A Novel Tool for the Analysis and Detection of Copy Number Variants Associated with Haemoglobinopathies

Abstract

Several types of haemoglobinopathies are caused by copy number variants (CNVs). While diagnosis is often based on haematological and biochemical parameters, a definitive diagnosis requires molecular DNA analysis. In some cases, the molecular characterisation of large deletions/duplications is challenging and inconclusive and often requires the use of specific diagnostic procedures, such as multiplex ligation-dependent probe amplification (MLPA). Herein, we collected and comprehensively analysed all known CNVs associated with haemoglobinopathies. The dataset of 291 CNVs was retrieved from the IthaGenes database and was further manually annotated to specify genomic locations, breakpoints and MLPA probes relevant for each CNV. We developed IthaCNVs, a publicly available and easy-to-use online tool that can facilitate the diagnosis of rare and diagnostically challenging haemoglobinopathy cases attributed to CNVs. Importantly, it facilitates the filtering of available entries based on the type of breakpoint information, on specific chromosomal and locus positions, on MLPA probes, and on affected gene(s). IthaCNVs brings together manually curated information about CNV genomic locations, functional effects, and information that can facilitate CNV characterisation through MLPA. It can help laboratory staff and clinicians confirm suspected diagnosis of CNVs based on molecular DNA screening and analysis.

Keywords: MLPA; copy number variants (CNVs); haemoglobinopathies.

Figure 1

Home page of the IthaCNVs tool. Filtering is based on the CNV location.

Figure 2

Descriptive analysis of the CNV dataset. (A) Haemoglobinopathy groups/phenotypes and variant functionality, (B) Haemoglobinopathy groups/phenotypes and variant type, (C) Affected genes associated with α-globin locus variants, (D) Affected genes associated with β-globin locus variants.