NEW YORK (GenomeWeb) – In a new study of the diagnostic yield of genomic testing for autism spectrum disorders, researchers from the Hospital for Sick Children, Toronto, have found that both chromosomal microarray analysis and whole-exome sequencing have value, and offer unique contributions to a molecular diagnosis of these disorders.
The study — published today in JAMA — also confirmed patterns seen in earlier studies, which showed genetic diagnosis rates appear to be significantly higher among children with certain physical anomalies or clinical characteristics.
Stephen Scherer, the study's first author, told GenomeWeb this week that he and his colleagues hoped to provide a more expansive representation of the power of genomic testing in the diagnosis of ASD in light of morphological or clinical subtypes, and to make a timely comparison of the results of array-based and exome-based strategies at a moment when exome sequencing is being increasingly adopted into clinical diagnostic labs.
"We had access to this cohort [for which] there was this extensive morphological testing, imaging, and full diagnostic workups, and we had been doing the microarrays all along … both in the clinical lab here and as part of our research study," Scherer said. "But now as exome sequencing is making it into the diagnostic labs here and in theUS, we [realized we] also needed to have some good numbers for both microarray and exomes."
Since recommendations were made several yeas ago that CMA be used as a first-tier diagnostic strategy for ASD, Scherer said the labs at the Hospital for Sick Children have ramped up to running 10,000 CMA tests per year.
"Essentially, every child that gets a diagnostic workup gets array testing around here," he said. "In comparison, exome sequencing is just starting to become common. … A big reason we did this is … a lot of people seem to think that the exome is going to find everything that CMA does. But it turns out it doesn't."
In their study, Scherer and his colleagues analyzed the results of chromosomal microarray analysis in a group of 258 unrelated children from Newfoundland and Labrador, Canada, who were consecutively referred from 2008 through 2013 from two developmental pediatric clinics in the province that perform multidisciplinary team assessments for ASD.
The researchers also tracked the results of whole-exome sequencing — using the Ion Proton and exonic amplification with the Ion AmpliSeq Exome Kit — in 95 of these cases to determine the molecular diagnostic yield, or the percentage of cases where either of these technologies identified a genetic alteration suspected to be linked to the development of ASD.
"Ideally, we would have done exome sequencing on all the samples, but we got enough with the 100 or so we did that we felt it was appropriate to publish," Scherer said.
Meanwhile, all the study subjects underwent detailed clinical assessments looking for major or minor physical abnormalities and were stratified based on this into three morphological groups: essential, equivocal, and complex.
Overall, among the 258 total children, CMA resulted in a molecular diagnosis in 24, or 9.3 percent, while exome sequencing yielded a variant linked to ASD in 8 of 95, or 8.4 percent of cases.
Among the children who underwent both CMA and WES testing, the estimated percentage with an identifiable genetic cause was a combined 15.8 percent, suggesting an added value in utilizing both methods in parallel, as well as highlighting the unique contribution of each.
Importantly, the researchers also found that the diagnostic yield for genetic testing was much higher — up to almost 40 percent — in study subjects who had more complex morphological or clinical presentations.
The combined yield for CMA plus exome sequencing in the different morphological groups was 6.3 percent in the essential subset, 28.6 percent in the equivocal, and 37.5 percent in the complex group
"In some ways, ASD as a whole can be looked at as the neurodevelopmental equivalent of capital-C cancer," Scherer said. "If you look at certain cancers like CML, the diagnostic yield of genetic testing is going to be much higher than for [all cancers]."
"It's similar here. If we can subgroup the autisms into one form or another, for example, if you look at the 20 percent with complex [presentations], you get a diagnostic rate up to 35 percent."
Moreover, he said, "With this we were looking at the lowest hanging fruits — the penetrant genes that are in our annotation. If we look deeper into combinations [of genes], where it becomes more of a risk score, then the numbers go up even more."
Clinically, understanding that genomic testing has a higher likelihood of identifying a diagnostic mutation or alteration in certain subgroups of patients could be important for creating strategies for how to best integrate these technologies into the process of assessing kids with suspected ASD.
Scherer said he and his team are continuing to collect subjects to increase their cohort. Within a year, he said they expect to double the number of cases.
As part of this ongoing effort, the team is also performing whole-genome sequencing on all subjects. According to Scherer, whole-genome sequencing should eventually replace the combination of exome sequencing and CMA, though not for several years.
In the meantime, the most important takeaway from the Toronto team's results, he said, is the necessity — as the field awaits eventual clinical whole-genome sequencing — to not rely on exome sequencing or arrays alone for a comprehensive screen of potential ASD-associated alterations.
"We've found previously that comparing data from all the studies that have done exome and microarray testing, the candidate gene list you get with the two is almost not overlapping," Scherer said.
The team's new data confirms this even further. "You can see that we are picking up really different [molecular] forms of autism depending on the technology," he said.