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The Saudi Human Genome Program: Bringing Genetic Testing to Routine Clinical Care
Saudi Arabia has a high incidence of inherited genetic diseases due the country’s tradition of consanguineous marriage. When close relatives marry, it increases the risk that parents could pass on recessive genetic mutations to their offspring. In 2015, according to an article in IEEE Pulse. it was estimated that 20 percent of the children born in the country were born with common genetic diseases such as diabetes and another 8 percent had inherited more severe diseases.
Genetic researchers at the King Faisal Specialist Hospital & Research Center (KFSHRC) began looking into genetic disease in the Saudi population in the late ‘90s. Years later, their efforts took shape in the form of the Saudi Human Genome Program (SHGP), a national project to study the genetic basis of disease in Saudi Arabia and the Middle East. The program formally launched at the end of 2013 with the goal of sequencing 100,000 individuals’ genomes using targeted next-generation sequencing.
In collaboration with Thermo Fisher Scientific, the SHGP designed and implemented a collection of 13 comprehensive gene panels that covered all known Mendelian rare diseases. The scientists behind the project aimed to make an immediate impact in three areas: reducing the time to diagnosis, increasing the accuracy and efficiency of diagnosis and leveraging the information generated to improve databases and overall knowledge around inherited disease in the Kingdom.
“The Saudi Human Genome Program was facilitated by advances in technology which provided us with the ability to rapidly sequence the genomes of individuals to understand the basis of disease and this became easily, then, related to the health and welfare of patients,” says Dr. Brian Meyer, chairman of the Department of Genetics at KFSHRC and one of the lead scientists on the project. “We were fortunate enough to have a collection of samples that allowed us to do this very quickly,” he adds. “By sequencing a large number of individuals with a diverse range of rare diseases, we got a picture of what was causing rare diseases in the population. That, in itself, led to better diagnostics for these diseases and an opportunity for prevention.”
His Highness Prince Dr. Turki bin Saud bin Mohammed Al Saud, president of King Abdulaziz City of Science and Technology (KACST), has stated that the SHGP is part of a larger initiative to advance scientific research and technological development across the Kingdom. According to the SHGP website, efforts to understand the population’s fundamental biological makeup “will drive direct and indirect advances in medical care for decades to come” by using genomic information to determine genetic risk and causality for “all health-related conditions.”
“In different populations, disease presentation at the gene level might be a little different, which requires each nation to develop its own database to enable its clinicians to provide a more personalized medicine approach,” says Dr. Sultan Al-Sedairy, who serves as executive director of the research center at KFSHRC. This approach is already paying off, as the data collected through the SHGP is enabling clinicians to make more precise diagnoses and arrive at diagnoses faster. Given the rapid turnaround time, it could serve as a routine service for any healthcare provider in the not-so-distant future.
According to Shire’s “Rare Disease Impact Report” a patient with a rare disease visits eight physicians, receives two to three misdiagnoses and must wait more than seven years before being correctly diagnosed. In contrast, the SHGP reported in 2015 that the team at KFSHRC was able to cut patients’ average diagnosis time down to one week, demonstrating that the time-consuming odyssey to identify rare disease can be reduced dramatically.
Dr. Meyer has incredible stories and examples of patients that have come into the hospital system in and out for weeks, months and, in some cases, even years. Now they’re able to provide an answer to parents around what’s going on with their children,” says Peter Silvester, president of the Life Sciences Group at Thermo Fisher.
“One of the unique aspects of the Saudi Human Genome Program was the ability to shift from basic research into translational research and then to apply that into the clinic,” says Silvester. “Dr. Sedairy and Dr. Meyer had the vision to sequence, or get genetic information from, a portion of the Saudi population, to be able to tailor inherited disease panels in the first instance to be able to look at the unique genetic makers for that population, and then put that into clinical practice in the King Faisal Hospital.”
In addition to enabling more effective and efficient diagnosis of genetic diseases, the SHGP is also empowering citizens to make health decisions to prevent disease in future generations. According to an article in Science, the number of families seeking genetic testing at KFSHRC’s prenatal diagnostics lab increased more than seven-fold from 2011 to 2016.
Currently, couples in Saudi Arabia must have their blood biochemically analyzed to determine if they’re carriers for two common genetic diseases. But if DNA testing was done instead, as the SHGP team hopes will one day be the case, the same sample could be used to test for thousands of diseases. “I think the ability to sequence and understand the genome of an individual has provided an opportunity for a better understanding of disease, for a better understanding of the patient, and, through that, better management of disease,” says Dr. Meyer.
The next phase of the SHGP will incorporate premarital testing to enable couples to identify carrier genes that might affect their future children. In 2017, Dr. Meyer and his team launched the national premarital carrier screening program using Thermo Fisher’s microarray technologies. Dr. Sedairy says the team hopes to identify markers for a number of genetic diseases, enabling the country to expand its screening program.
“Many people think precision medicine is a fad,” says Dr. Sedairy. “But it’s actually the reality of the new medicine that is going to be offered to the population at a much more expedited manner, at a much more precise manner, and a much more economically efficient manner.”