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The use of DNA chips in diagnostic testing

Posted in Diagnostic testing, Scientific research by Matt at WelcometoIllinois on December 1, 2008

I previously wrote about the use of “‘microarrays’ or gene chips in the genetic testing process and a new DNA test called array comparative genomic hybridization (aCGH). MIT Technology Review has an overview of the technology.

The DNA chip used in the study performs a process known as array comparative genomic hybridization (aCGH), which involves looking for an abnormal number of copies of particular segments of DNA. Normally, humans have two copies of each segment. Having extra or missing copies can result in serious medical problems. Each DNA chip contains hundreds of single-stranded DNA segments, each embedded in a piece of glass at a precise location. The researchers then add single-stranded, fetal DNA segments, usually taken from amniotic fluid. These strands are labeled red. Single-stranded DNA reference segments, which act as a control group and are labeled green, are also added to the chip. Once the fetal and control strands are bound with the embedded DNA, the arrangement of colors on the chip is imaged and analyzed by a computer.

“Basically we measured the color signal intensity,” said [Sau Wai Cheung, director of Baylor College of Medicine’s Cytogenetics Laboratory]. If the fetus has an extra copy of a particular segment of DNA, then the spot on the chip that corresponds to that DNA segment will appear more red than green. If the fetus is missing a DNA segment, the corresponding spot on the chip will appear more green than red. And if the fetus has the correct number of copies of the DNA segment, then the spot should appear yellow.

To put this in some context:

“The process normally used for prenatal diagnosis is karyotyping, which looks at the overall size and shape of chromosomes to identify problems. [Cheung] says the new research shows that DNA chips can reliably detect far smaller chromosomal abnormalities than karyotyping allows. And while these abnormalities may be small in size, they can have a big impact. “A lot of the diseases that we tested for [in this study] cause mental delays and problems with physical development,” said Cheung. Angelman syndrome, for example, can result in significant developmental problems and seizures.”

The study at Baylor included 300 cases and identified seven cases where the aCGH results provided new information about the risk of disease, “including two cases that would otherwise have been missed”. On the downside still requires an invasive testing procedure and has not been widely studied at this stage.

In fact, I previously mentioned the technique in the context of a warning from Leslie G. Biesecker of the federal government’s National Human Genome Research Institute, that the tests do not provide enough information to know whether genetic abnormalities will actual cause a disorder, or how severe the effects might be.

The MIT Technology Review story raises the same issue, as Diana Bianchi, professor of pediatrics, obstetrics, and gynecology at Tufts University School of Medicine and the editor in chief of Prenatal Diagnostics (which published details of the Baylor study): “The downside of aCGH is you pick up these copy-number variants that may or may not have clinical significance, and in the worst case [the impact] may be unknown.”

The reports adds: “Knowing that an unborn child has genetic abnormalities but not knowing how those might affect the child’s development could leave many parents scared and confused, Bianchi says.”

Of course that is the exact same issue that impact parents receiving screening and diagnostic test results today, but no one seems to bother about that.

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2 Responses

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