NEW YORK – Whole-genome sequencing can be a viable first-line diagnostic testing option, according to results from the Newborn Sequencing in Genomic Medicine and Public Health trial (NSIGHT2).
A team led by researchers from Rady Children's Institute for Genomic Medicine compared the effectiveness of rapid whole-genome or whole-exome sequencing in seriously ill infants with unknown diseases. The research team enrolled more than 200 sick infants into their study to undergo sequencing. Of those, two dozen were very ill and underwent ultra-rapid whole-genome sequencing, while the rest were randomized to undergo either rapid whole-genome or whole-exome sequencing.
While the researchers reported in the American Journal of Human Genetics today that rapid whole-genome and whole-exome sequencing had similar diagnostic rates in this cohort, they found rapid whole-genome sequencing had better analytical performance.
"Prior to this study, there was considerable evidence that rapid genomic sequencing was a useful diagnostic test for infants in ICUs who were suspected to have genetic diseases," David Dimmock, the senior medical director at Rady, and his colleagues wrote in their paper. "However, consensus with regard to optimal methods and scope of use was still lacking."
For this trial, the researchers sought to enroll a greater range of infants, as compared to previous efforts. In the past, clinical sequencing studies focused on infants in intensive care units with unknown, but suspected genetic diseases. Here, the researchers used broader inclusion criteria, but did, for instance, exclude infants for whom it was thought unlikely that a genetic diagnosis would change their clinical management or who had sepsis but were responding to therapy normally. In all, 213 infants enrolled in the study.
Eleven percent of these infants were too ill to undergo randomization and instead received ultra-rapid whole-genome sequencing, as that approach would provide the fastest possible route to diagnosis. Of the remaining 189 infants, 95 were randomized to receive whole-exome sequencing and 94 to whole-genome sequencing. They underwent sequencing within 96 hours of their admission to the NICU.
Both whole-genome and whole-exome sequencing had similar diagnostic rates, 19 percent and 20 percent, respectively. The time to diagnosis was also similar for the two groups, about 12 days.
But, the researchers uncovered differences in analytical performance between the whole-exome and whole-genome sequencing approaches. In particular, whole-genome sequencing uncovered more coding variants, more variants suspected to affect protein function, and more variants categorized as pathogenic or likely pathogenic by ClinVar than whole-exome sequencing. Because of this, the researchers said they were surprised that the two approaches had similar diagnostic rates.
However, they argued that the difference in the proportion of diseases diagnosed by whole-exome and whole-genome sequencing will likely change as experts' ability to interpret the pathogenicity of noncoding and structural variation improves. As it stands now, interpretation is largely confined to coding variation.
They noted, though, that one patient's renal hypodysplasia/aplasia 3 would have been missed if that infant had been assigned to the whole-exome sequencing arm, as the affected gene, GREB1L is not covered by whole-exome sequencing.
Ultra-rapid whole-genome sequencing, meanwhile, had a diagnostic rate of 46 percent and a median time to diagnosis of 2.3 days, which indicated to the researchers that it could be valuable as a first-tier test. In a previous study, the Rady researchers outlined their rapid pediatric sequencing approach, which involves bead-based genome library preparation and sequencing of paired 101-nucleotide reads.
The researchers added that a larger study of the diagnostic performance of these approaches is needed, especially as the understanding of pathogenic variants evolves.
In an email to GenomeWeb, Rady's Stephen Kingsmore, the first author of the paper, said this is the first of likely five papers from the NSIGHT2 study, and he and his colleagues are working on manuscripts related to enrollment and clinical utility. He added that enrollment into the study ended last October and they are still collecting outcomes data, which he said would be reported once that data collection ends.