Rapid detection and prenatal diagnosis of beta-thalassaemia: studies in Indian and Cypriot populations in the UK

Genotype-phenotype correlation of β-thalassemia spectrum of mutations in an Indian population

Coexistence of thalassemia, hemoglobinopathies and malaria has interested geneticists over many decades. The present study represents such a population from the eastern Indian state of Orissa. Children and their siblings (n=38) were genotyped for β-thalassemia mutations and genotype-phenotype correlation was determined. The major genotype was IVS 1.5 mutation: 26% homozygous (n=10) and 37% (n=14) double heterozygous with other mutations or hemoglobinopathies. Sickle hemoglobin was the major associated hemoglobinopathy (n=12, 32%). Other mutations found were Cd 8/9, HbE and Cd 41/42. The study population did not contain any IVS 1.1 mutations which is the second major Indo-Asian genotype. Genotype-phenotype correlation revealed that genotypes of IVS 1.5, Cd 8/9 Cd 41/42 alone or in association, exhibit severe, moderate and mild severity of thalassemia, respectively. Identification of the mutation at an early age as a part of new born screening and early intervention may help reduce the thalassemia-related morbidity.

Molecular basis of β-thalassemia in the western province of Saudi Arabia: identification of rare β-thalassemia mutations

This study aimed at the identification of the spectrum of mutations in patients with β-thalassemia (β-thal) in the western province of Saudi Arabia. Screening for the mutations was done using the polymerase chain reaction-amplification refractory mutation system (PCR-ARMS) technique to test for 12 mutations, and direct automated DNA sequencing for the unknown samples. The study included 172 patients; of these 15 patients had sickle cell anemia and one Hb S [β6(A3)Glu→Val, GAG>GTG]/β-thal. A total of 23 mutations were identified to cause the disease in the western area. Seven common mutations were responsible for the β-thal alleles in 78% of patients and could be detected by the ARMS technique: IVS-II-1 (G>A), IVS-I-110 (G>A), IVS-I-5 (G>C), codon 39 (C>T), codon 26 (G>A) [Hb E or β26(B8)Glu→Lys, GAG>AAG], frameshift codons (FSC) 8/9 (+G), and IVS-I-1 (G>A). DNA sequencing of uncharacterized alleles detected eight less common mutations: FSC 41/42 (-TCTT), IVS-I 25 bp deletion, codon 37 (G>A), FSC 44 (-C), Cap site +1 (A>C), IVS-I-6 (T>C), FSC 5 (-CT) and IVS-I-1 (G>T), and eight rare mutations: -87 (C>G), initiation codon -1 (T>G), codon 15 (G>A), FSC 16 (-C), FSC 20/21 (+G), codon 27 (G>A), IVS-I-130 (G>C) and IVS-II-837 (A>C). Four alleles were normal by DNA sequencing. Genetic heterogeneity was observed in this study, 10 mutations were of Asian or Asian/Indian origin, two were Kurdish, one Chinese, one Turkish, one Saudi, and the remainder were of Mediterranean origin. The presence of a large population of immigrants in the western province is responsible for the great heterogeneity at the molecular level, and for the difference observed in the frequencies of mutations from those reported in the eastern province of Saudi Arabia. Screening for β-thal mutations using PCR-ARMS for the seven most frequent mutations in the Saudi population followed by DNA sequencing of the unknown alleles could be useful for the implementation of a strategy for carrier detection and preimplantation genetic diagnosis in high risk families.

Application of diagnostic methods and molecular diagnosis of hemoglobin disorders in Khuzestan province of Iran

BACKGROUND:

The hemoglobinopathies refer to a diverse group of inherited disorders characterized by a reduced synthesis of one or more globin chains (thalassemias) or the synthesis of structurally abnormal hemoglobin (Hb). The thalassemias often coexist with a variety of structural Hb variants giving rise to complex genotypes and an extremely wide spectrum of clinical and hematological phenotypes. Hematological and biochemical investigations and family studies provide essential clues to the different interactions and are fundamental to DNA diagnostics of the Hb disorders. Although DNA diagnostics have made a major impact on our understanding and detection of the hemoglobinopathies, DNA mutation testing should never be considered a shortcut or the test of first choice in the workup of a hemoglobinopathy.

MATERIALS AND METHODS:

A careful three-tier approach involving: (1) Full blood count (2) Special hematological tests, followed by (3) DNA mutation analysis, provides the most effective way in which to detect primary gene mutations as well as gene-gene interactions that can influence the overall phenotype. With the exception of a few rare deletions and rearrangements, the molecular lesions causing hemoglobinopathies are all identifiable by PCR-based techniques. Furthermore, each at-risk ethnic group has its own combination of common Hb variants and thalassemia mutations. In Iran, there are many different forms of α and β thalassemia. Increasingly, different Hb variants are being detected and their effects per se or in combination with the thalassemias, provide additional diagnostic challenges.

RESULTS:

We did step-by-step diagnosis workup in 800 patients with hemoglobinopathies who referred to Research center of Thalassemia and Hemoglobinopathies in Shafa Hospital of Ahwaz Joundishapour University of medical sciences, respectively. We detected 173 patients as iron deficiency anemia (IDA) and 627 individuals as thalassemic patients by use of different indices. We have successfully detected 75% (472/627) of the β-thalassemia mutations by using amplification refractory mutation system (ARMS) technique and 19% (130/627) of the β-thalassemia mutations by using Gap-PCR technique and 6% (25/627) as Hb variants by Hb electrophoresis technique. We did prenatal diagnosis (PND) for 176 couples which had background of thalassemia in first pregnancy. Result of PND diagnosis in the first trimester was 35% (62/176) affected fetus with β-thalassemia major and sickle cell disease that led to termination of the pregnancy.

CONCLUSION:

Almost all hemoglobinopathies can be detected with the current PCR-based assays with the exception of a few rare deletions. However, the molecular diagnostic service is still under development to try and meet the demands of the population it serves. In the short term, the current generation of instruments such as the capillary electrophoresis systems, has greatly simplified DNA sequence analysis.

β-Thalassemia mutations in subjects with borderline HbA₂ values: a pilot study in North India

BACKGROUND

Interpreting hemoglobin high performance liquid chromatograms with borderline HbA₂ values is often problematic, especially in antenatal cases if the partner is a known thalassemia trait.

METHODS

We tested for underlying β-thalassemia mutations in 25 subjects with borderline HbA₂ values (between 3.0%-4.0%). Amplification refractory mutation system (ARMS-PCR) was used to detect the five common Indian β-thalassemia mutations: (IVS-I-5 (G>C), IVS-I-1 (G>T), codons 8/9 (+G), codons 41/42 (-TTCT) and 619 bp deletion). β-Globin gene sequencing was performed if no mutation was detected.

RESULTS

A β-globin gene defect was identified in 8 (32%) of the 25 cases with HbA₂ levels ranging from 3.5%-3.9%. ARMS-PCR revealed IVS-I-5 (G>C) in three, 619 bp deletion in two and codons 41/42 (-TTCT) in one case. Two cases had CAP +1 (A>C) mutation on gene sequencing. IVS-I-1 (G>T) and codons 8/9 (+G) were not found in this small cohort.

CONCLUSIONS

Mutation analysis should be offered to all at-risk couples with borderline HbA₂, especially those with values between 3.5% and 4.0% and microcytic hypochromic indices. Significant mutations different from those in other ethnic populations were seen in this small institution-based study.

An assessment of three noncommercial DNA extraction methods from dried blood spots for beta-thalassaemia mutation identification

INTRODUCTION

Dried blood spots (DBS) are currently the recommended sample collection method for newborn screening programmes in America. Early diagnosis of beta-thalassaemia screening is essential as it provides an added advantage especially in sickle cell disease. Beta-thalassaemia frequency is high in many poor countries, and the cost of using commercial DNA extraction kits can be prohibitive. Our study assessed three methods that use minimal reagents and materials to extract DNA from DBS for beta-thalassaemia identification.

METHODS

The methods assessed in this study were Tris-EDTA (TE) buffer-based method by Bereczky et al. (American Journal of Tropical Medicine and Hygiene 72, 2005, 249), NaCL/NaOH/Sodium dodecyl sulphate (SDS) method by Huang et al. (Human Genetics 84, 1990, 129) and NaOH method by Zhou et al. (Analytical Biochemistry 354, 2006, 159). Extracted DNA was amplified for three common beta-thalassaemia mutations in Malaysia.

RESULTS

Amplicons derived from TE buffer-based method were very faint and almost nonexistent while the NaCl/NaOH/SDS method did not produce any visible amplicons. The extraction using NaOH method produced visible bands that were comparable to the standard method using extraction kit.

CONCLUSION

The NaOH method is a simple method that uses minimal equipment and reagents that make it labour- and cost-effective. This method could be adopted by poorer countries to extract DNA for beta-thalassaemia mutation characterization.

Development and validation of a cost-effective in-house method, tetra-primer ARMS PCR assay, in genotyping of seven clinically important point mutations

The single nucleotide polymorphism (SNP) genotyping is currently considered as a particularly valuable tool for the diagnosis of different pathologies. For this reason, over the past several years a great deal of effort has been devoted to developing accurate, rapid, and cost-effective technologies for SNP analysis. Although a large number of distinct approaches has been reported each laboratory use one of the published methods based on their technical and economical capacity. This article presents an application of an in-house assay, tetra-primer ARMS PCR assay, and its application in SNP genotyping. We have shown that this assay could be more advantageous when compared with PCR-RFLP, real time PCR, and DNA sequencing. We have shown that the assay is successful in genotyping using archived paraffin-embedded tissues, heparinated samples and amniotic fluids with meconium. These low-costed (3$/reaction) assays could be completed within 3-4 h after specimen receipt allowing for a reasonable turn-around time in the laboratory. Since tetra-primer ARMS PCR assay does not require any special equipment, the assay could be set up in most clinical diagnostic laboratories.

Prenatal diagnosis of hemoglobinopathies in Hacettepe University, Turkey

Between 1983 and 2008, prenatal diagnostic procedures for identifying hemoglobinopathies were performed in 947 at-risk fetuses. Seventy-six percent of the fetuses were at risk for β-thalassemia major and 16% for sickle cell anemia; only a small percentage (7%) were at risk for compound heterozygosity of β-thalassemia and an abnormal hemoglobin of the β chain. The results of the study showed that β gene mutations in hemoglobinopathies have a very broad spectrum. Seven hundred and thirty of the 947 fetuses examined using the DNA technique showed 88 different combinations of 27 different mutations. Although the number of fetuses evaluated was far below the desired target, the termination of 261 affected fetuses provided both psychological and economic relief for the parents and was economically beneficial for the country in the long term.

Genetic predisposition to β-thalassemia and sickle cell anemia in Turkey: a molecular diagnostic approach

The thalassemia syndromes are a diverse group of inherited disorders that can be characterized according to their insufficient synthesis or absent production of one or more of the globin chains. They are classified in to α, β, γ, δβ, δ, and εγδβ thalassemias depending on the globin chain(s) affected. The β-thalassemias refer to that group of inherited hemoglobin disorders, which are characterized by a reduced synthesis (β(+)-thalassemia) or absence (β(0)-thalassemia) of beta globin (β-globin) chain production (1). Though known as single-gene disorders, hemoglobinopathies such as β-thalassemia and sickle cell anemia are far from being fully resolved in terms of cure, considering the less complex nature of the beta globin (β-globin) gene family compared to more complex multifactorial genetic disorders such as cancer. Currently, there are no definitive therapeutic options for patients with β-thalassemia and sickle cell anemia, and new insights into the pathogenesis of these devastating diseases are urgently needed. Here we address in detail the overall picture utilizing molecular diagnostic approaches that contribute to unraveling the population-specific mutational analysis of β-globin gene. We also present approaches for molecular diagnostic strategies that are applicable to β-thalassemia, sickle cell anemia, and other genetic disorders.

Molecular characterization of β-thalassemia intermedia: a report from Iran

Thalassemia intermedia is a clinical definition applied to patients whose clinical phenotype is milder than thalassemia major. To characterize different common mechanisms involving in pathogenesis of moderate to severe β-thalassemia intermedia, we have studied four factors in 38 Iranian patients with thalassemia intermedia: β-globin gene mutation, deletion in α-globin genes, presence of XmnI polymprphism and RFLP haplotype at β-globin gene cluster. The results showed that 84.4% of patients were associated with severe mutations in β-globin gene, mainly IVSII-1(G to A) (56.4%). The positive XmnI polymorphism was seen in 76.9% of the studied alleles which showed strong linkage to β° mutations and high level of fetal hemoglobin. Co-existence of α-globin gene deletions, β(+) mutation and the most frequent of RFLP haplotype (-/-, +/+, -/+, +/+, +/+, +/+, -/-) were seen in 7.7, 12.8 and 17.9%, respectively. In this group of our study it seems the main ameliorating factor in the patients was co-inheritance of a positive XmnI polymorphism with β° mutation especially IVSII-1, which were associated with increased production of fetal hemoglobin. However, the other probable genetic factors should be investigated to describe genotype-phenotype correlation in thalassemia intermedia patients.

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.

Easy, rapid, and cost-effective methods for identifying carriers of recurrent GJB2 mutations causing nonsyndromic hearing impairment in the Greek population

A variety of techniques have been developed for screening the GJB2 gene for known and unknown mutations, especially the most common mutation in the Caucasian population, the c.35delG. Other mutations that have been so far characterized in the GJB2 gene seem to have different geographical distributions, and therefore there is an interest in identifying recurrent mutations specific for each population and developing easy and rapid screening techniques. Here we present easy screening protocols for already identified recurrent mutations in the Greek population. Developing easy, rapid, and cost-effective screening methods will facilitate the detection of GJB2 recurrent mutation carriers, at large, in the Greek population.

Evaluation of the genetic basis of phenotypic heterogeneity in north Indian patients with thalassemia major

OBJECTIVES

To assess the molecular basis of phenotypic heterogeneity in north Indian patients with thalassemia major (TM).

METHODS

To determine the clinical severity, 130 patients of TM were studied for the age of first presentation and frequency of blood transfusion. The type of beta mutations, Xmn-1(G)gamma polymorphism and G6PD Mediterranean mutation was characterized. Analysis of the phenotypic presentation and the genotype was performed.

RESULTS

Majority (83.8%) presented before 1 year of age (mean 8.8 months). The caste distribution showed 41.6% were Aroras and 32.3% were migrants from Pakistan. IVS1-5(G-->C) was commonest (32.7%) and the common five Indian mutations comprised of 88.4% of alleles. The mean age of presentation with IVS1-5(G-->C), Fr 8/9, (+G) 619-bp del and IVS1-1(G-->T) homozygosity was 4.3, 6, 3.4 and 9.1 months respectively. Xmn-1(G)gamma status showed -/- in 66.9%, +/- in 26.1% and +/+ in 6.9% patients. Xmn-1(G)gamma-/- presented before 1 year of age. The mean age of presentation with +/+ was 18.3 months. Six hemizygous boys and one heterozygous girl with G6PD Mediterranean were found (prevalence 5.3%). Eight patients could be reclassified as thalassemia intermedia on follow up.

CONCLUSIONS

This study showed that majority of TM in north India present before 1 year of age and homozygous 619-bp deletion presents the earliest. The presence of Xmn-1(G)gamma polymorphism delays the presentation, is associated with the IVS 1-1 (G-->T) and shows variable improvement with hydroxyurea therapy. Based on the results of genotyping, reevaluation of patients can improve the outcome in a few patients.

Comprehensive and efficient HBB mutation analysis for detection of beta-hemoglobinopathies in a pan-ethnic population

Current methods that assay hemoglobin beta-globin chain variants can have limited clinical sensitivity when applied techniques identify only a predefined panel of mutations. Even sequence-based assays may be limited depending on which gene regions are investigated. We sought to develop a clinically practical yet inclusive molecular assay to identify beta-globin mutations in multicultural populations. We highlight the beta-globin mutation detection assay (beta-GMDA), an extensive gene sequencing assay. The polymerase chain reaction (PCR) primers are located to encompass virtually all hemoglobin beta locus (HBB) mutations. In addition, this assay is able to detect, by gap PCR, a common large deletion (Delta619 base pair), which would be missed by sequencing alone. We describe our 5-year experience with the beta-GMDA and indicate its capability for detecting homozygous, heterozygous, and compound heterozygous sequence changes, including previously unknown HBB variants. The beta-GMDA offers superior sensitivity and ease of use with comprehensive detection of HBB mutations that result in beta-globin chain variants.

Development of a quantitative real-time PCR assay for detection of unknown alpha-globin gene deletions

BACKGROUND

Alpha-Thalassemia is the most common inherited disorder of hemoglobin (Hb) synthesis in the world. Unlike beta-thalassemia, in which non-deletional mutations predominate, most of recognized alpha-thalassemia mutations include deletion of one or both alpha-globin genes. The importance of alpha-thalassemia detection is mainly due to its shared blood parameters with beta-thalassemia and its impact on discrimination between unknown alpha-thalassemia and normal HbA2 beta-thalassemia during thalassemia prevention program.

MATERIALS AND METHODS

Cases with hematologic profile of low MCV, MCH, and normal HbA2 were enrolled in this study. Common alpha-globin deletional mutations including alpha(3.7)kb, alpha(4.2)kb, alpha(20.5)kb, and alpha(MED) and point mutation including 5 nt, Constant Spring (CS), and C19 were checked using either GAP-PCR or ARMS-PCR. Cases with unknown molecular defects were investigated further by direct gene sequencing. Finally, further study was done for probable unknown deletions by gene dosage analysis using real-time PCR. For this, five pairs of primers were used spanning from theta-globin gene up to the 3' upstream of alpha(2) gene.

RESULTS

After validation of primers specificity and performing serial dilution analysis in order to calculate PCR efficiency, the assay was performed on normal samples and cases with known alpha-globin gene deletions as positive and negative controls, respectively. The assay was able to diagnose the control groups successfully. In 21 out of 29 unknown cases (72.4%), the assay showed various patterns of deletions in at 2 to 5 screened regions (theta gene up to the upstream of alpha2 gene). In 8 (27.6%) cases, deletions were seen in all regions.

CONCLUSION

Gene dosage study by quantitative real-time PCR can be suggested as a rapid and reliable assay to screen probable carrier of alpha-thalassemia for unknown alpha-globin gene deletions.

A new beta-chain haemoglobin variant with increased oxygen affinity: Hb Roma [beta115(g17)Ala-->Val]

BACKGROUND

Haemoglobin Roma [beta115(G17)Ala-->Val] is a new adult haemoglobin variant found in a patient presenting a mild hypochromia and microcytosis. We studied this previously uncharacterised variant in order to evaluate the effect on the structural and funcional properties of the Ala-->Val substitution at the alpha1beta1 interface.

METHODS AND RESULTS

The variant chain was identified by direct DNA sequencing of the beta-globin gene, which revealed a GCC-->GTC mutation in codon 115. This mutation was confirmed by mass spectrometric analysis of the tetramers and peptides. The oxygen-binding properties of the haemoglobin A/haemoglobin Roma mixture, in which the variant makes up 25% of the haemoglobins, showed a significant increase in oxygen affinity with respect to normal haemoglobin A, both in the absence and presence of 2,3-bisphosphoglycerate. The role of the betaG17 position, situated at the alpha(1)beta(1) interface, has been examined using computational models of haemoglobin Roma and other known betaG17 variants, in comparison with normal haemoglobin A.

CONCLUSIONS

This study suggests that the beta115(G17)Ala-->Val substitution at the alpha1beta1 interface is responsible for increased oxygen affinity and mild destabilisation of the haemoglobin Roma.

GENERAL SIGNIFICANCE

An amino acid substitution at the G17 position of the alpha1beta1 interface may result in stabilisation of the high affinity R-state of the haemoglobin molecule.

Hb Cardarelli [β86(F2)Ala→Pro]: A New Unstable and Hyperaffine Variant in Association with β+‐Thalassemia

Hb Cardarelli [beta86(F2)Ala-->Pro] is a new unstable and high oxygen affinity variant found in several members of a family from Naples, Southern Italy. A detailed structural and functional characterization of the variant was performed on two subjects, at both the protein and DNA level. The first patient exhibited 43% of the variant hemoglobin (Hb) without major hematological problems. The proband showed 82% of the abnormal Hb in association with beta(+)-thalassemia (thal) that caused relevant erythrocytosis requiring frequent phlebotomies. Structural investigation of the Hb variant by mass spectrometric methodologies identified the amino acid replacement as Ala-->Pro at beta86. The corresponding DNA mutation GCC-->CCC at codon 86 of the beta-globin gene was assessed by both DNA sequencing and amplification refractory mutation system (ARMS) techniques. Functional studies carried out on whole blood and diluted hemolysates from both patients demonstrated increased oxygen affinity, decreased Bohr effect, reduced heme-heme interaction and nearly halved 2,3-diphosphoglycerate (2,3-DPG) and chloride effects.

Establishment of prenatal diagnosis for β-thalassaemia: A step towards its control in a developing country

Beta-thalassaemia constitutes a major health burden on the limited health resources of India and prenatal diagnosis is seen as an important preventive measure to reduce the burden of the disease. Prenatal diagnosis has been offered to 99 women in 112 pregnancies by fetal DNA analysis, using a PCR-based Amplification Refractory Mutation System (ARMS) for the common and uncommon Indian mutations. Restriction fragment length polymorphism (RFLP) for the beta-globin gene was used when the mutation remained unidentified in one of the parents or to complement the ARMS result. In 53 cases the fetus tested had beta-thalassaemia trait (betaTT) (47.3%), 22 were normal (19.6%) and 31 had thalassaemia major (27.6%). In five cases (4.5%), a definitive report could not be given due to maternal contamination. In one case (0.9%), there was a misdiagnosis. Pitfalls encountered in the diagnosis were maternal contamination and occasional non-amplification of the primers. Having established a regional centre for the prenatal diagnosis for thalassaemia, the screening programmes will be enlarged both to identify carriers and prevent the birth of further homozygous children, even during the first pregnancy.

The IVS-II-1 (G → A) β0-Thalassemia Mutation inCISwith Hb A2-Troodos [δ116(G18)Arg → Cys (CGC →TGC)] Causes a Complex Prenatal Diagnosis in an Iranian Family

The beta-thalassemia (thal) minor phenotypes with normal Hb A2 levels and decreased MCV and MCH values are relatively rare beta-thal traits. Here, we describe a family with normal Hb A2 and decreased MCV and MCH levels. Amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) revealed the IVS-II-1 (G-->A) mutation in the beta-globin gene of the proband and her father. Direct sequencing of the gamma-globin gene of the proband and her father also revealed a previously reported variant called Hb A2-Troodos [gamma116(G18)Arg-->Cys] [in cis with the IVS-II-1 (G-->A) beta0-thal mutation]. This is the first case report of Hb A2-Troodos in association with the beta0 IVS-II-1 mutation. Reduced Hb A2 expression by a concomitant Hb A2 beta-thal in cis or trans, may cause problems in carrier diagnostics, and eventually in genetic counseling and prenatal diagnosis when insufficient molecular analyses are performed.

The Molecular Analysis of β-Thalassemia Mutations in Lorestan Province, Iran

Beta-Thalassemia (thal) is one of the most common genetic disorders in Iran and other countries. Getting information on the distribution of mutations in different ethnic groups of Iran is of fundamental importance for the purpose of health planning and prenatal diagnosis programs. One hundred and thirty chromosomes from 65 unrelated homozygous beta-thal patients were investigated for beta-globin gene mutations by amplification refractory mutation system-polymerase chain reaction (ARMS-PCR). The most common mutations of the Mediterranean region were examined in this study. Our results showed that the frameshift codons (FSC) 36/37 (-T) mutation, with a frequency of 33.8%, is the most common mutation in Lorestan Province. The other most frequent mutations were of the Mediterranean type and consisted of IVS-II-1 (G -->A), IVS-I-110 (G -->A), FSC 8/9 (+G) and IVS-I-5 (G -->C) with frequencies of 27.7, 11.5, 10.8 and 4.5%, respectively. The less frequent alleles, IVS-II-745 (C -->G), FSC 5 (-CT), IVS-I (25 bp deletion) and FSC 44 (-C) accounted for only 3.9% of the mutations. The unknown alleles comprised 7.7% of the mutations. These data showed that the spectrum of mutations found in Lorestan Province was different from those reported from other thalassemic regions of Iran and also of some neighboring countries.

First Spanish Case Of Thalassemia Major Due to a Compound Heterozygosity for the IVS-II-848 (C→A) And Codon 39 (C→T) Mutations Of The β-Globin Gene

This report describes the first case in Spain of a severe form of beta-thalassemia (thal) due to a compound heterozygosity for the IVS-II-848 (C --> A) and the nonsense codon 39 (C --> T) mutations. Five members of a family from Cadiz (southern Spain) were studied. The proband was an 8-year-old girl diagnosed as anemic at the age of 13 months. Her father had the codon 39 (C --> T) mutation and her mother the C --> A change at nucleotide (nt) 848 of IVS-II. Haplotype analysis showed that the proband was a compound heterozygote for haplotypes I [+ --> + +] and VII [+ --> +]. This is the first description in Spain of the IVS-II-848 (C --> A) mutation. It appears, from restriction fragment length polymorphism (RFLP) analysis, that this mutation has a different origin in the various populations, where it was found. This observation shows that in this case the association of a beta(0)- and a beta(+)-thal mutation does not lead to a thalassemia intermedia but to a severe thalassemia with very low hemoglobin (Hb) levels. From a therapeutic point of view, early introduction of a transfusion regimen may improve the clinical picture of these children, allowing for better development and growth.

Genotyping beta-globin gene mutations on copolymer-coated glass slides with the ligation detection reaction

BACKGROUND

Methods are needed to analyze small amounts of samples for variation in disease-causing genes. One means is to couple the sensitivity and multiplexing capability of the ligation detection reaction (LDR) with the use of simple glass slides specifically functionalized with a novel polymer coating to enhance sensitivity.

METHODS

We developed an array-based genotyping assay based on glass slides coated with copolymer (N,N-dimethylacrylamide, N,N-acryloyloxysuccinimide, and 3-(trimethoxysilyl)propyl methacrylate). The assay consists of an LDR with genomic DNA followed by a universal PCR (U-PCR) of genomic DNA-templated LDR product. The LDR occurs in the presence of 3 primers for each sequence variant under investigation: 2 distinguishing primers (allele specific and perfectly complementary to wild-type and mutant alleles) and 1 common locus-specific primer. The 2 allele-specific primers have different capture sequences for binding different complementary probes on a tag array. The LDR product templated from genomic DNA is made fluorescent during the U-PCR via incorporation of a Cy5-labeled universal primer into all LDR products; detection occurs on the coated glass slides.

RESULTS

The assay was designed to detect 7 prevalent mutations in the beta-globin gene (HBB, hemoglobin, beta) in a multiplex format, and signals for the different alleles are detected by their fluorescence. The assay was applied to 40 genomic DNA samples from both control individuals and patients with known beta-thalassemia mutations. Results show good correspondence between the patients' genotypes as assessed by DNA sequence analysis and those generated from the LDR assays.

CONCLUSIONS

The developed technology allows accurate identification of sequence variants in a simple, cost-effective way and offers good flexibility for scaling to other applications with different numbers of single-nucleotide polymorphisms or mutations to be detected.

Carrier Testing for Autosomal- Recessive Disorders

The aim of carrier testing is to identify carrier couples at risk of having offspring with a serious genetic (autosomal recessive) disorder. Carrier couples are offered genetic consultation where their reproductive options, including prenatal diagnosis, are explained. The Ashkenazi Jewish population is at increased risk for several recessively inherited disorders (Tay-Sachs disease, Cystic fibrosis, Canavan disease, Gaucher disease, Familial Dysautonomia, Niemann-Pick disease, Fanconi anemia, and Bloom syndrome). Unlike Tay-Sachs disease, there is no simple biochemical or enzymatic test to detect carriers for these other disorders. However, with the rapid identification of disease-causing genes in recent years, DNA-based assays are increasingly available for carrier detection. Approximately 5% of the world's population carries a mutation affecting the globin chains of the hemoglobin molecule. Among the most common of these disorders are the thalassemias. The global birth rate of affected infants is at least 2 per 1000 (in unscreened populations), with the greatest incidence in Southeast Asian, Indian, Mediterranean, and Middle Eastern ethnic groups. Carriers are detected by evaluation of red cell indices and morphology, followed by more sophisticated hematological testing and molecular analyses. The following issues need to be considered in the development of a carrier screening program: (1) test selection based on disease severity and test accuracy; (2) funding for testing and genetic counselling; (3) definition of the target population to be screened; (4) development of a public and professional education program; (5) informed consent for screening; and (6) awareness of community needs.

Detection of beta-thalassemia mutations using a multiplex amplification refractory mutation system assay

We developed two sets of a multiplex amplification refractory mutation system (M-ARMS) assay to identify specific beta-thalassemia (beta-thal) mutations that are common in Thailand. The first one was for the detection of mutants with codon 17 (A>T), IV S-I-1 (G >T)), codons 41/42 (-TCT T) and codons 71/72 (+A), while the second one was for the -87 (C>A), -28 (A>G) and IVS-II-654 (C>T). Application of the proposed assay to 282 persons with beta-thal trait revealed a positive result in 276 cases (97.8%). There were 258 cases (91.5%) positive for the set 1 M-ARMS assay and 18 cases (6.4%) were positive for set 2. Six cases (2.2%) were negative for both sets 1 and 2, and were further characterized by DNA sequencing. The mutations detected by the set 1 M-ARMS assay were 113 cases (40.1%) of codons 41/42, 95 (33.7%) of codon 17, 41 (14.5%) of IVS-I-1 and nine cases (3.2%) of codons 71/72, while by set 2 there were 12 cases (4.2%) of -28, four cases(1.4%) of -87 and two cases (0.7%) of IVS-II-654. Mutations undetectable by M-ARMS assay were two cases of codons 27/28 (+C), one case of codon 35 (C>A), one of codon 43 (G>T), one of -31 (A>G) and one of IVS-I-5 (C>G). The M-ARMS assay proved to be a valuable tool for the analysis of beta-thal mutations. The method is robust, accurate, simple, speedy and cost-effective. The application of this assay will facilitate genetic counseling and prenatal diagnosis for severe thalassemia in high-risk pregnancies.

Comparison of the mismatch-specific endonuclease method and denaturing high-performance liquid chromatography for the identification of HBB gene mutations

Background

Beta-thalassemia is a common autosomal recessive hereditary disease in the Meditertanean, Asia and African areas. Over 600 mutations have been described in the beta-globin (HBB), of which more than 200 are associated with a beta-thalassemia phenotype.

Results

We used two highly-specific mutation screening methods, mismatch-specific endonuclease and denaturing high-performance liquid chromatography, to identify mutations in the HBB gene. The sensitivity and specificity of these two methods were compared. We successfully distinguished mutations in the HBB gene by the mismatch-specific endonuclease method without need for further assay. This technique had 100% sensitivity and specificity for the study sample.

Conclusion

Compared to the DHPLC approach, the mismatch-specific endonuclease method allows mutational screening of a large number of samples because of its speed, sensitivity and adaptability to semi-automated systems. These findings demonstrate the feasibility of using the mismatch-specific endonuclease method as a tool for mutation screening.

β-Thalassaemia mutations and their linkage to β-haplotypes in Tamil Nadu in Southern India

A study for screening of beta-thalassaemia mutations by the Amplification Refractory Mutation System (ARMS) and haplotyping by Polymerase Chain Reaction (PCR) was undertaken because there was a paucity of data in Tamil Nadu in Southern India and to initiate a comprehensive prenatal diagnosis programme. A total of 294 alleles were analysed to study the nature of the mutations, of which 146 were beta-thalassaemia alleles. Only four types of beta-thalassaemia mutations were recorded. Of these, 128 alleles were of the variant IVS-1 nt 5 (G-->C). Thirteen had the mutation codon 41/42 (del TCTT), four had the mutation codon 8/9 (insert G) and one had the 619 bp deletion at the 3' end of the gene. The most common mutation, IVS-1 nt 5 (G-->C), was strongly associated with a single haplotype although the association was not absolute. The population of Tamil Nadu in Southern India seems to be ideal for initiating a prenatal diagnosis programme based on direct detection of mutation by ARMS coupled with RFLP linkage analysis.

Rapid detection of fetal Mendelian disorders: thalassemia and sickle cell syndromes

The inherited disorders of hemoglobin synthesis constitute the most common monogenic diseases worldwide. The clinical severity of beta-thalassemia major and the sickle cell syndromes targets them as priority genetic diseases for prevention programs, which incorporates population screening to identify heterozygotes,with the option of prenatal diagnosis for carrier couples. Rapid genotype characterization is fundamental in the diagnostic laboratory, especially when offering prenatal diagnosis. The application of real-time polymerase chain reaction (PCR) provides a means for rapid and potentially high-throughput assays, without compromising accuracy. It has several advantages over endpoint PCR analysis, including the elimination of post-PCR processing steps and a wide dynamic range of detection with a high degree of sensitivity. Although there are >180 mutations associated with the beta- thalassemia and sickle cell syndromes, the relatively small size of the beta-globin gene (<2,000 base pairs) and the proximity of most mutations facilitates the design of a minimal number of real-time PCR assays by using the LightCycler system (Roche Diagnostics [Hellas] A.E., Athens, Greece), which are capable of detecting the majority of most common beta-gene mutations worldwide. These assays are highly appropriate for rapid genotyping of parental and fetal DNA samples with respect to beta-thalassemia and sickle cell syndromes.

Beta-thalassemia mutations in western India

OBJECTIVE

To study occurrence of common mutations in the population of Gujarat and the most prevalent mutation in certain high-risk communities.

METHODS

The mutation screening was carried out using ARMS-PCR in children with beta thalassemia.

RESULTS

Population screening has identified certain communities like Sindhis, Lohana, Rajputs, and SC/ST/OBC to be at higher risk as compared to others. The most common mutation was IVS 1-5 (G-->C) followed by 619 bp deletions of the total cases coming to Gujarat.

CONCLUSION

Molecular evaluation for Thalassemia should be considered for families whose ethnicity indicates origin from high-risk community.

Molecular evidences of single mutational events followed by recurrent crossing-overs in the common delta-globin alleles in the Mediterranean area

The human delta-globin gene (HBD) is one of the beta-like globin genes expressed in adults. In the Mediterranean countries the carriers of delta-thalassemia defects or Hb A2-variants are >1% and about 40/70 known alleles have been found in families with this ethnic origin. The scope of this study was to investigate the variability of the gene and of the chromosomal background in order to highlight the origin and spreading of the delta-globin gene alleles in the Mediterranean area. We carried out the characterization of the delta-globin gene alleles and of RFLP-haplotypes, SNPs and one microsatellite associated with them in 231 carriers originating principally from East Sicily. Seventeen alleles were identified, of which five were new. The chromosomes associated with mutated alleles from unrelated carriers were 158; the allele Hb A2-Yialousa accounted for about 75% of relative frequency, Hb A2-Mitsero for about 8%. The alleles were associated with RFLP 5'-haplotypes "- - - -" or "+ - + +", prevalent in the Mediterranean area, except Hb A2-Mitsero associated with the 5'-haplotype "Benin" "- - - +" and the Hb A2' associated with "+ - - +", both of African origin. Each allele showed linkage with one haplotype with these exceptions. The Hb A2-Yialousa showed heterogeneity of the 5'-haplotype in 2/58 chromosomes; the Hb A2-Mitsero showed SNPs and (A)gamma-microsatellite typical of a "Benin" haplotype found associated with the Hb C and Hb S chromosomes; the Hb A2-Yialousa (14/58 chromosomes), Hb A2-Mitsero, Hb A2-Pylos, Hb A2-Fitzroy showed heterogeneity in the 3'-haplotypes and beta-globin gene SNPs. The Hb A2-Coburg was found associated with the haplotype "+ - + +/+ +" different from that already reported "- - - -/+ -". With the exception of this last allele, the linkage of each mutation with a core of RFLPs or SNPs around or inside the delta-globin locus suggested the unicentric origin of the mutations followed by recurrent recombination events causing the chromosomal background heterogeneity.

The clinical significance of the spectrum of interactions of CAP+1 (A→C), a silent β-globin gene mutation, with other β-thalassemia mutations and globin gene modifiers in north Indians

OBJECTIVES

To assess the clinical significance of the interactions of CAP+1 (A-->C), a silent beta-globin gene mutation, with other beta-thalassemia mutations and globin gene modifiers in north Indians.

METHODS

The clinical phenotypes associated with compound heterozygosity for the CAP+1 (A-->C) mutation with other beta-thalassemia mutations, together with the potential effect of the genetic modifiers alpha-thalassemia and the Xmn-1(G)gamma C-->T polymorphism were studied in 30 patients. The frequency of the CAP+1 (A-->C) polymorphism was determined and an analysis of the red cell indices, HbA(2) levels, iron status, and alpha-globin genes was carried out in 35 heterozygotes.

RESULTS

Based on an analysis of 1075 beta-thalassemia alleles the CAP+1 (A-->C) mutation constituted 3.2% of north Indians. There was a wide spectrum of phenotypic severity in compound heterozygotes; 18 of 30 were transfusion dependent. There was a very high frequency of the -/- genotype of the Xmn-1(G)gamma polymorphism in compound heterozygotes. Analysis of 35 heterozygotes indicated that approximately half were hematologically normal and therefore genuine 'silent' carriers.

CONCLUSIONS

Compound heterozygotes for CAP+1 (A-->C) and other severe beta-thalassemia alleles are phenotypically severe enough to necessitate appropriate therapy and counseling. The unexpected severity of these interactions may be due, in part, to the high frequency of beta-thalassemia alleles associated with the Xmn-1(G)gamma- allele in Indian populations. It is concluded that the CAP+1 (A-->C) mutation can pose serious difficulties in screening and counseling programs in populations in which it occurs at a significant frequency.

PCR-SSCP: a method for the molecular analysis of genetic diseases

Single strand conformation polymorphism (SSCP) is a reproducible, rapid and quite simple method for the detection of deletions/insertions/rearrangements in polymerase chain reaction amplified DNA. All the details for the use of PCR-SSCP are presented in the direction of genetic diseases (beta-thalassaemia, cystic fibrosis), optimum gel conditions, sensitivity and the latest modifications of the method, which are applied in most laboratories. This non-radioactive PCR-SSCP method can be reliably used to identify mutations in patients (beta-globin, CFTR), provided suitable controls are available. Moreover, it is widely used for mutation identification in carriers (beta-thalassaemia, cystic fibrosis), making it particularly useful in population screening.

Mutational spectrum of delta-globin gene in the Portuguese population

The phenotype of increased Hb A2 typical of beta-thalassaemia (beta-thal) carriers can be reduced to normal or borderline values because of the co-inheritance of a delta-globin gene (HBD, MIM #142000) mutation, which may lead to misinterpretation of diagnostic results. To know the spectrum of delta-globin mutations in the Portuguese population we performed a mutational analysis of the delta-globin gene in a group of 51 Portuguese beta-thal carriers presenting microcytosis, hypochromia and a normal/borderline Hb A2 level and in another group of 15 individuals suspected to have delta-globin structural abnormalities. The heterozygosity for the beta(+)IVS-I-6T-->C (HBB:c. 92+6T>C) mutation was the main cause for the mentioned atypical beta-thal carrier phenotype. Furthermore, eight individuals were double heterozygous for one common beta-thal mutation and the delta(+)Cd27G-->T mutation (Hb A2-Yialousa; HBD:c.82G>T). One of them also presented a novel delta-globin gene promoter mutation,-80G-->A (HBD:c.-130G>A), responsible for about 25% decrease of the promoter activity in transient expression assays. One the other hand, in the other group of 15 individuals suspected to have delta-globin structural abnormalities observed by biochemical methods, some known Hb A2 variants were identified - Hb A2' (HBD:c.49G>C), Hb A2-Babinga (HBD:c.410G>A), and Hb A2-Wrens (HBD:c.295G>A), and the novel Hb A2-Fogo [delta64(E8)(Gly-->Ser); (HBD:c.193G>A)]. This novel Hb A2 variant was observed segregating in linkage with Hb E (HBB:c.79G>A) in a three generation family. In conclusion, six different delta-globin mutations were found, being two of them new molecular defects. All delta-alleles identified were found linked to the expected beta-globin cluster haplotype. All mutations caused a low Hb A2 level and through this could lead to misdiagnosis when inherited together with a beta-thal allele.

High-Throughput Microtiter Well-Based Chemiluminometric Genotyping of 15 HBB Gene Mutations in a Dry-Reagent Format

Background: Hemoglobinopathies are the most common inherited diseases worldwide. Various methods for genotyping of hemoglobin, beta (HBB) gene mutations have been reported, but there is need for a high sample-throughput, cost-effective method for simultaneous screening of several mutations. We report a method that combines the high detectability and dynamic range of chemiluminescence with the high allele-discrimination ability of probe extension reactions for simultaneous genotyping of 15 HBB mutations in a high sample-throughput, dry-reagent format.

Methods: We genotyped the HBB mutations IVSI-110G&gt;A, CD39C&gt;T, IVSI-1G&gt;A, IVSI-6T&gt;C, IVSII-745C&gt;G, IVSII-1G&gt;A, FSC6GAG&gt;G-G, −101C&gt;T, FSC5CCT&gt;C−, IVSI-5G&gt;A, FSC8AAG&gt;−G, −87C&gt;G, IVSII-848C&gt;A, term+6C&gt;G, and HbS (cd6GAG&gt;GTG). The method used comprises the following: (a) duplex PCR that produces fragments encompassing all 15 mutations, (b) probe extension reactions in the presence of fluorescein-modified dCTP, using unpurified amplicons, and (c) microtiter well-based assay of extension products with a peroxidase-antifluorescein conjugate and a chemiluminogenic substrate. We used lyophilized dry reagents to simplify the procedure and assigned the genotype by the signal ratio of the normal-to-mutant–specific probe.

Results: We standardized the method by analyzing 60 samples with known genotypes and then validated by blindly genotyping 115 samples with 45 genotypes. The results were fully concordant with sequencing. The reproducibility (including PCR, probe extension reaction, and chemiluminometric assay) was studied for 20 days, and the CVs were 11%–19%.

Conclusions: This method is accurate, reproducible, and cost-effective in terms of equipment and reagents. The application of the method is simple, rapid, and robust. The microtiter well format allows genotyping of a large number of samples in parallel for several mutations.

Arterial ischemic stroke in a child with beta-thalassemia trait and methylentetrahydrofolate reductase mutation

Genetic and acquired disorders that foster a procoagulable state represent risk factors for stroke in childhood. Although an increased incidence of thromboembolic complications has been reported in patients with thalassemia, severe cerebral thromboembolism has rarely been observed in patients with beta-thalassemia minor. This article describes a case study of a 1-year-old boy who presented with left-sided hemiparesis, seizures, microcytic anemia, and recent infection with reactive thrombocytosis. Ischemic infarction in the territory of the right middle cerebral artery was confirmed by magnetic resonance imaging and magnetic resonance angiography. Genetic tests showed that the patient was heterozygous for the beta(degrees) -thalassemia IVS-I-1 mutation and homozygous for the methylentetrahydrofolate reductase C677T mutation. Based on these findings, it was concluded that the synergistic effects of multiple, genetic, and acquired prothrombotic risk factors brought about the hypercoagulable state that resulted in overt stroke in a thalassemic patient in early childhood.

Microsatellite Markers within —SEA Breakpoints for Prenatal Diagnosis of HbBarts Hydrops Fetalis

Background: We sought to develop a rapid prenatal diagnostic test for simultaneous detection of HbBarts hydrops fetalis and exclusion of maternal contamination.

Methods: We developed a multiplex quantitative fluorescent PCR (QF-PCR) test that detects the presence/ absence of 2 microsatellite markers (16PTEL05/16PTEL06) located within breakpoints of the Southeast Asia (—SEA) deletion. HbBarts hydrops fetalis (—SEA/—SEA) is diagnosed by absence of both markers, and maternal contamination of fetal DNA is excluded by absence of noninherited maternal alleles. Fetal and parental DNA samples from 50 families were analyzed in a blinded clinical validation study, and QF-PCR results were compared with their respective molecular genotypes.

Results: The multiplex QF-PCR results included correct diagnoses of HbBarts hydrops fetalis in 11 of the fetuses tested, correct verification as unaffected in 20 fetuses, and correct identification as either carriers (αα/—SEA) or unaffected homozygotes in 18. Misidentification as unaffected occurred for 1 carrier. Sensitivity for diagnosis of HbBarts hydrops fetalis was 100% [lower 95% confidence interval, 76.2%], and specificity was 100% (lower 95% confidence interval, 92.6%). None of the samples tested showed any traces of noninherited maternal alleles; thus false-positives because of maternal contamination were eliminated.

Conclusions: In this QF-PCR method, detection of maternally and paternally inherited fetal alleles allowed diagnosis of the double-deletion syndrome, and the ability to differentiate between these alleles allowed simultaneous exclusion of maternal contamination of the fetal genetic material. This novel strategy using cell-free fetal DNA in maternal plasma could form the basis for noninvasive testing for HbBarts hydrops fetalis.

Characterisation and confirmation of rare beta-thalassaemia mutations in the Malay, Chinese and Indian ethnic groups in Malaysia

AIMS

In Malaysia, about 4.5% of the Malay and Chinese populations are heterozygous carriers of beta-thalassaemia. The initial identification of rare beta-globin gene mutations by genomic sequencing will allow the development of simpler and cost-effective PCR-based techniques to complement the existing amplification refractory mutation system (ARMS) and gap-PCR used for the identification of beta-thalassaemia mutations.

METHODS

DNA from 173 beta-thalassaemia carriers and five beta-thalassaemia major patients from the Malay, Chinese and Indian ethnic groups were first analysed by ARMS and gap-PCR. Ninety-five per cent (174/183) of the 183 beta-globin genes studied were characterised using these two techiques. The remaining nine uncharacterised beta-globin genes (4.9%) were analysed using genomic sequencing of a 904 bp amplified PCR product consisting of the promoter region, exon 1, intervening sequence (IVS) 1, exon 2 and the 5' IVS2 regions of the beta-globin gene.

RESULTS

The rare beta-globin mutations detected in the Chinese patients were CD27/28 (+C) and CD43 (GAG-TAG), and -88 (C-T) in an Indian patient. Beta-globin mutations at CD16 (-C), IVS1-1 (G-A), IVS2-1 (G-A), -86 (C-G) and Haemoglobin South Florida (CD1, GTG-ATG) were confirmed in the Malay patients.

CONCLUSIONS

The seven rare beta-globin mutations and a rare haemoglobin variant confirmed in this study have been described in other populations but have not been previously described in Malaysian beta-thalassemia patients.

Identification of the four most common beta-globin gene mutations in Greek beta-thalassemic patients and carriers by PCR-SSCP: advantages and limitations of the method

In the present study we investigated whether the single-strand conformational polymorphism (SSCP) method could be employed to identify (rather than simply detect) the four most common beta-globin gene mutations in the Greek population: IVS-I-110, Cd39, IVS-I-1, and IVS-I-6. Using DNA from 50 beta-thalassemic patients and carriers, we amplified by PCR the appropriate 238-bp region of the human beta-globin gene, analyzed the reaction products by nondenaturing polyacrylamide gel electrophoresis, and visualized the bands by silver staining. Single-stranded DNA (ssDNA) fragments showed a reproducible pattern of bands that was characteristic of the mutations present. With the use of control samples containing six of the 10 possible combinations of the four most common beta-globin gene mutations, we were able to predict the mutations present in a quarter of the patients studied. Our predictions were confirmed independently by the amplification refractory mutation system (ARMS) method. We conclude that this non-radioactive PCR-SSCP method can be used to reliably identify mutations in patients, provided that suitable controls are available. Moreover, the method is easy to apply to the identification of mutations in carriers, which makes it particularly useful for population screening.

Multiplex tetra-primer amplification refractory mutation system PCR to detect 6 common germline mutations of the MUTYH gene associated with polyposis and colorectal cancer

BACKGROUND

We describe a simple tetra-primer amplification refractory mutation system PCR (T-ARMS-PCR) for detecting MUTYH mutations, which are associated with colorectal adenomas and colorectal cancer.

METHODS

We designed specific T-ARMS-PCR assays for 6 mutations (Y165C, G382D, 1395_7delGGA, Y90X, 1103delC, and R231H) selected on the basis of the frequency of their occurrence. We also designed a set of 3 multiplex T-ARMS PCR assays, each for detection of 2 mutations. We tested DNA samples from patients with attenuated or classic adenomatous polyposis coli and no detectable APC germline mutations.

RESULTS

All mutations were easily detected with both the specific and multiplex T-ARMS-PCR assays. Results were confirmed by DNA HPLC analysis in all 54 patients, and each mutation was confirmed by direct DNA sequencing.

CONCLUSIONS

T-ARMS-PCR does not require any special equipment, and it provides rapid, reproducible, and cost-effective detection of common MUTYH mutations. Multiplex T-ARMS-PCR allows the detection of 6 common MUTYH mutations with use of as few as 3 single tube PCR reactions. It could be useful to carry out large population-based epidemiologic studies.

Characterisation of beta-globin gene mutations in Malaysian children: a strategy for the control of beta-thalassaemia in a developing country

beta-thalassaemia major, an autosomal recessive hemoglobinopathy, is one of the most common single gene disorders in multi-racial Malaysia. The control of beta-thalassaemia major requires a multi-disciplinary approach that includes population screening, genetic counselling, prenatal diagnosis and the option of termination of affected pregnancies. To achieve this objective, the molecular characterisation of the spectrum of beta-globin gene mutations in each of the affected ethnic groups is required. We studied 88 consecutive unrelated individuals and their respective families with beta-thalassaemia (74 beta-thalassaemia major, 12 HbE-beta-thalassaemia, 2 with HbE homozygotes) and four individuals with beta-thalassaemia trait that contributed a total 180 alleles for study. Using a 2-step molecular diagnostic strategy consisting of amplification refractory mutation system (ARMS) to identify the 8 most common mutations followed by other DNA-based diagnostic techniques, a total of 177 (98.3 per cent) of the 180 beta-thalassaemia alleles were characterised. One out of 91 (1 per cent) of the Chinese alleles, one out of 46 (2.2 per cent) Malay alleles and one out of two Indian alleles remained unknown. A 100 per cent success rate was achieved in studying the Kadazandusun community in this study. A strategy to identify beta-globin gene mutations in Malaysians with beta-thalassaemia is proposed based on this outcome.

Nucleotide -88 (C-T) promoter mutation is a common beta-thalassemia mutation in the Jat Sikhs of Punjab, India

A study of beta-gene mutations in Jat Sikhs, a subcaste of Punjabis, revealed a very high prevalence (46%: 41/88) of the mild beta++ promoter region mutation -88 (C-T). Sixteen individuals presenting in homozygous form were clinically mild. Un-transfused patients had characteristic hematological findings: high Hb F (38.1-68.6%, mean 47.4%), high Hb A2 (5.7-9.8%, mean 6.88%), and the rest had adult hemoglobin. The 19 subjects with compound heterozygosity for -88 (C-T) and another beta-gene mutation presented both as thalassemia intermedia (four cases) and as thalassemia major (15 cases). One of the four patients with the milder phenotype had a second mild mutation, CAP+1 (beta++). In the other three cases with the milder phenotype, the second mutation was associated with the presence of the XmnI Ggamma polymorphism. Notably, the XmnI Ggamma was negative in all the -88 (C-T) alleles. None of the patients had associated alpha-thalassemia even in the thalassemia intermedia group. Haplotype analysis of the -88 (C-T) homozygous cases showed a single haplotype (+ - - - - + -) in all but two individuals. This haplotype is distinct from those described in the Africans with homozygous -88 (C-T), suggesting that the mutation in our population occurred independently.

High Incidence of 3-Thalassemia, Hemoglobin E, and Glucose-6-Phosphate Dehydrogenase Deficiency in Populations of Malaria-Endemic Southern Shan State, Myanmar

Samples from 916 members of various ethnic groups from malaria-endemic southern Shan State, Myanmar, were analyzed for 3-thalassemia (3-thal), 3-thalassemia (3-thal), abnormal hemoglobin variants, and glucose-6-phosphate dehydrogenase (G6PD) deficiency. Of these subjects, 530 (57.9%) were found to have at least one of these red cell genetic disorders. The overall frequencies for the various red cell genetic disorders were as follows: 3-thal, 37.5% (343/916); hemoglobin E (Hb-E), 20.3% (186/916); G6PD-Mahidol, 17.5% (160/916); and 3-thal, 0.3% (3/916). The frequencies of combined disorders were 6.9% (63/ 916) for 3-thal/Hb-E, 5.7% (52/916) for 3-thal/G6PD-Mahidol, 2.8% (26/916) for Hb-E/G6PD-Mahidol, 1.1% (10/916) for 3-thal/Hb-E/G6PD-Mahidol, and 0.1% (1/916) for 3-thal/3-thal/G6PD-Mahidol. Of the various ethnic and non-ethnic groups, the Bamar population showed the highest frequencies of 3-thal (56.9%, 177/311), Hb-E (28.3%, 88/311), and G6PD-Mahidol (21.2%, 66/311) (all duplicated and triplicated cases were included). In addition, 2 new mutations, an 3 gene triplication (/333(anti3.7); 0.2%, 2/916) and Hb-Neapolis (0.1%, 1/916), were detected. Our results showed that race was the dominant factor affecting the frequencies of red cell genetic disorders in malaria-endemic areas of Myanmar.

Molecular basis of thalassemia syndromes in Serbia and Montenegro

This study reports the molecular characterization of thalassemia syndromes in Serbian and Montenegrin populations. We identified eight beta-thalassemia mutations [codon 39 (C-->T), IVS-I-110 (G-->A), IVS-II-745 (C-->G), codon 44 (-C), -87 (C-->G), IVS-II-1 (G-->A), IVS-I-6 (T-->C), IVS I-1 (G-->A)] in 70 members of 29 families using polymerase chain reaction, reverse dot blot, amplification refractory mutation system and direct sequencing analysis. Hemoglobin (Hb) Lepore was found to be the most common cause of the thalassemia phenotype. Hb Sabine and alpha-thalassemia were detected as well. We also studied beta-globin gene cluster haplotypes and their association with the most common mutations. A novel haplotype associated with the Hb Lepore gene was identified. The results presented herein allowed the implementation of a prenatal diagnosis program in Serbia and Montenegro.