Use of next‐generation sequencing and candidate gene analysis to identify underlying defects in patients with inherited platelet function disorders

Abstract

SummaryBackgroundInherited platelet function disorders (PFDs) are heterogeneous, and identification of the underlying genetic defects is difficult when based solely on phenotypic and clinical features of the patient.ObjectiveTo analyze 329 genes regulating platelet function, number, and size in order to identify candidate gene defects in patients with PFDs.Patients/methodsTargeted analysis of candidate PFD genes was undertaken after next‐generation sequencing of exomic DNA from 18 unrelated index cases with PFDs who were recruited into the UK Genotyping and Phenotyping of Platelets (GAPP) study and diagnosed with platelet abnormalities affecting either Gi signaling (n = 12) or secretion (n = 6). The potential pathogenicity of candidate gene defects was assessed using computational predictive algorithms.ResultsAnalysis of the 329 candidate PFD genes identified 63 candidate defects, affecting 40 genes, among index cases with Gi signaling abnormalities, while 53 defects, within 49 genes, were identified among patients with secretion abnormalities. Homozygous gene defects were more commonly associated with secretion abnormalities. Functional annotation analysis identified distinct gene clusters in the two patient subgroups. Thirteen genes with significant annotation enrichment for ‘intracellular signaling’ harbored 16 of the candidate gene defects identified in nine index cases with Gi signaling abnormalities. Four gene clusters, representing 14 genes, with significantly associated gene ontology annotations were identified among the cases with secretion abnormalities, the most significant association being with ‘establishment of protein localization.’ConclusionOur findings demonstrate the genetic complexity of PFDs and highlight plausible candidate genes for targeted analysis in patients with platelet secretion and Gi signaling abnormalities.

Inherited platelet disorders: toward DNA-based diagnosis

“…73,85 The greatest diagnostic success for d-SPD has been in the multisystem syndromes such as Chediak Higashi syndrome and HPS, but most patients with nonsyndromic d-SPD remain undiagnosed. 86 In ongoing large-scale HTS projects such as Genotyping and Phenotyping of Platelets 87,88 and BRIDGE-BPD, 2,22,48 the lack of gene discovery for d-SPD, even in these large patient cohorts, highlights a need to analyze the noncoding regulatory regions of the genome via whole genome sequencing (WGS) while also exploring novel methods of data analysis and integration. We discuss such methods in more detail in the final section.…”

Whole exome sequencing identifies genetic variants in inherited thrombocytopenia with secondary qualitative function defects

“…WES and bioinformatics analysis were performed as described previously 8,15,16 ( Figure 1). The pathogenicity of variants was determined and called using the consensus guidelines as set out by the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG guidelines).…”

Targeted deep resequencing of ALOX5 and ALOX5AP in patients with diabetes and association of rare variants with leukotriene pathways

“…In addition, NGS studies, as applied to platelet function, provided significant results indicating that potentially damaging variants in platelet genes have low individual frequencies, but are collectively abundant among the population (45). Another previous study reported that potentially damaging variants are present in pedigrees with inherited platelet function disorders and may contribute to complex laboratory phenotypes (46). The genetic variants involved in the function of ALOX5 and ALOX5AP were described previously with mixed results regarding their involvement in the regulation of LT metabolism or vascularity, including platelet functions (7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17).…”