A reverse dot-blot method for rapid detection of non-deletion alpha thalassaemia

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.

Molecular Detection of Alpha Thalassemia: A Review of Prevalent Techniques

Alpha thalassemia (α-thalassemia) is an autosomal recessive disorder due to the reduction or absence of α globin chain production. Laboratory diagnosis of α-thalassemia requires molecular analysis for the confirmatory diagnosis. A screening test, comprising complete blood count, blood smear and hemoglobin quantification by high performance liquid chromatography and capillary electrophoresis, may not possibly detect all the thalassemia diseases. This review focused on the molecular techniques used to detect α-thalassemia, and the advantages and disadvantages of each technique were highlighted. Multiplex gap-polymerase chain reaction, single-tube multiplex polymerase chain reaction, multiplex ligation-dependent probe amplification, and loop-mediated isothermal amplification were used to detect common deletion of α-thalassemia. Furthermore, the reverse dot blot analysis and a single tube multiplex polymerase chain reaction could detect non-deletion mutation of the α-globin gene. Sanger sequencing is widely used to detect non-deletion mutations of α-thalassemia. Recently, next-generation sequencing was introduced in the diagnosis of both deletion and point mutations of α-thalassemia. Despite the advantages and disadvantages of different techniques, the routine method employed in the laboratory should be based on the facility, expertise, available equipment, and economic conditions.

Regulatory Mutation Study in Cases with Unsolved Hypochromic Microcytic Anemia and α-Major Regulatory Element Haplotype Analysis in Iran

α-Thalassemia (α-thal) is an inherited blood disorder with different clinical manifestations. Although genetic causes of anemia are identified routinely in the majority of α-thal cases, a pathogenic variant in a few cases remains undiagnosed. In this study, some reported regulatory mutations have been investigated in five unsolved α-thal carriers. α-Major regulatory element (α-MRE) haplotype analysis has also been performed in Iran for the first time. Four regions, including the HBA2 core promoter, the highly conserved sequence of hypersensitive-40 (HS-40), a region containing regulatory single nucleotide polymorphism (SNP) CR062116, and a region containing rs7203560, were screened for changes by Sanger sequencing in a total of five unsolved suspected α-thal carriers. The frequencies of α-MRE haplotypes B and C were also determined in control samples with normal hematological indices. No pathogenic variant was found in the investigated regions. Haplotype frequencies observed for B and C haplotypes fell into the range of frequencies observed in previous studies. The investigated genotypes in the control group were in the Hardy-Weinberg equilibrium. This study can provide evidence that there is no association between the B haplotype and microcytic hypochromic anemia. The cause of anemia remains a mystery in our unsolved cases, which demonstrates the need for further studies on the causes of hypochromic microcytic anemia in individuals with intact α- and β-globin genes without iron deficiency.

Noninvasive prenatal diagnosis for pregnancies at risk for β-thalassaemia: a retrospective study

OBJECTIVE

To evaluate the clinical feasibility of noninvasive prenatal diagnosis (NIPD) for β-thalassaemia using circulating single molecule amplification and re-sequencing technology (cSMART).

DESIGN

Through carrier screening, 102 pregnant Chinese couples carrying pathogenic HBB gene variants were recruited to the study. Pregnancies were managed using traditional invasive prenatal diagnosis (IPD). Retrospectively, we evaluated the archived pregnancy plasma DNA by NIPD to evaluate the performance of our cSMART assay for fetal genotyping.

SETTING

Chinese prenatal diagnostic centres specialising in thalassaemia testing.

POPULATION

Chinese carrier couples at high genetic risk for β-thalassaemia.

METHODS

Fetal cell sampling was performed by amniocentesis and HBB genotypes were determined by reverse dot blot. NIPD was performed by a newly designed HBB cSMART assay and fetal genotypes were called by measuring the allelic ratios in the maternal cell-free DNA.

MAIN OUTCOME MEASURES

Concordance of HBB fetal genotyping between IPD and NIPD and the sensitivity and specificity of NIPD.

RESULTS

Invasive prenatal diagnosis identified 29 affected homozygotes or compound heterozygotes, 54 heterozygotes and 19 normal homozygotes. Compared with IPD results, 99 of 102 fetuses (97%) were correctly genotyped by our NIPD assay. Two of three discordant samples were false positives and the other sample involved an incorrect call of a heterozygote carrier as a homozygote normal. Overall, the sensitivity and specificity of our NIPD assay was 100% (95% CI 88.06-100.00%) and 97.26% (95% CI 90.45-99.67%), respectively.

CONCLUSIONS

This study demonstrates that our cSMART-based NIPD assay for β-thalassaemia has potential clinical utility as an alternative to IPD for pregnant HBB carrier couples.

TWEETABLE ABSTRACT

A new noninvasive test for pregnancies at risk for β-thalassaemia.

Identification of a new β-thalassaemia variant Term CD+32(HBB: c.32A>C) in two Chinese families

AIMS

β-Thalassaemia is an inherited blood disorder caused by mutations in the β-globin gene cluster. Molecular characterisation of β-thalassaemia is essential for its diagnosis and management. More and more rare and novel mutations have been reported.

METHODS

Two Chinese families with β-thalassaemia from Fujian Province were recruited in this study. The phenotypes of the probands were confirmed through haematological analysis. Routine molecular analysis of thalassaemia was employed to identify the common mutations of thalassaemia. The rare and novel mutations were detected by direct DNA sequencing.

RESULTS

In family 1, the proband, a Chinese woman aged 31 years, showed elevated level of haemoglobin A2 (HbA2). No common mutations associated with β-thalassaemia were detected, whereas a rare mutation Term CD+32(HBB: c.32A>C) was identified through DNA sequencing. Subsequent investigation of the β-thalassaemia mutation in her family showed that her mother, her brother as well as her nephew also carried this mutation. In addition, both the proband's husband and her son carrying the rare --^THAI mutation exhibited decreased levels of MCH, MCH and HbA2. In family 2, the proband, a child aged 1 year, showed elevated level of HbA2, but had no common mutations of β-thalassaemia. The proband was identified carrying the mutation Term CD+32(HBB: c.32A>C), which was inherited from his mother.

CONCLUSIONS

In this study, we first report a rare β-thalassaemia mutation in Fujian Province, Southeast China. Moreover, our study also identified this rare mutation in humans. This finding has helped broaden the spectrum of β-thalassaemia mutations in our region and suggested that this rare mutation may be more prevalent in the Chinese population.

Molecular analysis of a large novel deletion causing α+-thalassemia

BACKGROUND

α-thalassaemia is an inherited blood disorder caused by mutations in the α-globin gene cluster. Recognizing the pathogenic α-globin gene mutations associated with α-Thalassemia is of significant importance to thalassaemia's diagnosis and management.

METHODS

A family with α-thalassaemia from Fujian, China was recruited for this study. The phenotype was confirmed through haematological analysis. Commercially available Gap-PCR genotypic methods were employed to identify the known deletions causing α-thalassemia. MLPA analysis was used to study the novel mutations; this was then confirmed through DNA sequencing and bioinformatics analysis.

RESULTS

The proband of the family belonged to Southeast Asian type (--^SEA) thalassaemia. None of the known mutations associated with α-thalassaemia were detected in this family's genetics, whereas a novel 6.9 kb deletion (16p13.3 g.29,785-36,746) covering the α2 gene on the globin gene cluster was identified with MLPA and confirmed through Sanger Sequencing. This data led us to propose a novel pathogenic deletion associated with α-thalassemia: -α^6.9 /--^SEA.

CONCLUSIONS

A novel α-thalassaemia deletion was identified in members of a Chinese family and subsequently analyzed. This finding has helped broaden the spectrum of pathogenic mutations leading to the development of α-thalassaemia, paving the way for improved disease diagnosis and management.

Simultaneous Genotyping of α-Thalassemia Deletional and Nondeletional Mutations by Real-Time PCR-Based Multicolor Melting Curve Analysis

α-Thalassemia, which is caused by defective synthesis of the hemoglobin α-globin chains, is the most commonly inherited recessive hemoglobin abnormality. Genetic detection of a defective α-globin gene is challenging because of a variety of large deletions of the α-globin gene cluster and nondeletional mutations. Separate detections of them are often required using complex and error-prone open-tube methods. We report a novel real-time PCR-based assay that can simultaneously genotype four major deletional and three common nondeletional mutations in two parallel reactions by using multicolor melting curve analysis. The turnaround time of this closed-tube assay was within 3.5 hours, the limit of detection was 5 ng of human genomic DNA per reaction, and as low as 5% mutant DNA could be detected in the mosaic samples. The assay was evaluated using 1213 precharacterized genomic DNA samples in a double-blind manner. All seven α-thalassemia mutations were accurately genotyped, yielding a 99.3% concordance with the comparison assays. The 14 discordant samples contained the HKαα allele that was undetected by the traditional methods. Considering its rapidity, ease of use, and accuracy, we concluded that our real-time PCR assay may be recommended as an alternative screening and diagnostic tool for α-thalassemia.

The first validated criteria for effective screening and a new simplified method for α-globin gene sequencing for diagnosis of uncommon α-globin mutations

No well-defined phenotypes that distinguish between unknown α- and β-globin mutations have been reported to date. Direct DNA sequencing of α-globin genes can be technically challenging, as α1- and α2-globin genes are nearly indistinguishable. To detect hemoglobin variants (HbXs) on Hb analysis, the entire β- and α-globin genes were directly sequenced using a newly developed sequencing protocol for α-globin genes. An algorithm to distinguish between α- and β-HbXs was constructed and subsequently validated in the independent validation group. Distinctive characteristics that can distinguish 39 α-HbXs from 24 β-HbXs were the presence of unidentifiable variants of HbA₂ and/or HbX of <37% on isoelectric focusing and <31% on high-performance liquid chromatography. Another set of 67 HbXs was employed to validate our algorithm. This accurately predicted 33 α-HbXs with 100% sensitivity and 97.1% specificity. Our sequencing protocol for α-globin genes was able to identify 11 rare mutations among all exons of both α-globin genes from 72 subjects. Six of these variants were first discovered in Thais. This is the first well-characterized algorithm for distinguishing unknown Hb variants in a large cohort. Our validated criteria and DNA sequencing procedure are highly efficient for molecular characterization of rare Hb mutations.

Identification of nondeletional α-thalassemia in a prenatal screening program by reverse dot-blot in southern China

The aim of this study was to demonstrate the performance of nondeletional α-thalassemia (α-thal) prevention using a reverse dot-blot method at a Mainland Chinese hospital. A prenatal control program for nondeletional Hb H disease was performed between January 2009 and December 2013. All couples were screened for α-thal trait, and for couples in which one partner tested positive for α(0)-thal, the other was subjected to screening for Hb Constant Spring (Hb CS, HBA2: c.427T > C) and Hb Quong Sze (Hb QS, HBA2: c.377T > C) mutations by reverse dot-blot assay. Prenatal diagnoses were offered in at-risk pregnancies. During the study period, 51,105 couples were found to be carrying α-thal; among these, 35 (0.07%) couples were found to be at-risk of conceiving an offspring with nondeletional Hb H disease, including 25 couples for Hb H-CS and 10 cases for Hb H-QS. Nine fetuses were diagnosed with nondeletional Hb H disease, and eight of the affected pregnancies were terminated. Detection of nondeletional α-thal is necessary for any prenatal diagnosis (PND) programs in Southeast Asian countries. Reverse dot-blot is a relatively simple method for simultaneous typing of common nondeletional α-thal mutations.

Implementation of newborn screening for hemoglobin h disease in mainland china

Hemoglobin H disease is the most severe non-fatal form of α-thalassemia syndrome characterized by pronounced microcytic hypochromic hemolytic anemia. It is predominantly seen in Southeast Asia, the Middle East and the Mediterranean. Studies suggest that hemoglobin H disease is not as benign a disorder as previously thought. Newborn screening for hemoglobin H disease is especially appealing because the screening test is based on the detection of hemoglobin Bart's (γ4) that is only possible within the newborn period. In this study, we reported on a 4-year period of newborn screening program at a mainland Chinese hospital, which detected 35 babies with hemoglobin H disease in a total of 26 152 newborns. The overall prevalence for hemoglobin H disease among all newborns in southern China is ~1 in 1,000. These children need appropriate follow-up and potential comprehensive care during their growth and development.

An improved reverse dot hybridization for simple and rapid detection of adefovir dipivoxil-resistant hepatitis B virus

Early detection of adefovir dipivoxil-resistant mutants during long-term treatment of chronic hepatitis B virus (HBV) infection with this drug is of great clinical importance. We developed an improved reverse dot hybridization test for simple and rapid detection of the rtA181V/T and rtN236T mutations associated with adefovir dipivoxil resistance in chronic hepatitis B patients. Probes were designed for genotypes B, C, and D of this resistance characteristic; a total of 70 clinical samples were analyzed with this improved reverse dot hybridization assay. Its usefulness was validated by comparing with sequencing data. Discordant results were confirmed by subclone sequencing. This reverse dot hybridization assay was sufficiently sensitive to detect 10(3) copies/mL; it also detected adefovir dipivoxil-resistant mutant strains when they comprised more than 5% of a mixed virus population. This reverse dot hybridization array correctly identified adefovir dipivoxil-resistant mutants; it had high concordance (98.5%) with direct sequencing data. There was no clear relationship between the HBV genotype and the development of adefovir dipivoxil-resistant mutants. This reverse dot hybridization assay proved to be simple and rapid for detection of rtA181V/T and rtN236T mutations associated with resistance to adefovir dipivoxil.

Analysis of alpha-hemoglobin-stabilizing protein (AHSP) gene as a genetic modifier to the phenotype of beta-thalassemia in Southern China

alpha-Hemoglobin-stabilizing protein (AHSP) is a molecular chaperon binding specifically to free alpha-globin. It is considered to be a potential modifier of beta-thalassemia. In order to find out if AHSP affects the phenotype of beta-thalassemia carriers in southern China, we analyzed AHSP gene in 365 beta-thalassemia subjects which was identified in 5789 consecutive blood samples from southern China. 8 SNPs were detected including two rare SNPs which were reported by us for the first time and two novel missense mutations. One missense mutation, A to T transversion at gene position 12750, substituting aspartic acid for valine at amino acid position 29 (AHSP D29V), was detected in three beta-thalassemia carriers respectively. The other AHSP missense mutation, 12831 A>T, which substitutes valine for glycine at amino acid position 56 (AHSP V56G), was identified in only one sample. Neither of the two missense mutations leads to obvious phenotypic change to the beta-thalassemia carries. A genetic association study between AHSP gene and the phenotype of beta-thalassemia subjects was conducted simultaneously. No significant association has been found between specific AHSP alleles or haplotypes and the disease severity of beta-thalassemia. Our study suggested that AHSP is not a significant genetic modifier of beta-thalassemia in southern China.

High-throughput beta-thalassemia carrier screening by allele-specific Q-primer real-time polymerase chain reaction

Based on a novel Q-primer real-time polymerase chain reaction (PCR) system, we designed allele-specific Q-primers for the detection of three beta-thalassemia mutations [Cd41/42(-TCTT), IVSI nt5 (G>C), and IVSII nt654 (C>T)] that have a high carrier frequency in Southeast Asia. With clear distinction between heterozygote and wild-type, DeltaC(t) (threshold cycle) values were defined. The results of evaluating 139 blinded samples by our system match perfectly with those obtained by the conventional reverse dot blot (RDB) method. With a 384-well plate that included replicates in the same analysis, our throughput reached 190 reactions per run with a turnaround time as short as 130 min, and the cost of consumables was as low as $1 (US) for each test.

Identification of a novel frameshift mutation at codon 53 (-T) in the beta-globin gene causing dominantly inherited beta-thalassemia in a Chinese Miao family

beta-thalassemia, one of the most common inherited disorders of hemoglobin synthesis in the world, is genetically heterogeneous with over 200 different beta-globin mutations worldwide. In this study, we describe a novel frameshift beta-thalassemia mutation at codon (cd) 53 (-T) in exon 2 of the beta-globin gene in a Chinese Miao family. In this family, all seven heterozygotes with this mutation presented with moderate anemia, jaundice, splenomegaly and elevated hemoglobin A2 levels. None of them had been transfused or carried any other known alpha/beta-globin mutation. Pedigree analysis indicated an autosomal dominant inheritance pattern in this family. Two new haplotypes "----+-+" and "--+++-+" were identified by restriction fragment length polymorphism (RFLP) haplotype analysis. The former was associated with the cd53 (-T) mutation and the latter only existed in one family member. Thus, a novel frameshift cd53 (-T) mutation may lead to mild thalassemia intermedia even though there is no statistically significant difference in beta-globin messenger RNA (mRNA) level between six heterozygotes and six normal subjects.

Validation of a reverse-hybridization StripAssay for the simultaneous analysis of common α-thalassemia point mutations and deletions

BACKGROUND

alpha-Thalassemia is a worldwide disease and considered to be a major public health problem in countries within the so-called thalassemia belt. The complex genetics of alpha-thalassemias requires diagnostic methods with the capacity to screen rapidly and accurately for common causative mutations.

METHODS

We developed and validated a reverse-hybridization assay (Alpha-Globin StripAssay) for the rapid and simultaneous detection of 21 alpha-globin mutations: two single gene deletions (-alpha(3.7); -alpha(4.2)), five double gene deletions [--(MED); --(SEA); --(THAI); --(FIL); -(alpha)(20.5)], alpha alpha alpha(anti-3.7) gene triplication, two point mutations in the alpha1 gene (cd 14 G>A; Hb Adana) and 11 point mutations in the alpha2 gene (initiation cd T>C; cd 19 -G; IVS1 -5nt; cd 59 G>A; Hb Quong Sze; Hb Constant Spring; Hb Icaria; Hb Pakse; Hb Koya Dora; polyA-1; polyA-2).

RESULTS

Reliable genotyping of recombinant mutant clones and reference DNA samples was achieved by means of two corresponding test strips presenting parallel arrays of allele-specific oligonucleotides. The entire procedure from blood sampling to the identification of mutations required less than 6 h, and hybridization/detection was manual or automated. The diagnostic potential of this Alpha-Globin StripAssay was carefully evaluated on 272 pre-typed samples in a multicenter validation study. In 96.14% of the cases, StripAssay typing was completely concordant with the reference methods.

CONCLUSIONS

The Alpha-Globin StripAssay proved to be a fast, easy-to-perform and reliable screening method to identify >90% of alpha-globin mutations in endemic areas worldwide.

A laboratory strategy for genotyping haemoglobin H disease in the Chinese

BACKGROUND

The thalassaemias are the commonest blood disorders worldwide, with South East Asia and southern China as areas of high prevalence. Accurate diagnosis of these disorders helps in clinical management with improved outcome.

METHODS

The alpha-globin genotypes of 100 Chinese patients in Hong Kong with haemoglobin H (Hb H) disease were characterised. Single-tube multiplex gap-PCR was used to detect --(SEA), -alpha(3.7) and -alpha(4.2), while Hb CS, Hb QS and codon 30 (DeltaGAG) were identified by single-tube multiplex amplification refractory mutation system (ARMS). Automated direct nucleotide sequencing of the amplified alpha2- and alpha1-globin genes was performed to characterise other non-deletional alpha-thalassaemia determinants.

RESULTS

In the 100 cases studied, 99 cases had --(SEA) in combination with deletional alpha(+)-thalassaemia or non-deletional alpha-globin gene mutation involving the alpha2-globin gene. In 70 cases of the deletional form, 43 cases showed the genotype of (--(SEA)/-alpha(3.7)) and 27 cases of (--(SEA)/-alpha(4.2)). Three of the 27 cases of (--(SEA)/-alpha(4.2)) were found to have Hb Q-Thailand linked in-cis with -alpha(4.2). The remaining 30 cases were of non-deletional form with the following genotypes: 11 cases of (--(SEA)/alpha(HbCS)alpha), 9 cases of (--(SEA)/alpha(HbQS)alpha), 3 cases of (--(SEA)/alpha(cd30 (DeltaGAG))alpha), 3 cases of (--(SEA)/alpha(cd31)alpha), 2 cases of (--(SEA)/alpha(poly-A)alpha), 1 case of (--(SEA)/alpha(HbWestmead)alpha) and 1 case of (--(non-SEA)/alpha(HbQS)alpha).

CONCLUSIONS

Based on two rapid diagnostic tests, multiplex gap-PCR and multiplex ARMS, more than 90% of the cases were genetically characterised. This laboratory strategy should be widely applicable for genetic diagnosis of alpha-thalassaemia.

The prevalence and spectrum of thalassemia in Shenzhen, Guangdong Province, People's Republic of China

Thalassemia (thal) is the most common autosomal disorder in southern China. The aim of the present study was to investigate the prevalence and spectrum of thalassemia mutations in the population of Shenzhen, Guangdong Province. In total, 3,711 samples from two hospitals in Shenzhen were subjected to hematological and molecular analysis. Of these, 241 (6.49%) were carriers of thalassemias, of which 161 (4.34%) had alpha-thal, 74 (1.99%) had beta-thal, and six (0.16%) had both alpha- and beta-thal. Three deletional and one nondeletional alpha-thal mutation, and nine beta-thal mutations were identified. Compared with other areas in Guangdong Province, the prevalence of thalassemia in Shenzhen was lower, while there was no evident difference for the spectrum of mutations. These results will provide a reference for prenatal testing and genetic counseling in the area.

Hemoglobin H hydrops fetalis syndrome resulting from the association of the - -SEA deletion and the alphaQuong Szealpha mutation in a Chinese woman

A case with Hb H hydrops fetalis syndrome resulting from the association of the - -(SEA) deletion and the alpha(Quong Sze)alpha mutation is reported. This is the first description of Hb H hydrops associated with the Hb Quong Sze mutation.

Study on molecular epidemiology of the alpha-thalassemias in Liuzhou City, Guangxi Autonomous Region, China

Guangxi is one of the provinces of Southern China with the highest incidence of alpha-thalassemia (thal). Liuzhou is the second biggest city in Guangxi. To find out the incidence of the various alpha-thal genotypes, and their distribution in the Liuzhou area, an F820 Blood Cell Analysis System was used to measure the parameters of red blood cells. A SPIFE Rapid Auto-Electrophoresis System was used to analyze the normal and abnormal hemoglobins (Hbs). Multiplex polymerase chain reaction (mPCR) was used to detect the alpha-globin genotypes. Thirty-two (2.05%) out of 7805 young couples undergoing pre-marriage counseling, were diagnosed as having an Hb H (beta4) disease. The study of 1228 cord blood samples revealed 138 newborn children carrying an alpha-thal determinant with nine different genotypes, thus making the total incidence of alpha-thal 11.24%. Among 185 cases of Hb H, 119 (64.1%) were confirmed as being deletional, and 66 cases (35.7%) nondeletional types. The severity of the Hb H diseases could be classified in the following order: alphaCSalpha/--SEA (alphaConstant (Spring)alpha/--Southeast Asia); alpha(-4.2)/--SEA; alpha(-3.7)/--SEA. Ten cases of alpha-thal determinants were found in combination with beta-thal. The mPCR technique can detect all kinds of combinations of the three common large deletions (--SEA, alpha(-4.2) and alpha(-3.7)) accurately and conveniently.

Molecular diagnosis of inherited disorders: lessons from hemoglobinopathies

Hemoglobinopathies constitute a major health problem worldwide, with a high carrier frequency, particularly in certain regions where malaria has been endemic. These disorders are characterized by a vast clinical and hematological phenotypic heterogeneity. Over 1,200 different genetic alterations that affect the DNA sequence of the human alpha-like (HBZ, HBA2, HBA1, and HBQ1) and beta-like (HBE1, HBG2, HBG1, HBD, and HBB) globin genes are mainly responsible for the observed clinical heterogeneity. These mutations, together with detailed information about the resulting phenotype, are documented in the globin locus-specific HbVar database. Family studies and comprehensive hematological analyses provide useful insights for accurately diagnosing thalassemia at the DNA level. For this purpose, numerous techniques can provide accurate, rapid, and cost-effective identification of the underlying genetic defect in affected individuals. The aim of this article is to review the diverse methodological and technical platforms available for the molecular diagnosis of inherited disorders, using thalassemia and hemoglobinopathies as a model. This article also attempts to shed light on issues closely related to thalassemia diagnostics, such as prenatal and preimplantation genetic diagnoses and genetic counseling, for better-quality disease management.

Oligonucleotide array for detection of common severe determinants of alpha thalassemia

A simple and an efficient oligonucleotide array was developed to identify common severe determinants of alpha (alpha) thalassemia. A total of 14 probes were designed to detect the most frequently three deletions (-alpha(3.7), -alpha(4.2), -(SEA)) and two non-deletions (alpha(Quong Sze), alpha(Constant Spring)). PCR products were amplified from human genomic DNA and allowed to hybridize with the oligonucleotide array. Hybridization was detected by fluorescence scanning, and alpha globin genotypes were assigned by quantitative analysis of the hybridization results. The efficiency and specificity of identifying alpha globin genotypes using the oligonucleotide arrays was evaluated by blinded analysis of 690 samples from unrelated individuals. The oligonucleotide array method described in this paper provides unambiguous detection of complex combinations of heterozygous, compound heterozygous and homozygous alpha thalassemia genotypes. The experimental results demonstrate that this methodological approach may be applied for screening and for hemological diagnosis in population at large.

The prevalence and spectrum of alpha and beta thalassaemia in Guangdong Province: implications for the future health burden and population screening

AIM

Thalassaemia is a good candidate disease for control by preventive genetic programmes in developing countries. Accurate population frequency data are needed for planning the control of thalassaemia in the high risk Guangdong Province of southern China.

METHODS

In total, 13397 consecutive samples from five geographical areas of Guangdong Province were analysed for both haematological and molecular parameters.

RESULTS

There was a high prevalence of carriers of alpha thalassaemia (8.53%), beta thalassaemia (2.54%), and both alpha and beta thalassaemia (0.26%). Overall, 11.07% of the population in this area were heterozygous carriers of alpha and beta thalassaemia. The mutation spectrum of alpha and beta thalassaemia and its constitution were fully described in this area. This study reports the true prevalence of silent alpha thalassaemia in the southern China population for the first time. In addition, two novel mutations that give rise to alpha thalassaemia, one deletion resulting in beta thalassaemia, and a rare deletion (--(THAI) allele) previously unreported in mainland China were detected. The frequency of the most common mutation, the Southeast Asian type of deletion (--(SEA), accounting for 48.54% of all alpha thalassaemias) was similar to the total of two alpha(+) thalassaemia deletions (-alpha(3.7) and -alpha(4.2), accounting for 47.49% of alpha thalassaemia).

CONCLUSION

Both alpha and beta thalassaemia are widely distributed in Guangdong Province of China. The knowledge gained in this study will enable the projected number of pregnancies at risk to be estimated and a screening strategy for control of thalassaemia to be designed in this area.

Alpha0 thalassaemia as a result of a novel 11.1 kb deletion eliminating both of the duplicated alpha globin genes

AIMS

To characterise a novel 11.1 kb deletion that eliminated both of the duplicated alpha globin genes, giving rise to a typical alpha0 thalassaemia phenotype in four carriers from a Chinese family.

METHODS

Haematological investigations were carried out on all family members. The seven common forms of alpha thalassaemia were screened for by the polymerase chain reaction (PCR) and Southern blotting was used to analyse the alpha globin gene cluster. DNA sequence analysis of the entire alpha1 and alpha1 globin gene region was carried out and reverse transcription (RT)-PCR was used to investigate the transcription levels of the alpha and beta globin genes.

RESULTS

The breakpoints were found to lie between coordinates 31695-31724 and 42846-42867 of the alpha globin gene cluster (NG_000006), with a total of about 11,135 nucleotides deleted. These sequences are involved in (CA)n repeats, suggesting a homologous recombination event. RT-PCR analysis gave a transcription level of the alpha globin gene in heterozygotes comparable with that of SEA deletion heterozygotes, confirming no output of alpha globin from the linked pair of alpha globin genes. The heterozygosity for this novel deletion was confirmed by PCR diagnosis in all four carriers from this family.

CONCLUSIONS

This rare mutation constitutes an additional heterogeneous defect causing alpha thalassaemia in the Chinese population.

Sequence variations of the ?-globin genes: Scanning of high CG content genes with DHPLC and DG-DGGE

The alpha-globin chains are encoded by two duplicated genes (HBA2 and HBA1, 5'-3') showing overall sequence homology >96% and average CG content >60%. alpha-Thalassemia, the most prevalent worldwide autosomal recessive disorder, is a hereditary anemia caused by sequence variations of these genes in about 25% of carriers. We evaluated the overall sensitivity and suitability of DHPLC and DG-DGGE in scanning both the alpha-globin genes by carrying out a retrospective analysis of 19 variant alleles in 29 genotypes. The HBA2 alleles c.1A>G, c.79G>A, and c.281T>G, and the HBA1 allele c.475C>A were new. Three pathogenic sequence variations were associated in cis with nonpathogenic variations in all families studied; they were the HBA2 variation c.2T>C associated with c.-24C>G, and the HBA2 variations c.391G>C and c.427T>C, both associated with c.565G>A. We set up original experimental conditions for DHPLC and DG-DGGE and analyzed 10 normal subjects, 46 heterozygotes, seven homozygotes, seven compound heterozygotes, and six compound heterozygotes for a hybrid gene. Both the methodologies gave reproducible results and no false-positive was detected. DHPLC showed 100% sensitivity and DG-DGGE nearly 90%. About 100% of the sequence from the cap site to the polyA addition site could be scanned by DHPLC, about 87% by DG-DGGE. It is noteworthy that the three most common pathogenic sequence variations (HBA2 alleles c.2T>C, c.95+2_95+6del, and c.523A>G) were unambiguously detected by both the methodologies. Genotype diagnosis must be confirmed with PCR sequencing of single amplicons or with an allele-specific method. This study can be helpful for scanning genes with high CG content and offers a model suitable for duplicated genes with high homology.

A thalassaemia array for Southeast Asia

The alpha and beta thalassaemias are the commonest genetic disorders worldwide. The homozygous state is associated with high morbidity and mortality, thus screening of at-risk pregnancies and prenatal testing are strongly advocated. A thalassaemia (thal) array has been designed using allele-specific arrayed primer extension (AS-APEX) for the simultaneous analysis of 15 non-deletion alpha-gene defects and 23 beta-gene mutations commonly found in southeast Asian countries, where thalassaemias are highly prevalent. This overcomes the problem of using multiple reverse dot blot analysis. The array showed 100% sensitivity and specificity in the detection of 120 beta-thal mutants and 35 non-deletion alpha-thal mutants. It is robust enough to be produced in a single place and shipped to other laboratories for use. The production cost of the array is low, each slide can be used for three different test samples and is therefore amenable to large scale antenatal screening in southeast Asian countries.

Evaluation of a single-tube multiplex polymerase chain reaction screen for detection of common alpha-thalassemia genotypes in a clinical laboratory

We prospectively compared a single-tube multiplex polymerase chain reaction (PCR) for detecting alpha-thalassemia with our current approach using 452 blood samples. Initial evaluation of 89 specimens revealed sensitivity and specificity, respectively, for the hemoglobin H inclusion body test (HbH prep) vs PCR for detecting alpha0-thalassemia carriers of 0.79 and 0.96 and for a mean corpuscular volume (MCV) of 82 microm3 (82 fL) or less, 1.0 and 0.45. Detection of all alpha-thalassemia genotypes was significantly lower for HbH prep and MCV (sensitivity and specificity, respectively: HbH prep, 0.48 and 0.96; MCV, 0.87 and 0.47). In a follow-up evaluation of patients with positive HbH prep results or suspected alpha-thalassemia prescreened by low MCV, the sensitivity and specificity, respectively, of HbH prep vs PCR increased to 0.97 and 0.93 for alpha0-thalassemia and 0.83 and 0.92 for any alpha-thalassemia. PCR detected alpha-thalassemia in 37.2% of 298 suspected alpha-thalassemia cases with suggestive indices but negative HbH prep results and no detectable hemoglobinopathy. This multiplex approach was more sensitive than the HbH prep for detecting all alpha-thalassemia genotypes, particularly alpha+-thalassemia; was particularly valuable for identifying carriers of alpha0-thalassemia at risk for offspring with hemoglobin Bart hydropsfetalis, regardless of other diagnosed hemoglobinopathies; and is an ideal adjunct to standard clinical screening protocols for detecting alpha-globin deletions.

Detection of severe nondeletional alpha-thalassemia mutations using a single-tube multiplex ARMS assay

Alpha-thalassemia is a common hereditary anemia due to decreased or absent synthesis of alpha-globin chains. The most common causes of alpha-thalassemia are deletions that remove one or both functional alpha-globin genes, with a small proportion of cases involving nondeletional mutations of the alpha2- or alpha1-globin genes. Herein, we describe a single-tube multiplex amplification refractory mutation system (ARMS) assay for rapid detection of six of the most common and severe nondeletional alpha-thalassemia mutations. These alleles are found predominantly among southeast Asian populations, and are associated with the most severe forms of hemoglobin (Hb) H disease or Hb H hydrops fetalis.

Robot printing of reverse dot blot arrays for human mutation detection

We report on a generally useful, partially automated, human mutation detection method based upon printing moderate density oligonucleotide arrays using a biorobot on activated nylon membranes. The Beckman Biomek 2000 was adapted to this task through fabrication of aluminum membrane filter holders and the development of an addressable Tool Command Language (Tcl) program, which can be invoked through BioScript. During program execution, a robot arm is moved along the x, y, and z axes to expel liquid, without dripping, from disposable barrier pipette tips and then to touch the drops on preactivated membranes. Printed arrays consist of alternating rows of oligonucleotides containing normal and mutant sequences. Hybridization of biotin labeled polymerase chain reaction products derived from human patient genomic DNA samples are visualized using chemiluminescent or chromogenic indicators. This technique allows unequivocal genotyping of 32 mutations at the beta-thalassemia locus (11p15.5) and of 34 mutations and one polymorphism at the cystic fibrosis transconductance membrane regulator locus (7p35).

Should we screen for globin gene mutations in blood samples with mean corpuscular volume (MCV) greater than 80 fL in areas with a high prevalence of thalassaemia?

AIMS

To investigate whether it is worthwhile, in areas where thalassaemia is common, to screen for globin gene mutations in subjects with a mean corpuscular volume (MCV) above 80 fL, especially in partners of known thalassaemia carriers.

METHODS

Blood samples from 95 subjects with MCV between 80 and 85 fL were screened for the presence of alpha globin gene mutations and the haemoglobin (Hb) E mutation.

RESULTS

Thirty four subjects harboured globin gene mutations. Of these, 31 had deletions of one alpha globin gene, one had Hb Constant Spring, and three had Hb E mutations.

CONCLUSION

Based on the above figures and known prevalence rates of thalassaemia carriers, it would seem worthwhile to screen for globin gene mutations in partners of known thalassaemia carriers, regardless of MCV, to identify pregnancies at risk of Hb H disease or Hb E/beta thalassaemia.

Single nucleotide polymorphisms of the factor IX gene for linkage analysis in the southern Chinese population

Carrier detection and prenatal testing for haemophilia B in Oriental populations have been hampered by the lack of informative markers within the factor IX (FIX) gene. We detected a T/C nucleotide variation at nucleotide 32770 in the poly-A region of the FIX gene in the mother of a haemophilia B child. Analysis of 139 unrelated alleles revealed a heterozygosity rate of 0.193, thus offering an additional marker for linkage analysis. Together with two other polymorphic sites (5' MseI and 3' HhaI) found in Chinese and Thai populations, these polymorphisms were useful in 66% of the families studied.

Genetic and clinical features of hemoglobin H disease in Chinese patients

BACKGROUND

Normally, one pair of each of the two alpha-globin genes, alpha1 and alpha2, resides on each copy of chromosome 16. In hemoglobin H disease, three of these four alpha-globin genes are affected by a deletion, a mutation, or both. We studied the alpha1-globin gene abnormalities and the clinical and hematologic features of Chinese patients with hemoglobin H disease in Hong Kong.

METHODS

We assessed the clinical features, hematologic values, serum ferritin levels, and liver function of 114 patients with hemoglobin H disease. We also performed echocardiography and magnetic resonance imaging of the liver and examined the two pairs of alpha-globin genes.

RESULTS

Hemoglobin H disease in 87 of the 114 patients (76 percent) was due to the deletion of three of the four alpha-globin genes (--/-alpha), a combination termed the deletional type of hemoglobin H. The remaining 27 patients (24 percent) had the nondeletional type of hemoglobin H disease, in which two alpha-globin genes are deleted and a third is mutated (--/alphaalphaT). All 87 patients with the deletional type of hemoglobin H were double heterozygotes in whom there was a deletion of both alpha-globin genes from one chromosome, plus a deletion of the alpha1 or alpha2 gene from the other chromosome (--/alpha- or --/-alpha). A variety of mutated alpha-globin genes was found in the patients with nondeletional type of hemoglobin H disease. Patients with the nondeletional type of the H disease had more symptoms at a younger age, more severe hemolytic anemia, and larger spleens and were more likely to require transfusions than patients with deletional hemoglobin H disease. The severity of iron overload was not related to the genotype.

CONCLUSIONS

Chinese patients in Hong Kong with the nondeletional type of hemoglobin H disease have more severe disease than those with the deletional type of the disease. Iron overload is a major cause of disability in both forms of the disease.