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Cytogeneticists Say Platform Choice a Question of Personal Preference, Circumstance

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CGH+SNP or just SNP? Geneticists who use microarrays for constitutional and cancer cytogenetics have never had so many choices. Four large vendors currently serve the market, and a number of other players sell a variety of designs optimized for different indications or communities.

But according to some longtime users of chromosomal microarrays, the decision of what platform to use often has more to do with the circumstances in which one adopts the technology.

"I think each platform has its pros and cons but [platform choice] has a lot to do with where you get into the microarray business," said Marilyn Li, director of Baylor College of Medicine's Cancer Genetics Laboratory.

Li told BioArray News that one of the reasons she first adopted Agilent Technologies' CGH platform in 2005 was because, at the time, there were no other arrays specifically geared to cytogeneticists.

"That's just the first animal I encountered," said Li.

Indeed, Affy and Illumina didn't release cyto-focused products until 2008, when Affy launched its Cytogenetics Research Solution and Illumina introduced its HumanCytoSNP-12 BeadChip (BAN 11/18/2008).

Li said that users have benefitted from vendors' interest in the market, and have chosen certain platforms over others based on those competitive dynamics.

"At a certain time one array might be better than another, and the competition between the vendors is great, so they are always trying to improve their arrays, platforms, and software," said Li.

In general, she said that Affy and Illumina's SNP arrays will offer genotype and loss of heterozygosity information in "much higher resolution" than CGH+SNP, but that Agilent's CGH+SNP arrays are "good for calling copy number."

To combine both of the approaches is "definitely a plus" she said, because SNPs are not distributed in the genome equally.

"If you only look at SNPs in the X chromosome, you are going to have a lot of holes, because you can't have too many variations in the X chromosome – and men only have one — especially in the exome regions," said Li. She acknowledged, though, that SNP array vendors have added content to overcome those limitations.

"Putting some copy number probes in will help, as Affy has done with CytoScan HD, which has a lot of copy number in addition to SNP probes," she said.

But, ultimately, the choice of whether to use a CGH+SNP array or a higher-resolution SNP array is the laboratory's preference, and also related to the context in which the platform is adopted, said Li.

That was the case for Daynna Wolf, a professor of pathology and laboratory medicine at the Medical University of South Carolina.

Wolf told BioArray News that at the time she was looking to adopt an array platform, Agilent had not yet debuted its CGH+SNP platform.

"I wanted to use a SNP array, and when I picked a platform there was only array CGH, not array CGH+SNP, so it was either Affy or Illumina, and in the end we went with Illumina because it worked out financially for us," said Wolf.

Though Agilent has since launched CGH+SNP arrays, Wolf is satisfied with her choice.

"Even with an array CGH+SNP chip, there's not enough SNP [content] there to pick up a lot of things," Wolf said. "The level of zygosity that we have seen on constitutional has been overwhelming," she added. "No one had any idea how much we were going to see, even in constitutional, so I am glad we went with a SNP array."

Robert Best, director of the division of genetics at the University of South Carolina School of Medicine, noted that his impression is that "people usually have a good reason for using the platform that they do, and that they are typically happy with their decisions."

Best told BioArray News that when it comes to finding the right platform, one has to "find what works and use the most efficient and economical way of doing it." He noted that the community may be using more density than it needs as it finds the balance between resolution and cost, and hypothesized that in the future, cytogeneticists may actually want lower-resolution chips to reduce the price of their services.

Wolf disagreed. She said that it was likely that the arrays favored in the community will be higher resolution.

"I see resolution going in one direction," said Wolf. "As things get cheaper, you will do more because you can."

Anwar Iqbal, director of the microarray CGH laboratory at the University of Rochester Medical Center, told BioArray News that, when it comes to deciding between CGH+SNP and SNP arrays, it's "all dependent on the needs of the institution."

"There is a market for both" kinds of arrays, said Iqbal, and he argued that there will continue to be. "It is a very rapidly evolving technology," he said. "It's possible the market will go from microarray to [next-generation sequencing], but microarrays are still going to be there for some time."

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