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2nd-Gen Platforms Can Do Targeted Sequencing


As second-generation sequencers from Roche/454, Illumina, and Life Technologies compete for targeted sequencing market share, researchers at the Scripps Research Institute and the J. Craig Venter Institute recently published an evaluation of the three platforms for this application.

The two teams, which used versions of the platforms that have since been updated, found they each suffered from non-uniform coverage and inherent systematic errors, making it difficult to use data from different platforms for the same study.

The research, which appeared in Genome Biology, began in October 2007 when the team sought to compare the ability of the three platforms to perform targeted sequencing in populations.

At the time, "it was clear from the whole-genome association studies that were coming out that there were going to be intervals in the genome associated with traits, and that deeper sequencing in populations was going to be required in order to try to identify the functional, or causative, variants underlying those associations," says senior author Kelly Frazer, director of genomic biology at the Scripps Genomic Medicine program, a collaboration between Scripps Health and the Scripps Research Institute.

In their study, the researchers used the Roche/454 GS FLX, Illumina Genome Analyzer I, and Applied Biosystems SOLiD 1 platforms to sequence a 260-kilobase interval in four individuals with unpaired reads.
The work was split between the Scripps Institute, which prepared the DNA for the entire study by long-range PCR and performed the sequencing on its Illumina Genome Analyzer, and the Venter Institute, which sequenced the amplified DNA on its 454 machine and sent it to ABI for SOLiD sequencing.

The JCVI also had Sanger sequencing data available from a previous study that covered 88 kilobases within the 260-kilobase region, against which the researchers benchmarked their second-generation sequence data. The Scripps researchers analyzed the alignments and base calls from all three platforms.

Julia Karow

Sequencing Notes

Lots of news for Helicos BioSciences recently: the company recorded its first product revenue — $36,000 — during the last quarter of 2008. It also is down to 71 employees from 2007's 114. Separately, Helicos has appealed a European Patent Office decision to maintain, in an amended form, a sequencing-related patent owned by Illumina, which Helicos first opposed in 2006.

Pacific Biosciences has been named the senior party in an ongoing US Patent and Trademark Office interference, involving a patent held by Life Technologies and a patent application filed by PacBio that both cover single-molecule sequencing technology. The USPTO's interference shows that the two companies are claiming ownership to related intellectual property.


GeneDx is offering its second diagnostic based on a next-gen sequencer. This one is for dilated-cardiomyopathy.

Funded Grants

$3,250,927/FY 2008
The San Diego Epigenome Center
Grantee: Bing Ren, Ludwig Institute for Cancer Research
Began: Sep. 29, 2008; Ends: Jun. 30, 2013

Ren and his colleagues will use this NIEHS funding to establish a center for epigenomics with a focus on human embryonic stem cells as well as hESC-derived early embryonic cell lineages. Ren's team will use high-throughput sequencing and other technologies to study "DNA methylation and chromatin modifications throughout the genome," the abstract says.

$118,317/FY 2008
A Novel Method for the Detection and Analysis of CpG Methylation Sites
Grantee: Mark Chee, Prognosys Biosciences
Began: Sep. 1, 2008; Ends: Aug. 31, 2009

NCI awarded this funding to Chee and Prognosys to develop "improved reagents that will allow for the efficient and accurate identification of 5-methyl cytosine residues in DNA. These reagents will enable the identification of 5meC sites with single-nucleotide precision and are compatible with a variety of high-throughput methods," according to the abstract.