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A survey of locus-specific database curation
  1. Richard G H Cotton2,
  2. Kate Phillips1,
  3. Ourania Horaitis1
  1. 1Genomic Disorders Research Centre, Melbourne, Australia
  2. 2Department of Medicine, The University of Melbourne, Melbourne, Australia
  1. Correspondence to:
 Professor R G H Cotton
 Genomic Disorders Research Centre, 7th Floor, Daly Wing, St Vincent’s Hospital, Fitzroy, VIC 3065, Australia; cotton{at}unimelb.edu.au

Abstract

It is widely accepted that curation of variation in genes is best performed by experts in those genes and their variation. However, obtaining funding for such variation is difficult even though up-to-date lists of variations in genes are essential for optimum delivery of genetic healthcare and for medical research. This study was undertaken to gather information on gene-specific databases (locus-specific databases) in an effort to understand their functioning, funding and needs.

A questionnaire was sent to 125 curators and we received 47 responses. Individuals performed curation of up to 69 genes. The time curators spent curating was extremely variable. This ranged from 0 h per week up to 5 curators spending over 4 h per week. The funding required ranged from US$600 to US$45000 per year. Most databases were stimulated by the Human Genome Organization-Mutation Database Initiative and used their guidelines. Many databases reported unpublished mutations, with all but one respondent reporting errors in the literature. Of the 13 who reported hit rates, 9 reported over 52 000 hits per year.

On the basis of this, five recommendations were made to improve the curation of variation information, particularly that of mutations causing single-gene disorder:

1. A curator for each gene, who is an expert in it, should be identified or nominated.

2. Curation at a minimum of 2 h per week at US$2000 per gene per year should be encouraged.

3. Guidelines and custom software use should be encouraged to facilitate easy setup and curation.

4. Hits per week on the website should be recorded to allow the importance of the site to be illustrated for grant-giving purposes.

5. Published protocols should be followed in the establishment of locus-specific databases.

  • HUGO-MDI, Human Genome Organization-Mutation Database Initiative
  • LSDB, locus-specific database

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Footnotes

  • Competing interests: None declared.

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