Utility and limitations of exome sequencing in the molecular diagnosis of pediatric inherited platelet disorders

Abstract

Inherited platelet disorders (IPD) are a heterogeneous group of rare disorders that affect platelet number and function and often predispose to other significant medical complications. In spite of the identification of over 50 IPD disease-associated genes, a molecular diagnosis is only identified in a minority (10%) of affected patients without a clinically suspected etiology. We studied a cohort of 21 pediatric patients with suspected IPDs by exome sequencing (ES) to: (1) examine the performance of the exome test for IPD genes, (2) determine if this exome-wide diagnostic test provided a higher diagnostic yield than has been previously reported, (3) to evaluate the frequency of variants of uncertain significance identified, and (4) to identify candidate variants for functional evaluation in patients with an uncertain or negative diagnosis. We established a high priority gene list of 53 genes, evaluated exome capture kit performance, and determined the coverage for these genes and disease-related variants. We identified likely disease causing variants in 5 of the 21 probands (23.8%) and variants of uncertain significance in 52% of patients studied. In conclusion, ES has the potential to molecularly diagnose causes of IPD, and to identify candidate genes for functional evaluation. Robust exome sequencing also requires that coverage of genes known to be associated with clinical findings of interest need to be carefully examined and supplemented if necessary. Clinicians who undertake ES should understand the limitations of the test and the full significance of results that may be returned.

FIGURE 1

Summary of ES performance characteristics for 53 gene IPD gene list. (A) Average coverage for 873 exons from 53 IPD genes at 20X sequencing depth from 265 exomes as defined in the Methods section. (B) Distribution of 2835 disease-associated variants from HGMD in 53 IPD genes. ES, exome sequencing; HGMD, Human genome mutation database; IPD, inherited platelet disorder [Color figure can be viewed at wileyonlinelibrary.com]

FIGURE 2

Molecular diagnostic yield using ES in IPD cohort as well as mode of inheritance. (A) Percentage displayed in each column represents the percentage of each diagnosis type from the total IPD cohort (n = 21 patients). Negative represents no suspected disease-causing variants or only likely benign / benign variants; Uncertain represents only variants of uncertain significance (VUS); Positive represents pathogenic or likely pathogenic variants consistent with disease inheritance pattern. (B) Mechanism of inheritance in patients with positive molecular diagnosis (n = 5 patients). AD, autosomal dominant; AR, autosomal recessive; Hom, homozygous; Comp het, compound heterozygous [Color figure can be viewed at wileyonlinelibrary.com]