Matt Roth for The New York Times
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. More Photos »
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.
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.”
This article has been revised to reflect the following correction:
Correction: February 19, 2013
An earlier version of this article misstated the name of a medicine taken by two teenagers who have a rare gene mutation. The drug is 5-hydroxytryptophan, not 5-hydroxytryptamine.
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