Article
Licensed
Unlicensed
Requires Authentication
ThalassoChip, an array mutation and single nucleotide polymorphism detection tool for the diagnosis of β-thalassaemia
-
Christos Shammas
Published/Copyright:
August 13, 2010
Abstract
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.
Received: 2010-3-2
Accepted: 2010-5-9
Published Online: 2010-08-13
Published in Print: 2010-12-01
©2010 by Walter de Gruyter Berlin New York
You are currently not able to access this content.
You are currently not able to access this content.
Articles in the same Issue
- Editorial
- Biomarkers of cardiovascular risk – matters of prediction and precision
- Reviews
- Inflammatory markers, cholesterol and statins: pathophysiological role and clinical importance
- C-reactive protein and venous thromboembolism: causal or casual association?
- Perspectives
- Statistical methods for assessment of added usefulness of new biomarkers
- Genetics and Molecular Diagnostics
- ThalassoChip, an array mutation and single nucleotide polymorphism detection tool for the diagnosis of β-thalassaemia
- General Clinical Chemistry and Laboratory Medicine
- Glycated hemoglobin vs. the oral glucose tolerance test for the exclusion of impaired glucose tolerance in high-risk individuals
- Impact of glucuronide interferences on therapeutic drug monitoring of posaconazole by tandem mass spectrometry
- Evaluation of D-dimer in the diagnosis of suspected aortic dissection
- Quantification of coagulation factor XIII activity by a thio-NADH based assay using factor XIII immuno-depleted plasma as a diluent for calibration
- Qualitative detection of the Marburg I alloenzyme of factor VII-activating protease by an immunoassay and its comparison to PCR testing
- Fatty acid composition of serum phospholipids in cystic fibrosis (CF) patients with or without CF related liver disease
- Development and validation of a combined method for the biomonitoring of omega-3/-6 fatty acids and conjugated linoleic acids in different matrices from human and nutritional sources
- Evaluation of the Sysmex UF-1000i® urine flow cytometer in the diagnostic work-up of suspected urinary tract infection in a Dutch general hospital
- Association between coffee consumption and the estimated glomerular filtration rate in the general Japanese population: preliminary data regarding C-reactive protein concentrations
- Lactic acid is of low predictive value for the diagnosis of bacterial infection in ventricular cerebrospinal fluid samples containing residual blood
- Accuracy of the Precision® point-of-care ketone test examined by liquid chromatography tandem-mass spectrometry (LC-MS/MS) in the same fingerstick sample
- Cancer Diagnostics
- Combination of polymorphisms within the HDAC1 and HDAC3 gene predict tumor recurrence in hepatocellular carcinoma patients that have undergone transplant therapy
- Global DNA methylation: comparison of enzymatic- and non-enzymatic-based methods
- Determination of biological variation of α-fetoprotein and choriogonadotropin (β chain) in disease-free patients with testicular cancer
- Infectious Diseases
- Investigation of the relationship between apolipoprotein E gene polymorphisms and hepatitis B virus infection in northern China
- Helicobacter pylori infection and the severity of gastritis are not associated with iron deficiency in a group of Brazilian patients
- Cardiovascular Diseases
- Proatrial natriuretic peptide is a better predictor of 28-day mortality in septic shock patients than proendothelin-1
- The relationship between aminoterminal propeptide of type III procollagen and heart rate variability parameters in heart failure patients: a potential serum marker to evaluate cardiac autonomic control and sudden cardiac death
- Relationship of hepatic steatosis and alanine aminotransferase with coronary calcification
- Letters to the Editor
- Novel mutation at codon 110 of the human APOE gene: impact on genotyping with fluorescent hybridization probes
- A simple, fast and inexpensive automated technique for measurement of plasma nitrite
- Development of an innovative serological test for detection of antibodies to Treponema pallidum
- Erratum
- Controversies on quotient reporting to standardise laboratory results
- Acknowledgement
- Acknowledgement
Keywords for this article
arrayed primer extension technology;
diagnostic test;
microarrays;
thalassaemia
Articles in the same Issue
- Editorial
- Biomarkers of cardiovascular risk – matters of prediction and precision
- Reviews
- Inflammatory markers, cholesterol and statins: pathophysiological role and clinical importance
- C-reactive protein and venous thromboembolism: causal or casual association?
- Perspectives
- Statistical methods for assessment of added usefulness of new biomarkers
- Genetics and Molecular Diagnostics
- ThalassoChip, an array mutation and single nucleotide polymorphism detection tool for the diagnosis of β-thalassaemia
- General Clinical Chemistry and Laboratory Medicine
- Glycated hemoglobin vs. the oral glucose tolerance test for the exclusion of impaired glucose tolerance in high-risk individuals
- Impact of glucuronide interferences on therapeutic drug monitoring of posaconazole by tandem mass spectrometry
- Evaluation of D-dimer in the diagnosis of suspected aortic dissection
- Quantification of coagulation factor XIII activity by a thio-NADH based assay using factor XIII immuno-depleted plasma as a diluent for calibration
- Qualitative detection of the Marburg I alloenzyme of factor VII-activating protease by an immunoassay and its comparison to PCR testing
- Fatty acid composition of serum phospholipids in cystic fibrosis (CF) patients with or without CF related liver disease
- Development and validation of a combined method for the biomonitoring of omega-3/-6 fatty acids and conjugated linoleic acids in different matrices from human and nutritional sources
- Evaluation of the Sysmex UF-1000i® urine flow cytometer in the diagnostic work-up of suspected urinary tract infection in a Dutch general hospital
- Association between coffee consumption and the estimated glomerular filtration rate in the general Japanese population: preliminary data regarding C-reactive protein concentrations
- Lactic acid is of low predictive value for the diagnosis of bacterial infection in ventricular cerebrospinal fluid samples containing residual blood
- Accuracy of the Precision® point-of-care ketone test examined by liquid chromatography tandem-mass spectrometry (LC-MS/MS) in the same fingerstick sample
- Cancer Diagnostics
- Combination of polymorphisms within the HDAC1 and HDAC3 gene predict tumor recurrence in hepatocellular carcinoma patients that have undergone transplant therapy
- Global DNA methylation: comparison of enzymatic- and non-enzymatic-based methods
- Determination of biological variation of α-fetoprotein and choriogonadotropin (β chain) in disease-free patients with testicular cancer
- Infectious Diseases
- Investigation of the relationship between apolipoprotein E gene polymorphisms and hepatitis B virus infection in northern China
- Helicobacter pylori infection and the severity of gastritis are not associated with iron deficiency in a group of Brazilian patients
- Cardiovascular Diseases
- Proatrial natriuretic peptide is a better predictor of 28-day mortality in septic shock patients than proendothelin-1
- The relationship between aminoterminal propeptide of type III procollagen and heart rate variability parameters in heart failure patients: a potential serum marker to evaluate cardiac autonomic control and sudden cardiac death
- Relationship of hepatic steatosis and alanine aminotransferase with coronary calcification
- Letters to the Editor
- Novel mutation at codon 110 of the human APOE gene: impact on genotyping with fluorescent hybridization probes
- A simple, fast and inexpensive automated technique for measurement of plasma nitrite
- Development of an innovative serological test for detection of antibodies to Treponema pallidum
- Erratum
- Controversies on quotient reporting to standardise laboratory results
- Acknowledgement
- Acknowledgement
