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Paired-end mapping reveals extensive structural variation in the human genome
Jan O Korbel1, Alexander Eckehart Urban, Jason P Affourtit
1Molecular Biophysics and Biochemistry Department, Yale University, New Haven, CT 06520, USA.
Science (New York, N.Y.)
|September 29, 2007
Summary
This study introduces paired-end mapping (PEM) to identify large structural variants (SVs) in the human genome. Researchers discovered over 1000 SVs, revealing greater human genetic diversity than previously thought.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Genomic structural variation (SV) encompasses large-scale alterations like deletions, duplications, and inversions.
- Understanding SVs is crucial for comprehending human genetic diversity and disease.
Purpose of the Study:
- To develop and apply a high-throughput sequencing method for identifying large structural variants (SVs) in the human genome.
- To characterize the landscape of SVs in different human populations and investigate their functional impact.
Main Methods:
- Introduction of high-throughput and massive paired-end mapping (PEM), a genome sequencing technique.
- Utilizing 454 sequencing and computational analysis to map DNA reads and identify SVs of approximately 3 kilobases or larger.
- Employing a novel pooling strategy and computational analysis to determine breakpoint junction sequences for over 200 SVs.
Main Results:
- Fine-mapping of over 1000 structural variants (SVs) in African and European individuals.
- Identification of shared and divergent SVs compared to a reference genome.
- Demonstration that the number of SVs in humans is significantly larger than previously hypothesized, with many potentially impacting gene function.
Conclusions:
- The study reveals a vast and underappreciated landscape of structural variation in the human genome.
- Paired-end mapping (PEM) is an effective method for large-scale SV detection.
- Insights into the mechanisms underlying structural variant formation in humans were gained.
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