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Illumina, ABI Test Whole Genome Sequences

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In anticipation of large-scale human resequencing studies like the 1,000 Genomes Project, Illumina and Applied Biosystems have separately been testing how comprehensively, quickly, accurately, and inexpensively their respective next-gen sequencing platforms can sequence a human genome.

At the Advances in Genome Biology and Technology conference in Marco Island in February, researchers from both companies presented preliminary data on the analysis of the same individual, a HapMap sample of African origin. Their results will be compared with those generated by other methods in order to determine how well the two platforms fare in finding SNPs and structural variants.

Both companies have been sequencing a HapMap sample, an anonymous African Yoruban man from Ibadan, Nigeria.

Illumina's and ABI's efforts are not the only next-generation whole-genome human sequencing projects: Last May, researchers from 454 Life Sciences and Baylor College of Medicine said they sequenced the genome of Jim Watson using 454's platform, a study that has yet to be published.

And last fall, scientists at the Beijing Genomics Institute said they used Illumina's platform to generate a first draft genome from a Chinese researcher, a study they intend to publish.

For six weeks, Illumina devoted eight sequencing machines — half the capacity of the former Solexa site in Little Chesterford, UK — to generate about 77 gigabases of data from 27 paired-end runs, according to David Bentley, the company's chief scientist. In total, the sequence, which represents approximately 20-fold coverage, covers about 92 percent of the human reference genome.

Applied Biosystems has not yet generated as much sequencing data as Illumina on the African HapMap sample. So far, ABI has analyzed 2.5 paired-end runs, adding up to roughly 21 gigabases of data, or 7-fold sequence coverage. The company plans to increase the sequence coverage eventually to 10- to 12-fold.

— Julia Karow

Sequencing Notes

Microchip Biotechnologies teamed with Mostafa Ronaghi at Stanford University to develop a front-end microfluidic-based sample prep system to speed up pyrosequencing projects.

Helicos Biosciences announced the sale and shipment of its first single-molecule sequencing instrument to genomic service provider Expression Analysis.

Scientists at the University of Washington and Washington State University are heading up an international effort to sequence the Rosaceae family genomes, in particular the apple.

The Stowers Institute's Chris Seidel started a Google group about the Illumina Genome Analyzer to give users a forum to exchange information.

Datapoint

95 percent
Washington University scientists have a draft sequence of the corn genome with 95 percent of its 2 gb genome.

Funded Grants

$210,495/FY2007
New Method for Direct Electronic Sequencing of DNA
Grantee: Andrew Hibbs, Electronic Biosciences
Began: Sep. 19, 2007; Ends: Aug. 31, 2008
The National Human Genome Research Institute funded Hibbs to work on a new method to sequence a single DNA molecule via direct electronic measurement of individual bases as they flow through a protein pore. The company works with Henry White at the University of Utah and David Deamer at the University of California, Santa Cruz.

$136,286/FY2007
Integrated Assembly Software for Sanger and Next Generation Sequence Technologies
Grantee: Timothy Durfee, DNAStar
Began: Sep. 1, 2007; Ends: Feb. 29, 2008
This project aims to develop and evaluate prototype software approaches targeted at the tremendous volume of data generated by next-gen sequencing platforms. According to the grant abstract, "This will require developing new algorithms that take advantage of the abundant data generated to overcome bottlenecks that have previously limited the accuracy and completeness of assemblies."

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