DOCSLIB.ORG

Highlights of the 'Gene Nomenclature Across Species' Meeting

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Highlights of the 'Gene Nomenclature Across Species' Meeting MEETING REPORT Highlights of the ‘Gene Nomenclature Across Species’ Meeting Elspeth A. Bruford* Project Coordinator, HUGO Gene Nomenclature Committee (HGNC), EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK *Correspondence to: E-mail: [email protected] Date received (in revised form): 24th February, 2010 Abstract The first ‘Gene Nomenclature Across Species’ meeting was held on 12th and 13th October 2009, at the Møller Centre in Cambridge, UK. This meeting, organised and hosted by the HUGO Gene Nomenclature Committee (HGNC), brought together invited experts from the fields of gene nomenclature, phylogenetics and genome assembly and annotation. The central aim of the meeting was to discuss the issues of coordinating gene naming across vertebrates, culminating in the publication of recommendations for assigning nomenclature to genes across multiple species. Meeting summary coorganiser of the meeting, kicked off by discussing The meeting began with a welcome and outline of the current work of the HGNC, ‘An Essential the agenda from Elspeth Bruford, one of the Resource for the Human Genome’. Matt outlined meeting organisers and the group coordinator for the roles of the HGNC, including a summary of the HUGO Gene Nomenclature Committee the process of symbol assignment, and its current (HGNC). HGNC has been based at the European efforts in coordinating gene naming across ver- Bioinformatics Institute (EBI) at Hinxton, UK, tebrates. He also highlighted instances where the since 2007. Since its inception in 1979, the lack of approved gene nomenclature for most mam- HGNC has been assigning gene symbols and malian genomes has resulted in valuable published names to all human genes, including pseudogenes data for these species being absent or confused in and non-coding RNAs. the genomic databases. He was followed by Janan The first session was chaired by Jennifer Harrow, Eppig, principal investigator of the MGI, who, in who leads the Human and Vertebrate Analysis and her talk, ‘What’s in a Name’, told us about current Annotation (Havana) group from the Wellcome nomenclature issues and activities for the mouse. Trust Sanger Institute (WTSI), also located on the As well as genes, the group at MGI also name Hinxton campus. This session was devoted to genetic markers, alleles, mutations and strains. introducing the three established gene nomencla- Current efforts are focused on creating a unified ture groups for mammals — namely HGNC, the gene catalogue for the mouse, by comparing gene Mouse Genome Nomenclature Committee models from the National Center for (MGNC) — based at the Mouse Genome Informatics Biotechnology Information (NCBI)’s Entrez Gene Database (MGI) at the Jackson Laboratory in database, the Ensembl database and the Havana Maine, USA — and the Rat Genome and group’s Vega database. The mouse genetics com- Nomenclature Committee, based at the Rat munity began naming genes in a standardised way Genome Database (RGD) in Milwaukee, long before the human community, with the first Wisconsin, USA. Matt Wright from the HGNC, Mouse Nomenclature Guide published in 1940. In # HENRY STEWART PUBLICATIONS 1479–7364. HUMAN GENOMICS. VOL 4. NO 3. 213–217 FEBRUARY 2010 213 MEETING REPORT Bruford 2003, the International Committee on nomenclature is identical to human where possible, Standardized Genetic Nomenclature for Mice, and and where a gene has been duplicated in Xenopus the Rat Genome and Nomenclature Committee relative to mammals the gene symbols are appended agreed to unify rules and guidelines for gene, allele with a numeral or letter suffix to indicate this. and mutation nomenclature in the mouse and rat. The newest nomenclature group, the Chicken It was therefore apt that Janan was followed by Gene Nomenclature Committee (CGNC; PMID: Mary Shimoyama from the RGD. Mary talked 19607656), also aims to name chicken genes based about ‘Nomenclature Assignment, Review and on the names assigned to human genes. Alan Resolution at the Rat Genome Database’, starting Archibald from the Roslin Institute, Edinburgh, with a discussion of the pipelines and software they UK, updated us on the progress of the CGNC, have established for naming rat genes, quantitative which has begun its naming efforts by transferring trait loci (QTLs) and strains, and for making the human gene symbols to 1:1 orthologues in nomenclature updates and orthology assignments chicken. To date, over 8,000 genes with a con- between rat, mouse and human. The state of the firmed 1:1 orthologue in human have been current rat genome assembly can prove problematic, assigned approved names by the CGNC. and there is a need to establish a core consensus rat After lunch, the third session turned to look at gene set in a manner similar to that of the other mammalian genomes that do not have an Consensus CDS (CCDS) projects that are currently established nomenclature group. Elizabeth in place for the human and mouse genomes Murchison from the WTSI spoke first on ‘Gene (PMID: 19498102). Other issues raised by Mary Annotation and Nomenclature in Marsupials and included problems with synchronising updates Monotremes’. While currently they are only rep- between databases, the need for timely adoption of resented by three ‘complete’ genomes in the public RGD gene nomenclature by some databases, and domain (namely those for the opossum, wallaby the lack of requirement for authors to use standar- and platypus), the important positions of these dised nomenclature in many journals. non-eutherian mammals in the vertebrate phylo- The second session was chaired by Derek geny mean that they should be able to teach us Stemple, head of the Vertebrate Development and some fascinating lessons about the evolution of the Genetics group at the WTSI, and focused on the mammalian genome. In most cases, marsupial and three further vertebrate nomenclature groups, start- monotreme genes do have clear eutherian ortholo- ing with a report from Monte Westerfield, the gues, but Elizabeth also discussed the platypus principal investigator of the Zebrafish Model defensin genes, which have shown us that dupli- Organism Database (ZFIN). Zebrafish gene names cation of these immune genes has independently are based on human names wherever possible, but resulted in the convergent evolution of venom in the symbols are written in lower case to distinguish both monotremes and reptiles. them from human gene symbols (which are in Chris Elsik and Ross Tellam, the analysis leaders upper case letters) or mouse/rat symbols (which of the Bovine Genome Sequencing and Analysis are lower case except for an initial upper case Consortium, then told us about the ‘Annotation of letter). Monte raised the important point that the Bovine Genome — the Easy and the Difficult’. species-specific mutants can drive the naming of This talk highlighted several common and recur- genes, such as the oep one-eyed pinhead gene in ring themes from the meeting: the importance of zebrafish, which is the orthologue of human high coverage and a quality genome assembly; the teratocarcinoma-derived growth factor 1 (TDGF1) necessity of producing a consensus gene set that is gene. The next speaker was Erik Segerdell from deposited in a centralised database (in this case the Xenbase, a Xenopus laevis and tropicalis resource Bovine Genome Database, www.bovinegenome. based at the University of Calgary in Alberta, org); and the need for expert input into specific Canada. As for zebrafish, Xenopus gene groups and families of genes. As currently there are 214 # HENRY STEWART PUBLICATIONS 1479–7364. HUMAN GENOMICS. VOL 4. NO. 3. 213–217 FEBRUARY 2010 Highlights of the ‘Gene Nomenclature Across Species’ Meeting MEETING REPORT no guidelines for assigning bovine gene symbols, of genes and over 400 mouse genes, there are only the 5,757 bovine gene models found in both around 120 sets of 1:1 orthologues, making the Ensembl and Entrez Gene, over 60 per cent have direct transfer of gene names between species different symbols assigned to them in each database, impossible without extensive manual curation. The so, clearly, there is a need for standardising the afternoon concluded with a lively discussion on nomenclature for this genome. Jim Reecy, the nomenclature guidelines across species, chaired by bioinformatics coordination leader of the USA’s Alan Archibald. All those present at the meeting National Animal Genome Research Program, then agreed that it would be useful to have a common talked to us about porcine gene annotation. To set of nomenclature rules that could be applied date, over 17,000 gene models have been annotated to any novel vertebrate genome, and that these in the swine genome, of which nearly 10,000 have would be based on human gene nomenclature but been projected from other species. Manual annota- also take into account species-specific character- tion, both from the Havana team at WTSI and istics. This should prove an invaluable resource for from community annotation, is now being used to assigning standardised gene names to newly refine these gene models. Jim also mentioned the sequenced genomes. International Society of Animal Genetics (ISAG), The next day, the proceedings began with two which is an established forum for the livestock gen- in-depth talks on complex gene families, following etics community. Its genome sequence workshops on from Lisa’s presentation the previous afternoon could provide an excellent opportunity for gene on zinc fingers. This session was chaired by Vasilis nomenclature committees to meet. The final Vasiliou from the University of Denver, Colorado, speaker of this session was Noelle Cockett, the USA, an expert in the aldehyde dehydrogenase sheep genome coordinator, based at Utah State family. The first talk came from Jed Goldstone University, USA, who updated us on the ‘Assembly from Woods Hole Oceanographic Institution in of the Ovine Whole Genome Reference Massachusetts, USA, who studies the evolution of Sequence’. The sheep genome is still in the early the cytochrome P450 (CYP) superfamily. While stages of assembly.
Load more

Recommended publications
  • Gene Nomenclature System for Rice
    Rice (2008) 1:72–84 DOI 10.1007/s12284-008-9004-9 Gene Nomenclature System for Rice Susan R. McCouch & CGSNL (Committee on Gene Symbolization, Nomenclature and Linkage, Rice Genetics Cooperative) Received: 11 April 2008 /Accepted: 3 June 2008 /Published online: 15 August 2008 # The Author(s) 2008 Abstract The Committee on Gene Symbolization, Nomen- protein sequence information that have been annotated and clature and Linkage (CGSNL) of the Rice Genetics Cooper- mapped on the sequenced genome assemblies, as well as ative has revised the gene nomenclature system for rice those determined by biochemical characterization and/or (Oryza) to take advantage of the completion of the rice phenotype characterization by way of forward genetics. With genome sequence and the emergence of new methods for these revisions, we enhance the potential for structural, detecting, characterizing, and describing genes in the functional, and evolutionary comparisons across organisms biological community. This paper outlines a set of standard and seek to harmonize the rice gene nomenclature system procedures for describing genes based on DNA, RNA, and with that of other model organisms. Newly identified rice genes can now be registered on-line at http://shigen.lab.nig. ac.jp/rice/oryzabase_submission/gene_nomenclature/. The current ex-officio member list below is correct as of the date of this galley proof. The current ex-officio members of CGSNL (The Keywords Oryza sativa . Genome sequencing . Committee on Gene Symbolization, Nomenclature and Linkage) are: Gene symbolization Atsushi Yoshimura from the Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581, Japan, email: [email protected] Guozhen Liu from the Beijing Institute of Genomics of the Chinese Introduction Academy of Sciences, Beijing, People’s Republic of China, email: [email protected] The biological community is moving towards a universal Yasuo Nagato from the Graduate School of Agricultural and Life system for the naming of genes.
    [Show full text]
  • Systematic Review of the Genetics of Sudden Unexpected Death in Epilepsy: Potential Overlap with Sudden Cardiac Death and Arrhythmia-Related Genes C
    SYSTEMATIC REVIEW AND META-ANALYSIS Systematic Review of the Genetics of Sudden Unexpected Death in Epilepsy: Potential Overlap With Sudden Cardiac Death and Arrhythmia-Related Genes C. Anwar A. Chahal, MBChB; Mohammad N. Salloum, MD; Fares Alahdab, MD; Joseph A. Gottwald, PharmD; David J. Tester, BS; Lucman A. Anwer, MD; Elson L. So, MD; Mohammad Hassan Murad, MD, MPH; Erik K. St Louis, MD, MS; Michael J. Ackerman, MD, PhD; Virend K. Somers, MD, PhD Background-—Sudden unexpected death in epilepsy (SUDEP) is the leading cause of epilepsy-related death. SUDEP shares many features with sudden cardiac death and sudden unexplained death in the young and may have a similar genetic contribution. We aim to systematically review the literature on the genetics of SUDEP. Methods and Results-—PubMed, MEDLINE Epub Ahead of Print, Ovid Medline In-Process & Other Non-Indexed Citations, MEDLINE, EMBASE, Cochrane Database of Systematic Reviews, and Scopus were searched through April 4, 2017. English language human studies analyzing SUDEP for known sudden death, ion channel and arrhythmia-related pathogenic variants, novel variant discovery, and copy number variant analyses were included. Aggregate descriptive statistics were generated; data were insufficient for meta- analysis. A total of 8 studies with 161 unique individuals were included; mean was age 29.0 (ÆSD 14.2) years; 61% males; ECG data were reported in 7.5% of cases; 50.7% were found prone and 58% of deaths were nocturnal. Cause included all types of epilepsy. Antemortem diagnosis of Dravet syndrome and autism (with duplication of chromosome 15) was associated with 11% and 9% of cases.
    [Show full text]
  • A Genetic Screen for Genes That Impact Peroxisomes in Drosophila Identifies
    bioRxiv preprint doi: https://doi.org/10.1101/704122; this version posted July 16, 2019. 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 4.0 International license. A genetic screen for genes that impact peroxisomes in Drosophila identifies candidate genes for human disease Hillary K. Graves1, Sharayu Jangam1, Kai Li Tan1, Antonella Pignata1, Elaine S. Seto1, Shinya Yamamoto1,2,3,4# and Michael F. Wangler1,3,4,# 1Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA 2Department of Neuroscience, BCM, Houston, TX 77030, USA 3Program in Developmental Biology, BCM, Houston, TX 77030, USA 4Jan and Dan Duncan Neurological Research Institute, Texas Children Hospital, Houston, TX 77030, USA #Corresponding authors: SY ([email protected]), MFW ([email protected]) Keywords: Drosophila, peroxisomes, BRD4, fs(1)h bioRxiv preprint doi: https://doi.org/10.1101/704122; this version posted July 16, 2019. 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 4.0 International license. Abstract Peroxisomes are sub-cellular organelles that are essential for proper function of eukaryotic cells. In addition to being the sites of a variety of oxidative reactions, they are crucial regulators of lipid metabolism. Peroxisome loss or dysfunction leads to multi- system diseases in humans that strongly affects the nervous system.
    [Show full text]
  • Indicators of the Molecular Pathogenesis of Virulent Newcastle
    www.nature.com/scientificreports OPEN Indicators of the molecular pathogenesis of virulent Newcastle disease virus in chickens revealed by transcriptomic profling of spleen Mohammad Rabiei1*, Wai Yee Low2, Yan Ren2, Mohamad Indro Cahyono3, Phuong Thi Kim Doan1,4, Indi Dharmayanti3, Eleonora Dal Grande1 & Farhid Hemmatzadeh1,2 Newcastle disease virus (NDV) has caused signifcant outbreaks in South-East Asia, particularly in Indonesia in recent years. Recently emerged genotype VII NDVs (NDV-GVII) have shifted their tropism from gastrointestinal/respiratory tropism to a lymphotropic virus, invading lymphoid organs including spleen and bursa of Fabricius to cause profound lymphoid depletion. In this study, we aimed to identify candidate genes and biological pathways that contribute to the disease caused by this velogenic NDV-GVII. A transcriptomic analysis based on RNA-Seq of spleen was performed in chickens challenged with NDV-GVII and a control group. In total, 6361 genes were diferentially expressed that included 3506 up-regulated genes and 2855 down-regulated genes. Real-Time PCR of ten selected genes validated the RNA-Seq results as the correlation between them is 0.98. Functional and network analysis of Diferentially Expressed Genes (DEGs) showed altered regulation of ElF2 signalling, mTOR signalling, proliferation of cells of the lymphoid system, signalling by Rho family GTPases and synaptogenesis signalling in spleen. We have also identifed modifed expression of IFIT5, PI3K, AGT and PLP1 genes in NDV-GVII infected chickens. Our fndings in activation of autophagy-mediated cell death, lymphotropic and synaptogenesis signalling pathways provide new insights into the molecular pathogenesis of this newly emerged NDV-GVII. Newcastle disease virus (NDV) has a worldwide distribution.
    [Show full text]
  • Identification of Common Gene Networks Responsive To
    Cancer Gene Therapy (2014) 21, 542–548 © 2014 Nature America, Inc. All rights reserved 0929-1903/14 www.nature.com/cgt ORIGINAL ARTICLE Identification of common gene networks responsive to radiotherapy in human cancer cells D-L Hou1, L Chen2, B Liu1, L-N Song1 and T Fang1 Identification of the genes that are differentially expressed between radiosensitive and radioresistant cancers by global gene analysis may help to elucidate the mechanisms underlying tumor radioresistance and improve the efficacy of radiotherapy. An integrated analysis was conducted using publicly available GEO datasets to detect differentially expressed genes (DEGs) between cancer cells exhibiting radioresistance and cancer cells exhibiting radiosensitivity. Gene Ontology (GO) enrichment analyses, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and protein–protein interaction (PPI) networks analysis were also performed. Five GEO datasets including 16 samples of radiosensitive cancers and radioresistant cancers were obtained. A total of 688 DEGs across these studies were identified, of which 374 were upregulated and 314 were downregulated in radioresistant cancer cell. The most significantly enriched GO terms were regulation of transcription, DNA-dependent (GO: 0006355, P = 7.00E-09) for biological processes, while those for molecular functions was protein binding (GO: 0005515, P = 1.01E-28), and those for cellular component was cytoplasm (GO: 0005737, P = 2.81E-26). The most significantly enriched pathway in our KEGG analysis was Pathways in cancer (P = 4.20E-07). PPI network analysis showed that IFIH1 (Degree = 33) was selected as the most significant hub protein. This integrated analysis may help to predict responses to radiotherapy and may also provide insights into the development of individualized therapies and novel therapeutic targets.
    [Show full text]
  • The Prepattern Transcription Factor Irx3 Directs Nephron Segment Identity
    Downloaded from genesdev.cshlp.org on October 8, 2021 - Published by Cold Spring Harbor Laboratory Press The prepattern transcription factor Irx3 directs nephron segment identity Luca Reggiani,1 Daniela Raciti,1 Rannar Airik,2 Andreas Kispert,2 and André W. Brändli1,3 1Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zurich, CH-8093 Zurich, Switzerland; 2Institute of Molecular Biology, Hannover Medical School, D-30625 Hannover, Germany The nephron, the basic structural and functional unit of the vertebrate kidney, is organized into discrete segments, which are composed of distinct renal epithelial cell types. Each cell type carries out highly specific physiological functions to regulate fluid balance, osmolarity, and metabolic waste excretion. To date, the genetic basis of regionalization of the nephron has remained largely unknown. Here we show that Irx3,a member of the Iroquois (Irx) gene family, acts as a master regulator of intermediate tubule fate. Comparative studies in Xenopus and mouse have identified Irx1, Irx2, and Irx3 as an evolutionary conserved subset of Irx genes, whose expression represents the earliest manifestation of intermediate compartment patterning in the developing vertebrate nephron discovered to date. Intermediate tubule progenitors will give rise to epithelia of Henle’s loop in mammals. Loss-of-function studies indicate that irx1 and irx2 are dispensable, whereas irx3 is necessary for intermediate tubule formation in Xenopus. Furthermore, we demonstrate that misexpression of irx3 is sufficient to direct ectopic development of intermediate tubules in the Xenopus mesoderm. Taken together, irx3 is the first gene known to be necessary and sufficient to specify nephron segment fate in vivo.
    [Show full text]
  • The Genetic Basis of Malformation of Cortical Development Syndromes: Primary Focus on Aicardi Syndrome
    The Genetic Basis of Malformation of Cortical Development Syndromes: Primary Focus on Aicardi Syndrome Thuong Thi Ha B. Sc, M. Bio Neurogenetics Research Group The University of Adelaide Thesis submitted for the degree of Doctor of Philosophy In Discipline of Genetics and Evolution School of Biological Sciences Faculty of Science The University of Adelaide June 2018 Table of Contents Abstract 6 Thesis Declaration 8 Acknowledgements 9 Publications 11 Abbreviations 12 CHAPTER I: Introduction 15 1.1 Overview of Malformations of Cortical Development (MCD) 15 1.2 Introduction into Aicardi Syndrome 16 1.3 Clinical Features of Aicardi Syndrome 20 1.3.1 Epidemiology 20 1.3.2 Clinical Diagnosis 21 1.3.3 Differential Diagnosis 23 1.3.4 Development & Prognosis 24 1.4 Treatment 28 1.5 Pathogenesis of Aicardi Syndrome 29 1.5.1 Prenatal or Intrauterine Disturbances 29 1.5.2 Genetic Predisposition 30 1.6 Hypothesis & Aims 41 1.6.1 Hypothesis 41 1.6.2 Research Aims 41 1.7 Expected Outcomes 42 CHAPTER II: Materials & Methods 43 2.1 Study Design 43 2.1.1 Cohort of Study 44 2.1.2 Inheritance-based Strategy 45 1 2.1.3 Ethics for human and animals 46 2.2 Computational Methods 46 2.2.1 Pre-Processing Raw Reads 46 2.2.2 Sequencing Coverage 47 2.2.3 Variant Discovery 49 2.2.4 Annotating Variants 53 2.2.5 Evaluating Variants 55 2.3 Biological Methods 58 2.3.1 Cell Culture 58 2.3.2 Genomic DNA Sequencing 61 2.3.3 Plasmid cloning 69 2.3.4 RNA, whole exome & Whole Genome Sequencing 74 2.3.5 TOPFlash Assay 75 2.3.6 Western Blot 76 2.3.7 Morpholino Knockdown in Zebrafish 79 CHAPTER III: A mutation in COL4A2 causes autosomal dominant porencephaly with cataracts.
    [Show full text]
  • Abundant and Dynamically Expressed Mirnas, Pirnas, and Other Small Rnas in the Vertebrate Xenopus Tropicalis
    Downloaded from genome.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press Letter Abundant and dynamically expressed miRNAs, piRNAs, and other small RNAs in the vertebrate Xenopus tropicalis Javier Armisen,1,2,3 Michael J. Gilchrist,1,3 Anna Wilczynska,2 Nancy Standart,2 and Eric A. Miska1,2,4 1Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, The Henry Wellcome Building of Cancer and Developmental Biology, Cambridge CB2 1QN, United Kingdom; 2Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom Small regulatory RNAs have recently emerged as key regulators of eukaryotic gene expression. Here we used high- throughput sequencing to determine small RNA populations in the germline and soma of the African clawed frog Xenopus tropicalis. We identified a number of miRNAs that were expressed in the female germline. miRNA expression profiling revealed that miR-202-5p is an oocyte-enriched miRNA. We identified two novel miRNAs that were expressed in the soma. In addition, we sequenced large numbers of Piwi-associated RNAs (piRNAs) and other endogenous small RNAs, likely representing endogenous siRNAs (endo-siRNAs). Of these, only piRNAs were restricted to the germline, suggesting that endo-siRNAs are an abundant class of small RNAs in the vertebrate soma. In the germline, both endogenous small RNAs and piRNAs mapped to many high copy number loci. Furthermore, endogenous small RNAs mapped to the same specific subsets of repetitive elements in both the soma and the germline, suggesting that these RNAs might act to silence repetitive elements in both compartments. Data presented here suggest a conserved role for miRNAs in the vertebrate germline.
    [Show full text]
  • Downloaded from the CAVA Integration with Data Generated by Pre-NGS Methods Webpage [19]
    Münz et al. Genome Medicine (2015) 7:76 DOI 10.1186/s13073-015-0195-6 METHOD Open Access CSN and CAVA: variant annotation tools for rapid, robust next-generation sequencing analysis in the clinical setting Márton Münz1†, Elise Ruark2†, Anthony Renwick2, Emma Ramsay2, Matthew Clarke2, Shazia Mahamdallie2,3, Victoria Cloke3, Sheila Seal2,3, Ann Strydom2,3, Gerton Lunter1 and Nazneen Rahman2,3,4* Abstract Background: Next-generation sequencing (NGS) offers unprecedented opportunities to expand clinical genomics. It also presents challenges with respect to integration with data from other sequencing methods and historical data. Provision of consistent, clinically applicable variant annotation of NGS data has proved difficult, particularly of indels, an important variant class in clinical genomics. Annotation in relation to a reference genome sequence, the DNA strand of coding transcripts and potential alternative variant representations has not been well addressed. Here we present tools that address these challenges to provide rapid, standardized, clinically appropriate annotation of NGS data in line with existing clinical standards. Methods: We developed a clinical sequencing nomenclature (CSN), a fixed variant annotation consistent with the principles of the Human Genome Variation Society (HGVS) guidelines, optimized for automated variant annotation of NGS data. To deliver high-throughput CSN annotation we created CAVA (Clinical Annotation of VAriants), a fast, lightweight tool designed for easy incorporation into NGS pipelines. CAVA allows transcript specification, appropriately accommodates the strand of a gene transcript and flags variants with alternative annotations to facilitate clinical interpretation and comparison with other datasets. We evaluated CAVA in exome data and a clinical BRCA1/BRCA2 gene testing pipeline.
    [Show full text]
  • The Human Gamma-Glutamyltransferase Gene Family
    Hum Genet (2008) 123:321–332 DOI 10.1007/s00439-008-0487-7 REVIEW The human gamma-glutamyltransferase gene family Nora Heisterkamp · John GroVen · David Warburton · Tam P. Sneddon Received: 9 November 2007 / Accepted: 6 March 2008 / Published online: 21 March 2008 © Springer-Verlag 2008 Abstract Assays for gamma-glutamyl transferase related genes or sequences. These sequences were given (GGT1, EC 2.3.2.2) activity in blood are widely used in a multiple diVerent names, leading to inconsistencies and clinical setting to measure tissue damage. The well-charac- confusion. Here we systematically evaluated all human terized GGT1 is an extracellular enzyme that is anchored to sequences related to GGT1 using genomic and cDNA data- the plasma membrane of cells. There, it hydrolyzes and base searches and identiWed thirteen genes belonging to the transfers -glutamyl moieties from glutathione and other extended GGT family, of which at least six appear to be -glutamyl compounds to acceptors. As such, it has a critical active. In collaboration with the HUGO Gene Nomencla- function in the metabolism of glutathione and in the con- ture Committee (HGNC) we have designated possible version of the leukotriene LTC4 to LTD4. GGT deWciency active genes with nucleotide or amino acid sequence simi- in man is rare and for the few patients reported to date, larity to GGT1, as GGT5 (formerly GGL, GGTLA1/GGT- mutations in GGT1 have not been described. These patients rel), GGT6 (formerly rat ggt6 homologue) and GGT7 (for- do secrete glutathione in urine and fail to metabolize LTC4. merly GGTL3, GGT4). Two loci have the potential to Earlier pre-genome investigations had indicated that encode only the light chain portion of GGT and have now besides GGT1, the human genome contains additional been designated GGTLC1 (formerly GGTL6, GGTLA4) and GGTLC2.
    [Show full text]
  • Decision Support for Molecular Diagnostic Laboratories Using Interactive Biosoftware Alamut V1.2
    EuroGentest Unit 5 New technologies Decision support for molecular diagnostic laboratories using Interactive Biosoftware Alamut v1.2 November 2007- February 2008 Prepared by: NGRL Manchester As part of the activities of: EuroGentest Unit 5 Quality Management and Accreditation / Certification of Genetic Testing within the work package WP5.4. EuroGentest Project Co-ordinator: Professsor Jean-Jaques Cassiman K.U.Leuven Center for Human Genetics/ Centrum Menselijke Erfelijkheid Gasthuisberg O&N Herestraat 49 Box 602 3000 Leuven Belgium The views expressed in this document are those of the work package participants and do not necessarily reflect the policies of the institutions or companies they are affiliated to. © July 2008 Copyright EuroGentest Network of Excellence Project 2005 - EU Contract no. FP6-512148 Table of contents Summary ii Acknowledgements ii Introduction 1 Background 1 Description of tool 1 Evaluation 3 Aim 3 Methods 3 Results 5 User interface and usability 5 Data sources 5 Applicability to diagnostic testing 8 Validity and accuracy 8 Conclusions 15 Glossary 16 Appendix A Tested Gene Variants 18 i Summary Alamut is a decision-support software application developed by Interactive Biosoftware for mutation diagnostics in medical molecular genetics. It is a client- server application that integrates genetic information from different sources to describe variants using HGVS nomenclature and to help interpret their pathogenic status. We evaluated Alamut in four areas: its user interface and usability; the suitability of its data sources; its applicability to diagnostic testing; and its validity and accuracy. Laboratories found the software intuitive and easy to use, and well adapted to diagnostic testing. Over 400 variants from 14 genes were tested.
    [Show full text]
  • Genetic Nomenclature Zhiliang Hu Iowa State University, [email protected]
    Animal Science Publications Animal Science 2012 Genetic Nomenclature Zhiliang Hu Iowa State University, [email protected] James M. Reecy Iowa State University, [email protected] Follow this and additional works at: http://lib.dr.iastate.edu/ans_pubs Part of the Agriculture Commons, Animal Sciences Commons, and the Genetics Commons The ompc lete bibliographic information for this item can be found at http://lib.dr.iastate.edu/ ans_pubs/170. For information on how to cite this item, please visit http://lib.dr.iastate.edu/ howtocite.html. This Book Chapter is brought to you for free and open access by the Animal Science at Iowa State University Digital Repository. It has been accepted for inclusion in Animal Science Publications by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Genetic Nomenclature Abstract Genetics includes the study of genotypes, phenotypes and the mechanisms of genetic control between them. Genetic terms describe the processes, genes, alleles and traits with which genetic phenomena are described and examined. In this chapter we will concentrate on the discussions of genetic term standardizations and, at the end of the chapter, we will list some terms relevant to genetic processes and concepts in a Genetic Glossary. Disciplines Agriculture | Animal Sciences | Genetics Comments This is a chapter from The Genetics of the Dog, 2nd edition, chapter 23 (2012): 496. Posted with permission. This book chapter is available at Iowa State University
    [Show full text]