutations in a Chinese cohort of 75 small RP families and 10 Usher syndrome families. Methods We performed a direct Sanger sequencing analysis of the USH2A gene to identify mutations for this cohort. Results We identified a total of eight mutations in four of the 75 small RP families (5.3%) and two mutations in one of the 10 Usher families (10%); all families were detected to have compound heterozygous mutations. In families with non- syndromic RP, we identified the compound heterozygous mutations p.Pro4818Leuand p.Leu2395Hisfs*19 in family No. 1234567890();,: 1234567890();,: 19114, p.Arg4493His and p.His1677Glnfs*15 in family No.19162, c.8559-2A > G and p.Arg1549* in family No.19123 and p.Ser5060Pro and p.Arg34Leufs*41 in family No.19178. We also identified the heterozygous mutations p.Arg3719His and p.Cys934Trp in family No.19124, which was the Usher syndrome family. -
HSPA8 Antibody (C-Term) Purified Rabbit Polyclonal Antibody (Pab) Catalog # Ap2872b
10320 Camino Santa Fe, Suite G San Diego, CA 92121 Tel: 858.875.1900 Fax: 858.622.0609 HSPA8 Antibody (C-term) Purified Rabbit Polyclonal Antibody (Pab) Catalog # AP2872b Specification HSPA8 Antibody (C-term) - Product Information Application IF, WB, IHC-P, FC,E Primary Accession P11142 Other Accession P63018, P63017, P19378, P19120, A2Q0Z1 Reactivity Human, Mouse Predicted Bovine, Hamster, Horse, Rat Host Rabbit Clonality Polyclonal Isotype Rabbit Ig Antigen Region 539-569 HSPA8 Antibody (C-term) - Additional Information Confocal immunofluorescent analysis of Gene ID 3312 HSPA8 Antibody (C-term)(Cat#AP2872b) with Hela cell followed by Alexa Fluor Other Names 488-conjugated goat anti-rabbit lgG (green). Heat shock cognate 71 kDa protein, Heat Actin filaments have been labeled with Alexa shock 70 kDa protein 8, Fluor 555 phalloidin (red). Lipopolysaccharide-associated protein 1, LAP-1, LPS-associated protein 1, HSPA8, HSC70, HSP73, HSPA10 Target/Specificity This HSPA8 antibody is generated from rabbits immunized with a KLH conjugated synthetic peptide between 539-569 amino acids from the C-terminal region of human HSPA8. Dilution IF~~1:10~50 WB~~1:1000 IHC-P~~1:10~50 FC~~1:10~50 Format Purified polyclonal antibody supplied in PBS with 0.09% (W/V) sodium azide. This Western blot analysis of lysates from rat antibody is prepared by Saturated H-4-II-E, mouse NIH/3T3 cell line (from left to Ammonium Sulfate (SAS) precipitation right), using HSPA8 Antibody (C-term) (Cat. # followed by dialysis against PBS. AP2872b). AP2872b was diluted at 1:1000 at each lane. A goat anti-rabbit IgG H&L(HRP) at Page 1/5 10320 Camino Santa Fe, Suite G San Diego, CA 92121 Tel: 858.875.1900 Fax: 858.622.0609 Storage 1:5000 dilution was used as the secondary Maintain refrigerated at 2-8°C for up to 2 antibody. -
Unique Variant Spectrum in a Jordanian Cohort with Inherited Retinal Dystrophies
G C A T T A C G G C A T genes Article Unique Variant Spectrum in a Jordanian Cohort with Inherited Retinal Dystrophies Bilal Azab 1,2,*,†, Zain Dardas 2,3,† , Dunia Aburizeg 2, Muawyah Al-Bdour 4 , Mohammed Abu-Ameerh 4, Tareq Saleh 5, Raghda Barham 6, Ranad Maswadi 7, Nidaa A Ababneh 6 , Mohammad Alsalem 8, Hana Zouk 9,10, Sami Amr 11 and Abdalla Awidi 6,* 1 Department of Human and Molecular Genetics, School of Medicine, Virginia Commonwealth University, Richmond, VA 23298-0565, USA 2 Department of Pathology and Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman 11942, Jordan; [email protected] (Z.D.); [email protected] (D.A.) 3 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA 4 Department of Ophthalmology, Jordan University Hospital, The University of Jordan, Amman 11942, Jordan; [email protected] (M.A.-B.); [email protected] (M.A.-A.) 5 Department of Basic Medical Sciences, Faculty of Medicine, The Hashemite University, Zarqa 13115, Jordan; [email protected] 6 Cell Therapy Center, The University of Jordan, Amman 11942, Jordan; [email protected] (R.B.); [email protected] (N.A.A.) 7 Department of Ophthalmology, Guy’s and St Thomas’ NHS Foundation Trust, London SE1 7EH, UK; [email protected] 8 Department of Anatomy and Histology, School of Medicine, The University of Jordan, Amman 11942, Jordan; [email protected] 9 Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, Citation: Azab, B.; Dardas, Z.; Cambridge, MA 02139, USA; [email protected] 10 Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, MA 02114, USA Aburizeg, D.; Al-Bdour, M.; 11 Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; Abu-Ameerh, M.; Saleh, T.; Barham, [email protected] R.; Maswadi, R.; Ababneh, N.A; * Correspondence: [email protected] (B.A.); [email protected] (A.A.); Alsalem, M.; et al. -
The Genetic and Clinical Landscape of Nanophthalmos in an Australian
medRxiv preprint doi: https://doi.org/10.1101/19013599; this version posted December 4, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license . 1 The genetic and clinical landscape of nanophthalmos in an Australian cohort 2 3 Running title: Genetics of nanophthalmos in Australia 4 5 Owen M Siggs1, Mona S Awadalla1, Emmanuelle Souzeau1, Sandra E Staffieri2,3,4, Lisa S Kearns2, Kate 6 Laurie1, Abraham Kuot1, Ayub Qassim1, Thomas L Edwards2, Michael A Coote2, Erica Mancel5, Mark J 7 Walland6, Joanne Dondey7, Anna Galanopoulous8, Robert J Casson8, Richard A Mills1, Daniel G 8 MacArthur9,10, Jonathan B Ruddle2,3,4, Kathryn P Burdon1,11, Jamie E Craig1 9 10 1Department of Ophthalmology, Flinders University, Adelaide, Australia 11 2Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Australia 12 3Department of Ophthalmology, University of Melbourne, Melbourne, Australia 13 4Department of Ophthalmology, Royal Children’s Hospital, Melbourne, Australia 14 5Centre Hospitalier Territorial de Nouvelle-Calédonie, Noumea, New Caledonia 15 6Glaucoma Investigation and Research Unit, Royal Victorian Eye and Ear Hospital, Melbourne, Australia 16 7Royal Victorian Eye and Ear Hospital, Melbourne, Australia 17 8Discipline of Ophthalmology & Visual Sciences, University of Adelaide, Adelaide, Australia 18 9Program in Medical and Population -
TOX3 Is Expressed in Mammary ER+ Epithelial Cells and Regulates ER
Seksenyan et al. BMC Cancer (2015) 15:22 DOI 10.1186/s12885-015-1018-2 RESEARCH ARTICLE Open Access TOX3 is expressed in mammary ER+ epithelial cells and regulates ER target genes in luminal breast cancer Akop Seksenyan1, Asha Kadavallore1, Ann E Walts2, Brian de la Torre1, Dror Berel3,4, Samuel P Strom5,6, Parinaz Aliahmad1, Vincent A Funari5 and Jonathan Kaye1,3,7* Abstract Background: A breast cancer susceptibility locus has been mapped to the gene encoding TOX3. Little is known regarding the expression pattern or biological role of TOX3 in breast cancer or in the mammary gland. Here we analyzed TOX3 expression in murine and human mammary glands and in molecular subtypes of breast cancer, and assessed its ability to alter the biology of breast cancer cells. Methods: We used a cell sorting strategy, followed by quantitative real-time PCR, to study TOX3 gene expression in the mouse mammary gland. To study the expression of this nuclear protein in human mammary glands and breast tumors, we generated a rabbit monoclonal antibody specific for human TOX3. In vitro studies were performed on MCF7, BT474 and MDA-MB-231 cell lines to study the effects of TOX3 modulation on gene expression in the context of breast cancer cells. Results: We found TOX3 expression in estrogen receptor-positive mammary epithelial cells, including progenitor cells. A subset of breast tumors also highly expresses TOX3, with poor outcome associated with high expression of TOX3 in luminal B breast cancers. We also demonstrate the ability of TOX3 to alter gene expression in MCF7 luminal breast cancer cells, including cancer relevant genes TFF1 and CXCR4. -
HSPA8 Antibody (N-Term) Purified Rabbit Polyclonal Antibody (Pab) Catalog # AW5209
10320 Camino Santa Fe, Suite G San Diego, CA 92121 Tel: 858.875.1900 Fax: 858.622.0609 HSPA8 Antibody (N-term) Purified Rabbit Polyclonal Antibody (Pab) Catalog # AW5209 Specification HSPA8 Antibody (N-term) - Product Information Application IF, WB, IHC-P, FC,E Primary Accession P11142 Other Accession P63018, P63017, P19378, O73885, P19120, A2Q0Z1 Reactivity Human, Mouse, Rat Predicted Bovine, Chicken, Hamster, Horse Host Rabbit Clonality Polyclonal Calculated MW H=71;M=71;Rat= 71 KDa Isotype Rabbit Ig Antigen Source HUMAN Confocal immunofluorescent analysis of HSPA8 Antibody (N-term)(Cat#AW5209) with HSPA8 Antibody (N-term) - Additional Information A2058 cell followed by Alexa Fluor 488-conjugated goat anti-rabbit lgG (green). Actin filaments have been labeled with Alexa Gene ID 3312 Fluor 555 phalloidin (red).DAPI was used to Antigen Region stain the cell nuclear (blue). 82-110 Other Names HSPA8; HSC70; HSP73; HSPA10; Heat shock cognate 71 kDa protein; Heat shock 70 kDa protein 8 Dilution IF~~1:10~50 WB~~1:1000 IHC-P~~1:10~50 FC~~1:10~50 Target/Specificity This HSPA8 antibody is generated from rabbits immunized with a KLH conjugated synthetic peptide between 82-110 amino acids from the N-terminal region of human HSPA8. Western blot analysis of lysates from Hela,A431,mouse NIH/3T3,rat H-4-Ⅱ-E cell line Format (from left to right), using HSPA8 Antibody Purified polyclonal antibody supplied in PBS (N-term)(Cat. #AW5209). AW5209 was Page 1/5 10320 Camino Santa Fe, Suite G San Diego, CA 92121 Tel: 858.875.1900 Fax: 858.622.0609 with 0.09% (W/V) sodium azide. -
Identification of Potential Key Genes and Pathway Linked with Sporadic Creutzfeldt-Jakob Disease Based on Integrated Bioinformatics Analyses
medRxiv preprint doi: https://doi.org/10.1101/2020.12.21.20248688; this version posted December 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Identification of potential key genes and pathway linked with sporadic Creutzfeldt-Jakob disease based on integrated bioinformatics analyses Basavaraj Vastrad1, Chanabasayya Vastrad*2 , Iranna Kotturshetti 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. 3. Department of Ayurveda, Rajiv Gandhi Education Society`s Ayurvedic Medical College, Ron, Karnataka 562209, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. medRxiv preprint doi: https://doi.org/10.1101/2020.12.21.20248688; this version posted December 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Abstract Sporadic Creutzfeldt-Jakob disease (sCJD) is neurodegenerative disease also called prion disease linked with poor prognosis. The aim of the current study was to illuminate the underlying molecular mechanisms of sCJD. The mRNA microarray dataset GSE124571 was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were screened.