A Randomized, Controlled Trial of the Analytic and Diagnostic Performance of Singleton and Trio, Rapid Genome and Exome Sequencing in Ill Infants

Abstract

The second Newborn Sequencing in Genomic Medicine and Public Health study was a randomized, controlled trial of the effectiveness of rapid whole-genome or -exome sequencing (rWGS or rWES, respectively) in seriously ill infants with diseases of unknown etiology. Here we report comparisons of analytic and diagnostic performance. Of 1,248 ill inpatient infants, 578 (46%) had diseases of unknown etiology. 213 infants (37% of those eligible) were enrolled within 96 h of admission. 24 infants (11%) were very ill and received ultra-rapid whole-genome sequencing (urWGS). The remaining infants were randomized, 95 to rWES and 94 to rWGS. The analytic performance of rWGS was superior to rWES, including variants likely to affect protein function, and ClinVar pathogenic/likely pathogenic variants (p < 0.0001). The diagnostic performance of rWGS and rWES were similar (18 diagnoses in 94 infants [19%] versus 19 diagnoses in 95 infants [20%], respectively), as was time to result (median 11.0 versus 11.2 days, respectively). However, the proportion diagnosed by urWGS (11 of 24 [46%]) was higher than rWES/rWGS (p = 0.004) and time to result was less (median 4.6 days, p < 0.0001). The incremental diagnostic yield of reflexing to trio after negative proband analysis was 0.7% (1 of 147). In conclusion, rapid genomic sequencing can be performed as a first-tier diagnostic test in inpatient infants. urWGS had the shortest time to result, which was important in unstable infants, and those in whom a genetic diagnosis was likely to impact immediate management. Further comparison of urWGS and rWES is warranted because genomic technologies and knowledge of variant pathogenicity are evolving rapidly.

Keywords: diagnosis; genetic disease; genomic medicine; infant; intensive care unit; precision medicine; ultra-rapid whole-genome sequencing; whole-exome sequencing; whole-genome sequencing.

Figure 1

Flow Diagram of the NSIGHT2 Randomized, Controlled, Blinded Trial Singleton analyses included variant validation and segregation analysis in trios, if samples were available, by Sanger sequencing or microarrays. RCHSD, Rady Children’s Hospital San Diego; NICU, level IV neonatal intensive care unit; PICU, regional pediatric intensive care unit; CVICU, regional cardiovascular intensive care unit; rWES, rapid whole-exome sequencing; rWGS, rapid whole-genome sequencing; urWGS, ultra-rapid whole-genome sequencing.

Figure 2

CONSORT Flow Diagram of the Number of Infants in ICUs Who Were Screened for Eligibility in NSIGHT2, Sequenced, and Received a Genetic Disease Diagnosis that Explained Their Presentation HIE, hypoxic ischemic encephalopathy.

Figure 3

Comparison of Time to Return of Results by rWES, rWGS, and urWGS in 213 Infants (A and B) Kaplan-Meier curves of time from sample receipt to first positive or negative report (A) or first positive report (B). (C) Gantt chart of the median times of the major components in clinical genomic sequencing for diagnosis of genetic diseases. Diagnoses that informed acute changes in management that had the potential to improve outcomes were reported verbally to clinicians provisionally before confirmatory testing of variants. Upon confirmation, all diagnoses were reported in writing.