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Affy, Hoping to Lure N. American Cancer Researchers, Integrates SNP 6.0, Exon Array

Affymetrix is now combining its SNP 6.0 genotyping array with its Human Exon 1.0 ST chips as part of an “integrated genomics solution” tailored specifically for cancer researchers, especially those in North America.
The move comes as Affy extends its Collaborations in Cancer Research Program, which it launched in Europe last year, to North America, and is intended to allow cancer researchers to survey gene-expression profiles, SNPs, and copy-number variations in the same study, according to the company.
Affy last year launched the SNP 6.0, a 1.8-million feature SNP genotyping array that also contains around 950,000 probes for copy number variations. The Human Exon 1.0 ST, which enables users to study gene-expression profiles and alternative splicing, has been on the market since 2005.
Ruby Gadelrab, Affy’s senior manager of academic marketing, told BioArray News this week that Affy decided to make the products available together for cancer research because they enable users to look at a variety of genomic parameters.
“A recent trend in high-profile journals shows [that] investigators want to be able to study multiple genomic parameters to get to their candidate genes quicker,” she said. “The purpose of CCRP is to enable studies such as this and to showcase these to the wider cancer community at events like the upcoming Integrated Genomics Conference series.” The series will be hosted by Affymetrix in May.
Gadelrab added that “using just one cancer sample on these two arrays enables researchers to study over six genomic parameters including gene expression, alternative splicing, exon expression, copy number, [loss-of-heterozygosity], and allele-specific copy number,” and would make the integrated tool attractive for some users.
Affy first launched its Collaborations in Cancer Research Program in Europe last year. The program, which the company plans to expand to the Asia-Pacific market later this year, enables select cancer researchers to access the newest Affymetrix technology and to work with the vendor to answer questions about using the platform and their research. Last week the company announced it is now working with 25 researchers in North America and Australia (see BAN 4/15/2005).
According to Gadelrab, CCRP researchers in general “want to be able to discover candidate genes and signatures implicated in disease mechanism and progression, classification, and prognosis. They also want to discover suitable candidates for drug targets implicated in drug efficacy and toxicity.”

“Realistically, I think the solution will need to be sought by the investigators rather than [by] relying on Affy.”

She added that the multi-genomic parameter approach to cancer studies has been reinforced by “recent literature trends show[ing] that combining copy number and LOH studies with gene expression studies enables researchers to focus their discovery of candidate genes, speed up their validation and reduce data complexity while still securing the most comprehensive view of the cancer genome.”
For example, in a recent issue of Molecular Cancer, researchers from the University of Milan used both Affy SNP arrays and gene-expression arrays to study clear cell renal carcinoma.
Some CCRP investigators are also looking at other genomic parameters, including methylation patterns and gene regulation as well as copy number and gene expression, she said. However, Gadelrab said that based on feedback, most customers are interested in “primarily a combination of gene expression, copy number, and LOH data integration.” Under these conditions, it made the most sense for Affy to pair the SNP 6.0 and the Human Exon 1.0 ST arrays, which the company will market with Partek’s Genomic Suite software.
A Tale of Two CCRP Participants
According to two of the newer CCRP participants, there are at least two benefits of joining the program rather than remaining regular Affy customers: being able to access new technology, and becoming part of the collaborative environment that Affy is attempting to create in which participants can swap data-analysis techniques and tackle research challenges together.
“In terms of benefits, it allows us to use of state-of-the-art microarray technology that’s been developed by Affymetrix,” said Norman Lee, a professor in the Department of Pharmacology and Physiology and the George Washington University Medical Center in Washington, DC.
“The other aspect is to get together with some of the other investigators that are part of this program to see what they are doing,” he added. “It gives us an opportunity to see how other labs are analyzing their data. So, it is a big advantage because we get to interact with other researchers.”
Lee’s research is focused on examining cancer disparities between, say, African-Americans and Caucasians, with a specific interest in prostate cancer, breast cancer, and colon cancer.
“The disparity question is a burgeoning area of focus in the cancer research community,” he said. “Something that is currently underway is the use of genomic approaches and strategies to understand cancer disparities. We will perform gene-expression profiling as that is one of our goals, coupled with genotyping and determination of copy number variation.”
Lee said that his lab “plans to perform association studies to help identify expression QTLs.” He added that he will also use the 6.0 to look at DNA copy-number variation. “This will be correlated with gene-expression differences in tumors derived from African-Americans and Caucasians. We hope to identify new markers or mechanisms pertaining to cancer disparities,” Lee said.
Ian Campbell, head of the Victoria Breast Cancer Research Consortium’s cancer genetics laboratory at Peter MacCallum Cancer Center in Melbourne, Australia, said that the main benefit of the CCRP will be to swap notes with fellow cancer researchers.
“This program aims to bring together researchers with similar interests so that we can share our experiences with these new technologies,” Campbell told BioArray News this week. “Many of us are probably encountering the same technical and analytical issues and have to struggle to find solutions on our own. By combining our experiences this collaboration should help us avoid re-inventing the wheel.”
According to Campbell, other researchers may hold the key to research bottlenecks that cannot be surmounted with help from Affy alone. “Affymetrix has never been good with data analysis and I still think it is an open question as to how useful their tools will be,” he said. “Realistically, I think the solution will need to be sought by the investigators rather than [by] relying on Affy.”
Like Lee’s lab, Campbell’s will look at multiple genomic parameters such as methylation and copy-number variation in ovarian cancer samples. He said a hidden benefit for CCRP participants will also ultimately be access to lower prices.
“It gives us access to arrays at a lower price, although I expect many of us were already getting discounted chips as we were either early-access users or were getting bulk order discounts,” he said. “In our context, Affy arrays are cheaper than [those of] their competitors, which allows us to do larger studies than would otherwise be possible.”

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