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As More Labs Introduce Array-based Prenatal Dx Tests, Debate Rages over Indication, Platform Choice


Cytogeneticists are increasingly adopting chromosomal microarrays for prenatal diagnostics, but have not yet reached a consensus when it comes to what kinds of cases should undergo array-based screening and which platform is best to use.

In addition, findings of unknown clinical significance continue to slow the uptake of the technology for prenatal testing, as some in the cytogenetics community hope that time, and experience, will put to rest most of the questions about the new technology and the data it provides.

The status of array-based prenatal testing was perhaps summed up best by Richard Choy, an associate professor of obstetrics and gynecology at the Chinese University of Hong Kong. In a presentation at the European Society of Human Genetics annual meeting — which was held in Nuremberg, Germany, two weeks ago — Choy said that arrays should replace karyotyping as a first-tier test for prenatal diagnostics. At the same time, he said that array technology is "not popular" in the cytogenetics community because of the questions surrounding it.

"It is not popular because there are too many issues," Choy told BioArray News at the meeting. One is the issue of correlating genotypes to certain phenotypes. Another is the existence of copy number variants of unknown significance. "Once these two issues have been solved, I am sure people will use arrays, because we really have increased the detection rate of pathological copy number variants," he said.

Choy and his colleagues in Hong Kong have been offering array-based prenatal testing since 2009. The lab designed its own array, called the Fetal DNA Chip, which is manufactured by Agilent Technologies. Choy's group chose to design its own array, rather than use an off-the-shelf offering, because the "spectrum of copy number variants is very different in the Chinese population" than in the Western population that has served as the basis for most commercial chips. It's an issue that sheds light on another issue confronting those who would like to offer array-based prenatal diagnostics: choice of platform.

Dom McMullan, head of molecular cytogenetics at the West Midlands Regional Genetics Laboratory in Birmingham, UK, told BioArray News at the meeting that his lab has decided to evaluate Affymetrix's CytoScan HD platform because the high-resolution chip can detect copy number neutral loss of heterozygosity. According to McMullan, autozygosity mapping is "particularly relevant in [places like] the [UK's] West Midlands with a large Asian population in which first cousin marriage is common, particularly in the Pakistani community" (BAN 7/3/2012 ).

Some geneticists have called for arrays to replace traditional, microscope-based karyotyping as a first-line test for prenatal diagnosis. Notably, a US National Institutes of Health-funded project found earlier this year that arrays are more informative than standard karyotyping, leading some to suggest that major professional organizations could revise their guidelines to recommend arrays as a first-tier test (BAN 2/21/2012).

But, according to McMullan, things are proceeding at a slower pace in the UK, where labs are looking to adopt chromosomal arrays only in pregnancies with an abnormal ultrasound scan. McMullan said that there is an ongoing seven-center study funded by the National Institute for Health Research that, upon conclusion, is likely to inform best practice in the UK moving forward.

"Reporting findings of unclear clinical significance has been a difficult area since the introduction of prenatal diagnosis by chromosome analysis," said McMullan. "It is not really a new problem, just likely to be more common with use of arrays and at a different level of resolution."

Ellen van Binsbergen, a clinical cytogeneticist at University Medical Center Utrecht, told BioArray News at the meeting that her lab has decided to implement array-based prenatal diagnostics in a "secure group" of cases with "severe" ultrasound abnormalities that are most often terminated.

"It feels good to provide an additional bit of information to the parents that gives them some reassurance that there actually was something wrong," said van Binsbergen. She noted that some cytogenetists feel apprehensive about offering chromosomal microarray analysis for lower-risk indications, such as advanced maternal age.

"You are going to wonder what happens if you encounter one of those autism-associated regions and you don't know if it is going to result in a phenotype," van Binsbergen said. "Most parents have a general knowledge of DNA, and when you use the word 'syndrome' they are going to freak out," she said. "So I think we should be aware of what indications you should allow to test for."

Van Binsbergen's lab is using an Agilent whole-genome comparative genomic hybridization array in its select prenatal cases. "We decided to use the same platform for prenatal that we are using for postnatal because I don't want to create a sense of false security," she said. "I want to look at the whole genome, not use a targeted chip for prenatal."

While cytogeneticists debate the indications for which chromosomal microarrays should be available, or what array is best to use, Francesco Fiorentino, director of Rome-based molecular genetics laboratory Genoma, told BioArray News at the meeting that in May his lab replaced karyotyping with chromosomal microarray.

Fiorentino said that the extent to which chromosomal microarrays are used in prenatal diagnostics is linked to the extent prenatal testing is done in a particular country. Since all couples are eligible for prenatal testing in the US, array-based screening is available too, he maintained.

"Once you go through invasive prenatal diagnosis, of course, the woman, or the couple, would like to have the best tool to detect something that is not detectable by traditional karyotyping," said Fiorentino. "We have been using karyotyping for over 40 years, but the time has come to use the new technology."

According to Fiorentino, Genoma ran an internal comparison of microarray and traditional karyotyping on 1,000 cases that found that arrays were a better tool for detecting constitutional abnormalities. A paper describing that study appeared last year, and a second has been submitted to a major journal, he said.

And, like Choy, McMullan, and van Binsbergen, Fiorentino has his own taste in technology. He said that Genoma has opted to use BlueGnome-manufactured bacterial artifical chromosome CGH arrays because of the platform's ability to work with scant sample materials and because the lower-resolution BAC arrays provide users with fewer results of unclear significance, demonstrating again that, when it comes to array-based prenatal testing, cytogeneticists are figuratively and literally all over the map.