Ambry Genetics this week rolled out StemArray, a new kit and service that enables researchers studying stem cells to detect genomic abnormalities that would ordinarily be missed by low-resolution karyotyping.
Manufactured by Agilent Technologies in multiplex format that provides four, 44,000-marker arrays on one slide, the chip offers a "higher-resolution approach" to standard karyotyping for stem cells, as well as increased coverage in known stem cell- and cancer-associated genes compared to Agilent's standard 44K CGH array, Ambry said.
The StemArray is designed for labs characterizing human embryonic stem cells or induced pluripotent stem cells. Aaron Elliott, an R&D scientist in Ambry's genomics division, told BioArray News last week that scientists using the StemArray will "be aware of the structural variants present in their cells and be more confident in the reliability of their experimental results."
According to Elliott, human embryonic stem cells and induced pluripotent stem cells that are cultured for an extended period of time are susceptible to chromosomal instability, which is a "big concern" for researchers. To date, stem cells have typically been characterized through traditional low-resolution karyotypic analyses, which can only identify large-scale aneuploidies over 5 megabases in size, Elliott said.
"Currently, the standard technique for characterizing human stem cell lines is G-banding metaphase karyotyping," said Elliott. "However, this technique is low resolution and can only identify large-scale aneuploidies."
In contrast, the Ambry StemArray has an average resolution of 43 kilobases throughout the genome and 24 kilobases in reference sequence genes. Specifically, compared to Agilent's catalog CGH arrays, the StemArray features increased probe coverage in more than 50 pluripotent-associated genes and in over 185 cancer-associated genes. The chip is currently priced "below $600," according to the firm.
"As human stem cells begin to make their way into clinical studies, it is essential that the cell lines be thoroughly characterized," Elliott said. Using the StemArray, scientists will "not only detect the extremely large copy number changes that can be found by karyotype, but also identify very small aberrations that occur during culture that could decrease the reproducibility and reliability of experimental data," he said.
Elliott said the StemArray was developed using Agilent's 44K comparative genomic hybridization array. Ambry modified the CGH chip's genomic backbone to increase the coverage in known stem cell and cancer-related genes. This additional coverage allows users to detect abnormalities in samples that the catalog CGH chips cannot detect due to lack of probes, he said.
Ardy Arianpour, director of business development in Ambry's genomics division, told BioArray News last week that the StemArray will complement Ambry's line of genomic services. The Aliso Viejo, Calif.-based company, which maintains a Clinical Laboratory Improvement Acts-compliant lab, is a certified Agilent and Illumina service provider. In that capacity it offers customers access to gene expression, genotyping, sequence capture, next-generation sequencing, and drug metabolism studies.
Last year, the company also launched a chromosomal microarray analysis service using an array designed by Baylor College of Medicine (see BAN 6/9/2009). Like the StemArray, its CMA chip is manufactured by Agilent.
It was Ambry's close relationship with Agilent, Arianpour said, that helped facilitate the development of the StemArray. The launch of StemArray marks "the first time an Agilent certified service provider will be offering a stem cell product [that] is array based," he noted.
Though manufactured by Agilent, Ambry owns the designs to the StemArray and will provide both the service, which has a turnaround time of two weeks, and kits to customers to "reduce the cost of karyotyping for stem cell companies, cores, academic researchers, and various clients," Arianpour said.
"Every scientist doing karyotype analysis is paying around $600 per sample today," said Arianpour. "We made sure that this product is within that same ballpark cost. However, they will receive better data [and will be able] to detect smaller duplications and deletions," he said of the cost. "As of right now we have it below the $600 mark."
Ambry is among a group of firms and researchers that are seeking to smooth stem cell research by enabling scientists to use higher-throughput technologies. South San Francisco, Calif.-based Fluidigm, for instance, is developing a stem cell integrated fluidic circuit that will simplify protocols developed to turn differentiated cells into stem cells, and to reprogram stem cells to redifferentiate in a desired way (see BAN 8/18/2009). The firm's IFCs are already being used by stem cell researchers in single-cell expression studies (see BAN 6/30/2009).
Other array companies that have worked with stem cell researchers include Illumina, Invitrogen, and Affymetrix, and the kinds of arrays that have been used in published studies range from whole-genome genotyping arrays to gene-expression and microRNA-expression profiling chips to chromatin immunoprecipitation (ChIP)-chip arrays. This month, for example, a group of researchers from Rensselaer Polytechnic Institute in Troy, NY, published a paper in Biotechnology and Bioengineering describing a three-dimensional cellular microarray platform to track stem cell fate and quantification of specific stem cell markers.