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Stanford Team Sequences Human Genome Using Helicos Technology

NEW YORK (GenomeWeb News) – Scientists from Stanford University reported online today in Nature Biotechnology that they have sequenced the genome of a Caucasian man using a Helicos Biosciences Heliscope single molecule sequencer.

Stanford University bioengineer and Helicos Co-founder Stephen Quake, who now chairs the company's scientific advisory board, sequenced his own genome — using a single Heliscope machine and four data collection runs — with help from two members of his lab: graduate student Dmitry Pushkarev and research technical manager Norma Neff.

The researchers reportedly generated billions of Heliscope sequence reads covering some 90 percent of the human reference genome at 28 times coverage. So far they have identified some 2.8 million SNPs and 752 copy number variations in the genome.

"This is the first demonstration that you don't need a genome center to sequence a human genome," Quake said in a statement. "This can now be done in one lab, with one machine, at a modest cost."

The team spent about four weeks and $48,000 on reagents to sequence the genome, co-author Neff told GenomeWeb Daily News.

She said the main advantage of the Heliscope over other sequencing platforms is the high output and ease of library preparation, which does not require DNA amplification or ligation prior to sequencing. "If I had three [Heliscopes] I could do a genome a week," Neff said.

Quake first mentioned the project in a guest blog for The New York Times in early March. GWDN's sister publication In Sequence carried a story on the sequencing project shortly thereafter.

But this is not the first application of Helicos' technology. Last April, researchers from Stanford, Helicos, and Ohio University reported that they had sequenced the roughly 7,000 base-pair genome of the M13 virus. And earlier this year, investigators from the Broad Institute reported at the Biology of Genomes meeting that they used the Helicos technology to find origins of replication in fission yeast genomes.

For the latest paper, the researchers first calibrated the performance and error rate for the Heliscope, a commercially available single molecule sequencing platform, by re-sequencing the Staphylococcus aureus genome.

They then tackled Quake's genome, generating billions of reads that varied in length from 24 to 70 bases (the average read length was 32 bases, the team reported).

Because a small percentage of nucleotides remain unlabelled, Neff explained, there are some "dark" nucleotides that appear as deletions during the sequencing process. The team used Helicos' software to assist in base calling and also corrected deletion errors by increasing their coverage of the genome, she said.

After mapping these reads to the human reference genome with IndexDP, the researchers found that their reads covered 2.5 billion bases, or 90 percent, of the reference.

To aid in SNP calling, co-author Pushkarev came up with an algorithm, dubbed UMKA. The algorithm predicted 2,805,471 SNPs in the genome. About 76 percent of these were also found in dbSNP, the researchers noted. When they compared the SNPs they had identified with those detected using SNP genotyping with the Illumina Human610-Quad SNP BeadArray, the researchers found 99.8 percent concordance between the two approaches. In addition, the researchers verified 100 of the SNPs by Sanger sequencing.

The team also found 752 CNVs in the genome — more than half of which are also present in the Database of Genomic Variants.

By sifting through his own genome, Quake has already found genetic variants thought to be linked to everything from a rare heart disorder to statin drug response. Others at Stanford are also examining Quake and his genome in an effort to find links between his genetic profile and his traits and family history. "Some of the doctors are starting to poke and prod me to see how they can couple my genome with medicine," he said in a statement.

The authors noted that there are still limitations to this and other sequencing technologies — including incomplete genome coverage and a lack of complete data on SNPs and structural variation.

Still, they argued, the approach they used lets researchers begin assessing sequence and CNV information "in virtually any lab using a single commercial instrument" — an advance that they say will "democratize access to the fruits of the genome revolution and may enable rapid and widespread adoption of individual genome sequencing in various scientific and medical contexts."

"Obviously this is sort of a landmark publication for Steve Quake and, because of that, it's also a landmark publication for Helicos," Patrice Milos, vice president and chief scientific officer for Helicos, told GenomeWeb Daily News. "We're really excited and thrilled."

Milos said Helicos has been working to create a machine that is easy to run and relies on simple upfront sample preparation — features that should make it feasible for a small group of individuals to do genome sequencing in independent labs.

"It really is exciting to think of how fast the technology has advanced," Milos said.

Those involved predict that the current paper represents the first of many genomes to be sequenced with the Heliscope. "We're calling Steve 'Patient Zero'," Neff said, noting that the genome may come in handy as a comparison tool for future sequencing projects using the Helicos technology. She said the team plans to use the Heliscope to sequence cancer genomes as part of a collaboration with Stanford's Stem Cell Biology and Regenerative Medicine Institute.

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