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New DNA test can diagnose genetic disorders in newborns in just 2 days

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For babies born with the rare genetic disorder phenylketonuria (PKU), their bodies are unable to break down a certain amino acid, which can lead to brain damage and seizures.  If found early enough, however, PKU is easily treated, and children with the condition can go on to live a normal life. But sometimes, genetic testing for disorders such as this one come too late, and narrow windows of opportunity for treatment can close up for good.

But now, parents and physicians can have answers regarding a baby’s genetic abnormalities in only a few short days.  Researchers from Children’s Mercy Hospitals & Clinics in Kansas City, Mo., have developed a new whole-genome sequencing technology capable of diagnosing genetic disorders in ICU newborns in just 50 hours – a significantly less amount of time than the 12 to 14 days needed for current screening techniques.

The ability to diagnose infants in such a short amount of time could help to speed up available treatments – as well as provide relief or knowledge to anxious parents.

“There are about 500 diseases that can present in a baby for which there’s a treatment,” Dr. Stephen Kingsmore, director of the Center for Pediatric Genomic Medicine at Children’s Mercy Hospitals and Clinics and lead author of the study, told FoxNews.com.  “But for diseases that don’t have treatment, this info can still be useful.  It gives parents and physicians an answer.  You can stop doing additional testing or stop giving futile treatments.  Parents can get counseling about whether this can recur in a future child and get advice about how intense treatments can be.”

Currently, there are more than 3,500 known genetic disorders – conditions caused by a mutation in a single gene – and the definitive method diagnose them is to sequence the mutated gene.  However, a big problem with gene sequencing up until now has been knowing exactly which gene to sequence, according to the researchers.  Each genome contains more than 3.1 billion nucleotides, and of those, three to four million variants exist.  In order to diagnose a condition, all of those variants need to be analyzed – a task that can take quite a long time.

To speed up this process, Kingsmore, along with fellow Children’s Mercy Hospital researcher Neil Miller, teamed up with the company Illumina – a group dedicated to technologies that analyze genetic variations.  Having announced in January the Illumina HiSeq 2500 – a high-speed sequencing device, the company approached Kingsmore and Miller to develop software that would go hand-in-hand with their new instrument.

That was how SAGA and RUNE were born.  After the Illumina HiSeq 2500 sequences the entire genome in less than 30 hours, the software applications then come into play. First, SAGA, which stands for sign-assisted genome analysis, helps physicians to determine which parts of the genome are significant depending on the patient’s symptoms.

“It allows them to click on buttons of symptoms that are corresponding in the baby – such as difficulty breathing, etc,” Kingsmore said.  “The computer then matches those particular symptoms and signs to the right parts of the genome and selects of those 3,500 genetic diseases, which ones are appropriate to test.  So it allows us to test the variants that are likely to cause a disease.”

To determine how effective SAGA was in determining a diagnosis, the researchers used the program on over 500 previously diagnosed cases, and the software was 99 percent accurate in selecting the right gene according to the patient’s symptoms.

RUNE solves the second part of the puzzle, which is determining how these variants impact the gene in which they occur.  Standing for rapid understanding of nucleotide-variant effect, RUNE essentially ranks the order of diseases that are on possibly on target for the variants that were found.

While the final results ultimately needed to be reviewed by a physician, Kingsmore said that sometimes a diagnosis was determined in less than two minutes.  The team tested their sequencing-software technology on nine newborns. Two of the cases, in which the babies had already died, were tested retrospectively to see if the technology worked.  

“One child had Menkes’ disease, which was sad because there’s a treatment, and if a diagnosis had been made when the baby was a newborn, it could have made a difference in quality of life,” Kingsmore said.

The rest of the babies tested were alive and were analyzed prospectively.  Of the five children tested, four accurate diagnoses were made.  Having shown the success of their new testing technique, the researchers hope to begin offering the sequencing-software technology to Children’s Mercy Hospital patients this November – and then eventually to hospitals across the country.

Kingsmore also hinted that their test could not only be beneficial for newborns, but also children, teenagers and even adults.  The symptoms of many genetic conditions, such as Charcot-Marie-Tooth (CMT), sometimes do not present until adulthood, and a rapid genetic test of this kind could also help to save the lives of older individuals.

As another added benefit, lives are not the only thing that could potentially be saved.  The researchers purport their new rapid testing technique can actually save money too.

“If we look at the (NICU), a hospital stay can cost a quarter of a million dollars quite easily,” Kingsmore said.  “Staying in a NICU bed for just one night can cost $8,000.  It’s horribly expensive …If we can diagnose these children fast and treat them fast, it can have huge benefits about how long they’re in the NICU.”

According to the researchers, the pros of 50-hour genome sequencing substantially outweigh any cons.

“Overall, it can save time, it can save lives, and a lot of times, it can save suffering,” Kingsmore said.