Fetal genome sequenced without the father's DNA

Who's your daddy? Clinicians seeking to pinpoint genetic diseases in developing fetuses may no longer need to know the identity of the father, thanks to a method for sequencing a fetus's genome using just a blood sample drawn from a pregnant woman.

Researchers have known for some time that during pregnancy a small amount of fetal DNA passes through the placenta and into the mother's bloodstream. Several commercially available genetic tests use this DNA to test for chromosomal abnormalities such as Down's syndrome in the fetus by simply drawing a blood sample from the pregnant woman's arm.

Such non-invasive testing of fetal genetics is attractive as other prenatal tests such as chorionic villus sampling and amniocentesis carry a small risk of miscarriage.

But to screen for other genetic diseases, clinicians would need to be able to look at a fetus's entire genome. Last month, researchers announced that the fetal genome could be sequenced by combining pieces of fetal DNA in a pregnant woman's blood with sequences from her own DNA and that of the father-to-be.

Stephen Quake of Stanford University, California, and colleagues have now taken this one step further by developing a sequencing method so precise it needs only the fetal DNA and the pregnant woman's genome sequence.

Twin methods

The group came at the problem in two different ways. The more difficult, but more complete, method uses DNA from the pregnant woman and the fetus to map out every last letter of the fetal genome. This approach has the advantage that it can pick up the 50 or so unique mutations that a fetus has but its parents do not. The sequence was 99.8 per cent accurate ? a figure the researchers determined by sequencing the cord blood after the birth.

An alternative, cheaper method sequences just the fetal "exome": the portion of the genome that codes for functional proteins. The researchers attempted to sequence the fetal exome during each of the three trimesters of its development. During the first trimester, they could map 75 per cent of the exome; by the third, they could map 99 per cent as there is more fetal DNA in the blood at this point.

Exome sequencing may be a more feasible option, says Dennis Lo of The Chinese University of Hong Kong. "Since everyone has these new mutations and most of us are still healthy, the possibility of them sitting in important sites is probably pretty low."

Whole genome sequencing also reveals far too much information, Lo thinks. "If you try to counsel [parents-to-be] with all that, it becomes very complicated," he says. Future research might focus on sharpening the genetic test for a few well-known diseases such as thalassaemia and phenylketonuria.

Journal reference: Nature, DOI: DOI: 10.1038/nature11251

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