A team of clinicians and bioengineers from Stanford University and Howard Hughes Medical Institute is reporting an exciting new technology that can revolutionize prenatal screening, and also calm the nerves of many expectant parents. A new technique, that scans fetal DNA present in the mother’s blood, can one day replace more invasive, and potentially dangerous, amniocentesis. In addition, the technique examines the fetal chromosomes directly, unlike the other noninvasive nuchal translucency test, that looks for secondary morphological characteristics through ultrasound.
Check out this exciting abstract by Stephen R. Quake, et. al. in the latest PNAS:
We directly sequenced cell-free DNA with high-throughput shotgun sequencing technology from plasma of pregnant women, obtaining, on average, 5 million sequence tags per patient sample. This enabled us to measure the over- and underrepresentation of chromosomes from an aneuploid fetus. The sequencing approach is polymorphism independent and therefore universally applicable for the noninvasive detection of fetal aneuploidy. Using this method, we successfully identified all nine cases of trisomy 21 (Down syndrome), two cases of trisomy 18 (Edward syndrome), and one case of trisomy 13 (Patau syndrome) in a cohort of 18 normal and aneuploid pregnancies; trisomy was detected at gestational ages as early as the 14th week. Direct sequencing also allowed us to study the characteristics of cell-free plasma DNA, and we found evidence that this DNA is enriched for sequences from nucleosomes.
More from the Howard Hughes Medical Institute:
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 noninvasive prenatal testing that relied on measurements of DNA in fetal cells present in the mother’s blood. The report said that the low prevalence of fetal cells – only about one in one million maternal cells – made it difficult to isolate enough of fetal cells to test for chromosomal abnormalities.
At the time, some researchers were trying to isolate fetal “cell-free DNA” from the mother’s blood. Cell-free DNA is fragmented double-stranded DNA that is in the debris of dying fetal cells. Isolating this DNA was a good idea, Quake said, but recovering the vanishingly small amount of fetal 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 amplify the fetal 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 fetus 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 fetal 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 analyze 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 fetuses 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.
Full article: Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood (.pdf) doi: 10.1073/pnas.0808319105
HHMI press release: New Blood Test for Down Syndrome…
Image credit: Wellcome images: Down syndrome human karyotype 47,XY,+21…