Tuesday, September 23, 2008

TGen Researchers Publish New Multiplexed Sequence Approach

[Source: By a GenomeWeb staff reporter , GenomeWeb News] - In a paper appearing online in Nature Methods this weekend, a team of researchers from the Translational Genomics Research Institute described a new multiplexed, targeted re-sequencing strategy for assessing regions of the human genome more quickly and efficiently.

The team used PCR amplicons to create degenerate, indexed DNA barcodes targeting specific regions of the genome before sequencing them with the Illumina Genome Analyzer. The multiplexed approach, they say, is an effective way to uncover genetic variation in genes of interest — an approach intended to facilitate cost-efficient re-sequencing on genes involved in particular diseases and conditions.

“In many cases, rather than sequencing the whole genome for ten people, researchers would rather sequence a dozen genes for 1,000 people,” co-lead author John Pearson, head of TGen’s Bioinformatics Research Unit, said in a statement.

The researchers tested their approach by simultaneously sequencing Encyclopedia of DNA Elements, or ENCODE, regions from the genomes of numerous HapMap individuals. Using its targeted resequencing approach, the team was able to identify genetic variants not previously described for these regions.

“Although whole-genome sequencing may be the primary motivator for improvements in sequencing technology, it is clear that next-generation technologies are immediately useful for focused, hypothesis-driven sequencing of linkage peaks, groupings of candidate genes or sequencing the entire known coding region of the human genome,” the authors noted. “In this report, we developed per-individual indexing of pooled PCR amplicons to carry out targeted sequencing.”

In the future, they added, pooled amplicons may also be replaced by other sample-preparation strategies, including genome partitioning. “[V]ariant discovery through the re-sequencing of all candidate regions implicated in a disease across genomes of dozens, possibly hundreds, of individuals could be considerably accelerated by merging multiplex capture, indexing, and next-generation sequencing approaches in a single protocol.”

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