Nature Medicine | Spoonful of Medicine

Microarrays outperform karyotyping in prenatal diagnoses

Testing fetal DNA for fine-scale copy number variations can reveal more genetic defects than standard karyotyping methods that look for genetic abnormalities in developing fetuses on a whole-chromosome level, according to the largest clinical trial of its kind.

“These findings will undoubtedly cause many clinical and laboratory geneticists to consider whether chromosomal microarrays should be recommended as a first-tiered prenatal diagnostic test,” says Cynthia Morton, director of cytogenetics at the Brigham and Women’s Hospital in Boston, who was not involved in the trial.

Karyotypic staining analyzes the composition and structure of chromosomes to reveal abnormal changes in chromosome number and shape that are commonly implicated in disease. This technique is currently the gold standard for detecting prenatal genetic defects, but is far from perfect. Karyotyping routinely misses small genetic aberrations and the method only works on cultured cells. To overcome these limitations, researchers have recently turned to a method known as ‘array-comparative genomic hybridization’, which relies on a small chip embedded with millions of molecular probes that recognize particular genomic DNA regions and pinpoint genetic abnormalities too small to be detected by current methods. And as an added bonus, it works on any tissue, living or dead.

Such ‘chromosomal microarrays’ have historically only been used in small scale studies for prenatal diagnostics. But now, a team led by Ronald Wapner, director of Maternal Fetal Medicine at the Columbia University Medical Center (CUMC) in New York, has tested fetal DNA from more than 4,400 expectant mothers at 29 centers across the US using both standard karyotyping and chromosomal microarrays. Microarray analysis, the researchers found, detected chromosomal deletions or duplications in 6% of cases in a group that was flagged as structurally abnormal by ultrasound but scored normal by karyotyping and also revealed genetic abnormalities in about 2% cases missed by karyotyping in another group with advanced maternal age.

“The advantage of microarrays is their high resolution and sensitivity, which allows detection of events at the level of genes, as opposed to the level of chromosomes for karyotyping,” says Wapner, who published the results today in the New England Journal of Medicine (NEJM).

Also today in NEJM, a team led by Uma Reddy, an obstetrician-gynecologist at the US National Institute of Child Health and Human Development in Bethesda, Maryland, compared the ability of microarrays and karyotyping to diagnose the cause of more than 500 stillbirths. Because of the challenges associated with culturing tissue from a dead fetus, karyotyping failed to give results in 30% of cases, whereas microarrays, which don’t require live cells, yielded a genetic culprit in 87% of stillbirth cases. “With microarrays, you are more likely to obtain a result, which is important for families waiting for answers,” says Reddy.

Chromosomal microarray diagnosis is not without its challenges, though. For one thing, the increased resolution of the technology means that microarrays can detect genetic variants without known phenotypes, although this problem should dissipate as new research emerges. For example, when Wapner and his colleagues first analyzed pilot data from their trial five years ago, they could not find disease associations in 2.5% of cases. When they reanalyzed the data this year, the rate fell to 1.5%.

Microarrays are also less informative than newer genetic techniques such as whole-genome sequencing. In the same issue of NEJM, Morton and her colleagues used DNA sequencing to identify the exact breakpoints of chromosomal rearrangements, something that microarrays are unable to do. In this way, they successfully diagnosed a genetic disorder known as CHARGE—coloboma of the eye, heart anomaly, atresia of the choanae, retardation and genital and ear anomalies—from the amniotic-fluid of a woman in the third trimester of her pregnancy.

There is a concern that the interpretation problem could be exacerbated as researchers move toward full genome sequencing in utero. However, according to Brynn Levy, director of the CUMC’s Clinical Cytogenetics Laboratory and also an investigator in the prenatal diagnostics and stillbirth trials, the transition from microarrays to sequencing prenatal diagnostics “will be easier in terms of the framework because we already set the paradigm.”

Because of the limited number of cases, the American College of Obstetrics and Gynecology (ACOG) was cautious in endorsing microarrays as a primary tool for prenatal diagnosis. Whereas there is still no official statement regarding these new findings, Levy expects ACOG to consider microarrays as the first tier of prenatal diagnostics considering the much larger size of the latest trial.

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