ThalassoChip, an array mutation and single nucleotide polymorphism detection tool for the diagnosis of β-thalassaemia.
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.
Shammas
Christos
C
Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.
Papasavva
Thessalia
T
Felekis
Xenia
X
Christophorou
Christos
C
Roomere
Hanno
H
Synodinos
Jan Traeger
JT
Kanavakis
Emmanuel
E
El-Khateeb
Mohammed
M
Hamamy
Hanan
H
Mahmoud
Tamara
T
Shboul
Mohammad
M
El Beshlawy
Amal
A
Filon
Dvora
D
Hussein
Ibtessam R
IR
Galanello
Renzo
R
Romeo
Giovanni
G
Kleanthous
Marina
M
D015342:DNA Probes / Q000592:standards; D006453:Hemoglobinopathies / Q000175:diagnosis / Q000235:genetics; D057166:High-Throughput Screening Assays / Q000379:methods*; D006801:Humans; D009154:Mutation; D020641:Polymorphism, Single Nucleotide; D012680:Sensitivity and Specificity; D055544:beta-Globins / Q000235:genetics; D017086:beta-Thalassemia / Q000175:diagnosis* / Q000235:genetics
D015342:DNA Probes; D055544:beta-Globins