In late March, the National Center for Genome Resources and the Mental Illness and Neuroscience Discovery Institute announced a partnership through which they would apply their technologies to tackling what they call the Schizophrenia Genome Project.
NCGR, a nonprofit research institute which has been performing genome sequence analysis since 1993, is a familiar member of the genomics community. This project represents something of a departure from the usual modus operandi of the group, which has traditionally offered sequence analysis to scientists rather than performing its own sequencing projects. But Stephen Kingsmore, president of NCGR, says this is an obvious next step for the institute, which is getting its feet wet by sequencing a pathogen with 454 technology. “Our core expertise is in genome sequence analysis,” he says. “The only difference here is we’ve got a project that we’re going to have to mine ourselves.”
That project will entail working closely with the MIND Institute, which has assembled a database of about 250 people who have schizophrenia. MIND uses that database in conjunction with high-resolution MRI technology and has “actually [been] able to image particular metabolic pathways in the brains of folks with schizophrenia,” Kingsmore says. He envisions using the database to stratify individuals based on any number of phenotypes and then performing genomic studies to try to find links. “If you start to combine a genetic approach with imaging technologies and very good clinical information as well, you could make schizophrenia a tractable disease,” he adds.
Next up: a pilot project on two or three people to determine whether sequencing the genome or the transcriptome will be the more promising approach, Kingsmore says. Then there’s the matter of funding for what will be an expensive, multi-year program. Kingsmore doesn’t anticipate trouble, saying that various funding sources will be considered. NCGR will apply for grants, but he says that his team has already been approached by pharmas and diagnostic companies that may be interested in contributing to the program’s coffers.
— Meredith Salisbury
Solexa reported an increased loss for the fourth quarter of 2005, despite solid revenue growth. Revenue increased from $23,000 in the last quarter of 2004 to $1.3 million for 2005’s Q4, while R&D expenses rose from $2.3 million to $4.9 million. Meanwhile, the company plans to add sales, marketing, and manufacturing staff to support the commercial release of its sequencing system.
NHGRI announced the latest plans for its large-scale sequencing network. The project with the highest priority will be to analyze 48 human DNA samples for structural variations larger than those found by the HapMap team. Second on the list is a plan to add high-density genome sequencing to the existing drafts of rhesus macaque, marmoset, and orangutan. Finally, the centers will add eight new mammals at low-density draft coverage. Those eight will be chosen from among these organisms: dolphin, elephant shrew, flying lemur, mouse lemur, horse, llama, mole, pika, kangaroo rat, and tarsier.
New Zealand’s HortResearch will release 150,000 ESTs from the apple genome into GenBank.
The Potato Genome Sequencing Consortium will begin at the very beginning: the Dutch government will fund €3 million for researchers to sequence the first potato chromosome. Scientists at consortium institutions, including the Netherlands Genomics Initiative and Wageningen University and Research Centre, hope to complete the starchy genome by 2010.
US Patent 7,016,788. Methods for classifying nucleic acids and polypeptides. Inventors: Joel Bader, Yi Liu, and Darius Dziuda. Assignee: CuraGen. Issued: March 21, 2006.
This invention includes “novel methods to identify, classify, quantify, and compare nucleic acids and polypeptides,” according to the abstract. More specifically, the methods provide “statistical scores for band-to-gene look-up from differential display experiments or fragment-based gene expression profiling. … [These] can serve to establish a cut-off low score such that genes with scores below the cut-off are assumed not to be expressed.”
US Patent 7,013,221. Iterative probe design and detailed expression profiling with flexible in situ synthesis arrays. Inventors: Stephen Friend, Roland Stoughton, Peter Linsley, and Julja Burchard. Assignee: Rosetta Inpharmatics. Issued: March 14, 2006.
According to the abstract, this patent covers techniques “that are useful for detecting and reporting a plurality of different target polynucleotide sequences in a sample, such as polynucleotides corresponding to a plurality of different genes expressed by a cell or cells.”
Financing round recently closed by Helicos BioSciences to help develop its single-molecule DNA sequencing technology. The funding brings to $67 million the total amount Helicos has raised since its start in 2004.