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Improved analysis of thousands of proteins in human plasma is poised to lead to the identification of diagnostic biomarkers, or altered patterns of proteins, for many diseases and health conditions. The development of new diagnostic tests of those plasma proteins is the primary goal of the Human Proteome Organization’s (HUPO’s) Human Plasma Proteome Project as well as many companies. However, HUPO leaders note that many technical hurdles persist and progress could be slowed without the adoption of rigorous standards for analyzing plasma proteins. “There is a big gulf between the analytical groups and the applications groups,” says Leigh Anderson, founder and CEO of the Plasma Proteome Institute. Proteomics researchers are only beginning to recognize that “the necessary technology is really not yet there to do good quantification over a wide enough dynamic range to develop diagnostics,” he says. The plasma proteome is hundreds of times larger than the ~30,000-gene human genome, because of splice variants, posttranslational modifications, and cleavage products. There could be >10 million peptides in a single vial of plasma or serum. In the most successful demonstration of its kind, a group led by Richard D. Smith, a scientist at the Pacific Northwest National Laboratory, recently identified ~4000 plasma proteins using FT ion cyclotron resonance MS. The method, which was described at the annual meeting of the American Association for the Advancement of Science in February, can detect low-abundance proteins, many of which would be little more than background noise with other MS methods. Many other groups are analyzing plasma with a protein-chip array SELDI/TOF MS system. SELDI is a surface-enhanced affinity capture technique that uses specific probe surfaces. A team led by researchers at the National Cancer Institute (NCI) and the U.S. Food and Drug Administration (FDA) used SELDI/TOF MS and a genetic algorithm to correctly identify the serum of 50 ovarian cancer patients. In all cases, the MS analysis distinguished the sera of ovarian cancer patients from healthy women or those
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with non-malignant tumors (Lancet 2002, 359, 572–577). “Unequivocally, we are confident in that data,” says Emanuel Petricoin, co-director of NCI’s Clinical Proteomics Program. However, the ability to find a pattern that is reproducible across laboratories, days, and machines is still in question. Correlogic Systems, a Marylandbased company, has developed an advanced version of Petricoin’s test as a commercial platform. Correlogic has licensed the OvaCheck test to Quest Diagnostics and Laboratory Corp. of America (LabCorp). Rather than provide it to healthcare companies, Quest and LabCorp were planning to perform the test in a centralized lab, a so-called home-brew arrangement that does not require FDA approval. VETERINARY DIAGNOSTIC LABORATORY, UNIVERSITY OF ILLINOIS AT URBANA–CHAMPAIGN
Growing plasma proteome sets stage for new diagnostics
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Human plasma proteome. Patterns of peptides in human plasma may reflect virtually every disease state.
At the same time, Keith Baggerly, an assistant professor of biostatistics and applied mathematics at the University of Texas M. D. Anderson Cancer Center, says the Petricoin group’s data are flawed by background noise at 1000 m/z and below and by procedural bias (Bioinformatics 2004, doi: 10.1093/bioinformatics/btg484). “Looking at the electronic noise region of the spectra, they are saying that they can separate can-
cers from normals, which suggests to us there is a systematic bias in how the cancers and normals were processed,” says Baggerly. “Based on the data that they have posted on the Web, we do not believe they have a test that works.” Although Petricoin’s group has improved the pattern recognition test, criticism has prompted Quest and LabCorp to hold off on marketing it. “We are undertaking meticulous and rigorous validation of the test,” says Laurie Park, vice president of investor relations at Quest. “Obviously, when you are running the test in a high-throughput environment, you want to make sure the test is reproducible.” A gynecological oncologist not connected to the company is leading the evaluation of the test. Meanwhile, Petricoin and his partner at NCI’s Clinical Proteomics Program, Lance Liotta, argue that Baggerly’s analysis is itself flawed. “They are not familiar with the physics of mass spectrometry,” says Liotta. A group led by James Glimm, a statistical expert at Brookhaven National Laboratory, analyzed the same data as the Texas group. However, Glimm’s group reported that 18 plasma-peptide biomarkers, most of which were
