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Agilent Makes Baylor-Designed CGH Arrays Available for Constitutional and Cancer Research


Baylor College of Medicine's department of molecular and human genetics has been an Agilent Technologies customer for nearly a decade, and the Santa Clara, Calif.-based microarray vendor has produced many iterations of custom-designed chips for BCM.

Recently though, BCM has been inundated with requests from external investigators to use those arrays for prenatal and pediatric constitutional testing as well as cancer research. The interest led BCM to agree recently with Agilent to make half a dozen of those array designs available as catalog products.

"We have been approached many times by colleagues and collaborators asking to use Baylor-designed arrays in their laboratories," Brandon Perthuis, director of business development at BCM's Medical Genetics Laboratories, told BioArray News this week.

He noted that the designs have taken years to create, and have been used on tens of thousands of samples. "We have now designed arrays sophisticated enough to detect single exon deletions and duplications in thousands of genes," said Perthuis. "This has led to new discoveries that would not have been possible with other array designs."

It has also led to demand from external researchers to gain access to the chips. According to Perthuis, the demand has become "significant enough to now enter into an agreement with Agilent to enable this process," he said. "Many labs now have the ability to perform microarray testing, and this new partnership with Agilent will grant these labs immediate access to array designs that have taken our department many years to create."

Baylor has unquestionably been an innovator in the implementation of array technology in prenatal, pediatric, and cancer research. Arthur Beaudet, who is chairman of the department of molecular and human genetics, oversaw the introduction of prenatal chromosomal microarray analysis in 2004. More recently, BCM investigators like Marilyn Li, director of its Cancer Genetics Laboratory, and Federico Monzon, director of molecular pathology within CGL, have discussed with BioArray News BCM's use of arrays and sequencing in cancer cytogenetics.

Heidi Kijenski, Agilent's clinical marketing director for genomics, this week provided additional detail on the six BCM array designs that are now available.

Three of the arrays are focused on postnatal research. Agilent is now offering CGH+SNP arrays on slides that contain two, 400,000-marker arrays; four, 180,000-marker arrays; or eight, 60,000-marker arrays. The company is also selling two prenatal designs: one in a 2x105K format and the other in the 4x180K format.

The final array, for cancer research, is available only in a 2x400K format. Each array contains more than 350,000 copy number markers and 60,000 SNPs.

Kijenski noted that the Baylor-designed arrays incorporate features such as exon coverage, whole genome coverage, SNP analysis for absence of heterozygosity and uniparental dysomy, mitochondrial genome coverage, and microRNAs. She said that, given the number of chips available, customers can "choose what works best for them based on the content and different throughput options."

She declined to provide a forecast for the arrays' adoption or what impact they might have on sales, but said the company has "had a lot of interest" since it first announced the collaboration at the American Society of Human Genetics meeting held last month in Boston.

According to Kijenski, BCM's recent decision to make its database available to external researchers may encourage adoption of the new chips. BCM's Perthuis noted that more than 50,000 samples have been processed on the array designs, allowing BCM to "generate custom tracks to help with interpretation of what may be considered benign variants, versus deleterious copy number changes."

BCM isn't the only major genetics laboratory to see its array designs become commercially available, though. Since 2009, Oxford, UK-based Oxford Gene Technology has commercialized nearly two dozen molecular arrays designed in collaboration with Madhuri Hegde, executive director of Emory Genetics Laboratory in Atlanta. BioArray News spoke with Hegde about Emory's collaboration with OGT last month.