By Vicki Brower

Special To BioWorld Today

Sequenom Inc. scientists have reported that an application of the company's DNA MassArray technology, BioMassPROBE, was able to detect with greater exactness than gel- or hybridization-based methods apolipoprotein E (Apo E) polymorphisms linked to Alzheimer's disease and atherosclerosis.

The study, published in the October issue of the European Journal of Clinical Chemistry and Clinical Biochemistry, provided a more definitive result for diagnostic DNA analysis — the exact mass value — of DNA from 100 unrelated individuals who had been screened for Apo E genotypes. Another advantage to Sequenom's method is that it can be automated, unlike gel-based or fluorescent methods.

The DNA MassArray uses high fidelity enzymatic methods and a proprietary SpectroChip functional array, which allows high-throughput via parallel processing and multiplexing. Mass spectrometry provides molecular weight information rapidly.

Using PCR, the segment of the gene between codons 112 and 158 was amplified and analyzed using Sequenom's BiomassPROBE, and was found to be in agreement with those found using conventional methods, such as restriction enzyme digestion.

In addition, results were easily interpreted and not at all ambiguous, as they are based on the objective criterion of molecular weight of nucleic acid fragments, said Hubert Koster, founder, president and CEO of the three-year-old company.

Diagnosis, Functional Genomics Key Applications

"BiomassPROBE is a highly reproducible assay for the analysis of substitution, deletion and insertion mutations in genes," said Koster. "Gel- or hybridization-based DNA analysis methodologies rely on subjective interpretations or sometimes difficult-to-interpret radioactive or fluorescent signals, and are time-consuming and hard to automate," he said.

"In contrast, BiomassPROBE provides the exact mass values of each of the diagnostic products analyzed, providing empirical data on which to make a diagnosis."

Sequenom is the result of a collaboration between Koster, a biochemist and molecular biologist formerly of the University of Hamburg in Germany, Charles Cantor, a biophysicist at Boston University, and Robert Cotter, a pharmacologist at Johns Hopkins University, in Baltimore.

Sequenom's technologies focus on high definition DNA analysis tools for industrial and life science applications. Its proprietary position is based on the analysis of nucleic acids from oligonucleotide arrays by mass spectrometry, which can be applied to drug development, medical diagnostics, forensics, agricultural biotechnology and environmental testing.

Its technologies, Koster said, will play an important role in the evolution of functional genomics and DNA diagnostics. It is on the clinical development side where Sequenom sees its technologies making the most impact in lowering development costs.

Diagnosis and disease monitoring also are areas its toolbox is bound to influence, Koster said. The company uses proprietary molecular biology, 2-D array formats — its SpectroChip — and proprietary surface chemistry to generate application tools including BiomassSIZE, BiomassPROBE, BiomassSCAN, BiomassSEQUENCE and BiomassINDEX.

These methodologies comprise molecular genetic procedures specially designed and optimized for applications with Biomass Spectrometry for more accuracy and cost effectiveness.

BiomassSIZE is a highly specific method for identifying amplified DNA products and can be used for accurate and direct detection of viral and other infectious disease particles such as hepatitis B and HIV. It can efficiently and accurately characterize the length as well as the authenticity of an amplified DNA fragment.

BiomassPROBE is a highly reproducible assay for the analysis of substitution, deletion and insertion mutations and for microsatellite sizing. This technology can impact the discovery process at several points, Koster said, such as identifying genomic localization of disease-candidate genes and genetic profiling for clinical trials, where it can identify a specific mutation or polymorphism.

BiomassSCAN compares molecular weights of restriction fragments of a diseased patient with those of healthy persons, revealing the localized region of a mutation to within about 20 bases. It is very rapid and Sequenom believes this will reduce the effort of diagnostic DNA sequencing by at least two orders of magnitude.

BiomassSEQUENCE is an optimized method of gel-based DNA sequencing employing mass spectrometry. It is a tool for clinical DNA analysis for cancer genetics to detect new mutations within disease-causing genes or to type mutations in highly variable gene regions. In drug development, it also can be used in candidate gene validation and genetic profiling of patients.

Like BiomassPROBE, BiomassSEQUENCE can also be applied in the areas of identity testing, plant engineering, and pollutant monitoring.

BiomassINDEX identifies differentially expressed genes and monitors gene expression. Gene expression profiling of cancer and other disorders can help in monitoring the disease progress and potential treatments, including monitoring genes which are differentially expressed due to environmental changes.

Company Seeking Partners To Market Products

Sequenom is seeking partnerships with major pharmaceutical and genomics companies to provide services, technology and tools based on DNA MassArray technology. In the future, it plans to implement its own functional genomics-based drug discovery and development programs. It also plans to offer DNA diagnostic services via licensing agreements involving its SpectroChip.

To date, the company has raised $12 million: $8 million in equity venture capital investments from the U.S., Europe and Israel; four grants worth $1.6 million; and $2.6 million in long-term loans.

At the beginning of 1995, Sequenom raised $5 million, and in May 1997, it raised an additional $3.5 million. Investors include Boston's Community Technology Fund, Amsterdam's Alpinvest, Munich and Boston's TVM fund, and Israel's Star Venture Fund. *

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