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Updated: Jun 2, 2026
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Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
Published on: April 4, 2018
ENGINES: exploring single nucleotide variation in entire human genomes.
Jorge Amigo1, Antonio Salas, Christopher Phillips
1Grupo de Medicina Xenómica, CIBERER, Universidade de Santiago de Compostela, Santiago de Compostela, Galicia, Spain. jorge.amigo@usc.es
BMC Bioinformatics
|April 21, 2011
Summary
A new tool, ENGINES, enables comprehensive population analysis of human genome variation data from large-scale sequencing projects. It provides fast access to genetic variant data, aiding medical and population genetics research.
Area of Science:
- Genomics
- Bioinformatics
- Population Genetics
Background:
- Next-generation sequencing generates vast amounts of human genome data, necessitating advanced analytical software.
- Existing tools lack comprehensive population analysis capabilities for large-scale genomic variation data.
- The 1000 Genomes project provides extensive population-specific genome data.
Purpose of the Study:
- To develop a scalable software tool for analyzing entire human genomes.
- To enable comprehensive population-level analysis of genetic variation.
- To facilitate exploration of Single Nucleotide Variations (SNVs) across diverse populations.
Main Methods:
- Developed ENGINES (ENtire Genome INterface for Exploring SNVs), a genetic variant site explorer.
- Utilized 1000 Genomes Phase I data (>7.3 billion genotypes, 28 million SNVs).
- Pre-processed data into a web-accessible data mart with query capabilities for population comparison, rs-number, chromosomal region, or gene searches.
Main Results:
- ENGINES efficiently handles and analyzes large-scale genetic variation data.
- The tool provides summary statistics, including allele frequency and FST values.
- Users can compare results with other SNP repositories like HapMap and Perlegen.
Conclusions:
- ENGINES offers fast and comprehensive access to large-scale variation data repositories.
- It enables rapid browsing of whole genome variation with detailed statistical information.
- Web interface and data mart scripts are available for public access.
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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%...
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%...
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