When Agencourt Bioscience won the sequencing contract for NIH’s Mammalian Gene Collection Project in January, there were some sour grapes among would-be competitors. Incyte Genomics had relinquished the contract when it shut down its contract sequencing facility last fall, and, according to grumblings overheard at a genomics meeting in Marco Island, it seems that the job was reassigned to Agencourt before some in the industry could blink.
As Agencourt hadn’t even been born yet back when bidding for the project originally took place, some were surprised to see the contract handed over to the company. But Agencourt genomic services product manager Joel Malek, formerly of TIGR’s microbial sequencing team, says Agencourt got a special invitation to apply for the job. “We had been advertising and that’s how [they] found us. We did not necessarily pursue an announcement.”
Still, it seems Agencourt won the bid fair and square: “We went through the typical bidding process … and the combination of our price, quality, and throughput, which is critical to this project, made us the most attractive bidder.”
Using an untold number of ABI 3700 sequencing instruments and Solid Phase Reversible Immobilization, a DNA-prep method developed by 28-year-old Agencourt co-chief scientist Kevin McKernan while he was in the Whitehead Institute’s technology development group, the company says it can process more than 20 million Phred 20 bases a day with average pass rates in excess of 85 percent. SPRI, which uses microscopic magnetic beads and binding reagents to isolate nucleic acids from biomolecular contaminants, was used at Whitehead, JGI, and Wash U. to purify about one-third of the DNA sequenced by the Human Genome Project, Malek says.
Now, Agencourt will employ the technology to help the MGC Project identify and sequence a representative full ORF clone for each human and mouse gene. “Our part of the contract is to generate sequences from ESTs so they can determine which have the full-length gene in them,” Malek explains. As soon as Agencourt determines which ones are full-length, they’re handed off to one of the groups assigned to sequence the full-length genes: Eric Green’s lab at the NIH, Anup Madan’s lab at the Institute for Systems Biology, Marco Marra’s British Columbia Genome Sequence Center, Richard Myers’ group at Stanford, or Richard Gibbs’ lab at Baylor College of Medicine.
For the one-year contract, Agencourt will be paid for each EST it generates. Malek won’t say what the amount is, but he expects to sequence 500,000 of them. To date, NIH has reportedly invested some $35 million on the Mammalian Gene Collection Project.
— Adrienne J. Burke