And although babies inherit one copy of each gene from mother and father, new mutations can arise that aren't found in the mother or the father's genes, which further complicates the analysis.
However, perhaps the biggest challenge is how to interpret all of the information, Evans said. Not only does it take time, researchers don't know what every mutation means as far as disease.
"When you do a whole genome sequence, you end up with millions of variants. The biggest challenge facing our field is to understand which variants are importantly clinically and which are meaningless," Evans said.
For example, Shendure noted, mutations on the BRCA1 and 2 genes are known to be associated with a much higher risk of breast cancer. But even after many years and tens of thousands of tests, researchers still come across mutations on those genes that they haven't seen before and therefore aren't sure if they really mean a heightened risk of breast cancer.
"We have only begun to scratch the surface in our ability to interpret the findings in a whole genome sequence," Evans said. "This should been seen as very much in the realm of research. It is not ready for clinical application."
What prenatal whole genome sequencing likely won't be used for anytime soon time is to predict a baby's likelihood of going on to develop common diseases such as heart disease and diabetes, experts said.
While there is plenty of research that links various mutations with a heightened risk of various diseases, genetics remains a poor predictor, Evans said. Instead, other, more obvious influences such as diet, exercise and whether a person smokes remain the best bet for predicting who's going to develop the more common chronic diseases, Evans said.
"Measuring weight and asking them a few questions about activity and lifestyle does a far better job of figuring out, for example, heart disease risk," Evans said.
Shendure agreed. "These single-gene disorders are the things we understand the best, and even there it's challenging," he said.
Read more about the Human Genome Project.
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