Quicker genome analysis improves detection of rare diseases
A new platform developed by researchers in Leuven and Ghent aims to speed up diagnosis of conditions from days to just hours
After the link between genetics and health disorders was established in the 1960s, technological advances gradually enabled better analysis to clarify the relationship. But to be practically useful for doctors, and not only for researchers, it was essential to reduce the cost and duration of the process. GAP, which combines innovative solutions in software and hardware, does just that.
GAP, short for Genome Analytics Platform, was developed by imec with the universities of Leuven (KU Leuven) and Ghent (UGent), the university hospital of Leuven (UZ Leuven) and ICT companies Western Digital, Bluebee and Agilent. UZ Leuven and KU Leuven’s department of human genetics already use applications based on the GAP insights for diagnosis and screening purposes.
48 samples in 48 hours
To map one’s genome, scientists first take a blood or saliva sample that contains the person’s DNA. That sample is then inserted in a sequencing machine, which composes that person’s full genetic code – consisting of about 3 billion letters. This raw output then needs to be pre-processed by software before it can be interpreted.
“While the pre-processing in the past took several days, we managed to shorten the duration to about one hour,” says professor Roel Wuyts, team lead at imec’s ExaScience Life Lab. “A sequencing machine can now process at once 48 samples in 48 hours.”
Each of these conditions is rare, but there are many different ones, so together they affect a considerable number of patients
The results still have to be interpreted by specialists, to be useful for doctors, which generally takes a few days. “But in future, artificial intelligence will separate the wheat from the chaff for the specialists by filtering out unnecessary info,” says Wuyts. “The technology will never replace the experts but will enable them to help patients better and faster.”
The solutions born out of the GAP project already help specialists at KU Leuven and UZ Leuven to find genetic reasons for otherwise unexplainable rare diseases that lead for example to mental disabilities, heart defects, immune deficiency or abnormal growth of limbs. In the best cases, which are not yet that frequent, that diagnosis also leads to an effective treatment.
“Each of these conditions is rare, but there are many different ones, so together they affect a considerable number of patients,” says professor Joris Vermeesch, head of KU Leuven’s department of human genetics. Each year, the specialists in Leuven have about 1,000 patients with a rare disease.
The genome analysis is vital to take decisions concerning major surgical interventions needed to save the life of newborn babies. “The in-depth information about defects in the genome can help to determine what is necessary to deal with life-threatening disorders of newborns, like heart problems,” says Vermeesch. “The detail of such knowledge is crucial as such surgery on infants brings many risks.”
Finally, this technological progress is important as well for the improvement of in vitro fertilisation techniques, as it allows doctors to better identify and select embryos without life-threatening abnormalities. “It improves our screening for chromosomal defects, one of the main causes of early pregnancy loss,” says Vermeesch.
The basic technology is already available, we now need to put the different parts together
In the future, Vermeesch believes, these applications can also be of great benefit for the early diagnosis of more common conditions such as diabetes or Crohn’s disease – in which more complex genetic factors play a role than in rare diseases. “In the long term, we might make up a full genome analysis of everyone, which would help not only to fine-tune treatments but even more importantly to prevent conditions from developing,” he explains.
Wuyts of imec is similarly optimistic, envisioning in the next five to 10 years the creation at imec of simple-to-use mobile devices that can be directly applied by doctors to examine a patient’s genome. “The ambition is that such a device can make an easy-to-interpret analysis in a few hours after inserting a DNA sample,” he says. “The basic technology is already available, we now need to put the different parts together.”
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