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Locus-specific mutation databases: pitfalls and good practice based on the p53 experience

Nature Reviews Cancer volume 6, pages 83–90 (2006)Cite this article

Abstract

Between 50,000 and 60,000 mutations have been described in various genes that are associated with a wide variety of diseases. Reporting, storing and analysing these data is an important challenge as such data provide invaluable information for both clinical medicine and basic science. Locus-specific databases have been developed to exploit this huge volume of data. The p53 mutation database is a paradigm, as it constitutes the largest collection of somatic mutations (22,000). However, there are several biases in this database that can lead to serious erroneous interpretations. We describe several rules for mutation database management that could benefit the entire scientific community.

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Figure 1: Frequency of p53 mutants in the Universal Mutation Database.
Figure 2: Activity of p53 mutants according to their frequency in the Universal Mutation Database.
Figure 3: p53 loss of function.

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Acknowledgements

Development of the UMD software is supported by grants from AFM to C.B. and M.C. Work of T.S. is supported by the ARC and ligue contre le cancer (comité de Paris). We are grateful to Richard Cotton for critical reading of this manuscript.

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Authors and Affiliations

  1. the Université P.M. Curie, 4 place Jussieu, Paris, 75005, France

    Thierry Soussi

  2. Department of Oncology-Pathology, the Karolinska Institute, Cancer Center Karolinska (CCK), Stockholm, SE-171 76, Sweden

    Thierry Soussi

  3. the Department of Clinical Oncology, Institute of Development, Aging, and Cancer, Tohoku University, Sendai, 980-8575, Japan

    Chikashi Ishioka

  4. the Laboratoire de Génétique Moléculaire et Chromosomique, Institut Universitaire de Recherche Clinique et CHU, CNRS UPR 1142, 641, avenue du Doyen Gaston Giraud, Montpellier, 34093, Cedex 5, France

    Mireille Claustres & Christophe Béroud

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Correspondence to Thierry Soussi.

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Related links

Related links

DATABASES

National Cancer Institute

breast cancer

colon cancer

hepatocellular carcinoma

lung cancer

OMIM

Marfan syndrome

von Hippel–Lindau syndrome

FURTHER INFORMATION

EMBL

GDB Human Genome Database

GenBank

Human Gene Mutation Database

Mutation Storage and Retrieval Program

Leiden Open Source Variation Database

MySQL

p53 database of the International Agency for Research on Cancer

Swiss-Prot

The p53 Database

Universal Mutation Database for p53

Waystation Project

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Soussi, T., Ishioka, C., Claustres, M. et al. Locus-specific mutation databases: pitfalls and good practice based on the p53 experience. Nat Rev Cancer 6, 83–90 (2006). https://doi.org/10.1038/nrc1783

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