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Custom Array Market Heats Up with New Affymetrix Offering, Luminex Universal Array


Need to order a custom-designed oligonucleotide array at 3AM? Now Affymetrix customers can do just that, with a new CustomExpress program and the company’s NetAffx website.

The CustomExpress program, which the company launched at the end of July for its EasyAccess customers, and will make available to all customers in October, enables customers to choose probe sets for up to 1,000 genes per chip, or up to 16,000 probes in total, from existing sets on Affymetrix’s prefabricated GeneChip arrays such as the U95 human genome set or the U74V2 mouse array.

Customers can design and order the arrays online through NetAffx, (, which is free to any customer or potential customer who registers. NetAffx includes links to a variety of public and private gene databases, and a search engine powered by collaborator Lion Biosciences’ SRS platform that allows customers to search for sequence information based on accession number, description, or Affymetrix ID.

“If a customer has done a genome-wide screen with a set of human arrays, and has identified up to 1000 [relevant] probe sets, the customer can make a file with those IDs, [and] do text-based ordering of the custom array on the site. Or if the customer knows they’re interested in a particular topic — say they want to look up the interleukins — they can pull up any probe set that matches that description and can select each by hand,” explained Liz Kerr, Affymetrix’s marketing director of gene expression.

The website ordering program offers an ongoing update to tell the customer how much space is left on the array and to warn the customer of accidental repeated probe set selections.

Turnaround time for these made-to-order arrays, which cost $250 each in addition to an undisclosed design fee, is currently four weeks.

This new program, which augments Affymetrix’s existing high-end custom services, has involved altering the photolithographic technique the company uses to synthesize oligonucleotides on the chip. Because photolithography involves designing a mold and specific masks for a group of arrays, it has not previously been thought of as adaptable to custom arrays.

“We don’t think people expected they could do this with photolithography,” said Affymetrix president Sue Seigel. “The CustomExpress program is a buster of that perception. We’ve gotten extremely favorable feedback from customers,”Seigel said.

The company makes arrays in batches of 90, and makes a mold for each batch. If a person orders 540 arrays or more, there is no design fee.

Currently, CustomExpress users are limited to probe sets available on Affymetrix prefabricated arrays. But over the next year, the company plans to expand the program to allow users to submit sequence that is not on any preexisting Affymetrix arrays.

This effort can be viewed as a way for Affymetrix to seize on what it perceives as a trend away from cDNA arrays and toward prefabricated ones for specialized arrays.

“Scientists have told us that after they performed their whole genome studies, they wanted to selectÖsubsets of genes for high volume or detailed follow up studies,” said Seigel.

These scientists, said Kerr, have been trying to use the cDNA arraying equipment for these studies, but have ended up getting too involved in developing the technology rather than answering scientific questions with it.

“Although a lot of customers wanted to make subsets of their own, they found the [arraying] technology too challenging, and were excited about having a plug and play solution,” Kerr noted.

CustomExpress can also be seen as an attempt to grab market share from competitor Agilent, which also offers custom probe arrays, by moving out of the more-is-better high-density space and into the medium-density arena. Affymetrix has said that it would like to gain an increased share of this market.

“This is a natural step,” said Kerr. “The one size fits all approach does not fit all any more.”


Luminex Challenges Affy with Universal Array

Shortly after Affymetrix announced its new CustomExpress custom array offering, Luminex also announced plans to develop a bead array-based custom offering, the universal microarray platform, with Tm Biosciences of Toronto, Canada.

The platform will be “a very simple and flexible method that will allow scientists to do advanced genetic research,” said Mark Chandler, Luminex’s CEO, in the company’s second quarter conference call. The company expects the platform, which it plans to introduce in the fourth quarter and will be able to accommodate gene arrays as well as protein arrays, to constitute a large part of its future business.

Users of this universal bead-based microarray platform will be able to design customized arrays, ordering their oligonucleotides one day, then receiving the arrays the next day, said Chandler.

With this entry into the research array market, Luminex, of Austin, Texas, said it plans to sharply undercut competitors such as Affymetrix.

With Affymetrix’s CustomExpress offering,” said Chandler, “it’s about a $25,000 expenditure just to get the chips into your lab. We’re going to be doing things much differently with our universal array. The arrays, which will involve oligonucleotides placed on luminex beads, will be “done at very low cost for overnight delivery. You can look at one gene or 1000 genes and not really increase the complexity of the process by a very great extent.”


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