A comprehensive bioinformatic analysis of 126 patients with an inherited platelet disorder to identify both sequence and copy number genetic variants.

Ibrahim Almazni,Neil V Morgan,Rachel J Stapley,Abdullah O Khan

doi:10.1002/humu.24114

Abstract

Inherited bleeding disorders (IBDs) comprise an extremely heterogeneous group of diseases that reflect abnormalities of blood vessels, coagulation proteins, and platelets. Previously the UK-GAPP study has used whole-exome sequencing in combination with deep platelet phenotyping to identify pathogenic genetic variants in both known and novel genes in approximately 40% of the patients. To interrogate the remaining "unknown" cohort and improve this detection rate, we employed an IBD-specific gene panel of 119 genes using the Congenica Clinical Interpretation Platform to detect both single-nucleotide variants and copy number variants in 126 patients. In total, 135 different heterozygous variants in genes implicated in bleeding disorders were identified. Of which, 22 were classified pathogenic, 26 likely pathogenic, and the remaining were of uncertain significance. There were marked differences in the number of reported variants in individuals between the four patient groups: platelet count (35), platelet function (43), combined platelet count and function (59), and normal count (17). Additionally, we report three novel copy number variations (CNVs) not previously detected. We show that a combined single-nucleotide variation (SNV)/CNV analysis using the Congenica platform not only improves detection rates for IBDs, suggesting that such an approach can be applied to other genetic disorders where there is a high degree of heterogeneity.

Highlights

Inherited bleeding disorders (IBDs) are a heterogeneous group of diseases that reflect abnormalities in blood vessels, coagulation proteins, and platelets
We show that a combined single‐nucleotide variation (SNV)/copy number variations (CNVs) analysis using the Congenica platform improves detection rates for IBDs, suggesting that such an approach can be applied to other genetic disorders where there is a high degree of heterogeneity
Many of these panels do not search for copy number variations (CNVs), and we, and others have not found definitively causative variants in approximately 40%–50% patients despite a strongly indicative inherited component for their bleeding (Bastida et al, 2018; Johnson et al, 2018; Johnson, Lowe, et al, 2016; Leinøe et al, 2017; Lentaigne et al, 2016). We address this by applying a newly established, comprehensive genetic analysis software that detects both single‐nucleotide variations (SNVs) and CNVs

Summary

| INTRODUCTION

Inherited bleeding disorders (IBDs) are a heterogeneous group of diseases that reflect abnormalities in blood vessels, coagulation proteins, and platelets. NGS panels can be employed in a clinical diagnostic setting or used for prescreening, filtering out patients with variants in known genes, and subsequently employing WES for those who may harbor variants in novel genes (Johnson et al, 2018; Simeoni et al, 2016) This approach was applied in the UK‐GAPP study where patients with known mutations in hemophilia A and B or coagulation mediated genes, known to cause bleeding were eliminated. We show its utility in interrogating a large cohort of patients recruited to the UK‐GAPP research study Using this approach, we perform a robust and comprehensive analysis to find both known and novel genetic variants with plausible association with disease, including rare CNVs not previously detected. Combined with extensive patient phenotypic studies, this provides a potent tool for the dissection of the genetic causes of bleeding in a cohort which, far, remains genetically unresolved despite an extensive clinical presentation of familial bleeding

| METHODS

| RESULTS

F11 SERPINC1 F13A1

Findings

| DISCUSSION