Blood test for Down syndrome

Researchers have developed a prenatal blood test that accurately detected Down syndrome and two other serious chromosomal defects in a small study of 18 pregnant women. If confirmed in larger trials, they say, the test would offer a safer and faster alternative to invasive prenatal tests such as amniocentesis that pose a small risk of miscarriage.

Researchers have long known that a pregnant woman's blood contains small amounts of DNA from the foetus. Howard Hughes Medical Institute researcher Stephen R Quake and colleagues at Stanford University devised an ingenious way to the scan foetal DNA present in the mother's blood to determine whether the foetus's cells contain extra chromosomes associated with several types of severe birth detects.

The test developed by Quake's team was more accurate than techniques used in previous efforts to diagnose aneuploidy by analysing foetal DNA. Aneuploidy occurs when there are either too many or too few chromosomes in cells. Down syndrome, for example, is caused by a trisomy — three copies instead of two — of chromosome 21.

“We believe this is the first demonstration of a universal, non-invasive test for Down and other aneuploidies,” said Quake, senior author of the research article, which was published online in the early edition of the Proceedings of the National Academy of Sciences (PNAS) on 6 October 2008. “We need a larger clinical study to understand a bit more about the best way to implement it, but I am highly optimistic it will be used as a diagnostic test in short order.”

With the new test, scientists only need to draw a small amount of blood from the woman. The blood is analysed and the results are available within a couple of days, said Quake, who is a bioengineer at Stanford.

Quake's interest in developing new technology to diagnose aneuploidies was sparked when he read a research article published in the journal Science in 2005. That article discussed new methods of non-invasive prenatal testing that relied on measurements of DNA in foetal cells present in the mother's blood. The report said that the low prevalence of foetal cells — only about one in one million maternal cells — made it difficult to isolate enough foetal cells to test for chromosomal abnormalities.

At the time, some researchers were trying to isolate foetal ‘cell-free DNA’ from the mother's blood. Cell-free DNA is fragmented double-stranded DNA that is in the debris of dying foetal cells. Isolating this DNA was a good idea, Quake said, but recovering the vanishingly small amount of foetal cell-free DNA remained a challenge.

After reading the Science article, Quake thought to himself, "A lot of my work is about counting molecules; this is one problem I know how to do." He had a brainstorm: where other researchers were developing various ways of amplifying the foetal DNA signal to distinguish it from maternal DNA, Quake proposed a bold shortcut — skipping that step entirely. After all, he observed, the point of screening was to spot extra chromosomes in the woman's blood sample. Whether the DNA being scanned was from the foetus or from the mother didn't matter. The objective, therefore, was simply to measure the amount of DNA in fragments mapped to the different chromosomes.

Conveniently, the cell-free DNA floating in the mother's blood circulation normally exists in short pieces, averaging 169 nucleotides in length. Quake proposed a ‘shotgun sequencing’ strategy where he would use the very latest high-throughput gene sequencing technology and equally powerful computers to identify millions of unique sequence ‘tags’ in the foetal DNA. Each of these tags was a 25 base-pair fragment of DNA. After the tags were identified, Quake's group could then map them to specific locations on the 23 pairs of chromosomes. By using this strategy, the researchers believed they could detect higher-than-normal amounts of DNA belonging to the three chromosomes involved in the most common aneuploidies — chromosomes 21, 18, and 13.

In the experiments reported in PNAS, Quake and his colleagues, including first author H Christina Fan, a graduate student in bioengineering at Stanford, used their new technique to analyse DNA in blood samples from 18 pregnant women who were undergoing invasive prenatal testing (and one man, for reference).

When the amounts of DNA corresponding to each chromosome were plotted on a graph, significant, above-normal peaks appeared when a chromosome was present in three copies instead of two. These signals enabled the scientists to correctly identify the 12 women who carried aneuploid foetuses and the six whose pregnancies were normal.

Their results matched those of amniocentesis or CVS test that were done on the women.

Quake said the shotgun-sequencing system is not only safer than invasive techniques but can also make a determination at an earlier gestational age, around 12 weeks.

Quake's group is now planning a follow-up study to evaluate the test in a larger group of patients.