Saudi geneticist Fowzan Alkuraya examines Muteb, a 6-year-old boy born with epilepsy and global developmental delay.

Thamer Al-Hassan

Saudi gene hunters comb country's DNA to prevent rare diseases

In a hospital conference room here in Saudi Arabia's capital, a lieutenant colonel in the Saudi army, dressed in fatigues and a black beret, stoically tells a story of genetic casualties. His and his wife's first child, born in 2004, seemed healthy at first, but at 6 months old the baby girl could not yet sit up and barely cried. Doctors in France, where the family was living at the time, found no explanation. "We were sure that lack of oxygen" during delivery had caused brain damage, the father says.

Although their next baby, a boy, was healthy, a second girl born 5 years later had similar developmental delays. Meanwhile, the officer's sister had given birth to six children, two healthy but four with similar medical problems: Each had crossed eyes and an IQ below 70, didn't talk, and didn't walk until about age 5.

Both the lieutenant colonel, who asked not to be identified, and his sister had married first cousins, who were also related. Suspicions that this close kinship played some role in their kids' problems led the two families to this clinic at King Faisal Specialist Hospital and Research Centre (KFSHRC) and into the care of Fowzan Alkuraya, a young Saudi geneticist who had recently returned from the United States. Some months after the families gave him DNA samples, Alkuraya delivered the results: All four parents carried one copy of the exact same disease mutation, a change of a single DNA base in a gene called ADAT3. Although the mutation was harmless to the parents because each retained a working copy of the gene, their severely disabled children had inherited two faulty copies. As a result, their cells couldn't make an enzyme that helps translate DNA into proteins.

Alkuraya's news brought the families some measure of comfort, and hope. "It was a big relief for my wife, for me, for my sister, for everyone" to know what had gone wrong, the officer says. Hoping to break their bad genetic luck, he and his wife decided they would turn to in vitro fertilization (IVF) and use preimplantation genetic diagnosis to select embryos that inherited no ADAT3 mutation. They now have 2-year-old twins, a boy and a girl. "And they are perfectly healthy," the father says.

The officer's family is one of hundreds that have come to Alkuraya, 39, who may be the country's leading genetics sleuth. His work is part of a boom in human genetics research in Saudi Arabia over the past decade, which has culminated in a Saudi version of a human genome project, called the Saudi Human Genome Program (SHGP). Largely because many Arabs marry cousins or other close relatives, the country, like others in the Middle East, has an increased rate of inherited genetic diseases—nearly double the rate in Europe and the United States and 10 times higher for certain disorders, according to some estimates. As a result, the country has long drawn Western scientists eager to bag disease genes new to science. But Alkuraya and other geneticists here at KFSHRC are bringing such research home.

Marital problems

Thanks to a culture that encourages marriages between first cousins, Saudi Arabia has one of the higher rates of consanguinity in the world, which has elevated its incidence of many inherited genetic diseases.

(Graphic) J. You/Science; (Data) Alan Bittles and Michael Black

They are harnessing cheap, next-generation DNA sequencing to pin down mutations underlying unexplained diseases, cranking through more than 10,000 cases in the past 5 years. Although most of the solved cases involve known mutations, some have yielded novel disease genes— more than 200 from Alkuraya's group alone, including ADAT3. The output of the relatively small team rivals that of larger groups of disease gene hunters in the United States and Europe, colleagues say. "I am very impressed with what [Alkuraya] has achieved in Saudi Arabia," says Joris Veltman, a human geneticist at Radboud University Medical Center in Nijmegen, the Netherlands.

Alkuraya and his colleagues hope the growing catalog of disease mutations they have found will not only help individual families with inherited diseases have healthy babies, but lead to premarriage DNA tests for young people that could bring down the high rate of those diseases here. The broader sequencing effort could also have payoffs beyond the Middle East. The country's closely related population should make it easier to identify "healthy knockouts"—people who lack both copies of a specific gene yet remain healthy and even gain protection against disease, providing clues to new drugs. "If there's any place they should be discovered, it's here," Alkuraya says.

But first, Saudi geneticists will have to get past the worsening budget crisis here triggered by the global drop in oil prices. Funding is on hold for the next phase of the overall genome project, and even ongoing research grants, including Alkuraya's, have been slashed this year. It's vital that his gene sleuthing and other genomics efforts in the country don't stall out, observers say. As human geneticist Daniel MacArthur of the Broad Institute in Cambridge, Massachusetts, notes, "There's no question the opportunities there are massive."

When DNA and culture clash

Outside the research wing of KFSHRC on the traffic-clogged streets here, women cannot mingle with unrelated men and must wear a loose black robe called an abaya. But in this surprisingly cosmopolitan space, women swap their abayas for lab coats and work side by side with male staff. Some take off their head scarves, but others retain their black face veils, known as niqabs, even in the lab.

Such adherence to tradition helps explain why about 40% or more of native Saudis—two-thirds of the country's 30 million people—still marry first cousins or other close relatives. The practice, once common in Europe, lives on in much of the Middle East today, helping preserve wealth and tribal ties. But the downside of consanguineous marriage is a relatively high risk for recessive genetic diseases, which develop when both the maternal and paternal copy of a gene are faulty. If both parents carry the same recessive disease mutation, their children have a 25% chance of inheriting two copies and developing the disease; and in the large families still common in Saudi Arabia, the genetic dice are rolled repeatedly. By one estimate, 8% of babies in Saudi Arabia are born with a genetic or partly genetic disease, compared with 5% in most high-income countries.

Often the diseases have never been seen before. For decades, Middle Eastern clinicians puzzled by these cases have called in European or U.S. scientists, who collected DNA samples from the afflicted families and claimed lead authorship on papers describing new disease genes. After the draft human genome was unveiled in 2001, the country's homogeneous population—made up of about two dozen major tribes descended from a small number of founders— also attracted broader genetics efforts. Brian Meyer, an Australian expat scientist who has long worked in Saudi Arabia and now chairs the KFSHRC genetics department, recalls a proposal from genome sequencing pioneer Craig Venter to launch a company modeled after Iceland's deCODE, which would have mined the DNA of Saudis for drug targets. The plan fizzled out because of local concerns about privacy and exporting genetic data for commercial purposes, however.

"The population wasn't ready," Meyer says. Saudi Arabia also declined to contribute DNA samples to HapMap, an international effort to map human genetic diversity that began in 2002. Middle Easterners are still virtually missing from human genome reference databases, a problem some Arab scientists are now trying to remedy.

In the late 1990s, however, the seeds of a Saudi genome effort began to take root. After finding that the mutations causing cystic fibrosis in Saudis were different from those in Europeans, KFSHRC geneticists began to do their own disease gene hunting. Alkuraya soon joined the chase.

Samel Al Samel and his wife, who have three severely disabled children, Ali (23), Manwa (16) and Muteb (6), talk to geneticist Fowzan Alkuraya. Hala, 10, also pictured, does not have her siblings’ genetic disease.

Thamer Al-Hassan

A star medical student from a small town in Saudi Arabia's north, Alkuraya says he realized that the nation's inherited diseases were a "major problem"—and an unparalleled research opportunity. After training in the United States in pediatrics and medical genetics, he completed a postdoc in developmental genetics at the Harvard University-affiliated Brigham and Women's Hospital in Boston and became first author on a 2006 paper in Science on a gene that controls palate formation.

Alkuraya could have found a U.S. faculty position and traveled to Saudi Arabia to collect disease cases, but he worried that "I would have felt like an opportunist." In 2007, he returned to launch his own research group at KFSHRC and nearby Alfaisal University. He's acutely aware of what he's missing compared with Boston: In Riyadh, he has no world-class experts from other disciplines down the hall with which to exchange ideas and faces long delays in getting reagents such as antibodies. To stay productive—he's published more than 270 papers since he got back—he juggles multiple projects. "You really need to anticipate everything ahead of time," he says.

In his gene hunt, Alkuraya takes advantage of a shortcut known as exome sequencing, which analyzes just the 1% of DNA in a genome that codes for proteins. Instead of scanning entire genomes for mutated genes, a disease hunter can just compare the exome of a sick child with one or two exomes of normal, healthy people, such as the child's parents—a process that takes weeks rather than years. In 2011, Alkuraya's team used that exome strategy for the first time to find a new disease gene: DOCK6, which causes limb malformations when mutated.

The team picked up its pace 3 years ago when Saudi Arabia announced plans for a 100,000-person genome project modeled after efforts in countries such as the United Kingdom and Iceland. Saudi leaders decided to focus a $40 million pilot project on diagnosing patients with single-gene diseases who are recruited by physicians at Saudi research institutions. That proved to be a "wise decision," says Sultan Al-Sedairy, the project's principal investigator and executive director of KFSHRC.

The Saudi genome team uses two shortcuts to find the culprit mutations. In one, instead of sequencing a patient's full exome, the genome project analyzes only the genes most likely to be involved in the condition—genes already tied to facial malformations for those with facial abnormalities, for example. The project assembled a team of some 90 geneticists, clinicians, and others, who developed 13 panels of known disease genes for conditions such as deafness, vision loss, heart disease, and metabolic disorders.

This "Mendeliome" approach, the SHGP reported in Genome Biology last year, diagnosed 43% of 2357 cases for about $75 to $150 a person within days. That success rate, from a cut-rate approach, impresses observers. (The team solved another 11% using costlier exome sequencing.) Although clinical geneticists in other countries have begun using gene panels before turning to exome sequencing, "people haven't systematically done it the way they have in Riyadh," says geneticist James Lupski of Baylor College of Medicine in Houston, Texas. "I think we can learn things from them."

We can't change the culture, but just by screening and prevention we can help people.

Dorota Monies, Polish expat researcher, King Faisal Specialist Hospital and Research Centre (KFSHRC)

If the Mendeliome strategy doesn't pinpoint the responsible mutation, the team can also try to take advantage of the second shortcut. When the child of a consanguineous union develops a recessive disease, the responsible mutation usually lies within a larger identical block of DNA inherited from both parents. Researchers can therefore ignore most of the child's exome and look for the mutation at fault by only probing these shared parental regions, which they find by scanning the DNA for known markers. "That gives us x-ray vision," Alkuraya says. "You know just where to look."

Getting the genes out

Beyond the practical payoff of diagnosing genetic diseases, the Saudi team is excited by the science it's generating. Among the more than 200 genes newly linked to human illness by Alkuraya's team is one called DNASE1L3 that causes an inherited form of lupus and is being pursued as a drug target for the immune disorder. The group has found dozens of additional genes that cause intellectual disability. Other genes are among the first known to be fatal in early embryonic development. Identifying mutations behind such failed pregnancies is difficult because it requires DNA from the lost embryo, but Alkuraya has enrolled pregnant mothers with a history of miscarriage and collects a fetal tissue sample when they show signs of miscarrying again.

He acknowledges that some of his published connections between genes and a disease are preliminary—often a mutation has only been found in one family so far—and that he doesn't do much of the functional work needed to pin down what these genes do. "My philosophy is always to get the genes out" so that other geneticists can build on them, Alkuraya says. The SHGP group soon plans to publish the full database of its genome data on more than 10,000 individuals.

Some of these data may also challenge previously reported gene-disease links. In a paper last month in Genome Biology, Alkuraya reports that hundreds of gene variants labeled as pathogenic in other databases are commonly found in Saudis without the relevant disease.

In the next phase of the SHGP, researchers want to study common disorders such as heart disease and diabetes—a rare inherited form of diabetes afflicts some Saudis—and personalize cancer therapies based on a person's DNA. Alkuraya also aims to recruit up to 10,000 people who receive health care at KFSHRC in hopes of finding healthy knockouts, a potential boon to drug developers. A Texas woman lacking the gene PCSK9, for example, led to a new class of drugs that drastically reduces cholesterol by mimicking the effect of the gene knockout. The hunt should be easier in Saudi Arabia's consanguineous population. "I'm really optimistic that we're going to find something like" PCSK9, Alkuraya says.

All of this will depend on funding, however. The Saudi government has approved $200 million in the budget of the country's main science agency, King Abdulaziz City for Science and Technology (KACST) here, to fund the next 5 years of the SHGP, including the purchase of the latest DNA sequencers, which Alkuraya hopes to use. But the money hasn't yet been released, and existing funds dwindled this year. Alkuraya's own grants have been cut by 50% and his lab has been unable to replace equipment for the past 2 years.

But Alkuraya says that for the moment, he's not too worried about his science. "I'm sitting on so much data. If I were to shut my lab down now, I could continue to write papers for the next 3 years."

A national screening effort

While the genomics research slows, what has been learned so far is starting to pay off for Saudi families. There is often little to be done for children who inherit a recessive disease, but genetic knowledge can save future children from a similar outcome. In addition to selecting IVF embryos without disease mutations, potential Saudi parents can turn to prenatal diagnosis if the wife is already pregnant. (Islamic law allows abortion to save the mother's life, and clerics in Saudi Arabia have ruled that this also applies before 120 days of gestation if she is likely to have a severely malformed fetus.)

Five years ago, about 80 families a year came to KFSHRC's prenatal diagnostics lab for genetic testing. Now, about 500 families annually seek testing, and as a result as many as 125 pregnancies have been terminated because the babies would have had severe or fatal diseases. "That's a huge economic burden on the country that we have eliminated," says geneticist Faiqa Imtiaz, who heads the hospital's prenatal testing lab.

Samel Al Samel and some of his children, three of whom have developmental problems. His eldest son, Mohammad (not pictured), is healthy, but after having a DNA test, learned that he is a carrier of the mutation that afflicted his siblings.

Thamer Al-Hassan

 

Ultimately, the Saudi genome team would like to screen all 150,000 Saudi couples who plan to marry each year for disease genes. Each couple is now required by the Ministry of Health to have their blood biochemically analyzed for signs they are carriers of sickle cell anemia and thalassemia, two genetic diseases that are common here. If DNA testing were done instead, "the same sample could be used for thousands of diseases," Meyer says. He says that the SHGP's next phase includes a plan to begin using a custom, chiplike device, known as a genotyping array, to screen couples' DNA samples for the 2300 most common disease mutations in the Saudi population.

Earlier screening, perhaps in high school before a marriage is arranged or a couple falls in love, might be even more effective, Alkuraya says. "We can't change the culture, but just by screening and prevention we can help people," adds his colleague Dorota Monies, a Polish expat researcher who has lived in Riyadh for more than a decade and who runs the DNA sequencers for the genome project.

Such a compulsory national test for that many genetic diseases would be "unparalleled in scale," says Stephen Kingsmore, a geneticist at Rady Children's Hospital in San Diego, California. The country would also have to greatly expand its cadre of genetic counselors—it now has just nine. "If you have proper counseling in the clinic, then they understand and stop the marriage," says Ayman Alsulaiman, a genetic counselor at KFSHRC who consults for the Ministry of Health's current premarital screening program. "With no proper counseling, they don't listen."

In the meantime, the Saudi team encourages parents who have a child with a genetic disorder to have their immediate and extended family tested, to reduce the risk in future births. This can be a sensitive matter, says Shatha Al Rasheed, a research genetic counselor with KACST. A mother may worry that her husband will take a second wife if he learns they both carry a disease gene. Or families may fear that their sons and daughters will never get married. But most families end up sharing the information: "I feel success stories are much more common than negative ones," Al Rasheed says.

Mohammad Al Samel, a 27-year-old medical student in his residency in Jeddah, Saudi Arabia, grew up with three siblings severely disabled by a mutation identified by Alkuraya's lab. After their diagnosis, Al Samel agreed to have his DNA tested and learned that he is a carrier of the same genetic flaw. His fiancée is also being tested, even though the two aren't related and she's unlikely to have the mutation. If she does, Al Samel says, they will still marry but consider "other solutions" such as IVF to avoid having a sick child.

"I didn't have brothers or sisters who were healthy enough to play with me, and we had to stay in the hospital for long times," he says. "I don't want my kids to have the same memories. You cannot imagine."