Agrawal Laboratory

About a year and a half ago, Robert Rothstein, MD, FAAP encountered a baby with a pattern of facial features and clinical findings that suggested a genetic syndrome. The available tests couldn’t pinpoint a diagnosis, and the family wanted a more definitive answer. So Rothstein and his colleagues transferred the newborn from Baystate Medical Center (Springfield, Mass.) to Boston Children’s Hospital — 90 miles away — for a more in-depth genetic workup.

By the time the parents met with the Boston Children’s team to discuss their baby’s genetic diagnosis, they were anxious and mistrustful. The neonatal intensive care unit (NICU) team in Boston suggested patching Rothstein into the family conferences and decision-making.

Suheil Day was born early, at 37 weeks. Aside from a slight head lag and mild muscle weakness, nothing seemed terribly amiss. But as the months progressed, he began having seizures.
 

“At the age of 4 to 5 months, he started waking up screaming and crying excessively, his eyes rolling up into his head,” says his mother, Nadeen.
 

Suheil’s physicians in Israel diagnosed him with West syndrome, an infantile spasm disorder, and treated him with adrenocorticotropic hormone. His seizures abated, but only for six months. After 15 other medications were tried without success, the Israeli hospital arranged for whole-exome sequencing to look for a genetic cause. The results showed variants in four genes. Two genes were ruled out after more testing; the other two were unknown.

A growing number of children with suspected genetic disorders are having their complete exomes sequenced, since it’s now often faster and cheaper to sequence all the protein-coding genes at once rather than test limited groups of genes. But even after whole-exome sequencing, 70 to 75 percent of children come away without a genetic explanation for their illness.

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More and more clinicians are sending these families to Pankaj Agrawal MD, MMSc, a neonatologist at Boston Children’s Hospital and medical director of the Gene Discovery Core at Boston Children’s Manton Center for Orphan Disease Research. The Core can then do a deeper dive. Its services are available to any patient or family looking for a second opinion, including families whose child is deceased.

Two rare groups of CF patients may reveal new approaches to treatment. They are outliers: patients whose disease progresses much more rapidly or slowly than is typical despite the same mutation.

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A Boston Children's team scoured the genomes of five outliers in search of genes that might modify the effects of the CF mutation and this explain these differences. They found several and are creating patient-specific stem cell models to further study the interactions of the modifier of CF genes. The team --physician scientist Ruobing Wang, stem cell scientists Carla Kim and George Q. Daley, and geneticist Pankaj Agrawal -- hopes that insights from outliers will lead to new treatments for CF patients who do not benefit from today's drugs.  

When the 1-year-old boy arrived from overseas, he was relying on total parenteral nutrition — a way of bypassing the digestive system to provide nutrients and calories completely intravenously — to survive. From the time of his birth, he had experienced unexplainable diarrhea. Answers were desperately needed.

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Sequencing his genes in search of clues, neonatologists and collaborators at the Manton Center for Orphan Disease Research at Boston Children’s Hospital identified a new gene mutation responsible for chronic congenital diarrhea — even finding a similar mutation in two other children as well.

The answer may be hidden in their genes.

Cystic fibrosis is an inherited disorder caused by genetic mutations that disrupt the normal movement of chloride in and out of cells. Among other health problems, cystic fibrosis compromises the lungs’ ability to fight infection and breathe efficiently, making it the most lethal genetic disease in the Caucasian population. Patients have an average lifespan of just 30 to 40 years.

Despite this narrow average lifespan, there is a big range in how severely cystic fibrosis (CF) affects the lungs and other organs depending on an individual’s specific genetic variation, and even in how long patients sharing the same, most common genetic mutation are able to survive with CF.

The first complete autopsy findings for a patient with AIFM1-associated disease are described in a paper from Morton et al. A novel variant in AIFM1 was identified in an infant who presented with severe metabolic acidosis, myopathy, and neuropathy. Shown here is a Gomori trichrome image of quadriceps muscle biopsy, 100×, showing features of mitochondrial myopathy including coarse stippling and scattered fibers with subsarcolemmal aggregates corresponding to mitochondria. (For details, see Morton et al., this issue; doi: 10.1101/mcs.a001560.)

Examining the tragedies of several families who each lost multiple children, two teams of researchers reveal a previously unappreciated role for a mitochondrial enzyme.

Head magnetic resonance imaging (MRI) findings in a female patient with severe mitochondrial disease presenting with developmental delay, hypotonia, lactic academia, and brain atrophy. Whole-exome sequencing identified two variants in the PMPCA gene, which encodes for α-mitochondrial processing peptidase (α-ΜPP), a protein likely involved in the processing of mitochondrial proteins. Shown here is the head MRI image of the patient at 6 months of age, which reveals cerebellar atrophy with enlarged interfolial spaces, whereas marked cerebral and cerebellar atrophy with enlarged ventricles were noted at 3 and 6 years. (For details, please see Joshi et al., this issue; doi: 10.1101/mcs.a000786.)

The coming year will see increased focus on genome sequencing of sick babies as an aid to their medical diagnosis and management. In 2013, the NIH funded four grantees across the U.S. to explore the use of genome sequencing in newborn health care for a period of five years, including a joint project from Boston Children’s and Brigham and Women’s Hospital. In the future, genomic sequencing may expand to all newborns as sequencing technologies get more affordable and sequence data get more interpretable. This may not only help improve care for those babies but also guide their families in making future decisions. —Pankaj Agrawal, MD, MMSC, Newborn Medicine Research Center, Boston Children’s Hospital

Sequencing a patient’s genome to figure out the exact source of his or her disease isn’t standard operating procedure — yet. But falling sequencing costs and a growing number of successes are starting to bring this approach into the mainstream, helping patients and families while advancing a broader understanding of their diseases.