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Joseph Washburn, U. of Michigan Comprehensive Cancer Center


At A Glance

Joseph Washburn, Supervisor, University of Michigan Comprehensive Cancer Center (UMCCC) DNA microarray facility BA in cell and molecular biology, University of Michigan.

What role do microarrays play at the cancer center?

Our facility is a core laboratory for the cancer center. The cancer center members, who are pretty much scattered throughout the University of Michigan, have both [cDNA] microarrays and Affymetrix services available to them. Most of [them] are doing basic science research. In a recent study, an investigator was using arrays to determine genes differentially expressed under a specific chemo-preventive drug in cell lines. [That drug is] ultimately going to be used pre- and post-treatment in human subjects. We also have investigators … working on early cancer events by using a variety of stem cells as their basis. Others take tissues obtained after biopsy to evaluate the gene expression effects pre- and post-drug or radiation treatments. Lastly, other typical investigators look at cancers after they have been removed from patients and correlate gene expression with clinical outcomes.

What types of microarrays do you use?

Affymetrix is one type, …the most ubiquitous is of course the U133A. For the [cDNA] microarray world, we have our [human] cancer [array], it has got 4,135 genes related to cancer. We also have a 5,000-gene array, [which] we call a biodiscovery array. Both the cancer array and the 5K discovery array were derived from ResGen cDNA clones. [Several institutions] found that up to 30 percent of the clones in that library may or may not be what ResGen says they are, [so] we tell people that upfront. We have a 5K mouse array as well, which is another clone set from ResGen. Pretty much everything else that we do is custom. [Users specify genes] and we locate the clones and put them on the array. [Or] they are not bringing any specific information about which genes they want [in which case] we do our best to identify those genes involved [and put them on the array.] Most people will do simple experiments; they will use our stock arrays. If they are doing gene discovery, we push the model of using Affymetrix, where you are looking at potentially 45,000 different probes for genes and trying to locate the few that are changed in your model, …and then we can subarray which genes are of interest onto a [cDNA] microarray, and you can do much larger experiments, such as time courses [or] drug concentrations. On a percentage basis, I would say probably 75 percent of the users use our stock arrays, probably about 20 percent use the Affymetrix, and about five percent then go on to do customs.

How long have you been offering Affymetrix services?

We started doing service work [in] February 2002. For cancer center members there is a discounted price, for University of Michigan members there is a direct cost-price, and then for everybody else, there is a direct-plus-indirect cost associated with the processing of Affymetrix GeneChips. We also sell our stock array to anybody; we even do custom arrays [for outsiders], but they need to pay for both direct and indirect costs. Our business is cancer center members, probably five percent is the rest of the university community, and probably five percent outside the university.

What''''''''s been the response to your Affymetrix service?

It''''''''s been quite positive. Many people like the robustness of the Affy process. From a reproducibility standpoint, the Affy system works quite well, and a lot of investigators like that. From the reliability of the data standpoint, I haven''''''''t yet heard negative feedback, so I usually consider that to be a good sign.

What is the biggest challenge you face?

The biggest challenge for the microarray world is reproducibility. The way we have evaluated it is to standardize as much of the entire process as possible. That starts from the production of the microarrays all the way through [to] the end users and the protocols they use.

Are you planning to add new technologies?

It depends. Basically it will be a cost issue. If we can achieve the ability to do additional technologies with the existing equipment or with a minimal investment in new equipment, we are definitely going to be getting into [them]. If it requires a huge capital infusion, I would suspect that eventually we would get into it as the investigators within the cancer center demand it. Being a core lab and not a primary research lab, we need to take the path more traveled. Probably the next technology we will adopt is going to be spotting proteins or spotting antibodies.

Lynx, Rosetta, Fujirebio Diagnostics, Randox join forces, UK''''''''s LGC, Zyomyx, Amersham

Lynx posts revenue Drop, plans MPSS database, seeks proteomics partner

Despite lighter R&D spending and a workforce reduction of 30 percent, Lynx Therapeutics reported last week that its second-quarter net loss continued to widen as revenues fell sharply. Total revenue for the period ended June 30 dropped to $2.9 million from $4.4 million one year ago. Atop that the company spent about $5.4 million on R&D, which is down from the $5.9 million it spent in the same period last year. Lynx''''''''s net loss in the current second quarter swelled to $5.5 million, or $0.23 per share, from $4.6 million, or $0.37 per share, year over year. The company stressed that excluding a $500,000 charge for the staff reductions made in April would have reduced the net loss from operations to $4.4 million. The reduction in per-share net loss was the result of some 11.4 million new shares hitting the market in the past year. The company said it had roughly $18 million in cash, cash equivalents, and short-term investments as of June 30. But Lynx is looking for new revenue streams: Kevin Corcoran, the company''''''''s CEO, said that "a prominent IT company has expressed interest in sponsoring construction of an MPSS [Massively Parallel Signature Sequencing] transcriptome database," which it wants to market to customers, and Lynx would supply it with MPSS data content. The company is also currently looking for a partner to commercialize its ProteinProfiler protein separation technology and has attracted interest "from many of the key players in bioinstrumentation," which are evaluating the technology at the moment, Corcoran said. Lynx also announced a new MPSS customer service agreement last week, with Cue Therapeutics, a Salt Lake City-based stem cell company.

Report: Rosetta Plans Expansion

Rosetta Inpharmatics has plans to expand. According to The Seattle Times, the Merck subsidiary is hoping to move into 133,000 square feet at South Lake Union in early 2004, and to boost the number of employees from 230 to 300 by the end of 2005.

Fujirebio Diagnostics and Randox join forces

Fujirebio Diagnostics of Malvern, Pa., and diagnostics company Randox of Crumlin, UK, plan to co-develop cancer diagnostics assays using Fujirebio''''''''s proprietary tumor marker antibodies and Randox''''''''s patented Biochip Array technology. Randox will pay Fujirebio Diagnostics based on future product sales.

Randox is the largest manufacturer of clinical chemistry diagnostic reagents in the UK. The company makes antibody and antigen microarrays for diagnostics, and is developing ones with sandwich immunoassays for thyroid hormones, fertility hormones, allergen-specific IgE''''''''s, antibiotic drug residues, and drugs of abuse, cardiac markers, and tumor markers. The company has also made a cytokine and growth factors chip.

UK''''''''s LGC Gets £2M to Develop Biotech Tools

The analytical laboratory LGC of Teddington, UK, won more than £2 million ($3.12 million) in eight government contracts to develop microarray technology, mass spectrometry methods, and other research tools, in collaboration with other companies and academic institutions. Under the larger of two microarray contracts, LGC will investigate the performance and comparability of microarrays for gene expression. The second contract aims to develop protein microarrays. The UK Department of Trade and Industry granted these contracts under its Measurements for Biology program, which is designed to improve measurement techniques and standardization in biotechnology.

Zyomyx pockets $27M in Series E round

Zyomyx of Hayward, Calif., raised $27 million in a Series E round of private-equity financing. The round was led by existing investor Credit Suisse First Boston Private Equity and included newcomers Lilly BioVentures and GE Life Science and Technology Finance. Zyomyx said the cash will help build up the commercialization infrastructure needed to launch its human cytokine protein-profiling biochip, due in early 2003.

Amersham Closes CodeLink Microarray Deal

Less than two weeks after announcing that it was acquiring Motorola''''''''s CodeLink microarray business, Amersham Bioscience has already signed a deal to provide the National Cancer Institute with the high-density spotted arrays, according to an Amersham company representative. The CodeLink arrays consist of 10,000-spot oligonucleotides, and are available in human, rat, and mouse varieties. While Motorola had been in discussions to provide the arrays to the NCI for some time, Amersham was able to close the deal quickly since the NCI is already one of its customers. The company did not disclose the terms of the deal. The representative said it is one of over 100 pending sales that Motorola turned over to Amersham recently.


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