Software speeds genome tests that could help sick infants

Software for whole-genome sequencing can speed the process from weeks to hours, according to a study published this week in Science Translational Medicine. The researchers, based at Children's Mercy Hospitals and Clinics in Kansas City, Mo., said that the results prove that whole-genome sequencing is, in fact, a realistic course of action for treating at least one kind of patient, according to an article in Technology Review: newborns with single-gene disorders that are difficult to diagnose.

Monogenic diseases frequently cause death in newborns, according to the researchers. But clinical testing is only available for a small percentage of the more than 3,500 such diseases currently characterized.

"Hence, an immense unmet need exists for improved molecular diagnosis in infants," the researchers said.

Using software developed by Neil Miller, director of informatics at Mercy's Center for Pediatric Genomic Medicine, the researchers were able to retroactively analyze the genomes of seven infants who died shortly after birth. Five were able to be accurately diagnosed with critical conditions within 50 hours.

According to an article in MedPage Today, two pieces of software were used: One, known as symptom- and sign-assisted genome analysis (SSAGA), centered clinical attention on genetic regions often linked to specific symptoms. The second, known as Rapid Understanding of Nucleotide variant Effect Software (RUNES), characterized the effects of genetic variants discovered.

"The first question is, 'what gene should we be looking at?'" Miller said, according to Technology Review. "The second important question is, 'what effect might each of the variants that we detected in each patient have on the gene that it occurs in?'"

The test costs roughly $13,500 per genome, study co-author Stephen Kingsmore of Mercy told MedPage Today. However, he added, when compared with the cost of a one-night stay in a neonatal unit--roughly $8,000--the cost difference could be negligible, if not favorable, for the test.

To learn more:
- here's the study's abstract
- read the Technology Review article
- check out the MedPage Today story

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