Frequently Asked Questions

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FAQ

Variation Databases and Related Sites (NEW LSDB LIST!)

Recommendations including Nomenclature Guidelines

Meeting Reports

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Meetings of Interest

Relevant Publications

Waystation / Central Database project

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How can I put my data on the Internet, do you have any software I can use?

Preparation of Content

This is an often asked and difficult question. We suggest these four steps:

(a) Check our list of Locus Specific Databases to see if the database already exists. If yes, contact the curator to submit your mutations to this database.

(b) If there is no database, contact Rania Horaitis to determine if someone else is already working on your gene/s of interest.

(c) Form a consortium of interested researchers and clinicians to spread the load and ensure longlevity of the database by having a community to find a new curator if necessary.

(d) Collect all mutations including polymorphisms and name them according to the Recommendations (see below). You may wish to publish this data as a review for a specialist journal such as Human Mutation (contact Rania) or other journal. This is a good incentive to collect the relevant information since a useful publication will be produced.

(e) Make sure to include "core" content that the "Content" Working Group of the MDI has proposed (see what information do I include? below).

Software

(f) You may choose to use software available to us, commercially available packages or create your own. We have designed custom made software that makes it easier for curators to create a database. Software that is currently made available by HGVS members to others is listed below including a reference, you must contact the curators/creators yourself:

LOVD; Leiden Open Variation Database

> to the Website

> to the Publication

How do I name my mutations?

The HGVS & HUGO MDI Nomenclature Working Group has proposed the following recomendations for naming of mutations. These have now become widely accepted.

(a) Antonarakis SE and the Nomenclature Working Group (1998) Recommendations for a Nomenclature System for Human Gene Mutations. Hum Mut 11: 1-3

(b) den Dunnen JT & Antonarakis SE (2000) Mutation nomenclature extensions and suggestions to describe complex mutations: A discussion. Hum Mut 15: 7-12

Detailed descriptions and examples are available online here.

What information do I need to include in a database?

Compatibility between different databases is both desirable and necessary. The Content Working Group of the MDI has made recommendations as to the bare minimum of data for cohesiveness. We strongly urge you to read these papers before preparing your database to make your database more meaningful & useful. Of course other data particular to your disease or gene may be included and we encourage this.

Essential content

1. A unique identifier must be issued by the database for each allele
2. The source/report of the data
3. The context of the allele; Ref. Seq. Acc. No.;DDBJ/EMBL/GenBank
4. (a) The name of the allele using the guidelines above e.g. 1425G->A
(b) Description of the change as fully as possible
5. A document showing the "biography" of the database and a map of its details.
6. A minimum set of links to other databases should be included for mutual compatibility. e.g. OMIM
7. The date when the database was last updated.

Scriver C.R., Nowacki P.M., and Lehvaslaiho H. (1999) Guidelines and Recommendations for Content, Structure and Deployment of Mutation Databases. Hum Mut 13: 344-350

Scriver CR, Nowacki PM, Lehvslaiho H. (2000) Guidelines and recommendations for content, structure, and deployment of mutation databases: II. Journey in progress Hum Mut 15: 13-15

Optional content to make a database more interesting and useful

Obviously the list can vary depending on the gene/s however here are a few items of content that would make a variation database of more interest.

HUGO-approved Gene symbol
Chromosome Region
Gene information
Location Exon/Intron
Phenotype (if any)
RNA effect
Protein effect
Detection method
Clinical information about disease for clinicians & patients
Geographic origin
Ethnic origin
Expression studies
List of contributors to db
List of associations and organisations

See also: Claustres M., Horaitis O., Vanevski M.,and Cotton R.G.H. (2002) Time For A Unified System Of Mutation Description and Reporting: A Review of Locus Specific Mutation Databases Genome Res 12:680-688

How can I help?

You can help by either joining the HGVS if you are not already a member, and participating in community discussions that occur via email, or by attending our meetings this way your opinions will be heard.

Other questions?

Please contact Rania