DNA Test for Babies Pinpoints Mutations, Speeding Diagnosis

By GINA KOLATA

Published: October 3, 2012

From the day she was born, the girl had seizure after seizure. Doctors at Children’s Mercy Hospital in Kansas City, Mo., frantically tried to keep her alive. Weeks passed and every medication failed. Finally, her family decided to let their baby go, and the medical devices were withdrawn. She was 5 weeks old.

Her doctors suspected a genetic disorder, and as it happened the hospital had just begun a study of a new technique for quickly analyzing the DNA of newborns, zeroing in on mutations that can cause disease.

This new method, published on Wednesday in the magazine Science Translational Medicine, is a proof of concept — a demonstration in four babies that it is possible to quickly scan a baby’s entire DNA and pinpoint a disease-causing mutation in a couple of days instead of the more typical weeks or months.

The study’s investigators said the test could be one of the first practical fruits of the revolution in sequencing an individual’s entire DNA.

For the baby with seizures, her doctors provided a sample of her blood. The analysis took only 50 hours and provided an answer. The baby had a mortal gene mutation so rare that it had only been reported once before.

If only, said Dr. Joshua E. Petrikin, one of the baby’s doctors, the test could have been done within days of the baby’s birth.

“There was no treatment, there was not anything that could have changed the outcome,” Dr. Petrikin said “But we could have more appropriately counseled the family and bypassed what had to have been intense suffering.”

The baby, he explained, was heavily sedated, medicated and intubated for her entire brief life.

The idea behind the test is to take advantage of what is known about disease symptoms to narrow the search for genetic aberrations. And that, said Dr. Joe Gray, an expert in genome analysis at Oregon Health and Science University, “is a good step in the right direction.”

“It’s a big genome,” said Dr. Gray, who was not involved with the study. “How do you know what part of it to search?”

While more research needs to be done before the test is ready for widespread use, he applauded the effort. “If people don’t push the envelope like this, then we won’t get there,” Dr. Gray said.

About one in 20 babies in newborn intensive care units has a genetic disease and all too often, no one can figure out what it is. Scientists identified the faulty genes for about 3,500 of 7,500 known genetic diseases, said the paper’s authors, adding that about 500 have treatments.

To test their method, the investigators tried it with two babies whose disease had been diagnosed only through an autopsy. They quickly found the genetic causes. Then they tried the method on four babies who were seriously ill with suspected genetic diseases, including the baby with seizures. They quickly found the mutated gene in three of the four.

The investigators also sequenced the DNA of an older brother of one of the babies who had the same genetic disorder — his organs were reversed. His heart was on the right, instead of the left, for example. This caused a heart defect that was corrected by surgery. The parents had been told the child had a condition that would not happen again. Then their second baby had the same problem. The researchers found a new genetic defect, never seen before, that they suspect was the cause. They contacted doctors and discovered more than 100 other children with the same unexplained defect. Now the investigators are checking to see if some have the mutation, which would indicate it caused the problem. Then the parents could know of a prenatal diagnosis for future pregnancies.

The baby whose disease remained a mystery was another of Dr. Petrikin’s patients. When he was born, some skin was missing over his eyebrows and in patches on his scalp. Over weeks, he developed severe blistering, eventually losing nearly all the skin in his mouth and on his body and dying of an infection.

“We still don’t know what caused it,” Dr. Petrikin said. 

  With the new method, a computer program searches for genes based on the baby’s symptoms. And because it only focuses on genes that cause diseases in newborns, it avoids an ethical dilemma: findings that are unrelated to the problem at hand. In sequencing and analyzing the entire DNA, researchers may discover, for example, aberrations leading to conditions that occur only in adults. Do parents really want to know that their sick baby has a gene that increases the risk of Alzheimer’s disease?

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“They did it right, and you rarely hear that from an ethicist,” said Dr. Lainie Friedman Ross, an ethicist and professor of pediatrics at the University of Chicago. Dr. Ross, who praised the researchers for deliberately avoiding such incidental findings, was also not involved with the study.

The method is expensive, though, costing about $13,500. It is not yet covered by insurance.

But Dr. Stephen F. Kingsmore, director of Children’s Mercy’s center for pediatric genomic medicine, expects to show it is cost effective and hopes insurers will pay for it. He noted that each day a baby spends in intensive care costs about $8,000, so any test that reduces that time would quickly pay for itself. A test that reveals a uniformly fatal genetic disease, for example, can allow parents and doctors to know that continuing life support in the hope the baby will improve is futile and only causing suffering. In the meantime, Dr. Kingsmore said, he is hoping a philanthropist will help defray the costs.

To develop the test, the researchers used every clue about the sick newborn. Was the baby floppy? Was her cry abnormal, her breathing labored? A computer program factored in the symptoms and searched the baby’s DNA sequence for mutated genes that might be responsible.

A gene sequencing company, Illumina, had a new machine with a prototype in Essex, England, that could sequence DNA in 25 hours, so researchers sent samples of babies’ blood there. The results, a hard drive full of data, were sent by Federal Express for analysis at the Missouri hospital. By the end of November, the hospital expects to have its own machine on site.

Although genetic causes for the diseases were found in three of the four babies, the diseases had no treatments — except for surgery for the brothers — and that baby was the only one who survived.

The biggest surprise for Dr. Kingsmore, though, was that the families greatly valued having a diagnosis.

When a baby has a mysterious disease, he said, the family often embarks on a terrifying diagnostic odyssey. “Test after test is performed,” he said. “Some tests are invasive, the child is suffering. The child is getting worse and worse – most spend their entire lives in the hospital and there is no answer.”

Just knowing the answer can be a comfort. “Providing a definitive diagnosis somehow brings closure,” Dr. Kingsmore said. “It is something they can name.” 

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