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Clinical Chemistry and Laboratory Medicine (CCLM)

Published in Association with the European Federation of Clinical Chemistry and Laboratory Medicine (EFLM)

Editor-in-Chief: Plebani, Mario

Ed. by Gillery, Philippe / Lackner, Karl J. / Lippi, Giuseppe / Melichar, Bohuslav / Payne, Deborah A. / Schlattmann, Peter / Tate, Jillian R.

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ThalassoChip, an array mutation and single nucleotide polymorphism detection tool for the diagnosis of β-thalassaemia

Christos Shammas1 / Thessalia Papasavva1 / Xenia Felekis1 / Christos Christophorou1 / Hanno Roomere2 / Jan Traeger Synodinos3 / Emmanuel Kanavakis3 / Mohammed El-Khateeb4 / Hanan Hamamy4 / Tamara Mahmoud4 / Mohammad Shboul4 / Amal El Beshlawy5 / Dvora Filon6 / Ibtessam R. Hussein7 / Renzo Galanello8 / Giovanni Romeo9 / Marina Kleanthous1

1Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus

2Asper Biotech Ltd., Tartu, Estonia

3Department of Medical Genetics, Athens University Medical School, Athens, Greece

4National Center for Diabetes, Endocrinology and Genetics, University of Jordan, Amman, Jordan

5Hematology Department of the Pediatric Hospital, Cairo University, Cairo, Egypt

6Department of Hematology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel

7Center of Excellence for Genome Research in Medicine, King AbdulAziz University, Jeddah, Saudi Arabia

8Department of Science, Biomedicine and Biotechnology, University of Cagliari, Cagliari, Italy

9European Genetic Foundation, Bologna, Italy

Corresponding author: Marina Kleanthous, PhD, Head, Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology and Genetics, 6 International Airport Ave., Ag. Dhometios, P.O. Box 23462, Nicosia, Cyprus Phone: +357 22392652, Fax: +357 22392615,

Citation Information: Clinical Chemistry and Laboratory Medicine. Volume 48, Issue 12, Pages 1713–1718, ISSN (Online) 1437-4331, ISSN (Print) 1434-6621, DOI: https://doi.org/10.1515/CCLM.2010.331, August 2010

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Background: The detection and diagnosis of β-thalassaemia for populations with molecular heterogeneity, or diverse ethnic groups, has increased the need for the development of an array high-throughput diagnostic tool that can deliver large scale genetic detection. We report on the update and validation of the ThalassoChip, a β-thalassaemia genetic diagnostic tool which is based on arrayed primer extension (APEX) technology.

Methods: ThalassoChip slides with new and redesigned probes were prepared for testing the microarray. Six hundred and sixty DNA samples collected from eight Mediterranean countries were used for standardisation, optimisation and validation of the ThalassoChip. The β-globin gene region was amplified by PCR, the products were hybridised to the probes after fragmentation and the APEX reaction followed.

Results: The ThalassoChip was updated with new probes and now has the ability to detect 57 β-globin gene mutations and three single nucleotide polymorphisms (SNPs) in a single test. The ThalassoChip as well as the PCR and APEX reactions were standardised and optimised using 500 DNA samples that were previously genotyped using conventional diagnostic techniques. Some probes were redesigned in order to improve the specificity and sensitivity of the test. Validation of the ThalassoChip performed using 160 samples analysed in blinded fashion showed no error.

Conclusions: The updated version of the ThalassoChip is versatile, robust, cost-effective and easily adaptable, but most notably can provide comprehensive genetic diagnosis for β-thalassaemia and other haemoglobinopathies.

Clin Chem Lab Med 2010;48:1713–8.

Keywords: arrayed primer extension technology; diagnostic test; microarrays; thalassaemia

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