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University of Chicago, Mayo, Sanger Institute, Wellcome Trust, ABI, Affy, The Guilford Genomic Medicine Project, NHGRI, NIH, Roche, Epigenomics, Large Scale Biology


University of Chicago Licenses PGx Test to Mayo

University of Chicago researchers licensed a pharmacogenomics test for colorectal cancer patients to the Mayo Clinic, the university said two weeks ago.

The UGT1A1 test determines which patients are likely to have an adverse reaction to Pfizer's Camptosar, a key component of the standard first-line treatment for advanced cancers of the colon and rectum.

Through this licensing agreement, the clinic's reference laboratory, Mayo Medical Laboratories, will provide the test to patients nationwide.

Mayo acquired an exclusive license from the university, as well as the right to sub-license the test.

Mayo recently sub-licensed the rights under the University of Chicago patent to Third Wave Technologies. While Third Wave received FDA approval for the genetic test in August, only patients enrolled in studies at the University of Chicago previously had access to it.

In June, the FDA relabeled Camptosar to include a warning that patients with a particular UGT1A1 genotype should receive a lower starting dose.

Sanger Institute Receives $590M from Wellcome Trust

The Wellcome Trust Sanger Institute has received a five-year award totaling £340 million ($590 million) from the Wellcome Trust biomedical research charity.

The funds will be used to continue the institute's research on cancer, malaria, and diabetes, including a Cancer Genome Project that focuses on identifying the majority of mutations involved in the development of breast, lung, and kidney cancer.

ABI Licenses Affy Microarray Patents for Gene Expression Analysis

Applied Biosystems has licensed "a number" of Affymetrix patents "related to the manufacture, sale, and use of microarrays for gene expression analysis," the companies said two weeks ago.

Applera, the parent company of Applied Biosystems, has taken a non-exclusive, worldwide license to the patents.

ABI said that it will use the licenses to expand its Expression Array system and to enable customers "to use that system for gene expression, research and development purposes."

The companies did not disclose further details of the licensing agreement.

Affymetrix Appearing on S&P Midcap 400 Index as of Dec. 30

Standard & Poor's has added Affymetrix to its S&P MidCap 400 Index as of Dec. 30.

Affy has joined Beckman Coulter and Invitrogen, the only other genomic tool vendors tracked by the Index.

The Index, launched in 1991, tracks a diverse group of medium-sized US companies, according to These companies have a market capitalization of between $2 billion and $10 billion, according to the service. said the MidCap 400 "is an important benchmark for many fund managers who invest in this segment" and it "contains solid firms with good track records that are simply not large enough to be included in the much larger S&P 500 index."

The Index's current constituents can be seen here.

Congressional Defense Spending Bill Contains $2.2M for NC Genomics Project

The US House of Representatives approved a defense spending bill last week that included $2.2 million for a genomic project in North Carolina, a Congressman from that state said last week.

The Guilford Genomic Medicine Project, a collaboration between UNC-Greensboro, Moses Cone Health System, and Duke University, will receive $2.2 million in funding, said Rep. Howard Coble, R-NC.

The project will genetically test Guilford County veterans to help develop personalized health care plans.

NHGRI Pledges $420M to Support Genome Sequencing Centers; Adoption of New Tech Encouraged to Reduce Costs

The National Human Genome Research Institute has allocated $130 million for fiscal year 2006 to renew its large-scale sequencing program, according to a request for applications published on the National Institutes of Health website.

NHGRI allocated up to $420 million in total costs, to be awarded over four years, the solicitation said. The institute expects to make three to five awards, for a maximum period of four years. The earliest anticipated start date is Nov. 1, 2006.

NHGRI is encouraging the adoption of next-generation sequencing technologies that it expects to reduce the cost of large-scale sequencing projects by five-fold or more over the next four years. The institute "recognizes that the renewal of its genomic sequencing program comes at a time when significant advance(s) in genomic sequencing technology can be anticipated," the RFA said. "In renewing the sequencing program, NHGRI intends to provide adequate funding to encourage sequencing centers to explore adoption of the new technologies. Therefore, the applicant should discuss the new sequencing technologies and should describe any plans s/he has for implementation of one or more of them."

The RFA said that improvements in sequencing technology "have allowed the NHGRI to decrease the amount of funding for the program in each of the last four years, from a high of over $180 million to its current FY 2006 level of $133 million, while more than tripling output over that time."

NHGRI said in the RFA that centers funded under the program will continue a number of comparative genomic sequencing projects that are generating data for annotating the human genome, "while an increasing fraction of the sequencing capacity will be directed to medical sequencing, which is expected to result in the identification of genomic changes implicated in heritable disease and the elucidation of the genetic changes associated with cancer."

The program will also focus on sequencing eukaryotic pathogens and "vectors of human disease," NHGRI said.

Letters of intent are due Jan. 11, and applications must be received by April 11, 2006.

More information can be found here.

NIH Pledges $7M for Genotyping of Diabetes and Diabetic Complications

Three NIH institutes have collectively allocated $3 million for fiscal year 2006 to fund diabetes research projects, according to a request for applications published on the National Institutes of Health website.

The National Heart, Lung, and Blood Institute; the National Institute of Allergy and Infectious Disease; and the National Institute of Diabetes and Digestive and Kidney Diseases intend to commit $3 million in fiscal year 2006 and $2 million each for 2007 and 2008. The organizations expect to make five to seven awards, for a maximum period of three years, the solicitation said. The earliest anticipated start date is Sept. 15, 2006.

Applicants should focus on a strategy for high-density genotyping of two existing DNA sample collections: Epidemiology of Diabetes and its Complications and Genetics of Kidneys in Diabetes.

No funding should be requested for whole-genome genotyping, as the genotyping costs for whole-genome analyses will be borne separately by the NIDDK, NIH said. Funds may be requested for "limited genotyping" in a candidate gene.

Genotyping data will be stored in an NIDDK repository and shared with the research community one year after it is generated, NIH said.

Letters of intent are due March 14, 2006 and applications must be received by April 12, 2006.

More information can be found here.

Without Roche, Epigenomics Completes Validation Study for Prostate Cancer Dx

Epigenomics will develop a DNA methylation test for prostate cancer on its own after erstwhile partner Roche Diagnostics decided to back out of their alliance, the company said this week.

Epigenomics has recently completed a successful a validation study for the test, the company said.

Epigenomics and Roche signed a three-year agreement in 2003 to develop molecular diagnostic and pharmacogenomic assays for colon, breast, and prostate cancer, as well as tests to predict response to anti-cancer drugs.

Berlin-based Epigenomics today said that Roche had discontinued the prostate cancer alliance and decided not to maintain its option for an exclusive license. The Swiss diagnostics giant will continue collaborating with Epigenomics for the remaining indications, according to an Epigenomics official.

The prostate cancer test uses DNA methylation markers to determine cancer aggressiveness, according to Epigenomics. The company said it had completed a study involving paraffin-embedded samples from 605 patients and that it had validated three of its biomarkers. If completed, such a test would be useful in helping physicians prescribe treatment to patients, Epigenomics said.

Predictive Diagnostics Closes Doors as Nasdaq Delists LSBC

Faced with delisting from the Nasdaq exchange, Large Scale Biology has shuttered its operations, including its proteomics subsidiary, Predictive Diagnostics, Pharmacogenomics Reporter sister publication GenomeWeb News has learned.

LSBC disclosed its plan in a filing with the US Securities Exchange Commission. Though the filing did not mention Predictive Diagnostics' fate, when GenomeWeb News called the company for details this week a recorded message said, "Effective December 23, 2005, Predictive Diagnostics, Inc. has ceased operations. Calls to this number will not be returned."

GenomeWeb News has reported LSBC's financial woes in the past. After its stock price plummeted to less than $1 per share in June, Nasdaq threatened to delist the company unless the share price went back up in 180 days.

According to the SEC filing, LSBC's stock ceased trading at the end of trading on Dec. 23.

Filed under

The Scan

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Lupus Heterogeneity Highlighted With Single-Cell Transcriptomes

Using single-cell RNA sequencing, researchers in Nature Communications tracked down immune and non-immune cell differences between discoid lupus erythematosus and systemic lupus erythematosus.

Rare Disease Clues Gleaned From Mobile Element Insertions in Exome Sequences

With an approach called MELT, researchers in the European Journal of Human Genetics uncovered mobile element insertions in exomes from 3,232 individuals with or without developmental or neurological abnormalities.

Team Tracks Down Potential Blood Plasma Markers Linked to Heart Failure in Atrial Fibrillation Patients

Researchers in BMC Genomics found 10 differentially expressed proteins or metabolites that marked atrial fibrillation with heart failure cases.