Effectiveness of exome and genome sequencing guided by acuity of illness for diagnosis of neurodevelopmental disorders

Abstract

Neurodevelopmental disorders (NDDs) affect more than 3% of children and are attributable to single-gene mutations at more than 1000 loci. Traditional methods yield molecular diagnoses in less than one-half of children with NDD. Whole-genome sequencing (WGS) and whole-exome sequencing (WES) can enable diagnosis of NDD, but their clinical and cost-effectiveness are unknown. One hundred families with 119 children affected by NDD received diagnostic WGS and/or WES of parent-child trios, wherein the sequencing approach was guided by acuity of illness. Forty-five percent received molecular diagnoses. An accelerated sequencing modality, rapid WGS, yielded diagnoses in 73% of families with acutely ill children (11 of 15). Forty percent of families with children with nonacute NDD, followed in ambulatory care clinics (34 of 85), received diagnoses: 33 by WES and 1 by staged WES then WGS. The cost of prior negative tests in the nonacute patients was $19,100 per family, suggesting sequencing to be cost-effective at up to $7640 per family. A change in clinical care or impression of the pathophysiology was reported in 49% of newly diagnosed families. If WES or WGS had been performed at symptom onset, genomic diagnoses may have been made 77 months earlier than occurred in this study. It is suggested that initial diagnostic evaluation of children with NDD should include trio WGS or WES, with extension of accelerated sequencing modalities to high-acuity patients.

Fig. 1. Diagnoses and inheritance patterns in 100 NDD families tested by genome or exome sequencing

(A) Diagnostic outcomes in 100 families. (B) Inheritance pattern in 45 families. AR, autosomal recessive.

Fig. 2. Clinical features of patients CMH301, CMH663, CMH334, and CMH335

(A to C) Patient CMH301, with multiple congenital anomalies–hypotonia–seizures syndrome 2 (PIGA, c.68dupG, p.Ser24LysfsX6) at ages 2 (A), 6 (B), and 10 years (C). (D) Infant CMH663, with compound heterozygous mutations in the mitochondrial malate/citrate transporter (SLC25A1). (E) Male patients CMH334 (left) and CMH335 (right) with X-linked Rett syndrome (MECP2, c.419C>T, p.A140V) and their mother.

Fig. 3. Expression of GPI-anchored proteins on peripheral blood cells of patient CMH301

CMH301 was diagnosed with multiple congenital anomalies–hypotonia–seizures syndrome 2. Flow cytometric signals corresponding to CMH301 are shown by the green lines, his mother CMH303 is shown in blue, and a normal control is shown in red. Erythrocytes were stained with anti-CD59 antibodies. Granulocytes, B cells, and T cells were stained with fluorescent aerolysin (FLAER). The orange line represents an unstained normal control. The x axis is the number of cells. The y axis is fluorescence intensity, representing the abundance of protein expression on the cell surface. CMH301 has normal expression of CD59 and decreased expression of GPIanchored proteins on granulocytes, B lymphocytes, and T lymphocytes.

Fig. 4. Effect of citrate supplementation on urinary citrate and 2-hydroxyglutarate in patient CMH663

CMH663 had combined d-2- and l-2-hydroxyglutaric aciduria. CMH urinary citrate reference value for normal urine is >994 mmol/mol creatinine. CMH urinary 2-OH-glutarate reference value for normal urine is <89 mmol/mol creatinine.