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Originally published February 18, 2013 at 5:20 PM | Page modified February 19, 2013 at 10:38 AM

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DNA tests give hope where there was none

DNA sequencing has become less expensive and is beginning to transform life for patients and families who have often spent years searching for answers to illnesses that are difficult to diagnose otherwise.

The New York Times

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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, 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,” Sukin said.

Desperate to find out what is wrong with Eli, now 8, the Sukins, of The Woodlands, Texas, 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 available only 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 five 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 Chung, professor of pediatrics and medicine at Columbia University.

“Most people originally thought of using it as a court of last resort,” 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 also can 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 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.

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,’” Debra Sukin said.

In November 2011, when Eli was 6, Sukin consulted Dr. Arthur Beaudet, a medical geneticist at Baylor who had 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,” 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. “My son needs someone who literally is holding his hand. He runs; he doesn’t know ‘no.’ And he does not talk.”

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, Retta 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,” Retta 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 Gibbs, the head of Baylor’s gene-sequencing program, and Dr. James 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.

Retta Beery has made it her mission to tell her children’s story and to encourage families to seek testing.

But 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.”

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