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.

Population based frequency of naturally occurring loss‐of‐function variants in genes associated with platelet disorders

“…14 Next generation sequencing (NGS) has enhanced diagnostic capabilities, but causal variants often remain uncharacterized. 15 These disorders may not be diagnosed until an invasive procedure causes excessive bleeding, or may be misdiagnosed as autoimmune unless additional affected family members are identified. 16 Because platelet-related genes can be associated with increased risk of myelodysplastic syndrome (MDS), malignancy, bone marrow failure, cardiac arrhythmias, cataracts, deafness, or renal failure, molecular characterization is important for defining prognosis and guiding clinical decisions.…”

Horizon Scan Of Clinical Laboratories Offering Pharmacogenetic Testing

“…For gene panels, individual genes have differing levels of evidence of clinical validity. 24–26 With the exception of the gene pairs CYP2C9 / VKORC1 for warfarin and CYP2C9 / HLA-B for phenytoin (brand name Dilantin), all of the CPIC guidelines focus on a single gene-drug or gene–drug class interaction. The combined effect of variations in multiple genes relevant to a given medication remains largely unknown, though some test developers have suggested that combinatorial PGx testing, including genes involved in pharmacokinetic and pharmacodynamic pathways, may provide a more comprehensive prediction of drug response by using proprietary algorithms to predict drug safety 27 and may reduce medication costs.…”

Diagnosis of Inherited Platelet Disorders on a Blood Smear

“…However, interpretation of genetic findings can be difficult especially in patients without a peculiar clinical picture. In fact, NGS usually detects many variants of unknown or uncertain significance, whose correlation with the patient's phenotype is unresolved, and over-interpretation is a major risk [73][74][75][76][77]. Data from big case series reported so far indicated that NGS is able to achieve a diagnosis in nearly 50% of IPD patients suffering from congenital thrombocytopenia, and in nearly 25% of those with inherited platelet function disorder.…”