Characterization of beta-thalassaemia mutations using direct genomic sequencing of amplified single copy DNA

Global Globin Network and adopting genomic variant database requirements for thalassemia

Thalassemia is one of the most prevalent monogenic disorders in low- and middle-income countries (LMICs). There are an estimated 270 million carriers of hemoglobinopathies (abnormal hemoglobins and/or thalassemia) worldwide, necessitating global methods and solutions for effective and optimal therapy. LMICs are disproportionately impacted by thalassemia, and due to disparities in genomics awareness and diagnostic resources, certain LMICs lag behind high-income countries (HICs). This spurred the establishment of the Global Globin Network (GGN) in 2015 at UNESCO, Paris, as a project-wide endeavor within the Human Variome Project (HVP). Primarily aimed at enhancing thalassemia clinical services, research, and genomic diagnostic capabilities with a focus on LMIC needs, GGN aims to foster data collection in a shared database by all affected nations, thus improving data sharing and thalassemia management. In this paper, we propose a minimum requirement for establishing a genomic database in thalassemia based on the HVP database guidelines. We suggest using an existing platform recommended by HVP, the Leiden Open Variation Database (LOVD) (https://www.lovd.nl/). Adoption of our proposed criteria will assist in improving or supplementing the existing databases, allowing for better-quality services for individuals with thalassemia. Database URL: https://www.lovd.nl/.

The role of molecular diagnostic testing for hemoglobinopathies and thalassemias

Hemoglobin disorders are among the most common genetic diseases worldwide. Molecular diagnosis is helpful in cases where the diagnosis is uncertain and for genetic counseling. Protein-based diagnostic techniques are frequently adequate for initial diagnosis. Molecular genetic testing is pursued in some cases, particularly when a definitive diagnosis is not possible and especially for the purpose of assessing genetic risk for couples wanting to have children. The expertise available in the clinical hematology laboratory is essential for the diagnosis of patients with hemoglobin abnormalities. Initial diagnoses are made using protein-based techniques such as electrophoresis and chromatography. Based on these findings, genetic risk to an individual's offspring can be assessed. In the setting of β-thalassemia and other β-globin disorders, coincident α-thalassemia may be difficult to diagnose, which can have potentially serious consequences. In addition, unusual forms of β-thalassemia caused by deletions in the β-globin locus cannot be definitively characterized using standard techniques. Molecular diagnostic testing has an important role in the diagnosis of hemoglobin disorders and is important in the setting of genetic counseling. Molecular testing also has a role in prenatal diagnosis to identify fetuses affected by severe hemoglobinopathies and thalassemias.

Advances in droplet digital polymerase chain reaction on microfluidic chips

The PCR technique has been known to the general public since the pandemic outbreak of COVID-19. This technique has progressed through three stages: from simple PCR to real-time fluorescence PCR to digital PCR. Among them, the microfluidic-based droplet digital PCR technique has attracted much attention and has been widely applied due to its advantages of high throughput, high sensitivity, low reagent consumption, low cross-contamination, and absolute quantification ability. In this review, we introduce various designs of microfluidic-based ddPCR developed within the last decade. The microfluidic-based droplet generation methods, thermal cycle strategies, and signal counting approaches are described, and the applications in the fields of single-cell analysis, disease diagnosis, and pathogen detection are introduced. Further, the challenges and prospects of microfluidic-based ddPCR are discussed. We hope that this review can contribute to the further development of the microfluidic-based ddPCR technique.

Next-Generation Sequencing (NGS) and Third-Generation Sequencing (TGS) for the Diagnosis of Thalassemia

Thalassemia is one of the most heterogeneous diseases, with more than a thousand mutation types recorded worldwide. Molecular diagnosis of thalassemia by conventional PCR-based DNA analysis is time- and resource-consuming owing to the phenotype variability, disease complexity, and molecular diagnostic test limitations. Moreover, genetic counseling must be backed-up by an extensive diagnosis of the thalassemia-causing phenotype and the possible genetic modifiers. Data coming from advanced molecular techniques such as targeted sequencing by next-generation sequencing (NGS) and third-generation sequencing (TGS) are more appropriate and valuable for DNA analysis of thalassemia. While NGS is superior at variant calling to TGS thanks to its lower error rates, the longer reads nature of the TGS permits haplotype-phasing that is superior for variant discovery on the homologous genes and CNV calling. The emergence of many cutting-edge machine learning-based bioinformatics tools has improved the accuracy of variant and CNV calling. Constant improvement of these sequencing and bioinformatics will enable precise thalassemia detections, especially for the CNV and the homologous HBA and HBG genes. In conclusion, laboratory transiting from conventional DNA analysis to NGS or TGS and following the guidelines towards a single assay will contribute to a better diagnostics approach of thalassemia.

Professionally responsible management of the ethical and social challenges of antenatal screening and diagnosis of β-thalassemia in a high-risk population

Thalassemias are among the most frequent genetic disorders worldwide. They are an important social and economic strain in high-risk populations. The benefit of β-thalassemia screening programs is growing evident but the capacity to diagnose fetal β-thalassemia exceeds the treatment possibilities and even when treatment before birth becomes feasible, difficult decisions about the relative risks will remain. This paper can be of practical and ethically justified aid when counseling women about screening, diagnosis, and treatment of β-thalassemia. It takes in consideration various social challenges, medical issues such as antenatal screening, preimplantation genetic diagnosis, prenatal diagnosis, non-invasive prenatal testing and prenatal therapy. We also describe the Sardinian experience in applying and promoting high-risk population screening and diagnosis programs and future trends in the management of β-thalassemia.

Borderline HbA2 levels: Dilemma in diagnosis of beta-thalassemia carriers

There is inconsistency in the exact definition of diagnostic levels of HbA₂ for β thalassemia trait. While many laboratories consider HbA₂ ≥4.0 % diagnostic, still others consider HbA₂ ≥3.3 % or HbA₂ ≥3.5 % as the cut-off for establishing β thalassemia carrier diagnosis. This is because, over the years, studies have described β thalassemia carriers showing HbA₂ levels that lie above the normal range of HbA₂ but below the typical carrier range of β thalassemia. These, "borderline HbA₂ levels", though not detrimental to health, are significant in β thalassemia carrier diagnosis because they can lead to misinterpretation of results. In this review, we have evaluated the prevalence of borderline HbA₂ levels and discussed the causes of borderline HbA₂ values. We have also compiled an extensive catalogue of β globin gene defects associated with borderline HbA₂ levels and have discussed strategies to avoid misdiagnosing borderline HbA₂ β thalassemia carriers. Our analysis of studies that have delineated the cause of borderline HbA₂ levels in different populations shows that 35.4 % [626/1766] of all individuals with borderline HbA₂ levels carry a molecular defect. Among the positive samples, 17 % [299/1766] show β globin gene defects, 7.7 % [137/1766] show α thalassemia defects, 2.7 % [49/1766] show KLF1 gene mutations, 2.3 % [41/1766] show the co-inheritance of β and α thalassemia, 2.0 % [37/1766] show the co-inheritance of β and δ thalassemia and 1.8 % [32/1766] show α globin gene triplication. It appears that a comprehensive molecular work up of the β globin gene is the only definite method to detect borderline HbA₂ β thalassemia carriers, especially in populations with a high prevalence of the disease. The presence of associated genetic or acquired determinants may subsequently be assessed to identify the cause of borderline HbA₂.

A Long, Fulfilling Career in Human Genetics

I have been fortunate and privileged to have participated in amazing breakthroughs in human genetics since the 1960s. I was lucky to have trained in medical school at Dartmouth and Johns Hopkins, in pediatrics at the University of Minnesota and Johns Hopkins, and in genetics and molecular biology with Dr. Barton Childs at Johns Hopkins and Dr. Harvey Itano at the National Institutes of Health. Later, the collaborative spirit at Johns Hopkins and the University of Pennsylvania were important to my career. Here, I describe the thrill of scientific discovery in two diverse areas of human genetics: DNA haplotypes and their role in solving the molecular basis of beta thalassemia and the role of retrotransposons (jumping genes) in human biology. I hope that this article may inspire others who love human genetics as much as I do.

A rare gene variation cap +1 (A>C) (HBB: c. -50A>C) associated with codon 5 (-CT) (HBB: c.17_18delCT) mutation in Syrian family

Background

CAP+1 [A>C] (HBB:c.‐50A>C) is a rare silent β‐thalassemia (β‐thal) mutation. Carrier individuals of this mutation show borderline hemoglobin (Hb), mean corpuscular volume (MCV) and Hb A2 levels. This mutation was previously reported in combination with different β‐thalassemia mutations, leading to variable phenotypes.

Case presentation

Here, we describe for the first time the combination of silent CAP+1 [A>C] (HBB:c.‐50A>C) mutation with β⁰ codon 5 [‐CT] (HBB:c.17_18delCT) mutation in a Syrian proband, leading to beta thalassemia intermedia (TI).

Conclusions

The compound heterozygotes of the silent CAP+1 (A>C) together with another severe beta gene mutation, are phenotypically severe enough to present at an early age and require appropriate therapeutic modalities.

Novel α0-Thalassemia Deletion Identified in an Indian Infant with Hb H Disease

We report the identification of a large deletion of the α-globin gene cluster, which removed both HBA2 and HBA1 and included the region from HBZ to HBQ1 on chromosome 16 (16p13.3). The α⁰-thalassemia (α⁰-thal) deletion was discovered in an Indian family residing in New Zealand. The proband was a 3-month-old female, who presented with a Hb H disease of unknown molecular origin. Routine hematology showed marked hypochromic microcytic anemia, with numerous Hb H inclusion bodies. In the absence of iron deficiency, there was a strong clinical suspicion of α-thal. On initial screening using a multiplex gap polymerase chain reaction (gap-PCR), only the common rightward deletion (-α^3.7) was detected. Investigation of the proband's mother and father revealed the mother was heterozygous for the -α^3.7 deletion, while none of the seven most common pathogenic α-thal deletions were detected in the father. Multiplex ligation-dependent probe amplification (MLPA) was employed to detect the presence of a novel α⁰-thal deletion in both the proband and her father. For the proband, the α⁰-thal deletion in combination with the -α^3.7 deletion, eliminated three copies of HBA consistent with a clinical diagnosis of Hb H disease.

From Prenatal to Preimplantation Genetic Diagnosis of β-Thalassemia. Prevention Model in 8748 Cases: 40 Years of Single Center Experience

The incidence of β-thalassemia in Sardinia is high and β-39 is the most common mutation. The prevention campaign started in 1977 and was performed in a single center (Microcitemico Hospital, Cagliari, Sardinia, Italy). It was based on educational programs, population screening by hematological and molecular identification of the carriers. Prenatal and pre-implantation diagnosis was offered to couples at risk. 8564 fetal diagnosis procedures using different invasive approaches and analysis techniques were performed in the last 40 years. Trans-abdominal chorionic villous sampling was preferred due to lower complication risks and early diagnosis. Chorionic villous DNA was analyzed by PCR technique. 2138 fetuses affected by β-thalassemia were diagnosed. Women opted for termination of the pregnancy (TOP) in 98.2% of these cases. Pre-implantation genetic diagnosis (PGD) was proposed to couples at risk to avoid TOP. A total of 184 PGD were performed. Initially, the procedure was exclusively offered to infertile couples, according to the law in force. The success rate of pregnancies increased from 11.1% to 30.8% when, crucial law changes were enacted, and PGD was offered to fertile women as well. Forty years of β-thalassemia prevention programs in Sardinia have demonstrated the important decrease of this severe genetic disorder.

Molecular Diagnosis of Thalassemias and Hemoglobinopathies: An ACLPS Critical Review

OBJECTIVES

To describe the use of molecular diagnostic techniques for patients with hemoglobin disorders.

METHODS

A clinical scenario is presented in which molecular diagnosis is important for genetic counseling. Globin disorders, techniques for their diagnosis, and the role of molecular genetic testing in managing patients with these disorders are described in detail.

RESULTS

Hemoglobin disorders, including thalassemias and hemoglobinopathies, are among the commonest genetic diseases, and the clinical laboratory is essential for the diagnosis of patients with these abnormalities. Most disorders can be diagnosed with protein-based techniques such as electrophoresis and chromatography. Since severe syndromes can result due to inheritance of combinations of globin genetic disorders, genetic counseling is important to prevent adverse outcomes. Protein-based methods cannot always detect potentially serious thalassemia disorders; in particular, α-thalassemia may be masked in the presence of β-thalassemia. Deletional forms of β-thalassemia are also sometimes difficult to diagnose definitively with standard methods.

CONCLUSIONS

Molecular genetic testing serves an important role in identifying individuals carrying thalassemia traits that can cause adverse outcomes in offspring. Furthermore, prenatal genetic testing can identify fetuses with severe globin phenotypes.

Systematic comparison of two whole-genome amplification methods for targeted next-generation sequencing using frozen and FFPE normal and cancer tissues

Sequencing key cancer-driver genes using formalin-fixed, paraffin-embedded (FFPE) cancer tissues is becoming the standard for identifying the best treatment regimen. However, about 25% of all samples are rejected for genetic analyses for reasons that include too little tissue to extract enough high quality DNA. One way to overcome this is to do whole-genome amplification (WGA) in clinical samples, but only limited studies have tested different WGA methods in FFPE cancer specimens using targeted next-generation sequencing (NGS). We therefore tested the two most commonly used WGA methods, multiple displacement amplification (MDA-Qiagen REPLI-g kit) and the hybrid or modified PCR-based method (Sigma/Rubicon Genomics Inc. GenomePlex kit) in FFPE normal and tumor tissue specimens. For the normalized copy number analysis, the FFPE process caused none or very minimal bias. Variations in copy number were minimal in samples amplified using the GenomePlex kit, but they were statistically significantly higher in samples amplified using the REPLI-g kit. The pattern was similar for variant allele frequencies across the samples, which was minimal for the GenomePlex kit but highly variable for the REPLI-g kit. These findings suggest that each WGA method should be tested thoroughly before using it for clinical cancer samples.

Molecular basis of β thalassemia and potential therapeutic targets

The remarkable phenotypic diversity of β thalassemia that range from severe anemia and transfusion-dependency, to a clinically asymptomatic state exemplifies how a spectrum of disease severity can be generated in single gene disorders. While the genetic basis for β thalassemia, and how severity of the anemia could be modified at different levels of its pathophysiology have been well documented, therapy remains largely supportive with bone marrow transplant being the only cure. Identification of the genetic variants modifying fetal hemoglobin (HbF) production in combination with α globin genotype provide some prediction of disease severity for β thalassemia but generation of a personalized genetic risk score to inform prognosis and guide management requires a larger panel of genetic modifiers yet to be discovered. Nonetheless, genetic studies have been successful in characterizing the key variants and pathways involved in HbF regulation, providing new therapeutic targets for HbF reactivation. BCL11A has been established as a quantitative repressor, and progress has been made in manipulating its expression using genomic and gene-editing approaches for therapeutic benefits. Recent discoveries and understanding in the mechanisms associated with ineffective and abnormal erythropoiesis have also provided additional therapeutic targets, a couple of which are currently being tested in clinical trials.

Mobile Genome Express (MGE): A comprehensive automatic genetic analyses pipeline with a mobile device

The development of next-generation sequencing (NGS) technology allows to sequence whole exomes or genome. However, data analysis is still the biggest bottleneck for its wide implementation. Most laboratories still depend on manual procedures for data handling and analyses, which translates into a delay and decreased efficiency in the delivery of NGS results to doctors and patients. Thus, there is high demand for developing an automatic and an easy-to-use NGS data analyses system. We developed comprehensive, automatic genetic analyses controller named Mobile Genome Express (MGE) that works in smartphones or other mobile devices. MGE can handle all the steps for genetic analyses, such as: sample information submission, sequencing run quality check from the sequencer, secured data transfer and results review. We sequenced an Actrometrix control DNA containing multiple proven human mutations using a targeted sequencing panel, and the whole analysis was managed by MGE, and its data reviewing program called ELECTRO. All steps were processed automatically except for the final sequencing review procedure with ELECTRO to confirm mutations. The data analysis process was completed within several hours. We confirmed the mutations that we have identified were consistent with our previous results obtained by using multi-step, manual pipelines.

Genetic Basis and Genetic Modifiers of β-Thalassemia and Sickle Cell Disease

β-thalassemia and sickle cell disease (SCD) are prototypical Mendelian single gene disorders, both caused by mutations affecting the adult β-globin gene. Despite the apparent genetic simplicity, both disorders display a remarkable spectrum of phenotypic severity and share two major genetic modifiers-α-globin genotype and innate ability to produce fetal hemoglobin (HbF, α₂γ₂).This article provides an overview of the genetic basis for SCD and β-thalassemia, and genetic modifiers identified through phenotype correlation studies. Identification of the genetic variants modifying HbF production in combination with α-globin genotype provide some prediction of disease severity for β-thalassemia and SCD but generation of a personalized genetic risk score to inform prognosis and guide management requires a larger panel of genetic modifiers yet to be discovered.Nonetheless, genetic studies have been successful in characterizing some of the key variants and pathways involved in HbF regulation, providing new therapeutic targets for HbF reactivation.

Molecular Epidemiological Characterization and Health Burden of Thalassemias in the Chaoshan Region, People's Republic of China

Thalassemia is one of the most prevalent inherited disease in southern China. However, there have been only a few epidemiological studies of thalassemia in the Chaoshan region of Guangdong Province, People's Republic of China (PRC). A total of 6231 unrelated subjects in two main geographical cities of the Chaoshan region was analyzed for thalassemia. Seven hundred and thirty-six cases of suspected thalassemia carriers with microcytosis [mean corpuscular volume (MCV) <82.0 fL] were found by complete blood cell (CBC) count, and were tested by reverse dot-blot gene chip to reveal a total of 331 mutant chromosomes, including 278 α-thalassemia (α-thal) alleles and 53 β-thalassemia (β-thal) alleles. The most common α-thal mutations were the Southeast Asian (- -(SEA)), followed by the -α(3.7) (rightward) and -α(4.2) (leftward) deletions. The two most common β-thal mutations were HBB: c.316-197C>T and HBB: c.126_129delCTTT, accounting for 69.81% of the β-thal defects in the studied individuals. In addition, a rare mutation, Cap +1 (A>C) (HBB: c.-50A>C) was described for the first time in the Chaoshan region. Our results gave a heterozygote frequency of 5.31% for common α- and β-thal in the Chaoshan region, and also indicated a higher prevalence of thalassemia with a heterozygote frequency of 6.29% in Chaozhou, followed by Shantou (3.37%). This study provided a detailed prevalence and molecular characterization of thalassemia in the Chaoshan region, and will be valuable for developing a strategy for prevention of thalassemia and reducing excessive health care costs in this area.

Investigation of sensitivity, specificity and accuracy of Tetra primer ARMS PCR method in comparison with conventional ARMS PCR, based on sequencing technique outcomes in IVS-II-I genotyping of beta thalassemia patients

PURPOSE

Beta thalassemia is one of the most important hematic diseases all around the world and solving the problems caused by this abnormality is strongly dependent on precise detection and reliable screening of high-risk couples. The aim of our study was the investigation of sensitivity, specificity and accuracy of Tetra primer ARMS PCR method comparing with conventional ARMS PCR, based on sequencing technique outcomes for genotyping of IVS-II-I mutation in beta thalassemia patients.

METHODS

Fifty seven samples including two homozygote, 49 heterozygote and 6 normal specimens were analyzed by Tetra primer ARMS PCR and conventional ARMS PCR methods. DNA was extracted by the standard method of salting out for leukocyte genomic DNA extraction of blood specimens and a high pure PCR template preparation kit was used for DNA purification of CVS samples. The results obtained by Tetra primer ARMS PCR and conventional ARMS PCR methods were compared with gold standard technique, i.e. sequencing.

RESULTS

All three parameters including specificity, sensitivity and accuracy were 100% for Tetra primer ARMS PCR method, while they were 100%, 92.45% and 92.7% for conventional ARMS PCR technique respectively. Comparing with Tetra primer ARMS PCR which represented 100% agreement with sequencing method, conventional ARMS PCR technique only showed 47.1% agreement, because of 4 discordant results.

CONCLUSION

Tetra primer ARMS PCR method is an almost reliable, sensitive and accurate technique and it is suggested that it can be used as a complementary method for diagnostic cases instead of conventional ARMS PCR method. This suggestion originated with perfect rate of agreement between outcomes of sequencing method, as a gold standard method of detecting the mutations, and Tetra primer ARMS PCR technique comparing with conventional ARMS PCR method.

Identification of three new nucleotide substitutions in the β-globin gene: laboratoristic approach and impact on genetic counselling for beta-thalassaemia

PURPOSE

Over the past two decades, a wide range of available methods for DNA analysis have allowed us to identify defects in globin genes associated with haemoglobin disorders and to correlate specific mutations with phenotypic expression. The purpose of this study was to evaluate the nature of three new nucleotide changes, mutation or single nucleotide polymorphism, found in the beta-globin gene, to conduct an appropriate genetic counselling.

PATIENTS AND METHODS

We report the molecular study performed in three probands and their families, sampling during the screening programme conducted at the Laboratory for Molecular Prenatal Diagnosis of Hemoglobinopathies at Villa Sofia-Cervello Hospital in Palermo, Italy.

RESULTS

This work allowed us to report three new nucleotide substitutions of the β-globin gene: a substitution of the nucleotide 16 in the CAP site area (HBB: c.-35 A>G), a substitution of the nucleotide 478 in the second intron (HBB: c.316-373) in association with β-haemoglobin variant Hb G Copenhagen (HBB:c.142G>A) and a substitution of the nucleotide 1656 within the 3' UTR (HBB: c.*+182 G>A) in association with the 1393-bp deletion (NG_000007.3:g.70060_71452del1393).

CONCLUSION

The present work emphasizes the importance of reporting the observed nucleotide changes to the Haemoglobin Variant Database, especially in the case of new or rare undefined mutations, to facilitate the determination of their phenotypic expression and the possible interactions with known molecular defects and to formulate an appropriate genetic counselling for couples at risk.

The molecular basis of β-thalassemia

The β-thalassemias are characterized by a quantitative deficiency of β-globin chains underlaid by a striking heterogeneity of molecular defects. Although most of the molecular lesions involve the structural β gene directly, some down-regulate the gene through distal cis effects, and rare trans-acting mutations have also been identified. Most β-thalassemias are inherited in a Mendelian recessive fashion but there is a subgroup of β-thalassemia alleles that behave as dominant negatives. Unraveling the molecular basis of β-thalassemia has provided a paradigm for understanding of much of human genetics.

Separation principles of cycling temperature capillary electrophoresis

High throughput means to detect and quantify low-frequency mutations (<10(-2) ) in the DNA-coding sequences of human tissues and pathological lesions are required to discover the kinds, numbers, and rates of genetic mutations that (i) confer inherited risk for disease or (ii) arise in somatic tissues as events required for clonal diseases such as cancers and atherosclerotic plaque.While throughput of linear DNA sequencing methods has increased dramatically, such methods are limited by high error rates (>10(-3) ) rendering them unsuitable for the detection of low-frequency risk-conferring mutations among the many neutral mutations carried in the general population or formed in tissue growth and development. In contrast, constant denaturing capillary electrophoresis (CDCE), coupled with high-fidelity PCR, achieved a point mutation detection limit of <10(-5) in exon-sized sequences from human tissue or pooled blood samples. However, increasing CDCE throughput proved difficult due to the need for precise temperature control and the time-consuming optimization steps for each DNA sequence probed. Both of these problems have been solved by the method of cycling temperature capillary electrophoresis (CTCE). The data presented here provide a deeper understanding of the separation principles involved in CTCE and address several elements of a previously presented two-state transport model.

Is the poly A (T>C) mutation a causative factor for misdiagnosis in second trimester prenatal diagnosis of β-thalassemia by fetal blood analysis on high performance liquid chromatography?

We report the problems in diagnosis faced by two families referred for prenatal diagnosis of thalassemia where cordocentesis and fetal blood analysis by high performance liquid chromatography (HPLC) had to be done. The Hb A levels of the fetal blood measured by HPLC on the VARIANT™ Hemoglobin Testing System were 1.2 and 6.7%, respectively, suggestive of a heterozygous β-thalassemia (β-thal) fetus in the first case and a normal fetus in the second case. In one family, one of the parents had a borderline Hb A(2) level and in the other, one parent had normal RBC indices. However, DNA sequencing, done later, showed that in the first case the fetus was a compound heterozygote for the IVS-I-5 (G>C) and the polyadenylation signal site [poly A (T>C)] mutation, while in the second case, the fetus was homozygous for the poly A mutation. This emphasizes that characterization of β-thal mutations must be done whenever one of the parents has a borderline Hb A(2) level or normal RBC indices, and one should not rely on fetal blood analysis by HPLC for prenatal diagnosis of β-thal so as to avoid misdiagnosis.

A melting curve analysis--based PCR assay for one-step genotyping of β-thalassemia mutations a multicenter validation

The increasing number of disease-causing mutations demands a simple, direct, and cost-effective diagnostic genotyping technique capable of detecting multiple mutations. This study validated the efficacy of a novel melting curve analysis-based genotyping assay (MeltPro HBB assay) for 24 β-thalassemia mutations in the Chinese population. The diagnostic potential of this assay was evaluated in 1022 pretyped genomic DNA samples, including 909 clinical cases of β-thalassemia minor or major, using a double-blind analysis in a multicenter validation study. Reproducibility of the assay was 100%, and the limit of detection was 10 pg per reaction. All 24 β-thalassemia mutations were accurately genotyped, and β-thalassemia genotypes were correctly determined in all 1022 samples, yielding overall sensitivity and specificity of 100%. The concordance rate was 99.4% between this assay and the reference method. It was concluded that the MeltPro HBB assay is useful for reliable genotyping of multiple β-thalassemia mutations in clinical settings and may have potential as a versatile method for rapid genotyping of known mutations because of its high throughput, accuracy, ease of use, and low cost.

History and current status of newborn screening for hemoglobinopathies

The impact of hemoglobinopathies on healthcare in the United States, particularly sickle cell disease (SCD), has been significant. Enactment of the Sickle Cell Anemia Control Act in 1972 significantly increased the federal interest in the SCDs and other hemoglobinopathies. Only since May 1, 2006, have all states required and provided universal newborn screening for SCD despite a national recommendation to this effect in 1987. In this article, we review the history of screening for SCD and other hemoglobinopathies, along with federal and state activities that have contributed to improved health outcomes for patients with SCD, as well as current newborn screening practices. We also chronicle the federal activities that have helped to shape and to refine laboratory screening and diagnostic proficiency. Finally, we review molecular testing strategies that have evolved and outline their possible future impacts on disease detection and outcome improvement.

The significance of the hemoglobin A(2) value in screening for hemoglobinopathies

BACKGROUND AND OBJECTIVE

The inherited hemoglobinopathies are a large group of disorders that include thalassemias and hemoglobin variants. Accurate determination of the carrier phenotype is essential for detecting couples at risk for producing offspring with hemoglobinopathy. Heterozygous beta-thalassemia is usually silent at the clinical level. His phenotype is characterized by microcytosis and hypochromia with increased hemoglobin A(2) (HbA(2)) value. Therefore, HbA(2) determination plays a key role in screening programs for hemoglobinopathy. The aim of this review is to address and suggest an approach for reducing or abolishing hemoglobinopathy screening mistakes.

DESIGN AND METHODS

Quantitative methods for HbA(2) value determination, comment on the accuracy of the test and on the interpretation of data were discussed. The most probable diagnostic conclusion based on the HbA(2) level, hemoglobin pattern, hematological parameters and iron markers was suggested in this review.

RESULTS

Hemoglobinopathies are the only genetic disease where it is possible to detect carriers using hematological findings rather than DNA analysis. However, hematological diagnosis is sometimes presumptive, and in these cases, DNA analysis becomes necessary. Complete screening is based on the detection of red cell indices, HbA(2), HbF and hemoglobin variant values. In particular, HbA(2) determination plays a key role in screening programs for beta-thalassemia because a small increase in this fraction is one of the most important markers of beta-thalassemia heterozygous carriers.

CONCLUSION

Genetic factors both related and unrelated to the beta- and alpha-globin gene clusters, iron metabolism, endocrinological disorders, and some types of anemia, together with intra- and inter-laboratory variations in HbA(2) determination, may cause difficulties in evaluating this measurement in screening programs for hemoglobinopathies. Therefore, knowledge of all these issues is important for reducing or eliminating the risk of mistakes in screening programs for hemoglobinopathies.

Detection of Two Rare β-Thalassemia Alleles Found in the Tunisian Population: Codon 47 (+A) and Codons 106/107 (+G)

We here present the first report of the detection of two rare beta0-thalassemia (thal) mutations in the Tunisian population: codon 47 (+A) and codons 106/107 (+G). To the best of our knowledge this is the second report of the codon 47 (+A) mutation, the first being identified in a Surinamese subject. The codons 106/107 (+G) mutation was first described in American Blacks, subsequently in Egyptians and Palestinians, and now in Tunisians. These mutations were detected by denaturing gradient gel electrophoresis (DGGE) screening followed by automated nucleotide sequencing. The former was found in two related beta-thal major patients in the homozygous state, while the latter was identified in a homozygous state in a transfusion-dependent beta-thal subject and in a sickle cell beta-thal patient. Both mutations are in linkage disequilibrium with haplotype V and sequence framework 2. Given the known wide spectrum of beta-thal alleles in the Tunisian population, the present report further confirms such heterogeneity. The knowledge of an updated spectrum of beta-thal alleles in Tunisia must allow the implementation of a more efficient screening strategy for genetic counseling and prenatal diagnosis.

A Different Molecular Pattern of β‐Thalassemia Mutations in Northeast Brazil

The main hereditary hemoglobin (Hb) disorders of clinical significance in Brazil are sickle cell disease and beta-thalassemia (thal). The sickle gene was introduced by the slave trade, whereas beta-thal was introduced later, due to a massive immigration (mostly by Italians) between 1870 and 1953, mainly to the southeast region of Brazil. Molecular studies performed in the southeast of the country showed a marked prevalence of the nonsense mutation at codon 39 (C --> T) (47-54%), leading to severe forms of beta0-thal. However, the northeast region of the country has a different demographic history, characterized by the absence of the massive Italian immigration. Owing to this and since the majority of cases of beta-thal in Pernambuco, a state located in the northeast of the country, have mild or intermediate clinical and laboratory features, we would predict a different spectrum of beta-thal mutations in this region. We examined 60 unrelated patients (86 beta-thal chromosomes) under regular clinical follow-up in Pernambuco: 6 were regularly transfused beta-thal major subjects, 20 had beta-thal intermedia, 20 had Hb S/beta-thal and 14 were beta-thal trait individuals. The following mutations were found: IVS-I-6 (T --> C) 62.8%, IVS-I-1 (G -->A) 15.1%, IVS-I-5 (G --> C) 9.3%, IVS-I-110 (G --> A) 8.2%, codon 39 (C --> T) 3.5%, and codon 30 (AGG --> AGC) 1.1%. These data show different patterns of beta-thal mutations in two regions of Brazil, demonstrating a thus far unrevealed heterogeneity of the disease in the country.

Simple, efficient, and cost-effective multiplex genotyping with matrix assisted laser desorption/ionization time-of-flight mass spectrometry of hemoglobin beta gene mutations

A number of common mutations in the hemoglobin beta (HBB) gene cause beta-thalassemia, a monogenic disease with high prevalence in certain ethnic groups. As there are 30 HBB variants that cover more than 99.5% of HBB mutant alleles in the Thai population, an efficient and cost-effective screening method is required. Three panels of multiplex primer extensions, followed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry were developed. The first panel simultaneously detected 21 of the most common HBB mutations, while the second panel screened nine additional mutations, plus seven of the first panel for confirmation; the third panel was used to confirm three HBB mutations, yielding a 9-Da mass difference that could not be clearly distinguished by the previous two panels. The protocol was both standardized using 40 samples of known genotypes and subsequently validated in 162 blind samples with 27 different genotypes (including a normal control), comprising heterozygous, compound heterozygous, and homozygous beta-thalassemia. Results were in complete agreement with those from the genotyping results, conducted using three different methods overall. The method developed here permitted the detection of mutations missed using a single genotyping procedure. The procedure should serve as the method of choice for HBB genotyping due to its accuracy, sensitivity, and cost-effectiveness, and can be applied to studies of other gene variants that are potential disease biomarkers.

Genotyping of bovine kappa-casein (kappa-CNA, kappa-CNB, kappa-CNC, kappa-CNE) following DNA sequence amplification and direct sequencing of kappa-CNE PCR product

Genomic DNA isolated from blood and semen of dairy cattle with known kappa-casein (kappa-CN) genotypes was subjected to Southern blot hybridization and polymerase chain reaction (PCR) using up to 14 restriction endonucleases. kappa-casein genotypes AA, AB and BB were identified using Hin dIII and Hin fI while genotypes with kappa-CNC and kappa-CNE were misidentified. Direct sequencing of the PCR product (kappa-CN EE) showed a substitution of guanine (kappa-CNA,B) by adenine (kappa-CNE) which creates a HaeIII restriction site. Therefore using PCR followed by Hin dIII or HinfI and Hae III digest allows discrimination between kappa-casein A, B and E directly at the DNA level.

Distinct modes of gene regulation by a cell-specific transcriptional activator

The architectural layout of a eukaryotic RNA polymerase II core promoter plays a role in general transcriptional activation. However, its role in tissue-specific expression is not known. For example, differing modes of its recognition by general transcription machinery can provide an additional layer of control within which a single tissue-restricted transcription factor may operate. Erythroid Kruppel-like factor (EKLF) is a hematopoietic-specific transcription factor that is critical for the activation of subset of erythroid genes. We find that EKLF interacts with TATA binding protein-associated factor 9 (TAF9), which leads to important consequences for expression of adult beta-globin. First, TAF9 functionally supports EKLF activity by enhancing its ability to activate the beta-globin gene. Second, TAF9 interacts with a conserved beta-globin downstream promoter element, and ablation of this interaction by beta-thalassemia-causing mutations decreases its promoter activity and disables superactivation. Third, depletion of EKLF prevents recruitment of TAF9 to the beta-globin promoter, whereas depletion of TAF9 drastically impairs beta-promoter activity. However, a TAF9-independent mode of EKLF transcriptional activation is exhibited by the alpha-hemoglobin-stabilizing protein (AHSP) gene, which does not contain a discernable downstream promoter element. In this case, TAF9 does not enhance EKLF activity and depletion of TAF9 has no effect on AHSP promoter activation. These studies demonstrate that EKLF directs different modes of tissue-specific transcriptional activation depending on the architecture of its target core promoter.

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.

Mutation detection by cycle sequencing

Candidate genes are screened for mutations by a DNA sequencing procedure known as cycle sequencing. First, a segment of the candidate gene is PCR amplified from the genomic DNA of an affected individual. The PCR product is then subjected to multiple rounds of further amplification in a thermal cycler using a heat-stable DNA polymerase in the presence of different dideoxynucleotides and a radiolabeled primer. The resulting 32P-labeled sequence reaction products are fractionated on a denaturing polyacrylamide gel and visualized by autoradiography. DNA segments on the order of 200 bp from 10 to 30 individuals can be screened on each gel. Cycle sequencing eliminates the need to subclone genomic fragments or PCR products, which makes it a much simpler method than conventional sequencing for identifying mutations.

Protein chip for detection of DNA mutations

A large number of human genetic diseases, bacterial drug resistances, and single-nucleotide polymorphisms are caused by gene mutations. Rapid and high-throughput mutation detection methods are urgently demanded. A protein chip method for detection of single-base mismatches and unpaired bases of DNA was developed using a genetic fusion molecular system Trx-His6-(Ser-Gly)6-Strep tagII-(Ser-Gly)6-MutS (THLSLM). The THLSLM coding sequence was constructed by attaching Strep tag II and mutS gene to the vector pET32a (+) sequentially with insertion of a (Ser-Gly)6 coding sequence before and behind Strep tagII gene, respectively. The fusion protein THLSLM was expressed in Escherichia coli AD494 (DE3) and purified using Ni(2+)-chelation affinity resin. The results of bioactivity assay showed that THLSLM both binds to mismatched DNA and interacts with streptavidin. THLSLM was immobilized on the chip matrix coated with the streptavidin through Strep tagII-streptavidin binding reaction. The resulting protein chip was used to detect the mismatched and unpaired mutations in the synthesized oligonucleotides, as well as a single-base mutation in rpoB gene from Mycobacterium tuberculosis, with high specificity. The method could potentially serve as a platform to develop the high-throughput technology for screening and analysis of genetic mutations.

Analysis of beta globin mutations in the Indian population: presence of rare and novel mutations and region-wise heterogeneity

Beta thalassaemia is a major public health problem in India. A comprehensive database of the spectrum of mutations causing beta thalassaemia in the Indian population is necessary. This study in which a large number of patients with beta thalassaemia including those from certain regions that were not explored earlier shows a great heterogeneity of mutations. Several novel and rare alleles that have not been reported earlier in the Indian population have been identified, and mutations differ in frequency in different regions of the country. This information on the spectrum of mutations has implications for the control of beta thalassaemia in a population with complex ethnic background and also on the genotype-phenotype correlation of the disease.

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.

Functional characterization of core promoter elements: the downstream core element is recognized by TAF1

Downstream elements are a newly appreciated class of core promoter elements of RNA polymerase II-transcribed genes. The downstream core element (DCE) was discovered in the human beta-globin promoter, and its sequence composition is distinct from that of the downstream promoter element (DPE). We show here that the DCE is a bona fide core promoter element present in a large number of promoters and with high incidence in promoters containing a TATA motif. Database analysis indicates that the DCE is found in diverse promoters, supporting its functional relevance in a variety of promoter contexts. The DCE consists of three subelements, and DCE function is recapitulated in a TFIID-dependent manner. Subelement 3 can function independently of the other two and shows a TFIID requirement as well. UV photo-cross-linking results demonstrate that TAF1/TAF(II)250 interacts with the DCE subelement DNA in a sequence-dependent manner. These data show that downstream elements consist of at least two types, those of the DPE class and those of the DCE class; they function via different DNA sequences and interact with different transcription activation factors. Finally, these data argue that TFIID is, in fact, a core promoter recognition complex.