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Closing gaps in the human genome with fosmid resources generated from multiple individuals
Donald Bovee1, Yang Zhou, Eric Haugen
1Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington 98195, USA.
Nature Genetics
|December 25, 2007
Summary
Researchers filled over 26 gaps in the human genome
Area of Science:
- Genomics
- Human Genetics
Background:
- The International Human Genome Sequencing Consortium published the human genome sequence in 2004, but over 340 gaps remained.
- Euchromatic regions of the human genome contain most genes and were incompletely sequenced.
Purpose of the Study:
- To close remaining gaps in the euchromatic region of the human genome.
- To analyze the sequence and characteristics of previously unknown euchromatic DNA.
Main Methods:
- Utilized fosmid resources from multiple individuals to target specific gaps.
- Sequenced and analyzed 2,488,842 base pairs of previously unknown euchromatic DNA.
Main Results:
- Successfully closed 26 euchromatic gaps (10% of 250), including two on chromosome 19.
- Identified 363,114 base pairs of novel euchromatic sequence.
- Found 30.7% of closed gaps to be polymorphic, enabling complete gene annotation and mRNA assignment.
- Gap sequences showed a 2.3-fold enrichment in segmental duplications compared to the whole genome.
Conclusions:
- Fosmid libraries are a valuable resource for completing the human euchromatic genome.
- Not all gaps in "finished" genomes are inherently difficult to sequence.
- The newly sequenced regions provide critical data for gene annotation and understanding genome structure.
