Randomized Clinical Trial of First-Line Genome Sequencing in Pediatric White Matter Disorders

Abstract

Objective: Genome sequencing (GS) is promising for unsolved leukodystrophies, but its efficacy has not been prospectively studied.

Methods: A prospective time-delayed crossover design trial of GS to assess the efficacy of GS as a first-line diagnostic tool for genetic white matter disorders took place between December 1, 2015 and September 27, 2017. Patients were randomized to receive GS immediately with concurrent standard of care (SoC) testing, or to receive SoC testing for 4 months followed by GS.

Results: Thirty-four individuals were assessed at interim review. The genetic origin of 2 patient's leukoencephalopathy was resolved before randomization. Nine patients were stratified to the immediate intervention group and 23 patients to the delayed-GS arm. The efficacy of GS was significant relative to SoC in the immediate (5/9 [56%] vs 0/9 [0%]; Wild-Seber, p < 0.005) and delayed (control) arms (14/23 [61%] vs 5/23 [22%]; Wild-Seber, p < 0.005). The time to diagnosis was significantly shorter in the immediate-GS group (log-rank test, p = 0.04). The overall diagnostic efficacy of combined GS and SoC approaches was 26 of 34 (76.5%, 95% confidence interval = 58.8-89.3%) in <4 months, greater than historical norms of <50% over 5 years. Owing to loss of clinical equipoise, the trial design was altered to a single-arm observational study.

Interpretation: In this study, first-line GS provided earlier and greater diagnostic efficacy in white matter disorders. We provide an evidence-based diagnostic testing algorithm to enable appropriate clinical GS utilization in this population. ANN NEUROL 2020;88:264-273.

Trial registration: ClinicalTrials.gov NCT02699190.

Conflict of interest statement

Potential Conflicts of Interest

J.F. and R.J.T. are employees of Illumina. Illumina employees participated in trial design, review of genomic data, and revision of the manuscript. The other authors have no conflicts to report. Illumina provided in kind support by providing Clinical Laboratory Improvement Acts (CLIA)/College of American Pathologists (CAP) certified GS; however, all study activities, including randomization, patient review, trial coordination, and statistical analysis occurred at the academic institutions involved without direct input or support from Illumina.

© 2020 American Neurological Association.

Figures

FIGURE 1:

LeukoSeq trial design and principal results. (A) Overall recruitment and enrollment of the cohort examined in this study. (B) The trial employed a time-delayed crossover design with one-third of individuals assigned to the immediate genome sequencing (GS) arm and two-thirds of individuals receiving standard of care (SoC) for 4 months followed by GS. Of the 9 individuals assigned to immediate- GS, none received a diagnosis during the study period using SoC, 5 received a diagnosis using GS, and 4 did not achieve a diagnosis. Of the 23 individuals undergoing SoC with delayed-GS, only 5 individuals achieved a diagnosis with SoC approaches. Fourteen individuals achieved a diagnosis using GS, and 4 individuals did not achieve a diagnosis. Two patients noted in the black box at the top right received a diagnosis prior to randomization. (C) Distribution of cases solved by modality (SoC or GS) and broad class of white matter disorder. NR = not resolved; WGS = whole genome sequencing.

FIGURE 2:

Time to diagnosis with genome sequencing (GS) or standard of care (SoC). (A) Median time to diagnosis (weeks) in either the immediate-GS or delayed-GS arms. Overall time to diagnosis correlates with time to access to GS for the majority of the cohort. Note that for patients solved by SoC diagnostic techniques in the SoC arm, all individuals who received a diagnosis received it within 2 weeks of enrollment, although for the remainder of the cohort SoC approaches continued until crossover. (B) Kaplan–Meier analysis of the proportion of individuals achieving a diagnosis for the immediate-GS versus delayed-GS arms, demonstrating time to diagnosis from enrollment in individuals achieving a diagnosis only. The time to diagnosis was significantly shorter in the immediate-GS group (p = 0.04, log-rank test). The likelihood of diagnosis using SoC approaches was greatest <5 weeks after the onset of testing; afterward, only GS resolved cases.

FIGURE 3:

Accuracy of magnetic resonance imaging (MRI) pattern recognition prior to agnostic testing. Thirty-two MRIs were reviewed by clinicians experienced in the diagnosis of leukodystrophy patients. If the ultimate diagnosis was a canonical leukodystrophy, at least one of the reviewers correctly identified the MRI pattern and the diagnosis (8/10). High certainty of the category of disease if the final diagnosis was a mitochondrial leukoencephalopathy (4/4) was demonstrated. If the final diagnosis was neither a mitochondrial disease nor a leukodystrophy, MRI pattern recognition never identified the correct diagnosis (0/18 cases).

FIGURE 4:

Diagnostic testing algorithm for patients with a suspected white matter (WM) disorder. A decision flow chart to determine appropriate diagnostic approaches given clinical assessment and magnetic resonance imaging (MRI) pattern analysis is shown. First- line biochemical testing, including very long chain fatty acids (VLCFAs), lysosomal enzymes, and urine organic acids (UOAs), and in the appropriate context cholestenol levels, are recommended to provide rapid diagnosis for treatable leukodystrophies. If the MRI pattern cannot be associated with a previously recognized leukodystrophy, rapid genome sequencing (GS; if available) should be pursued to shorten the diagnostic odyssey and provide the greatest likelihood of definitive diagnosis. Targeted molecular testing may be considered if the clinical picture or MRI is characteristic of a single specific recognizable disorder but does not demonstrate the same level of efficacy as broader exome sequencing or GS testing in the absence of salient clinical features. LP, likely pathogenic; P = pathogenic