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New Method for Targeted Resequencing

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Researchers at Stanford University’s Genome Technology Center and their colleagues have coupled a multiplexed DNA-amplification method with next-generation sequencing to resequence multiple human cancer genes in parallel and at lower cost than traditional methods.

Unlike traditional PCR, results provided by the DNA-amplification technology, also known as the selector technology, allow researchers to amplify many different DNA regions in a single reaction tube.

The researchers used 454 Life Sciences’ sequencing technology in their proof-of-concept study, which was published in Proceedings of the National Academy of Sciences in May. They are now testing the technology in a larger project that will use other new sequencing platforms, including Illumina’s Genetic Analyzer.

For the pilot study, the researchers, led by Ron Davis and colleagues at the Stanford Genome Technology Center, used the selector technology to amplify 10 cancer genes comprising 177 exons from genomic DNA derived from cancer cell lines.

Combining multiplexed DNA amplification and next-gen sequencing could significantly lower the cost and time of large-scale, targeted resequencing projects, and make such studies possible in smaller laboratories that do not have access to the same infrastructure as large genome centers, according to the researchers.

“This is a really great (and important) step forward in the right direction,” according to Jay Shendure, a researcher in George Church’s group at Harvard University. Shendure, who has been working on a similar amplification method and was not involved in this study, called the results “impressive.”

Methods to amplify subsets of the human genome will be crucial for targeted resequencing studies.

“Even with new [sequencing] technologies, sequencing of a complete human genome will continue to be prohibitively expensive for most investigators, and most of the immediate demand will lie in targeted resequencing,” Shendure says.
— Julia Karow

Short Reads

Applied Biosystems shipped its first SOLiD next-generation sequencing instrument to Stanford University through an early access program, and is developing new applications for the system through collaborations with other academic institutions. Those expected to participate in the early access program include the Joint Genome Institute, Washington University, Baylor College of Medicine, the Genome Institute of Singapore, and the University of Kiel in Germany.

454 Life Sciences and the Human Genome Sequencing Center at Baylor have finished sequencing, verifying, and annotating the genome of James Watson. 454 handled the sequencing and Baylor verified and interpreted the data for the project, which took two months and cost less than $1 million.

A team of researchers from the UK and Canada sequenced the genome of Clostridium botulinum, the bacteria that produces botulinum neurotoxin and the causative agent of botulism. The genome contains a chromosome with 3.9 million base pairs and 3,650 predicted genes and a plasmid with 16,344 base pairs and 19 predicted genes.

Aryx Therapeutics will use GenomeQuest’s sequence search service in intellectual property research related to its retrometabolic drug studies. The software is used to evaluate the patentability and competitive landscape for gene sequences.

Patents

US Patent 7,223,536. Methods for detecting single nucleotide polymorphisms. Inventors: David Wright, Maria Milla, James Nadeau, and G. Terrance Walker. Assignee: Becton, Dickinson. Issued: May 29, 2007.
The patent covers “methods for detecting and identifying sequence variations in a nucleic acid sequence of interest using a detector primer,” according to the abstract. “The methods are particularly well suited for detecting and identifying single nucleotide differences between a target sequence of interest (e.g., a mutant allele of a gene) and a second nucleic acid sequence (e.g., a wild type allele for the same gene).”

US Patent 7,230,093. Method of sequencing by hybridization of oligonucleotide probes. Inventors: Radoje Drmanac and Radornir Crkvenjakov. Assignee: Callida Genomics. Issued: June 12, 2007.
According to the abstract, this patent covers a sequencing-by-hybridization method in which up to 100,000 probes “are used to determine sequence information by simultaneous hybridization with nucleic acid molecules bound to a filter.” It adds, “Sequence generation can be obtained for a large complex mammalian genome in a single process.”

Data Point

-5.6%
Shares in Helicos were down 5.6 percent, or $0.50, on May 24, the company’s first day of public trading. Shares were priced around $8.50. Helicos became the first pure-play next-gen sequencing company to be publicly traded.

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