Exome Sequencing Diagnoses Neurodevelopmental Disorders

Ricki Lewis, PhD

December 05, 2014

Whole-exome and whole-genome sequencing can end the "diagnostic odyssey" that many families of children with neurodevelopmental disorders (NDD) undergo and can directly affect care, while costing less than conventional genetic testing, a new study shows.

The study, published in the December 3 issue of Science Translational Medicine, follows the experiences of 100 families, presenting several illuminating case studies.

NDD, including intellectual disability, global developmental delay, and autism, are challenging to diagnose at the molecular level because of overlapping symptoms and genetic heterogeneity. They affect 3% of all children.

Whole-exome sequencing (WES) or whole-genome sequencing (WGS) can add precision by helping describe new disorders, reveal atypical or incomplete presentations of known disorders, and identify comorbidities, researchers write.

Sarah Soden, MD, a developmental pediatrician at the Center for Pediatric Genomic Medicine at Children's Mercy Kansas City, and colleagues evaluated WES and/or WGS to retrospectively diagnose 119 children with NDD from the first 100 families enrolled at the center, which opened 3 years ago.

The children had characteristics associated with recognized inherited conditions, evaluated with the tool Phenomizer, but their overall phenotypes did not match any of the 2400 monogenic neurologic disorders.

The researchers used an "acuity-guided" approach that stratified participants by acute or nonacute presentation. "We have ambulatory patients who have been on the diagnostic odyssey on average 7 years; 85 families fell into that group," Dr Soden told Medscape Medical News. They underwent WES.

"Fifteen families had acutely ill patients who were mostly in neonatal and pediatric ICUs [intensive care units]. We tested those children with our STAT-Seq or rapid whole-genome sequencing," in collaboration with Illumina, Dr Soden said. It takes only 50 hours and can pick up gene variants that WES misses, she added.

Children in the nonacute group had global developmental delay/intellectual disability, whereas those in the acute group had seizures, hypotonia, and central nervous system anomalies. Parent-child trios were tested for most families.

Typical diagnostic odysseys included single-gene and chromosome tests, neuroimaging, biopsies, cerebrospinal fluid examination, and electromyography.

Diagnosis-by-Genomics Adds Speed and Precision

Of the 100 families, 45 (53 of 119 children) received molecular diagnoses after undergoing WES or WGS, the authors report.

"It's what we'd been hoping all along would be the case," Robert Marion, MD, chief, Division of Genetics, The Children's Hospital at Montefiore, Albert Einstein College of Medicine, Bronx, New York, who was not involved in the research, told Medscape Medical News. "The findings are spectacular."

The results are even more encouraging than those of other recent investigations, although comparisons are still somewhat apples-and-oranges. Two papers and an editorial in a recent issue of JAMA are compelling.

Lee and colleagues from the University of California at Los Angeles performed WES on 814 consecutive cases and diagnosed 26% overall (213 of 814). Yang and associates from Baylor College of Medicine, Houston, Texas, also used WES and diagnosed 25.2% (504 of 2000) of cases.

Calculations based on sequencing families (parent-child trios or parents and more than one child) led to better rates of diagnosis in the current study. Dr Soden and coauthors molecularly diagnosed 45% of their 100 families, and Lee et al diagnosed 31% (127 of 410) when considering trios. In addition, the phenotypes in the Lee and Yang studies were not restricted to neurologic conditions.

In the current study, WES led to diagnosis of 40% (34 of 85) of families with children with nonacute NDD. Rapid WGS led to diagnosis of 73% (11 of 15) of the families with acutely ill children. Even though the sequencing took 50 hours, 6 to 10 days total were required to analyze findings.

"The younger (acute) kids hadn't been worked up in the past, whereas the nonacute group eliminated kids with easy diagnoses," Dr Marion pointed out. "This justifies doing WES or WGS earlier."

The results indicate that genomics technology has transcended the point at which sequencing exomes and genomes costs less than sequencing individual genes. For the nonacute patients, previous testing cost on average $19,100 per family, compared with up to $7640 per family or $2996 per individual for WES or WGS. Exome sequencing might have provided diagnoses up to 77 months earlier, the researchers extrapolated, taking off another 10 months using WGS.

Comparing the costs for individual cases is even more compelling. Negative results on diagnostic testing for the first two enrollees, sisters, exceeded $35,000, with 45 subspecialist visits. A year later, two other siblings had WES at the first subspecialist visit, and the total cost was $3248.

Change in Care

The study is the first to demonstrate that genome-based diagnosis can directly affect patient care of infants and children with NDD. For nearly half of the families (49%), the results changed the interpretation of clinical findings and in some cases even care.

"New treatments were started, some unnecessary treatments were stopped, and some cases were sent for referrals to other subspecialists or for other tests for comorbid conditions," Dr Soden told Medscape Medical News.

 
All clinical geneticists doing this now have stories like mine. We have all been touched by this technology. Dr Robert Marion
 

Twelve of the 119 children (10.1%) received new treatments, and 5 (4.2%) had treatment discontinued; in 18 (15.1%) cases, comorbidity entered the diagnostic picture. Five cases (4.2%) were atypical presentations and "three new genes are included in our total tally," Dr Soden said.

The findings validate what clinical geneticists have already noted on a case-by-case basis. Dr Marion, who has led several families on a genome-guided end to their diagnostic quests, isn't alone. "All clinical geneticists doing this now have stories like mine. We have all been touched by this technology."

Intriguing Cases

The paper presents several cases. A boy with seizures, autism, tremor, unsteady gait, and dysmorphic features had a new variant in PIGA, which encodes a phosphatidylinositol glycan anchor biosynthesis protein. Known patients had died in infancy, but the boy, now 10 years of age, produces sufficient truncated protein to survive.

Another child had atypical KBG syndrome due to a variant in the ANKRD11 gene, but she hadn't been diagnosed because she does not have the associated macrodontia and hypertelorism. A third child had a mitochondrial disorder that explained respiratory symptoms. NA-K-citrate supplements improved muscle tone, alertness, and head control and halted the respiratory episodes.

Sequencing, however, hasn't extinguished clinical instinct. Dr Soden described a "fascinating pair of sisters whose exomes and those of their parents didn't result in a diagnosis. But given that the sisters had very similar features, we felt strongly that there was still something to find."

The sisters shared developmental delay, autism, hypotonia, and hypoglycemia, but one had low muscle mass and premature adrenarche and the other had apnea, bradycardia, and seizures.

WGS identified 156 candidate genes, narrowed down to the MAGE-like 2 gene, within the Prader-Willi region of chromosome 15. Neither parent had the variant, indicating gonadal mosaicism. Exome sequencing had missed the gene because it is intronless and in a GC-rich region.

Limitations of the study include lack of a control group, collection of data primarily by chart review, the retrospective nature of the diagnostic sequencing, and use of treatments tried only on a few patients due to the rareness of diseases. The acuity-based design precluded direct comparison of WES and WGS.

According to Dr Soden, genome-based diagnosis will spread from research centers to subspecialty care.

Dr Marion looks ahead to applying WES/WGS more widely and earlier, as part of newborn screening.

"In medicine today we wait for people to develop symptoms and treat them," he said. "But when we know what they will develop, we can predict and prevent. That will change the whole practice of medicine."

The researchers and Dr Marion have disclosed no relevant financial relationships.

Sci Transl Med. 2014;6:265ra168 Abstract

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