This story was originally posted on June 17.
Encouraged by the resolution and speed of chromosomal microarray analysis, as well as several recent studies that compared CMA with conventional cytogenetics, more laboratories are turning to array technology to better understand the genetics of pregnancy loss.
At the same time, labs are facing challenges related to the price of the assays, which in some cases can cost close to $2,000 per analysis, as well as how to communicate findings of unknown clinical significance to mothers at risk of miscarriage.
Stephanie Romero, a maternal fetal medicine fellow at the University of Utah in Salt Lake City, discussed the advantages and pitfalls of using arrays to study pregnancy loss at the Association of Genetic Technologists meeting, held last week in Las Vegas.
In her presentation, Romero portrayed the need for array technology as "real," because as many as one in three women experience pregnancy loss in their reproductive lives. At the same time, conventional cytogenetics such as molecular karyotyping and fluorescence in situ hybridization often fail as cytogeneticists are unable to culture samples obtained from miscarriages and stillbirths, also known as products of conception, in up to 40 percent of cases. In comparison, arrays can obtain data from POC that fail to culture, she noted.
She also praised arrays' ability to detect "very small" deletions and duplications and loss of heterozygosity, the "very accurate" results they provide, and a "fast turnaround" of about seven days.
Other factors that caused Romero to adopt array technology were two National Institute of Child Health and Human Development-sponsored studies that appeared in the New England Journal of Medicine in December 2012 (BAN 12/11/2012).
One study, led by NICHD's Uma Reddy, focused exclusively on stillbirth, and found that arrays provided a genetic diagnosis 87 percent of the time, versus karyotyping, which yielded results 71 percent of the time. Another study, led by Columbia University Medical Center's Ronald Wapner, indicated that chromosomal microarrays can provide more clinically relevant information than traditional karyotyping in prenatal cases, and recommended that the technology should become the standard approach in prenatal diagnostics going forward.
"I began using [CMA] clinically in July 2012, after seeing the preliminary results of my own research as well as the publications in the NEJM by Dr. Reddy about the use of CMA in stillbirth and by Dr. Wapner about use of CMA in prenatal diagnosis," said Romero.
"I think that the combination of the two papers … were quite significant, and that as a result many more practitioners will be using CMA," she added. "Within maternal fetal medicine, it did receive substantial attention."
While Reddy, Wapner, and their coauthors suggested arrays become a first-tier test in detecting the causes of pregnancy loss and prenatal diagnostics, Romero said she has taken a more nuanced approach to implementing the technology, which, in the case of her lab, is Affymetrix's CytoScan HD.
"In my clinical practice, I am offering it to patients with losses greater than 10 weeks or if it is their third loss or beyond at less than 10 weeks," said Romero. "I have also been offering it to patients who have babies with anomalies on ultrasound or who have abnormal serum screening but whose karyotype from amniocentesis or [chorionic villi sampling] shows no abnormality."
She added that she also uses CMA in research projects to test samples from subjects with pregnancy loss less than 20 weeks, with no attention to their pregnancy history.
Some of the reasons that Romero has opted to use arrays in select circumstances include the cost of the technology, certain technical limitations, and the conundrum of communicating findings of unknown significance back to patients.
In her talk, she said that CMA can cost about $1,900 per analysis, which is roughly four times the price tag of FISH, and more than seven times the cost of conventional karyotyping. Another issue is reimbursement. "CMA is not always covered by insurance," said Romero, "and in cases where it is not, most patients simply cannot afford it." She added that CMA is "also not helpful in diagnosis of tetraploidy or defining translocations, which can be important causes of pathology."
But the biggest problem confronting labs that would like to implement CMA is what Romero referred to in her talk as "toxic knowledge." While most patients are eager to learn more about the genetic factors that may be the cause of their pregnancy loss, Romero said that some have had a negative reaction to obtaining ambiguous array results.
"We are working closely with the genetic counselors and pathologists at our institution to develop some protocols for how we will deal with this tricky issue," Romero said. "As with many other areas in prenatal care, there is a careful balance to be struck between full disclosure of all results on one end, and revealing only that information which someone arbitrarily designates as worthy of discussion on the other."
Like Romero, Sheri Hedrick also recently began using CMA to test POC. Hedrick, a cytogeneticist at Nationwide Children's Hospital in Columbus, Ohio, presented a poster at AGT describing her lab's validation of Agilent Technologies' comparative genomic hybridization arrays to test POC.
In the poster, Hedrick and colleagues reported how arrays were able to yield results from degraded DNA samples as well as contaminated cultures, making it a "viable avenue of study," in her words, for POC samples.
"One of the things that's really great about it is that the microarrays can go on the POC that don't grow," Hedrick told BioArray News at the conference. "Sometimes the baby will die in utero and you won't know for two weeks," she said. "You can tell by looking at the sample that it's not going to grow, though we still try," Hedrick added. "But if that doesn't grow, we can always send it over for microarray, and we can get results from the dead sample, because they only need the DNA, they don't need to grow it out."
Hedrick agreed with Romero that arrays offer some advantages over karyotyping.
"There is a lot you can't see from just karyotyping," Hedrick said. "Tissue chromosomes are quite tight, so if you have a microdeletion or microduplication, there's a lot that you can't see," she said.
At the same time, she noted similar limitations to array technology.
"You have to remember that it's not showing balanced rearrangements, so if you are looking for the cause of a miscarriage, a sample could have a balanced rearrangement and it wouldn't show," said Hedrick. "If the baby did have a translocation, she could have it the next time and the next time, and you wouldn't see that with the array."
Because of these limitations, plus similar issues regarding cost and reimbursement, Hedrick said that Nationwide is currently "reflexing to microarray" in necessary cases, rather than using it as a first-tier test.
Romero said that she believes other cyto labs are taking a similar approach, though that could change if more insurance companies decide to reimburse the tests.
"The word I hear from colleagues at other institutions is that they are doing a similar 'karyotype with reflex to microarray if normal' in cases of prenatal diagnosis," said Romero. "I bet the limiting factor for most is cost, but once insurance companies begin to pick it up more reliably, it will become a common testing modality."
With regard to other new technologies, Romero described the use of next-generation sequencing for testing POC as "experimental" and "not yet widely available," an opinion that Hedrick agreed with.
"I don't have much to say about sequencing," said Romero. "It is not anything we are doing, and I don't think we'll be picking it up any time soon."