Rapid and reliable detection of alpha-globin copy number variations by quantitative real-time PCR

Alpha-thalassemia is the most common human genetic disease worldwide. Copy number variations in the form of deletions of alpha-globin genes lead to alpha-thalassemia while duplications of alpha-globin genes can cause a severe phenotype in beta-thalassemia carriers due to accentuation of globin chain imbalance.

It is important to have simple and reliable methods to identify unknown or rare deletions and duplications in cases in which thalassemia is suspected but cannot be confirmed by multiplex gap-PCR. Here we describe a copy number variation assay to detect deletions and duplications in the alpha-globin gene cluster (HBA-CNV).

Results:
Quantitative real-time PCR was performed using four TaqMan(R) assays which specifically amplify target sequences representing both the alpha-globin genes, the -alpha3.7 deletion and the HS-40 region.

The copy number for each target was determined by the 2-DeltaDeltaCq method. To validate our method, we compared the HBA-CNV method with traditional gap-PCR in 108 samples from patients referred to our laboratory for hemoglobinopathy evaluation.

To determine the robustness of the four assays, we analyzed samples with and without deletions diluted to obtain different DNA concentrations. The HBA-CNV method identified the correct copy numbers in all 108 samples.

All four assays showed the correct copy number within a wide range of DNA concentrations (3.2-100 ng/muL), showing that it is a robust and reliable method. By using the method in routine diagnostics of hemoglobinopathies we have also identified several deletions and duplications that are not detected with conventional gap-PCR.

Conclusions:
HBA-CNV is able to detect all known large deletions and duplications affecting the alpha-globin genes, providing a flexible and simple workflow with rapid and reliable results.

Author: Runa M GrimholtPetter UrdalOlav KlingenbergArmin P Piehler
Credits/Source: BMC Hematology 2014, 14:4

Published on: 2014-01-24

News Provider: EUPB â€“ European Press Bureau

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