Whole-genome sequencing is truly amazing. If every one of us were decoded tomorrow, scientists would no doubt figure out the cause of a slew of now-mysterious diseases.

The trouble is, doing it right (that is, thoroughly) is pretty expensive: the cheapest option right now is Complete Genomics, which does genome sequencing for $20,000 a pop for institutes willing to buy in bulk.

Researchers are now considering a cheaper option. Rather than sequence the 3 billion basepairs of the entire genome — 99% of which is ‘junk’ DNA — why not focus only on the regions that code for proteins, called exons?

There are two main drawbacks to this so-called ‘whole-exome’ approach. First, the price of whole-genome sequencing is dropping extremely quickly. So the money you spend today on just the exome might buy you the the entire frickin’ genome next year. Second, junk DNA isn’t really junk, so limiting your search to the exome may mean that you’re bypassing important (read: disease-causing) stuff.

Nevertheless, it looks like the exome camp is making some headway. Last week marked the first time that a whole-exome project found the cause of a genetic disorder: Miller syndrome. From Nature News:

Shendure and his colleagues have now sequenced the exomes of two siblings and two unrelated individuals who all suffered from a single-gene disorder called Miller syndrome, which is characterized by facial malformations and limb abnormalities, such as a cleft palate and absent or webbed fingers and toes. Although the disease was first described 30 years ago, its genetic basis has remained elusive.

The researchers compared the exomes of Miller-affected individuals to exome sequences from eight healthy, unrelated individuals. This approach flagged a single candidate gene called DHODH, which encodes an enzyme that is essential for making some of the building blocks used in DNA and RNA. Shendure’s team then directly sequenced DHODH in four more Miller-affected individuals and found that they too all had mutations in this gene. No similar mutations were found in 100 unaffected individuals. The findings are published online today in Nature Genetics.

“This is the first demonstration of whole-exome sequencing for a new disease-gene discovery,” says Richard Lifton, a geneticist at Yale University School of Medicine in New Haven, Connecticut, who was not involved in the work. This first discovery is only the tip of the iceberg, he adds. “I think there are large classes of Mendelian traits that will be found by whole-exome sequencing.”