DNA Test for Rare Disorders Becomes More Routine

Debra Sukin and her husband were determined to take no chances with her second pregnancy. Their first child, Jacob, who had a serious genetic disorder, did not babble when he was a year old and had severe developmental delays. So the second time around, Ms. Sukin had what was then the most advanced prenatal testing.

                        
Sam Bosley of Frederick, Md., going shopping with his daughter, Lillian, 13, who has a malformed brain and severe developmental delays, seizures and vision problems.

The test found no sign of Angelman syndrome, the rare genetic disorder that had struck Jacob. But as months passed, Eli was not crawling or walking or babbling at ages when other babies were.

“Whatever the milestones were, my son was not meeting them,” Ms. Sukin said.

Desperate to find out what is wrong with Eli, now 8, the Sukins, of The Woodlands, Tex., have become pioneers in a new kind of testing that is proving particularly helpful in diagnosing mysterious neurological illnesses in children. Scientists sequence all of a patient’s genes, systematically searching for disease-causing mutations.

A few years ago, this sort of test was so difficult and expensive that it was generally only available to participants in research projects like those sponsored by the National Institutes of Health. But the price has plunged in just a few years from tens of thousands of dollars to around $7,000 to $9,000 for a family. Baylor College of Medicine and a handful of companies are now offering it. Insurers usually pay.

Demand has soared — at Baylor, for example, scientists analyzed 5 to 10 DNA sequences a month when the program started in November 2011. Now they are doing more than 130 analyses a month. At the National Institutes of Health, which handles about 300 cases a year as part of its research program, demand is so great that the program is expected to ultimately take on 800 to 900 a year.

The test is beginning to transform life for patients and families who have often spent years searching for answers. They can now start the grueling process with DNA sequencing, says Dr. Wendy K. Chung, professor of pediatrics and medicine at Columbia University.

“Most people originally thought of using it as a court of last resort,” Dr. Chung said. “Now we can think of it as a first-line test.”

Even if there is no treatment, there is almost always some benefit to diagnosis, geneticists say. It can give patients and their families the certainty of knowing what is wrong and even a prognosis. It can also ease the processing of medical claims, qualifying for special education services, and learning whether subsequent children might be at risk.

“Imagine the people who drive across the whole country looking for that one neurologist who can help, or scrubbing the whole house with Lysol because they think it might be an allergy,” said Richard A. Gibbs, the director of Baylor College of Medicine’s gene sequencing program. “Those kinds of stories are the rule, not the exception.”

Experts caution that gene sequencing is no panacea. It finds a genetic aberration in only about 25 to 30 percent of cases. About 3 percent of patients end up with better management of their disorder. About 1 percent get a treatment and a major benefit.

“People come to us with huge expectations,” said Dr. William A. Gahl, who directs the N.I.H. program. “They think, ‘You will take my DNA and find the causes and give me a treatment.’ ”

“We give the impression that we can do these things because we only publish our successes,” Dr. Gahl said, adding that when patients come to him, “we try to make expectations realistic.”

DNA sequencing was not available when Debra and Steven Sukin began trying to find out what was wrong with Eli. When he was 3, they tried microarray analysis, a genetic test that is nowhere near as sensitive as sequencing. It detected no problems.

“My husband and I looked at each other and said, ‘The good news is that everything is fine; the bad news is that everything is not fine,’ ” Ms. Sukin said.

In November 2011, when Eli was 6, Ms. Sukin consulted Dr. Arthur L. Beaudet, a medical geneticist at Baylor.

“Is there a protein missing?” she recalled asking him. “Is there something biochemical we could be missing?”

By now, DNA sequencing had come of age. Dr. Beaudet said that Eli was a great candidate, and it turned out that the new procedure held an answer.

A single DNA base was altered in a gene called CASK, resulting in a disorder so rare that there are fewer than 10 cases in all the world’s medical literature.

“It really became definitive for my husband and me,” Ms. Sukin said. “We would need to do lifelong planning for dependent care for the rest of his life.”

Now, when doctors bill for medical services, insurers pay without as many questions. And Eli’s schools recognize how profound his needs are. “This isn’t just some kid with dyslexia,” his mother said, adding: “My son needs someone who literally is holding his hand. He runs, he doesn’t know ‘no.’ And he does not talk.”

The typical patient with a mystery disease has neurological problems, and is often a baby or a child. There are reasons for that.

Many people with such diseases do not live into adulthood or die in their 20s. Furthermore, Dr. Beaudet said, “if you randomly — as nature does — come along and dash any gene you like, the most sensitive function to go out is brain function.”

That may also be one reason cures are so rare, even if the gene defect is known.

Many such patients are like 13-year-old Lillian Bosley. She has never learned to speak. Her hands and feet are contracted and turned inward. Her brain is malformed. She has severe developmental delays, seizures and vision problems.

Lillian’s parents, Sam and Michelle Bosley of Frederick, Md., sought answers from specialist after specialist, until they finally stumbled onto gene sequencing. It did not give them a diagnosis.

But Sherri Bale, a medical geneticist and the managing director of GeneDx, the company that did the sequencing, has not given up. Maybe in a few years, when more is known about rare diseases, she will figure it out.

Mr. Bosley, meanwhile, is hopeful but resigned.

“In the end, I don’t know that it would change anything,” he said. “Maybe it is one of life’s mysteries.”

But the experience of the Beerys of San Diego raises the hopes of other families.

Retta and Joe Beery’s twins, born in 1996, were not meeting developmental milestones.

At 1 year, the babies, Alexis and Noah, could not crawl. Their muscle tone was so poor that anyone who held them had to support their backs. They vomited profusely every day.

The Beerys eventually got a diagnosis, cerebral palsy, which turned out to be wrong.

When the twins were 5, Ms. Beery realized that Alexis, who was more affected, had all the symptoms of an unusual disease, dopa-responsive dystonia. Her muscles would involuntarily contract and her limbs would twist. Her eyes would roll upward. She had tremors and seizures.

A University of Michigan neurologist gave Alexis L-dopa, a drug used to treat Parkinson’s disease. It alleviated most of her symptoms, but eventually she had breathing problems.

“We were back in this world of specialists,” Ms. Beery said. Two pulmonologists, three ear, nose and throat specialists, three allergists. Eighteen months of doctor visits and tests, with no answer.

The answer came in August 2010, when Dr. Gibbs, the head of Baylor’s gene sequencing program, and Dr. James R. Lupski, also at Baylor, agreed to sequence the twins’ entire genome as part of a research program. They discovered that Alexis and Noah had an extremely rare mutation in a gene, SPR, that knocked out synthesis of both dopamine and another neurotransmitter, serotonin.

The twins started taking 5-hydroxytryptamine, which the body converts to serotonin, along with L-dopa. Alexis, who had been unable to participate in any sport because of her difficulty breathing, was running track three weeks later. Noah’s tremors went away. His handwriting and his eye-hand coordination improved.

Ms. Beery has made it her mission to tell her children’s story and to encourage families to seek testing. But Dr. Beaudet, the Baylor geneticist, cautions that very few families get such a happy ending.

“Theirs,” he said of the Beerys, “is the world’s poster story for this kind of activity.” 

Source : New York Times ( 18th feb 2013 )