New technique permits rapid prenatal test for Down syndrome, other conditions

Researchers have invented a faster technique for prenatal testing of Down syndrome and other birth defects that could provide results within just a few hours instead of a few weeks.

Parents currently wait about two weeks to get the results of a test - either amniocentesis or chorionic villus sampling - to detect Down syndrome and other birth defects that involve an abnormal number of chromosomes. With this new method, the genetic material obtained from the cells of the fetus can be accurately tested using a bioengineering technique that requires little waiting time.

'As any anxious parent who has had an amnio knows - I've been through this twice - there's a great deal of stress while you're waiting to find the results,' said Stephen Quake, PhD, professor of bioengineering and lead author of the study. 'It would be phenomenal to get the answer right away.'

The study will be published in the Oct. 1 issue of the American Chemical Society's journal Analytical Chemistry, and is available now online. The researchers next plan to begin clinical trials of the new test using actual clinical samples, with the possibility of it being available to the public within a year.

The rapid test was made possible with a microfluidic chip, often called a 'lab on a chip' because it can perform many tests at once, based on groundbreaking work by Quake and his colleagues.

To conduct their study, Quake and bioengineering graduate student Christina Fan used genomic DNA from two cultures of cells grown in the laboratory. One consisted of a normal human cell line and the other had human cells with the Down variant.

Instead of using the conventional prenatal testing technique termed karyotyping - which requires the cells to be cultured in a lab for two weeks - the researchers used a process known as 'digital polymerase chain reaction.'

The digital PCR was performed on the microfluidic chip, which has many tiny channels that convey vast amounts of information. The samples were loaded onto the chip and then partitioned into thousands of chambers by microscopic mechanical valves so that there is less than one DNA molecule per compartment.

The PCR reaction contains fluorescent probes that bind to DNA. While PCR was performed, the compartments containing individual DNA molecules lit up, while those without DNA did not glow. Researchers could then count DNA molecules from the samples and determine which samples had the extra chromosome that indicates Down syndrome.

Simply put, digital PCR is a way to count molecules, Quake said.

'We take the molecules from the sample we're interested in and distribute them in lots of chambers. What we're doing is using thousands of different test tubes,' he said.

The microfluidic chip is a device that makes this division into a thousand different test tubes automatically. Without the chip, this method would be impractical, Quake added.

'The test can be completed in two to three hours,' said Fan. 'It's pretty easy.'

The microfluidic chip used in the study is a commercial product made by Fluidigm, a biotech company Quake co-founded in 1999. Quake owns stock in the company and is chair of its scientific advisory committee.

Other rapid prenatal tests exist, but they lack the precision of digital PCR and have a variety of practical limitations, Quake said.

Jane Chueh, MD, clinical associate professor of obstetrics at Lucile Packard Children's Hospital, said many physicians have been hesitant to use these other tests because they don't provide as much information as the conventional karyotyping method, and they prefer to wait to give parents all the results at one time.

'I think this could be fabulous,' said Chueh. 'But it has to be as good as a conventional amnio. I think you'd probably still have to do the culture for more details.' She's referring to the detection of other abnormal or damaged chromosomes, such as inversions, that can't be found by counting but can cause disorders such as mental retardation.

Quake and Fan also hope to someday make this test available using blood samples, ultimately avoiding the necessary invasive needle extraction of amniotic fluid for the prenatal test, Quake said.

'In the last 10 years, scientists have discovered fetal genetic material floating in the blood of the mother,' Fan said. 'We're trying to apply this digital PCR technique to blood samples. That's the ultimate test.'