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Nomenclature: The Language of Genomics Ruth Lovering HUGO Gene Nomenclature Committee

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Presentation on theme: "Nomenclature: The Language of Genomics Ruth Lovering HUGO Gene Nomenclature Committee"— Presentation transcript:

1 Nomenclature: The Language of Genomics Ruth Lovering HUGO Gene Nomenclature Committee

2 The Role of HGNC # Assign approved gene symbols # Collate and curate data # Maintain symbol database (Genew) # Co-ordination with other public databases # Guidelines White et al (Genomics 1997) Updated guidelines, Genomics April 2002, in press

3 Definition of a Gene HGNC A gene is a DNA segment that contributes to phenotype/function. In the absence of demonstrated function a gene may be characterized by sequence, transcription or homology. [White et al 1997]

4 Definitions Gene name: a brief and specific description which conveys the character or function of the gene/gene product, but does not attempt to describe everything known about it. Gene Symbol: an abbreviation/acronym of the gene name, designated by upper-case Latin letters or by a combination of upper-case letters and Arabic numerals.

5 Approved Symbol # Unique # Meaningful – –M55108 – –CFTR – –cystic fibrosis transmembrane regulator # Systematic –ABCA4 –ATP-binding cassette, sub-family A (ABC1), member 4 # Cross-species – –FZD – –frizzled

6 14,363

7 Data Management Database: Genew (ver 3.0) # Stable numerate HGNC IDs # Sequence data store, local BLAST # Automatic updates from Locuslink, GDB, MGD, SWISS-PROT # Streamlined tracking system for correspondence # Will be upgraded to enable online editing

8 Genew Data Flow Other Database Files LocusLink: Approved Symbol, LocusLink ID, OMIM ID, RefSeq SWISS-PROT: Approved Symbol, SWISS- PROT ID, Sequence Accession ID GDB: Approved Symbol, GDB ID, Gene Name, Cytogenetic Location MGD: Reserved mouse gene symbols and names. (Not Exported) Data Submissions  Authors  Journals  Literature Review  Chromosome Sequencing Projects  Gene Families  Homologs from other species Genew Public Data Private Data Online Text Files Online Genew Search Engine Search Retrieval Gene Symbol Gene Name Alias Cytogenetic Location OMIM Number PMID

9 Databases Using Approved Symbols Ensembl GENATLAS GeneCards The Genome Database (GDB) Human Gene Mutation Database LocusLink MGD, Mouse Genome Informatics Online Mendelian Inheritance in Man SWISS-PROT UCSC Human Genome Project Working Draft

10 The Benefits of Approved Nomenclature # One gene symbol # User friendly # Simplified information retrieval # Database co-ordination # Efficient use of resources # Systematic assignment of new symbols

11 Quote of the Day: “I would rather use someone else’s toothbrush, than their nomenclature”

12 When Do You Name a Gene? # When you want to publish it # When you want to talk about it # When you want to add it to a database But only when you have some information about it

13 Source of Information for Symbol Assignment # Confidential Submissions # Literature # Domain structures # Other databases # Specialist advice

14 Symbol Assignment by Sequence Highly similar # Assign next available symbol in the family series Identical sequence # Verify approved symbol Highly similar, known pseudogene # Assign a symbol in the family series with the suffix “P” Moderately similar # Assign appropriate symbol with the suffix “L” for like No Homology #C#orf# (chromosome # open reading frame #) # C#orf# (chromosome # open reading frame #) # D#S# (DNA segment number) # KIAA#

15 Chromosome 20 Genes without symbols Approved symbols Approved prior to collaboration Currently approved 895

16 Chromosome 21 Approved prior to collaboration Currently approved 288 Genes without symbols Approved symbols

17 Chromosome 22 Approved prior to collaboration Currently approved 679 Genes without symbols Approved symbols

18 Why Use Approved Nomenclature? # Standardisation # Communication of information # Manual curation # Data storage, management and analysis # Community collaboration # Consistency across species # Linking genes to disease and physiology

19 The work of the HGNC is supported by NIH contract N01-LM (60% total) and by the UK Medical Research Council (40%). Dr Sue Povey Dr Hester Wain Dr Elspeth Bruford Dr Ruth Lovering Dr Michael Lush Dr Mathew Wright HUGO Gene Nomenclature Committee


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