A Diagnostics & Imaging Week

Illumina (San Diego) reported a collaboration with the Institute of Translational Medicine and Therapeutics (ITMAT) at the University of Pennsylvania (Philadelphia), the Broad Institute, and the National Heart, Lung, and Blood Institute's (NHLBI, Bethesda, Maryland) Candidate-gene Association REsource Consortium (CARe) to develop a customized chip for vascular disease.

Called the IBC (ITMAT, Broad, CARe) chip, this array will be developed to analyze more than 55,000 single-nucleotide polymorphisms (SNPs) in candidate genes selected for cardiovascular and other associated phenotypes. Using Illumina's iSelect Custom Genotyping BeadChip, researchers will assess the genetic diversity within pathways of about 2,100 genes believed to underpin primary and secondary vascular disease processes, such as blood pressure, myocardial infarction, heart failure, stroke, insulin resistance, metabolic disorders, dyslipidemia (changes in lipid levels in the blood), and inflammation. At the study's completion, more than 120,000 samples from large population studies and clinical trials will be analyzed for genetic links to vascular disease.

The collaboration, led by the University of Pennsylvania, the Broad Institute and the CARe Consortium is the first major cardiovascular initiative to use the iSelect Infinium Custom Genotyping array. iSelect custom panels enable researchers to focus on specific disease-related or pathway-related SNPs. The multi-sample BeadChip format increases throughput and shortens sample processing time.

"The University of Pennsylvania's interest in customizing this genotyping panel to tackle vascular-disease research underscores the creative ways the research community is working with Illumina to unravel the complexities of human disease," said Jay Flatley, president/CEO of Illumina. "Our whole-genome genotyping technology continues to raise industry standards by delivering unparalleled data quality, format and content flexibility, and cost-effectiveness. This is helping researchers accelerate discoveries that will help us better understand, cure, and ultimately prevent disease."

Illumina is a developer of life-science tools and integrated systems for the large-scale analysis of genetic variation and biological function.

In other agreements:

• Exact Sciences (Marlborough, Massachusetts) reported that it has signed a letter of intent with Laboratory Corporation of America Holdings (LabCorp; Burlington, North Carolina) to further strengthen and expand their relationship related to Exact's stool-based DNA technologies for colorectal cancer (CRC) screening.

Specific provisions of the letter of intent preserve the economic value of the prior relationship, including all royalties on PreGen-Plus sales as well as $40 million of existing milestone payments that Exact may receive from LabCorp. The letter of intent also provides for an additional $2.5 million milestone payment related to the inclusion of sDNA testing in the updated CRC screening guidelines, Medicare reimbursement and specified increases in sales of PreGen-Plus. Exact and LabCorp remain committed to the launch of Version 2 of Exact's stool-based DNA technology in the first half of 2008. This improved version demonstrated 88% sensitivity for detecting colorectal cancer in a recent multi-center study.

Current operating plans, which assume Exact's timely optimization and validation of its Version 2 technology as well as the intended relocation to a smaller facility, should allow further decreases in expenses beyond the anticipated marketing and sales reductions. Going forward, Exact said it intends to direct its resources and energies on the following: Pursuing inclusion of sDNA in the updated CRC screening guidelines; obtaining Medicare coverage for sDNA technology; obtaining and broadly exploiting the value of Exact's CRC technology and intellectual property

Exact Sciences uses applied genomics to develop screening technologies for use in the detection of cancer.

LabCorp takes part in geonomic testing.

• Affymetrix (Santa Clara, California) and Partners HealthCare (Boston) reported that they have extended their translation research collaboration with a new contract array manufacturing (CAM) supply agreement, enabling Partners researchers to transform recent microarray discoveries into fully validated, laboratory-developed molecular diagnostic tests. The array-based tests will help physicians better diagnose and tailor treatments for individual patients, the companies said.

Affymetrix will create custom microarrays based on the recent discovery data from Partners researchers. The arrays will be used to produce molecular diagnostic tests, which will then be validated and implemented in Partners HealthCare's CLIA (Clinical Laboratory Improvement Amendments)-certified environments. The team at Partners will begin focusing on array-based tests for hypertrophic cardiomyopathy (HCM) and will explore many indications in a large number of diseases.

The latest agreement builds on the success of the parties' translational research collaboration. For the past year, researchers at Harvard Medical School (Boston), Partners HealthCare and HPCGG have been using the Affymetrix technology to identify genetic sequences and signatures associated with a number of complex diseases. The clinically relevant data will now be used to develop the molecular diagnostic tests.

Affymetrix' GeneChip microarray platform offers a number of unique benefits and advantages for developing and implementing molecular diagnostic tests.