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AmberGen Secures $600K to Develop Allergy Test on Illumina's BeadXpress Platform

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AmberGen is developing a microbead-based, multiplexed, in vitro pediatric allergy test. The diagnostic is designed to enable the detection of multiple allergen-specific IgE antibodies in blood, according to a company executive.

The National Institutes of Health recently awarded the privately-held biotech $600,000 to support the project. AmberGen received the funds on March 15 as phase I of a Small Business Innovation Research grant through the Advanced Technology program of the National Institute of Allergy and Infectious Disease. The grant will expire on Feb. 28, 2013.

Mark Lim told BioArray News this week that the company aims to design an assay that will "detect, with high sensitivity, several hundred allergens simultaneously from a single drop of blood and automatically process [samples from] over 100 patients in one hour."

Lim is director of proteomics at Watertown, Mass.-based AmberGen, and principal investigator on the project.

AmberGen plans to format its assay to run on on Illumina's BeadXpress system using AmberGen's internally developed protein production, isolation, and bead attachment technologies. BeadXpress consists of a dual-color laser detection system that identifies unique holographic codes embedded in microbeads, and detects the signal intensity associated with each bead so users can survey up to 384 loci per assay, according to Illumina.

Lim said that AmberGen decided to use the BeadXpress because, "compared to other commercially available bead platforms," the BeadXpress offers "digital barcoding for higher potential coding capacity, a bio-friendly glass bead surface for low assay background, and a 2-color fluorescence readout, for maximum flexibility and data normalization."

As part of the phase I project, AmberGen will collaborate with Illumina and with Lynda Schneider, director of the allergy program at Children's Hospital in Boston. Based on the outcome of the phase I work, AmberGen plans to apply for phase II SBIR funding, as well as seek non-federal investment funds to commercialize its allergy test and, ultimately, submit the test to the US Food and Drug Administration for clearance.

Lim did not provide a timeline for when AmberGen hopes to submit its test to the FDA, but said that the company plans to "accelerate FDA-clearance" by "working closely with its clinical and industry partners specializing in this area."

According to Lim, AmberGen decided to craft a diagnostic for pediatric food allergies because the proportion of the population that has such allergies is increasing. "Current assessments show that [between] 5 and 8 percent of all children in the US have food allergies," Lim said. Additionally, 40 percent of afflicted children have a history of "severe and potentially deadly anaphylactic reactions," he said.

Lim's numbers hold up. The Food Allergy and Anaphylaxis Network, a Fairfax, Va.-based non-profit, estimates the number of children in the US with food allergies is about 6 million, or 8 percent of the total pediatric population. And a study released in 2008 by the Centers for Disease Control and Preventionnoted that there was about an 18 percent increase in food allergy between 1997 and 2007, and that food allergies result in over 300,000 ambulatory-care visits a year among children.

"Early and correct identification of food allergen triggers can be in some cases life-saving by allowing for diligent food avoidance," said Lim. He added that allergen proteins are often hidden in the "most unlikely of places."

"A milk protein and potent allergen is sometimes used as filler in hot dogs; and whey, another milk protein allergen, is found in a host of processed foods such as chicken nuggets," Lim said. "Food allergies are difficult to diagnose based on symptoms alone," he said. "The picture is further complicated by the fact that it is common for a child to have multiple different food allergies."

AmberGen's initial panel will target 21 proteins from the top eight pediatric food allergens — milk, soy, wheat, egg, peanuts, tree nuts, fin fish, and shellfish — and their many component allergen proteins. The panel will be expanded to other foods and environmental allergens in the future, Lim said.

According to the grant's abstract, cell-free expressed protein allergens will be compared to purified natural protein allergens on the BeadXpress, and those results will be compared with measurements obtained from Thermo Fisher Scientific's ImmunoCAP, a cellulose solid-phase-based qualitative in vitro assay that is widely used for blood-based allergy testing.

If the firm is successful in its plans to develop, validate, and receive regulatory clearance for the test, its most immediate competitor in the market, though, will be another Thermo Fisher Scientific product: the ImmunoCAP ISAC assay, which relies on fluorescence-based detection to survey 112 allergen components from 51 allergen sources using microarrays. Like AmberGen's planned test, the ImmunoCAP ISAC relies on a blood sample to make a diagnosis.

Another competitive offering will be Genesis Diagnostics' Genarrayt Microarray 200+ Food IgG test. Cambridge, UK-based Genesis launched the Genarrayt platform, which is based on an enzyme-linked immunosorbant assay, in April 2008. A number of labs have since adopted it for food intolerance testing, such as India's Super Religare Laboratories (BAN 6/23/2009).

According to AmberGen's grant abstract, while protein arrays have been adopted for allergen testing, shortcomings of the technology include "limited sensitivity, reproducibility, scalability, and expense of manufacture." This has prevented protein arrays from replacing the more common blood-based tests, such as ImmunoCAP or Siemens' Immulite, where each allergen is assayed in a separate reaction vessel.

A Bead-based Approach

AmberGen was one of two organizations to win Illumina's VeraCode Assay Design Challenge in 2010. The other winner was Royal Women's Hospital in Melbourne, Australia. While AmberGen won the contest with an assay for detecting protein biomarkers associated with colorectal cancer, Lim said that the firm has experience with the platform, and has developed methods for formatting antigens on BeadXpress for immune response profiling in a "variety of fields including allergies, autoimmune diseases, and cancer."

The company has also developed its own approach for protein analysis on the BeadXpress. According to the grant's abstract, this assay offers cell-free protein expression for "uniform and reproducible production of highly pure allergen components," low immunogenic protein attachment to the bead surface, and a dual-tag/dual-laser allergen method of detection that provides "normalization and reduced assay variance."

Illumina secured FDA clearance for BeadXpress two years ago (5/4/2010). Since then, a number of other firms have adopted the platform for diagnostics. For example, Portuguese genetic testing firm CGC Genetics offers several tests on the BeadXpress (BAN 12/21/2010).

Looking ahead, Lim said that AmberGen is also interested in designing higher multiplex assays for allergen testing. The company has developed a mass-spectrometry-based, multiplexed bead-microarray platform called Bead-GPS, which is designed for "ultra-high-plex proteome-scale biomarker discovery," such as for blood-based biomarkers; as well as a platform for screening drug-protein interactions, he said.

According to AmberGen, Bead-GPS relies on photocleavable mass-tags to code a protein library as well as interacting prey molecules such as other proteins, all displayed on individual beads randomly arrayed at high-density in a MALDI substrate plate. The firm claims that Bead-GPS can be used to identify "millions of different mass-tag combinations" originating from bait-prey interactions occurring on individual beads in the high-density array. Suggested applications include drug library screening, global functioning screening, and multianalyte analysis.

The NIH awarded AmberGen a separate, two-year, $600,000 SBIR I grant to develop the Bead-GPS platform last year (BAN 12/6/2011).

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