Skip to main content
Premium Trial:

Request an Annual Quote

In Some European Clinical Cytogenetic Labs, Arrays Have Become Primary Sample-Analysis Tool

Premium

By Justin Petrone

After years of selectively offering array-based tests to patients, some European clinical cytogenetic labs have recently begun using arrays as the primary sample-analysis tool in their services, rather than traditional cytogenetic methods like molecular karyotyping or fluorescent in situ hybridization.

According to several European cytogeneticists interviewed by BioArray News, the switch to arrays occurred over the past year as a result of falling array prices and because lab techs have become more confident in their ability to interpret results as they have gained more experience with the technology.

"In the beginning, only patients with a normal cytogenetic karyotype were allowed to continue on with array analysis," said Nicole deLeeuw, a clinical cytogeneticist at the Radboud University Nijmegen Medical Center Department of Human Genetics in the Netherlands.

"Now, in at least three centers in the Netherlands, we decided to put arrays first because basically you get a three-in-one outcome within one test," she said. "Instead of cytogenetics and FISH and [multiplex ligation-dependent probe amplification screening], with genome-wide array analysis, you can pick up all imbalances with one test."

DeLeeuw said the other Dutch centers that have decided to put arrays first are the Department of Human Genetics at the University Medical Center Groningen and the Center for Human and Clinical Genetics at Leiden University Medical Center.

Trijnie Dijkhuizen, a clinical cytogenetist at Groningen, confirmed with BioArray News that her lab decided last year to screen patient samples with arrays before using other technologies, saying arrays "are first, and in addition we do some cytogenetics," referring to FISH and MLPA.

According to Dijkhuizen, "all eight" academic medical centers in the Netherlands that provide clinical cytogenetic services offer array diagnostics, though they are in different stages of adopting the technology. In addition to Nijmegen, Groningen, and Leiden, the other five centers that offer array-based testing are the Department of Clinical Genetics at University Hospital Maastricht; the Institute of Clinical Genetics at Erasmus MC in Rotterdam; the University Medical Center Utrecht; the VU University Medical Center in Amsterdam; and the Academic Medical Center at the University of Amsterdam.

Across the border in Belgium similar protocol shifts are underway. Joris Vermeesch, associate professor at the Department of Human Genetics at the University of Leuven, told BioArray News this week that clinical cytogeneticists who send samples to Leuven for analysis are now requesting arrays first, while Björn Menten of the Center for Medical Genetics at Ghent University Hospital said his facility is increasingly using arrays in a clinical setting.

Like Nijmegen's deLeeuw, Menten and colleagues first started using arrays as the primary technology about six years ago for research purposes, and have recently begun using the tools in the clinic.

"In the beginning, we selected patients for array analysis. Now that prices are dropping, we can offer it to everyone," Menten told BioArray News. "Really, since the beginning of 2009, it has completely moved to diagnostics. [For instance,] in postnatal cases it is replacing normal karyotyping. All patients will now have microarray analyses performed."

Early Adopters

According to Vermeesch, cytogenetic labs in the Netherlands and Belgium have been among the earliest adopters of array technology in Europe, though there are other "leading laboratories" that have begun using the technology, including the Department of Molecular Medicine at the Karolinska Hospital in Stockholm, Sweden; and the Cyprus Institute of Neurology and Genetics in Nicosia.

In Vermeesch’s lab, the switch to arrays has evolved over more than six years. In the past, Vermeesch has used both bacterial artificial chromosome arrays as well as oligonucleotide-based chips to analyze neonatal samples, but in June he began evaluating arrays designed by Oxford Gene Technology for prenatal diagnostics (see BAN 6/30/2009).

At Nijmegen, arrays took a similar route into the clinic. "We started offering these services in 2003 and we had a solid report at the end of 2004," deLeeuw said. "In 2003 and 2004, the numbers of requests were limited and only clinical geneticists were able to ask for array-based diagnostics in a very selective population of patients. We did that partly because we wanted to gain experience and offer them more than routine cytogenetic analysis."

[ pagebreak ]

According to deLeeuw, Nijmegen began offering its array services on a homemade platform before switching to a genome-wide bacterial artificial chromosome array, which it used until 2006 when it adopted the Affymetrix platform. She said that the center currently uses the firm's 250K SNP chip.

Cytogeneticists at Groningen, meantime, began using homemade arrays in 2003 and switched to an Agilent Technologies platform four years later, Dijkhuizen said. Menten's lab in Ghent also recently adopted the Agilent platform for use in its clinical services.

"We started with BAC arrays and evolved to Agilent arrays," Menten said. "There is a lot of discussion on which array you should use. It's hard to say what the best strategy is," he said.

"In Belgium, we are also interested in research to detect new genes that are important for congenital abnormalities,” he added. “That's why we want to have a whole-genome array — so you can detect new things."

Over the same past few years in which these labs began switching to arrays, they also began experiencing a growing case load. During its first year of offering its service, for example, Nijmegen dealt with fewer than 100 cases, deLeeuw said. Last year, the number swelled to 950, while as of Sept. 30 the center had handled 1,700 cases in 2009, she said.

Leuven's Vermeesch reported that the center expects to serve 1,500 patients this year, up from around 200 patients in 2006. "We expect further growth in the coming years," Vermeesch added.

Groningen's Dijkhuizen and Ghent's Menten also reported sizable increases in case numbers, resulting in part from increased availability of commercially made array platforms. Groningen runs about 600 samples per year, Dijkhuizen said, and Ghent deals with about 1,000 cases a year, according to Menten.

Regulations and Reimbursement

As the use of arrays in early-adopter cytogenetics labs evolved from research projects to diagnostics, labs typically validated their array-based approaches internally before offering them to clinical geneticists.

"Whenever we started using an array, we validated the controls, then proved with the array that we could detect at least as many aberrations as we could with cytogenetics and FISH," said deLeeuw.

"After the numbers increased and we could guarantee a certain reporting time, we spread the news," she said of the service.

According to deLeeuw, Dutch centers have not gone through a formal approval process to begin offering their tests as diagnostics. Instead, the eight centers that offer array-based clinical cytogenetic testing have set the rules on how to best run such services.

"We did not request permission from an institute, but we did discuss it with colleagues in other clinical genetic centers, about how to report, when to report, et cetera," deLeeuw said. "It's always been with the other eight centers that offer this testing in the Netherlands that we have discussed it together."

In addition, the five labs that use Agilent-manufactured platforms and the three that use Affy regularly meet, she said.

In Belgium, both Menten and Vermeesch needed approval from ethics committees at their respective institutions before they could formally begin offering their array-based tests as clinical diagnostics. "The regulations in Belgium are not that strict. We don't really need to have approval for these tests," said Menten. "We need approval from an ethics committee at the hospital."

As in the Netherlands, Belgian clinical cytogenetics labs have sought to collectively regulate the way they provide their services. Menten said that working groups formed within the Belgium Society for Human Genetics have sought to tackle issues related to array-based testing, both in a prenatal and neonatal context.

According to Menten, all genetic centers in Belgium that offer array-based cytogenetic testing take part in the discussions. "Even though we are using different kinds of arrays, we agree that you should offer same kind of counseling and services to your patients," he said.

[ pagebreak ]

While centers in the Netherlands and Belgium have been able to introduce their services under relatively liberal regulatory conditions, representatives from both countries expect greater regulation in coming years, partially due to reimbursement issues.

In the Netherlands, where private insurance is mandatory for residents, centers have been getting reimbursed by private insurers, but at a fraction of the cost of the test, as all cytogenetic tests are reimbursed at the same rate. "In the Netherlands, no matter what you request, whether it is routine cytogenetic analysis, FISH, or arrays, there's a certain amount of money you get for any of these tests," said deLeeuw.

According to deLeeuw, it would make sense to set a new reimbursement amount for array-based tests, which would require additional validation of the tests.

"There have to be some changes. It's quite an expensive technique," said Groningen's Dijkhuizen. "It costs more than we get for it. There is always tension between the financial aspects of the service and doing as much as possible for patients."

Menten said that, as in the Netherlands, Ghent received "limited reimbursement" for doing molecular genetic testing in Belgium, which has a dual state- and private-insurance-based healthcare system. While it covers current costs, it will be expensive for Ghent to upgrade to higher-density arrays in the future, according to Menten.

"The situation is definitely going to change in Belgium. Probably within some years we will have to get some accreditation," Menten said. "The test should be further validated and we should apply further standards," he said. "You can offer the test if you don't do this, but if you won't get paid for doing the test."

Menten said that undergoing further validation and refining the test process to meet the standards of the state will be, in the end, a "good thing." He said that there "should be some regulations so that any lab can't start up and offer a test without any quality control."

Leuven's Vermeesch also forecast increased regulation for array-based cytogenetic tests. "In the future, I expect [external quality assurance] schemes to become activated as well as a formal reimbursement system to come into place," he said.

The Scan

Back as Director

A court has reinstated Nicole Boivin as director of the Max Planck Institute for the Science of Human History, Science reports.

Research, But Implementation?

Francis Collins reflects on his years as the director of the US National Institutes of Health with NPR.

For the False Negatives

The Guardian writes that the UK Health Security Agency is considering legal action against the lab that reported thousands of false negative COVID-19 test results.

Genome Biology Papers Present Epigenetics Benchmarking Resource, Genomic Architecture Maps of Peanuts, More

In Genome Biology this week: DNA methylation data for seven reference cell lines, three-dimensional genome architecture maps of peanut lines, and more.