By Allison Proffitt
August 4, 2017 | PerkinElmer announced the launch of PerkinElmer Genetics' clinical genomics services yesterday. Whole genome and whole exome sequencing will be offered through its laboratories in the U.S., India, and China.
“A lot of labs are doing gene panels and exomes,” Dr. Madhuri Hegde, vice president and chief scientific officer for laboratory services of PerkinElmer's Diagnostics business group told Diagnostics World News. “[We are now doing] whole genome sequencing on the [Illumina] NovaSeq platform… and doing from the dried blood spot card.”
PerkinElmer already offers a global genomic lab testing platform that performs screening and diagnostic testing, specializing in newborn screening and high throughput next generation sequencing for rare inherited diseases. Newborn screening is done from a dried blood spot card, a collection of blood spots usually made by pricking a newborn’s heel. The new sequencing services use those dried blood spot cards.
PerkinElmer has done side-by-side validation of a dried blood spot card-extracted DNA, blood-extracted DNA, and saliva-extracted DNA and been able to optimize performance using PerkinElmer’s well-established systems, robotics, and DNA extraction technology called chemagen, Hegde said. The result is high quality sequencing without the cost of additional collection kits.
But Hegde argues that the greatest value from the new PerkinElmer offerings is how the sequencing connects to the existing PerkinElmer test menu. PerkinElmer Genetics processes more than 500,000 samples a year through its Pittsburgh, Penn. and Branford, Conn. CLIA-certified clinical labs. The testing menus include newborn screening, biochemical profiling, 2nd tier molecular confirmatory testing, and Sanger sequencing.
“Most of NGS sequencing comes back with a lot of variants of unknown significance,” she said. “Many times when you pick up a variant of unknown significance, you need to have a functional assay to look at [biochemical] levels, so you can resolve that variant of unknown significance. In our Pittsburgh lab, we can do those biochemical assays… Sequencing is not a standalone solution. It, paired with biochem, is very critical.”
PerkinElmer plans to initially focused on newborn and ViaCord customers, but has also developed a biochemical and molecular testing menu to meet the needs of other segments, such as pharmaceutical companies, and the markets it serves in China and India. Hegde said that in a neonatal intensive care unit, whole genome sequencing can be returned in 10-12 days; biochemical data can be returned in 72 hours. "Bringing all that together in analysis is a huge advantage," she said.
The services are not intended to be direct-to-consumer testing. “That’s not what we’re doing right now; that’s not the intention,” Hegde said. “We’ll watch how things evolve in the LTD [laboratory developed test] world, but tests have to be ordered through a physician and results will be returned to a physician.”
PerkinElmer does have genetic counselors on staff in the Pittsburgh lab and in the Indian lab. The genetic counseling division is expanding, Hegde said. Counseling in this case is focused mostly toward the ordering physicians. In newborn screening, in particular, genetic counselors call doctors with findings immediately because quick action is often essential.
Doctor Services
The clinical laboratory and testing market is becoming crowded, and PerkinElmer is distinguishing its offering from the crowd in several ways. In addition to offering a full menu molecular and confirmatory testing, Hegde said the company is working on ways to empower the doctors who are delivering results.
PerkinElmer has no contact with the patients or families, Hegde said, so the company is exploring partnerships with genetic counseling firms to help ordering physicians connect families to licensed counselors for extended counseling. PerkinElmer has also developed an extensive database of foundations around the world for different genetic diseases. If a test report includes a particular diagnosis, PerkinElmer can inform the ordering physician of foundations dedicated to the disease.
“Physicians really don’t have the time to go hunting for all of these things,” Hegde said. “The clinical report has to be returned in such a way that they not only get the results and the interpretation, but they also get information on what they can do for the patient.”
Press materials for the new whole genome and whole exome sequencing call the tests “affordable.” Hegde declined to attach a number to that—citing volume discounts and partnerships with disease foundations—but she did emphasize that the cost was lower than current offerings. “It is definitely below the current industry price that you can find anywhere,” she said. “We are not adding on cost. Whatever the list price is, it includes everything: the genetic counseling component, reporting.”
The data analysis is done by PerkinElmer’s team of five American Board of Medical Genetics board-certified lab directors, and the sequencing price also includes curation. One of the advantages of doing genome sequencing, Hegde said, is generating “unbiased sequence. When you are doing an exome, you are basically doing target selection, which would result in dropout of regions. But genome data can stored, and you can revisit the data as long as you want.”
PerkinElmer has set up a pipeline for active curation of genomes, Hegde said. As new gene evidence comes out, genome interpretations are constantly being updated. “It’s not like we do this every six months, or every year. This is an active curation process,” Hegde said. “This will be incorporated into our reporting structure. We will do reanalysis of the data and we will communicate actively if there’s a finding that needs to be addressed.”
Because PerkinElmer is not selling or communicating with patients directly, new information will be communicated to the ordering physician. Sometimes the doctor will be in touch with the patient; sometimes she won’t be. Re-contact is a problem across the industry, Hegde said. “This isn’t a problem unique to us. It’s a problem in general. Families move. But from our side, whatever we can do, we will always do it.”