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Related Concept Videos

Next-generation Sequencing03:00

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
Genetic Variation01:25

Genetic Variation

Genetic variation is the diversity in DNA sequences found among individuals of the same species. This diversity is crucial for a species' survival because it helps organisms adapt to environmental changes. Genetic variation begins with fertilization, where an egg and sperm cell merge. Each of these cells carries 23 chromosomes, up to 46 in the fertilized egg. Chromosomes are long DNA strands that contain genes, the basic units of heredity.
Genes exist in different versions called alleles, which...
Principles of Pharmacogenetics: Types of Genetic Variants01:27

Principles of Pharmacogenetics: Types of Genetic Variants

The human genome is over 99.9% identical between individuals, yet genetic differences exist at millions of bases. The human genome contains approximately 3 million variant positions per individual, many of which are heterozygous, contributing to genetic diversity and individual traits. Genetic variations include single-nucleotide polymorphisms (SNPs), insertions, deletions, and copy number variations (CNVs).SNPs, the most common variation, involve single-base changes in DNA. These can be...
Genomics02:02

Genomics

Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
Comparing Copy Number Variations and SNPs02:26

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.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...

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Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
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LOVD v.2.0: the next generation in gene variant databases.

Ivo F A C Fokkema1, Peter E M Taschner, Gerard C P Schaafsma

  • 1Center of Human and Clinical Genetics, Department of Human Genetics, Leiden University Medical Center, Leiden, Nederland.

Human Mutation
|April 27, 2011
PubMed
Summary

The Leiden Open-source Variation Database (LOVD) v.2.0 enhances gene variation data management for researchers and clinicians. This platform-independent tool offers flexibility, security, and supports high-throughput sequence analysis.

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Area of Science:

  • Genomics and Bioinformatics
  • Human Genetics
  • Database Development

Background:

  • Locus-Specific Databases (LSDBs) are crucial for cataloging gene sequence variations linked to human phenotypes.
  • Existing LSDBs often lack flexibility and standardization, hindering data integration and accessibility for researchers and clinicians.
  • The Human Genome Variation Society (HGVS) provides recommendations for variant description, emphasizing the need for standardized databases.

Purpose of the Study:

  • To introduce Leiden Open-source Variation Database (LOVD) v.2.0, an enhanced platform-independent, web-based LSDB package.
  • To improve flexibility, functionality, and data management capabilities for storing and querying human gene sequence variations.
  • To promote standardization and interoperability among LSDBs through a robust and user-friendly system.

Main Methods:

  • Development of a platform-independent, web-based LSDB package (LOVD v.2.0) following HGVS recommendations.
  • Implementation of a relational database structure with separate tables for patients and sequence variants, linked for comprehensive data retrieval.
  • Inclusion of features for dynamic column addition, support for high-throughput sequencing data, and robust security measures.

Main Results:

  • LOVD v.2.0 offers enhanced flexibility, allowing storage of sequence variants across multiple genes per patient and custom data fields.
  • The database structure facilitates fast queries and integrates seamlessly with high-throughput sequencing data, as demonstrated by the X-chromosomal Mental Retardation LOVD installation.
  • Currently, 71 public LOVD installations host 3,294 gene variant databases with 199,000 variants in 84,000 patients, indicating widespread adoption.

Conclusions:

  • LOVD v.2.0 provides a powerful, flexible, and secure solution for managing gene variation data, supporting both clinical and research applications.
  • The platform's design promotes LSDB standardization and database interoperability, crucial for advancing genomic medicine.
  • Free server space and support are offered to encourage the establishment of new LSDBs, further promoting data sharing and collaboration.