RainDance Targeted Gene Panels Are in High Demand at Greenwood Genetic Center’s CAP/CLIA Lab
At Greenwood Genetic Center (GGC), a South Carolina-based nonprofit medical genetics institute that offers clinical genetic services and diagnostic testing, a targeted panel analyzing genes commonly implicated in X chromosome-linked intellectual disability (XLID) has rapidly become one of the most frequently ordered tests.
Monica Basehore, PhD, Director of the CAP- and CLIA-certified Molecular Diagnostic Laboratory at GGC, says that the XLID test is based on a next-generation sequencing workflow using targeted gene panels from RainDance Technologies and sequencing on Life Technologies’ SOLiD 5500 platform.
Basehore joined GGC in 2008, and her primary responsibilities include directing operations of the clinical diagnostic laboratory, overseeing lab technicians, reviewing and interpreting molecular test results, writing diagnostic reports for the referring physicians, performing new assay development, and offering training to diagnostic laboratory fellows. All of these activities center on the CAP- and CLIA-certified lab, which means everything has to be conducted under quality controlled protocols with documentation, validation, and attention to detail. For any tool brought into the lab — from commercial reagents to new technology platforms — Basehore’s team must follow in-house validation protocols. Once that process has been accomplished, “then we can offer the test diagnostically,” she says.
Basehore’s facility has a veritable cornucopia of testing options — each geared toward detecting a particular type of DNA-based mutation. Multiplex ligation-dependent probe amplification (MLPA), for example, is used to identify large deletions or duplications. Southern blotting works best for triplet repeat expansions, while sequencing is used for detecting single nucleotide changes, such as point mutations or single-basepair deletions or duplications. Using all of these technologies and more, Basehore’s team processes some 7,500 samples per year. “Ultimately our goal is to get patients accurate results in the quickest time possible from a test that costs them the least amount of money,” Basehore says.
That goal led Basehore to RainDance, which offered a targeted sequencing solution that fit her needs and had been highly recommended to her by colleagues in the diagnostic field. “When we design these targeted panels for analysis by next-generation sequencing, we need to enrich for just those regions that we’re interested in,” says Basehore, who uses the RDT 1000. While her lab is planning to add exome sequencing to its repertoire, “we do not currently plan to take away the targeted panels,” Basehore says. “You get much better coverage when you’re using a targeted panel. If you know where you need to be looking, using a targeted panel is the best way to go.” Targeted sequencing also avoids the clinical challenge of incidental findings, which is far more common with exome or whole genome sequencing. Basehore says her team “has been very happy” with RainDance’s platform, which provides excellent coverage of targeted regions.
Indeed, the GGC Molecular Diagnostic lab has recently ramped up the number of tests it can offer using RainDance’s targeted sequencing approach. After launching their first two panel tests — the 90-gene XLID panel in late 2010 and a 62-gene syndromic autism panel in early 2012 — Basehore’s team has spent the last several months working to validate and offer four new tests. In early 2013, they launched a 74-gene panel for lysosomal storage disorders; a highly targeted, 10-gene panel for common causes of skeletal dysplasias; and a 31-gene panel for connective tissue disorders such as Marfan syndrome. Up next is a 103-gene panel for epilepsy that is currently undergoing GGC’s stringent validation process.
As Basehore and her team consider all available sequencing options, they continue to forge ahead with gene panels on the RainDance platform. Basehore is so pleased with the platform that she encourages prospective users to contact her to find out more about how it works and her team’s experience using it. “Talking to people who are using it is some of the best help you can get when choosing a technology,” she says. “We’d be happy to serve as a reference.”
— Meredith Salisbury