In the News

From GenomeWeb Daily News, June 1, 2010

Affomix, U Montreal PGx Centre, and Montreal Heart Institute Ink PGx Deal

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – Antibody company Affomix today announced a collaboration with the University of Montreal Pharmacogenomics Centre and the Montreal Heart Institute to develop companion diagnostic biomarkers for cardiovascular disease.

Under the agreement, the financial terms of which were not disclosed, Affomix and the PGx Centre will partner to develop reagents for the quantitative profiling of candidate biomarkers in a multiplex manner. The PGx Centre has identified a panel of proteins it believes may be predictive of patient response to novel anti-atherosclerotic agents.

In a statement, Jean-Claude Tardif, director of the Research Center at the Montreal Heart Institute, said, "Having the ability to consistently measure these cardiovascular proteins represents a key first step in identifying important biomarkers that will help us better understand atherosclerosis and how patients respond to certain medications."

Based in Branford, Conn., Affomix develops monoclonal antibodies using its proprietary technology, called Y2H Express, that it says improves upon traditional yeast two-hybrid technology in terms of antibody specificity.

In January, Affomix and the City of Hope announced a collaboration to determine the clinical use of "digital proteomics" using next-generation sequencing. In December, it signed an agreement with Kalgene Pharmaceuticals to select antibodies with potential diagnostic and therapeutic use in breast cancer.

Second Annual Consumer Genetics Conference - The Spotlight Shines on Boston June 2-4, 2010

The Opportunities, Risks, and Realities

(CAMBRIDGE, Massachusetts – November 16, 2009) -  The media spotlight will shine again on Boston from June 2-4, 2010 as the Consumer Genetics Conference hosts its yearly conference at the Hynes Convention Center.  The Consumer Genetics Conference has established itself as the premier event for the convergence of the consumer market, genetics technology market, and healthcare/diagnostics market.

Last year’s Consumer Genetics Conference reached overcapacity levels in terms of attendees, and was covered by three major news networks, as well as over 12 national and local television programs – all filming onsite. 

This year, the conference, is limiting the number of available attendee slots in order to prevent overcrowding in the conference halls and exhibit areas. A preliminary schedule has been released on its website. 

The conference attracted as speakers, accomplished CEO’s and genetics thought leaders such as:  Francis Collins, now Director of the National Institutes of Health, George Church, Professor of Genetics at Harvard Medical School, and Jay Flatley, CEO of Illumina.  Also present, and in some cases presenting on genetics and consumer products, were large consumer focused companies such as Procter and Gamble, L’Oreal, and MedCo. Flatley unveiled the first prescription ever written for genome sequencing, as well as a genome sequence iPhone application.  Given these consumer/patient focused products as well as advancements in the field; Collins speculated that the conference would grow to 6X its size within two years.  

This year’s conference will continue to highlight cutting edge technologies, such as those offered by Affomix. These new technologies may enable point of care diagnostics, and response to treatment determinations, utilizing proteomics techniques on genomic-based platforms.  “Until now, there was no pipeline to produce the Affome™, a collection of monoclonal antibodies against all protein targets in the proteome, or a way to measure complex protein mixtures.” stated Mike Snyder, Department Chair of Genetics at Stanford and a co-founder of Affomix.  “Rapid production of high quality monoclonal antibodies fused to nucleic acid backbones could provide a paradigm shift not only in proteomics research, but also in point of care diagnostics and personalized medicine,” Snyder continued.

“The conference is a one of kind of event offering the convergence of perspectives from thought leaders in genetics and medicine, the consumer product industry, the law, and the venture capital community,” stated John Boyce, Conference Founder, Co-Founder of Delphi Bio, and President of DNA Like Me, Inc.  “We have chosen our speakers and subjects carefully, and thus created an unbiased forum where opinions (pro and con), can be voiced and where critical information can be disseminated,” Boyce continued.

The Consumer Genetics Conference

The Consumer Genetics Conference was developed and launched in 2008 and will host its second annual event in Boston at the Hynes Convention Center from June 2-4, 2010.  It is hosted and owned by DNA Like Me, with initial sponsorship funding provided by Delphi Bio www.delphibio.com,

Contact Information

John Boyce, DNA Like Me, Inc.,

877-362-7461 x701

From CURE News, Summer 2009

Affomix Presents at CURE/Yale BioHaven Series

Rounding out the 2008-2009 CURE/Yale BioHaven Entrepreneurship seminar series was a presentation May 6 by Affomix Corporation, a development-stage company based in Branford, CT. The company has proprietary technology for rapid, automated, high-throughput selection of human monoclonal antibodies (mAbs).
Introduced by Paul Pescatello, president and CEO of CURE, the speakers were Michael Sherman, Ph.D., president and co-founder of Affomix, and Michael P. Weiner, Ph.D., vice president, Molecular Sciences at Affomix and a co-founder of the company.

Also on hand for the presentation was John J. Boyce IV, co-founder of Delphi Bio, LLC, who is serving as co-head of business development, sales, and marketing for Affomix.

Michael Snyder and Sherman Weissman, both professors at Yale University, are also co-founders of Affomix.

The Affomix mission, the company says, is to commercialize proprietary mAbs, mAb microarrays, and mAb libraries for research, drug discovery, and diagnostic and therapeutic applications, including those for the sensitive and accurate detection of protein levels in biological samples.

The company is built on the premise that simultaneous tracking and quantitation of the proteome will dramatically increase understanding of cellular phenomena.

Currently the methods used for measuring antibody-protein interactions are throughput limited, and measuring post-translationally-modified proteins is neither high throughput nor sensitive enough, the company says.

Designed to improve on the traditional yeast two hybrid process, Affomix Y2Hexpress™ technology is designed to select mAbs that possess high levels of affinity and specificity toward their antigens.

The company currently has an automated assembly-line process capable of manufacturing antibodies against 150 targets per week. To date Affomix has generated antibodies against about 250 protein targets.

The company also intends to apply its patented proprietary technology in other areas of proteomic research, such as using fluidics and emulsion technologies to interrogate post-translationally modified proteins; providing a service; that allows protein-protein interaction reactions to be carried out in solution and captured on chips or beads for semi quantitative measurement; and using methods to interrogate mAb-antigen interactions on a substrate, for quantitative measurement.

Affomix says its ultimate objective is to mine its extensive human mAb libraries to generate the human Affome™, a comprehensive library of mAbs that can be used to detect and quantify all proteins in the human proteome.

Affomix says it is perfecting a proprietary protein quantitation technology to enable the development of highly multiplexed proteome arrays. "If you have an interest in generating antibodies against a lot of different targets and want to do it in a rapid and cost-effective manner, then come see us because we can help you," Michael Sherman says.

Affoxmix completed a $7 million Series A Financing in February 2008. Four Seasons Ventures and Connecticut Innovations joined founding investor Elm Street Ventures in the financing.

From BioCentury, The Bernstein Report on BioBusiness, May 25, 2009, Page A10/21

Affomix: Whole proteome arrays

By Stephen Hansen, Staff Writer

Antibody arrays are a more accurate tool for measuring protein levels in biological samples than commonly used mRNA-based methods. But the cost and time needed to generate antibodies has limited the space that can be covered to a few protein families.

Affomix Corp. has developed an automated yeast hybrid antibody screening technology that it believes will cut time and cost enough to develop a whole proteome antibody array. “What we want to do is generate a proteome multiplex array,” President Michael Sherman told BioCentury. “We want the scientists to be able to take a biological sample of any type, whether it’s serum or a tumor sample, and be able to use our array to get an indication of the level of all the proteins in that sample.” According to Sherman, arrays that measure mRNA expression in biological samples are useful in most cases for detecting the presence of a protein, but not sufficiently accurate to specifically quantify protein levels. “About half of the proteins in the proteome cannot be accurately measured by looking at mRNA expression levels,” said Sherman, who also is a partner at Elm Street Ventures. One reason is the difference in the rates of production and breakdown of mRNAs and their corresponding proteins. Another is that proteins such as hormones and growth factors are produced in one cell but taken up by another, so mRNA may not be present in a particular cell even though the protein is. Developing an antibody array that covers the entire proteome is a logical solution, because the ability of antibodies to target specific proteins. According to Sherman, Affomix has made that a possibility by automating the process of antibody screening to generate antibodies in a fraction of the time and at a much lower cost than can be done by other screening technologies.

The company has two automated technologies: Y2HExpress, a yeast two-hybrid technology; and Phage ESCape, a phage display technology for generating antibodies that have post-translational modifications that cannot be reproduced in yeast. Like phage display, both technologies generate human single-chain variable fragments that can be used for research or diagnostic purposes, or converted into IgG antibodies for use as therapeutics. Unlike phage display, Y2H Express does not require creation of an antigen to generate the antibody, which Sherman said is costly and time-intensive. Instead, the genetic information for the antigen is inserted into the yeast. “It is much less expensive and much faster to make the gene for the antigen than it is to make the antigen itself,” he told BioCentury. Additionally, the company has modified the yeast two-hybrid process. The details are not disclosed. But Sherman did say labor-intensive steps that are difficult to automate, such as centrifugation, filtration and washing, are eliminated. Sherman said Affomix’s system allows the company to generate antibodies against 150 targets per week. In contrast, he said, a single researcher would be hard pressed to do 50 targets in a year with a manual yeast two-hybrid system, and it would take a phage display system months to select antibodies against 100+ targets. Affomix plans to launch both antibody screening technologies this summer as a service for life science researchers and other companies. It plans to incorporate a rights clause into its service contracts that would allow Affomix to use resulting antibodies in a proteome multiplex array, thus allowing the company to generate revenues and build up its antibody inventory at the same time. “We would make these antibodies, let people use them for whatever reason they want to use them, and retain the rights to use them as part of a very large population of antibodies on our own array,” Sherman said. Affomix already has a contract with an undisclosed diagnostics company and is in discussions with others to generate antibodies for research, diagnostic and therapeutic use. On the way to developing a whole proteome multiplex array, Sherman said Affomix would develop and market antibody arrays for specific protein families. He expects the first array to be available within a matter of months. In January 2008, Affomix raised about $7 million in a series A round, which could be the company’s last financing. Sherman said revenues from the service business should allow Affomix to be self sustaining. Y2HExpress was developed by VP of Molecular Sciences Michael Weiner while he was working at an undisclosed pharma, from which the biotech has a license. The terms of the license are not disclosed.   

Antibody Firm Affomix Readies to Launch Service Biz in the Summer; Technology for PTM Differentiation in the Works

April 07, 2009, Newsletter: ProteoMonitor

Antibody firm Affomix, founded about a year ago, is ready to launch a custom antibody service business using a technology that it said significantly improves the affinity and specificity of the antibodies while shortening the production time as compared to other methods such as yeast two-hybrid.

The company will begin providing the service commercially during the summer, after it has moved from its current 4,000-square-foot office to a 12,000-square-foot facility in New Haven, Conn., at the end of this month.

The company is also refining its technology so that it will be able to distinguish proteins that have undergone post-translational modifications from those that haven't.

The company, which launched in January 2008 with $7 million in venture capital, has performed work for one client in order to validate its approach, and is in discussions with other pharmaceutical and biotechnology firms and consortia, Mike Sherman, Affomix's president, told ProteoMonitor last week. Sherman is also a partner in Elm Street Ventures, one of the investors in Affomix.

Along with Sherman the other co-founders of Affomix are Michael Snyder and Sherman Weissman, both professors at Yale University and Michael Weiner, who has held various positions at a number of life science shops.

While antibody production is a relatively crowded business, it also is one with plenty of room for improvement. Indeed, two of the most cited reasons for the low adoption of antibody microarrays in proteomics research are the poor quality of antibodies and the low number of antibodies that are available.

Affomix, Sherman said, aims to address these bottlenecks by defining a so-called "affome" — an antibody equivalent to the proteome and genome.

"Our ultimate aim is to generate the affome, an antibody set against virtually all proteins in the human proteome," Sherman said. The plan is to do that in two steps: the first is to develop antibodies against at least two epitopes of every protein in the human proteome. Then, a second generation of its core technology will be used to select antibodies against polymorphisms, mutations, and post-translational modifications.

Ultimately, he added, the antibodies developed by Affomix, which are monoclonal, would allow researchers to measure and track proteins in a manner similar to NMR and mass spectrometry but in a cost-effective way.

Y2H That Discriminates

The basis for Affomix's technology is the yeast two-hybrid system. However, Weiner has also developed a proprietary step that improves antibody specificity. It is that method, Sherman said, that distinguishes Affomix from other antibody firms in the market.

The company starts with a library of antibodies generated in yeast cells, then uses Weiner's method to excise those antibodies that are non-specific. While Sherman spoke only in general terms about the technology, called Y2H Express, developed by Weiner, he said that it addresses one of the biggest issues when it comes to antibody development — antibodies that don't work.

The poor quality of antibodies is well known in the research field. In conference talks and interviews, Matthias Uhlén, a professor at the Royal Institute of Technology and the catalyst behind the Human Protein Atlas, has said that more than half of the commercially available antibodies the HPA has received for testing don't work.

The National Cancer Institute was concerned enough about the issue that in late 2007, it began an initiative, as part of its proteomics program, to improve antibody development and characterization by creating an antibody-characterization laboratory at its Frederick, Md., facility [See PM 11/29/07].

According to Sherman, about 95 percent of antibodies from a typical yeast two-hybrid study will be non-specific. Affomix has "gone through our library and rinsed out the antibodies that we know right from the get-go that are likely to be non-specific and that right away improves the chances that the antibodies we find will be specific to 30 percent," he said.

The company has done work with one client, which Sherman declined to identify, but that wanted to "kick the tires and … see how well we could perform." The client picked 10 proteins that it was interested in using, grouped into three categories: proteins for which antibodies that work already exist; those for which antibodies are commercially available but don't work properly; and those for which antibodies don't exist.

Affomix was able to develop antibodies against all 10 proteins, Sherman said, and is now ready to generate and send them to the client.

The other major problem with antibodies is that while there are plenty of them on the market, they target many of the same proteins. By some estimates, commercially available antibody arrays contain fewer than 600 antibodies. But Affomix's technology is not dependent on antigen quantity, which opens up its potential ability to generate antibodies against all proteins in the human proteome, according to Sherman.

"We are of the opinion that if you look at … enough epitopes of the protein, and if you do it properly," antibodies can be developed against all proteins, Sherman said. So far, he added, "we have not been stumped."

To date, Affomix has generated antibodies against about 250 protein targets.

Currently, Affomix has an automated assembly-line process capable of manufacturing antibodies against 150 targets per week, "and that's scaleable, [although] we don't need to scale it at the present time."

It takes three to four weeks from the time a customer puts in an order for Affomix to identify which part of the protein to target and to develop the antibody. By comparison, a comparable experiment using a classical yeast two-hybrid experiment would take three to four months, Sherman said.

While a customer has proprietary rights over how an antibody generated by Affomix is used, Sherman said that he expects Affomix either to have rights to the antibody itself, or that there would be no IP restrictions on them at all so that it can offer the antibodies to other customers.

Affomix is also looking to address a growing market in proteomics research, analysis of post-translational modifications. Mass spec-based methods such as electron-transfer dissociation and collision-induced dissociation have been developed for PTM work, but the Affomix technology would make the work cheaper and simpler, according to Sherman.

"If we're able to come up with a set of monoclonal antibodies … that allow customers to distinguish between modified and non-modified proteins and put that together with our protein quantitation technology, then … you wouldn't need mass-spec hardware or to send samples out for analysis by mass-spec companies," Sherman said. "The procedure would be straightforward and amenable to multiplexing.

"The way we're contemplating this somewhere down the pike, you'd apply your biological sample to an antibody capture array, or a pair of matched arrays, and in one fell swoop, measure how much of each protein you're looking for is present in the sample and then what portion of each of the proteins is post-translationally modified," he added.

Currently, while certain antibodies can disclose whether a protein has a phosphate group on its tyrosine, for example, no antibodies exist that can distinguish between modified and non-modified proteins.

"We want to provide a product and services that will allow people to do things in proteomics that they can't do … effectively with proteomics," Sherman said.

He declined to elaborate on the technology that Affomix has developed for PTM differentiation, but said it would be agnostic to the kind of modification. He added that he hopes it will be "ready for prime time" in a few months.

Industry Veterans

If the founders of Affomix seem familiar, it's because they have extensive experience in the life sciences business: Sherman, Snyder, and Weissman are three-quarters of the team behind Proteometrix, a company founded in 2001 to commercialize protein microarray technology developed by Snyder, one of the pioneers in the protein and antibody microarray field [See PM 01/28/02]. Proteometrix was purchased in 2004 by Invitrogen, now a division of Life Technologies, which sells the technology under the ProtoArray brand.

Meanwhile, Weiner has held various positions at Stratagene, 454 Life Sciences, and GlaxoSmithKline.

The company will eventually offer antibodies off-the-shelf, but it is in no rush to enter the catalog antibody business, Sherman said. "[It] is our ability to select antibodies in a very comprehensive and rapid and remarkably cost-effective manner that makes it practical to contemplate making a chip to measure 20,000 different proteins," he said. "We are in a service mode and we're telling customers, 'If you have an interest in generating antibodies against a lot of different targets and want to do it in a rapid and cost-effective manner, then come see us because we can help you.'"

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