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Comparing Copy Number Variations and SNPs

Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
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Curating gene variant databases (LSDBs): toward a universal standard.

Jacopo Celli1, Raymond Dalgleish, Mauno Vihinen

  • 1Human and Clinical Genetics, Leiden University Medical Center, Leiden, Netherlands.

Human Mutation
|October 13, 2011
PubMed
Summary
This summary is machine-generated.

This study details the crucial process of curating gene variant databases, also known as Locus-Specific DataBases (LSDBs). It outlines essential tasks, steps, and potential issues for creating reliable, quality-assured genetic variant information.

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Area of Science:

  • Genetics and Bioinformatics
  • Clinical Diagnostics
  • Database Management

Background:

  • Gene variant databases, or Locus-Specific DataBases (LSDBs), are vital resources for collecting and presenting genetic sequence variant information.
  • These databases are frequently utilized in DNA-based diagnostics, offering clinicians and researchers access to global gene variant data and their functional impact (pathogenicity).
  • Despite extensive literature on gene variant databases, the specific processes of database curation remain under-documented.

Purpose of the Study:

  • To address the gap in literature regarding the practical aspects of gene variant database curation.
  • To provide an overview of the tasks, methodologies, and challenges involved in curating Locus-Specific DataBases (LSDBs).
  • To lay the groundwork for establishing standardized guidelines for quality-assured gene variant database curation.

Main Methods:

  • Leveraging extensive practical experience in Locus-Specific DataBase (LSDB) curation.
  • Drawing upon contributions to database curation training courses.
  • Descriptive overview of curation tasks, procedural steps, and identified issues.

Main Results:

  • Detailed description of the tasks inherent in gene variant database curation.
  • Step-by-step procedural guidance for effective database curation.
  • Identification and discussion of common issues encountered during the curation process.

Conclusions:

  • The paper provides a foundational overview of gene variant database curation processes.
  • This work is a preliminary step towards developing comprehensive guidelines for quality-assured LSDBs.
  • Effective curation is essential for the reliability and utility of gene variant databases in diagnostics and research.