New hope for critically ill babies as test diagnoses genetic diseases in days instead of weeks
Doctors at Children's Mercy Hospital in Kansas sequenced genetic code of four newborns
Super-quick genetic test reveals DNA variations that point to around 3,500 rare diseasesThe test is projected to cost £8,300. Doctors pointed out that intensive care units can cost £5,000 a night to run

|

UPDATED:

12:57 GMT, 4 October 2012

Critically ill babies could be diagnosed with genetic diseases in just days rather than weeks, thanks to a new rapid gene unravelling machine.

Doctors at Children's Mercy Hospital in Kansas sequenced the entire genetic code of four gravely ill newborns and identified genetic diseases in three of them in just 50 hours. This was quick enough to help them
make vital treatment decisions.

Genetic sequencing involves analysing 3.2 billion chemical 'bases' or 'letters' that make up the human genetic code.

Four gravely ill newborns had their entire genetic code sequenced in 50 hours at Children's Mercy Hospital in Kansas

Four gravely ill newborns had their entire genetic code sequenced in 50 hours at Children's Mercy Hospital in Kansas

50 hours to diagnosis: How the process works

50 hours to diagnosis: How the process works

It can reveal DNA variations that point to around 3,500 rare diseases. Many of these conditions are fatal but around 500 have treatments available.

Up til now the process was viewed by
medics as too slow and expensive to pursue.

Study author, Dr Stephen Kingsmore: 'It is now feasible to decode an entire genome and provide interim results back to the physician in two days.'

The study tested two software programs developed at Children's Mercy that were used in conjunction with a high-speed gene sequencer from Illumina called HiSeq 2500, which can sequence an entire genome in about 25 hours.

The company helped pay for the study and company researchers took part in it.

Next-generation gene sequencing machines have driven down the cost of whole genome sequencing, but making practical use of the data has been more challenging, largely because of the time it takes to analyse all of the data.

Dr Stephen Kingsmore led the study into the new ultra-fast genetic testing

Dr Stephen Kingsmore led the study into the new ultra-fast genetic testing

As many as a third of babies admitted
to a neonatal intensive care unit in the United States have some form
of genetic disease. Treatments are currently available for more than 500
diseases, but identifying them quickly has been a problem.

Typically,
genetic testing on newborns using conventional methods takes four to
six weeks, long enough that the infant has either died or been sent
home.

'Up until now, they have really had to practice medicine blindfolded,' Dr Kingsmore said.

Dr
Neil Miller, director of informatics at Children's Mercy, said the
software programs help doctors identify which genes to test, and analyze
the data quickly.

One
of these programs, called SSAGA, allows doctors to order this test based
on the child's symptoms, without having to know in advance which genes
to test for.

The
software only maps genes associated with the child's symptoms. SSAGA
does this for nearly 600 diseases, but the team is expanding this to
include all 3,500 known disease genes, Miller told the briefing.

The team developed a second software program called Runes that helps determine which of the suspected genes was most likely to be the cause of the child's illness.

In the study, the team tested the system on four seriously ill babies whose conditions were suspected of having a genetic cause. One of the boys was found to have a heart defect that the team discovered is also shared by his six-year-old brother. The infant underwent heart surgery and has survived. While two of the other three babies were diagnosed with rare conditions they sadly all passed away.

How the cost of decoding genomes has dramatically fallen since 2008

How the cost of decoding genomes has dramatically fallen since 2008

Dr Carol Saunders,who helped interpret the study results said the study could give parents more information
about the cause of their child's illness and allow them to make
decisions about what kinds of treatments they wanted to pursue.

The test is projected to cost £8,300 ($13,500), but the team believes that may be worth it given the high cost of care in a neonatal intensive care unit, which runs roughly £5,000 ($8,000) per night.

The next move is to broaden the test to include 100 or more babies to determine the benefits, costs and potential problems linked with the testing.

Because the Illumina machine was not available in the United States, the team had to discount the time it took to ship the blood samples to Britain, where the actual sequencing was done.

But Kingsmore said the hospital expects to receive its own HiSeq 2500 machine next month. Eventually, the hospital hopes to have its
testing validated, so the researchers can do genetic testing on newborns
in hospitals across the United States.