WGA Speeds Diagnosis of Devastating Seizure Disorder in Kids

Damian McNamara

August 17, 2018

Whole-genome analysis (WGA) may offer much more rapid and cost-effective clinical diagnosis of a rare, but devastating, epilepsy syndrome in infants, new research shows.

Investigators found WGA, consisting of whole-genome sequencing and comprehensive variant discovery, revealed infantile epileptic encephalopathy (EIEE) in 14 infants for whom previous genetic tests had not yielded a diagnosis.

This strategy, investigators note, supports WGA as a superior diagnostic strategy compared with whole-exome sequencing or use of gene panel testing.

"Our results suggest that this approach achieves a very high diagnostic rate and is a more economical solution to diagnosis than traditional tests," principal investigator Aaron Quinlan, PhD, associate professor of human genetics and biomedical informatics at the University of Utah in Salt Lake City, told Medscape Medical News.

The study was published online August 13 in npj Genomic Medicine.

Severe Impairment, Early Death

EIEE presents in the first months of life and causes intractable seizures with multiple seizure types, including generalized tonic, myoclonic, hemiclonic, focal tonic, and other seizure types. The prevalence is unclear; the condition only affects a subset of all infants with seizures at about 1.2 of 1000 live births, the investigators report.

These children typically have developmental delays and severe intellectual impairment and progress to severe psychomotor impairment and early death, they note.

Although there are several potential causes, including structural brain malformations, birth injury, and inborn error of metabolism, most EIEE cases are presumed to have a genetic basis.

More than 50 different genes have been described in EIEE. While gene panel and whole-exome sequencing can be less costly and time-consuming than WGA, diagnostic yields for these two approaches typically remain below 60%.

Furthermore, diagnostic testing using traditional methods can take years and can be costly, so "improving the speed and reducing the cost associated with genetic tests would have substantial clinical impact," the researchers note.

For these reasons and others, Quinlan, lead author Betsy Ostrander, MD, and colleagues turned to WGA.

The researchers retrospectively studied 14 newborns for whom previous genetic testing before age 6 months was inconclusive. The retrospective cohort included babies born between 2004 and 2016 and followed as outpatients.

DNA samples from each newborn and both parents were extracted from blood or saliva. Researchers performed whole-genome sequencing using TruSeq DNA PCR-free libraries (Illumina) and the Illumina HiSeq X Ten System at a minimum of 60x median whole-genome coverage.

They identified genetic changes present in the newborn and not in either parent via a proprietary algorithm they developed. A forthcoming publication will detail their RUFUS reference-free de novo variant-calling algorithm, which in this instance detected all diagnostic and putative disease causing mutations in a single step. Sanger sequencing confirmed the genetic mutations identified in the study.

Rapid, Definitive Diagnosis

Using the online GEMINI genetic database, the investigators found single de novo mutations in known EIEE-associated genes for 9 of the 14 participants.

They report a high confidence of pathogenicity for these mutations. Another "interrogation tool" called gene.iobio helped them identify a likely pathogenic mutation in a tenth participant.

Remarkably, these techniques allowed the researchers to identify these 10 mutations in less than 5 minutes. In a noteworthy contrast, one study participant was older than 16 years upon a definitive EIEE diagnosis.

Expanding the investigation beyond regions of DNA associated with EIEE allowed researchers to find new mutations and structural changes to DNA for the remaining newborns.

Three of the genetic mutations identified with WGA were not detected in patients who underwent earlier whole-exome sequencing. In addition, a de novo mutation detected in another patient could be detected only with this more comprehensive approach. 

They identified some known EIEE gene mutations and others not previously associated with the condition. They also discovered unexpected structural changes to the DNA of the children, including genetic duplication and missense variations.

"Given that there are dozens of genes known to underlie EIEE, I was not surprised that multiple genes were implicated in our study," said Quinlan, who is also associate director of the Utah Science Technology and Research Center for Genetic Discovery.

"However, a key insight and surprise from our study was the connection to structural rearrangements. The characterization of these types of genomic changes is a key strength of my lab, and it was very rewarding for us to use these methods to solve the genetic basis of EIEE," he added.

Cost-effective

WGA can be cost-effective, the researchers note, even with a current cost that ranges between $5000 and $15,000.

Each study participant received a minimum of 24 diagnostic tests, for an average cost of $30,866 (range, $16,592 - $50,348). The total cost associated with pursuing a diagnosis for the entire cohort was $432,121.

"As genome sequencing costs continue to decline, we suggest that this approach is the best clinical diagnostic, especially since it can identify all forms of causal mutations," Quinlan said.

Another advantage of WGA is that it can be performed in a clinical setting with a turnaround time of 14 days or less.

WGA "is best suited to developmental disorders and other Mendelian diseases typically caused by mutations in single genes," Quinlan said. More complex disorders are rarely diagnosable with this approach, he added

 "We would like to expand this approach to the diagnosis of a broader range of neurological disorders," said Quinlan. "Ultimately, we will strive to establish genome sequencing as the frontline test for the diagnosis of rare diseases at the University of Utah.

"Excellent Approach"

Commenting on the findings for Medscape Medical News, Fernando Scaglia, MD, professor of molecular and human genetics, Baylor College of Medicine in Houston, Texas, said that whole-genome analysis is "excellent approach, and it's an approach we will eventually starting using clinically at Baylor."

"This [study] demonstrates this strategy has a higher diagnostic yield than whole-exome sequencing."

Scaglia agreed that the cost of whole genome sequencing is coming down.

In terms of clinical implications, he added, "When you get a result sooner you can, in some cases, choose a more appropriate therapy. Also, the patient can also be brought into a clinical trial."

"For EIEE, whole-genome sequencing seems to be the way to do it."

Grants from the National Institutes of Health's National Genome Research Institute and National Institute of General Medical Sciences supported the study. Quinlan and Scaglia have disclosed no relevant financial relationships.

NPJ Genom Med. Published online August 13, 2018. Full text

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