Mutation Databases

David Baux, CHU Montpellier, Montpellier, France
Souphatta Sasorith, CHU Montpellier, Montpellier, France
Anne Bergougnoux, Université de Montpellier, Montpellier, France
Mireille Claustres, Université de Montpellier, Montpellier, France

Published online: September 2017

DOI: 10.1002/9780470015902.a0005315.pub2

Abstract

Mutation databases were developed in the 1990s and since then being a hot topic in the field of human molecular genetics. They have been constantly evolving, from a single gene to whole genome, from a few patients to whole populations, bringing the community to face multiple challenges, from the ethical and technical aspects of data sharing to the new methods to be developed to bring precision medicine to the patient. The new sequencing technologies, generating worldwide an uninterrupted flow of variants from patients and from the general population, challenge the information technology capacities of genetic centres. Huge databases are now present in multiple copies inside the institutions in high‐performance computing environments and are used to filter, interpret and prioritise variants in disease studies in order to facilitate the work of thousands of geneticists overwhelmed with the big data.

Key Concepts

  • Mutation databases appeared in the 1990s and were designed to store, organise and share genetic data.
  • The main categories were central databases, which gathered all variants, and locus‐specific databases, which were focused on one gene/disease with an expert curator.
  • The advent of high‐throughput sequencing changed the paradigm: central databases are becoming more and more experts and locus‐specific databases more and more genomic.
  • High‐throughput sequencing also brought a new category of databases for fast variant interpretation.
  • The main current issue is data sharing: success is linked to data quality, availability and usability.

Keywords: DNA variant; genetic databases; high‐throughput sequencing; locus‐specific databases; data sharing; variant prioritisation

Figure 1. Main categories of genetic databases. Types of genetic databases are labelled in orange, with key examples in yellow. Arrows show examples of data integration in dbSNP. The blue curly brace highlights the UCSC web browser that includes data from all databases.
Figure 2. Evolution in the number of variants reported in dbSNP from 2005 (HapMap project) to 2017. The graph represents the number of submitted (blue) and validated variants (pink) for each dbSNP version. M: millions
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Related Sub-Topics:

Bioinformatics and Genetic Disease | Techniques and Tools in Clinical Genetics | Computational Molecular Biology | Bioinformatics
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Article Title: Mutation Databases
 
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Baux, David, Sasorith, Souphatta, Bergougnoux, Anne, and Claustres, Mireille(Sep 2017) Mutation Databases. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0005315.pub2]