Multiplex Gap-polymerase Chain Reaction Research Articles

Occurrence of the – –SEA, – –THAI and – –FIL α-Thalassemia-1 Carriers from a 7-Year Study at Ramathibodi Hospital, Bangkok, Thailand

α-Thalassemia (α-thal) is one of the most common genetic diseases in Thailand. Homozygosity of α-thal-1 (– –/– –) and compound heterozygosity of α-thal-1/α-thal-2 (– –/–α) leads to Hb Bart's (γ4) hydrops fetalis and Hb H (β4) disease, respectively. In order to better control and provide prevention of α-thal disease, the prevalence of α-thal-1 carriers and the types of genotypes in the Thai population should be known. A 7-year retrospective study, employing multiplex gap-polymerase chain reaction (gap-PCR) of 31,632 blood samples from Ramathibodi Hospital, Mahidol University, Bangkok, revealed an α-thal-1 carrier rate of 14.40% with the – –SEA (NG_000006.1: g.26264_45564del19301), – –THAI (NG_000006.1: g.10664_44164del33501) and – –FIL (NG_000006.1: g.11684_43534del31851) genotypes, constituting frequencies of 14.21, 0.18 and 0.01%, respectively. Although the – –FIL genotype is rare in the Thailand, its detection should be included in future α-thal screening programs.

The molecular characterization of Beta globin gene in thalassemia patients reveals rare and a novel mutations in Pakistani population

IntroductionA multicentre study (including four cities in Pakistan) aimed to investigate the frequency and spectrum of alpha and beta thalassemia genetic mutations and XmnI polymorphism of the Gamma Globin gene. MethodsOne hundred and sixty one beta thalassemia patients, identified on the ground of haematological parameters, were screened for mutations of the Alpha (HBA2 and HBA1) and Beta (HBB) Globin genes as well as Gamma (HBG2) Globin gene, -158 Gγ XmnI polymorphism, using a combination of multiplex GAP polymerase chain reaction (PCR), Sanger sequencing and restriction fragment length polymerase (RFLP) based PCR. ResultsMutations of at least one HBB gene was identified in 157 of 161 patients screened. Among 16 identified mutations in the beta gene, HBB:c.27_28insG (p. Ser10Valfs*14) was the most prevalent. α−3.7 and α−4.2 deletions were co-inherited with beta thalassemia mutations. Rare mutations such as HBB:c.–138C > T and HBB:c.315 + 1G > A were also identified. One novel variant (HBB:c.-148T > A), two rare mutations [HBB:c.332T > C (p.Leu111Pro); HBB:c.92G > C (p.Arg31Thr] and a novel association, HBB:c.[92G > C (p.Arg31Thr)] and [-92C > G], were reported for the first time in our study. HBG2:c.-211C > T base-pair substitution (historically described as -158 GγXmnI polymorphism) was present in 36% of the patients. ConclusionHeterogeneity in clinical and haematological parameters in TM, show that monogenic disorders can present with a wide spectrum of disease severity. Our studies identified rare and novel mutations that will be useful in the prevention of highly prevalent disease of thalassemia in Pakistan following nationwide awareness campaign.

Evaluation of α-Globin Gene Mutations Among Different Ethnic Groups in Khuzestan Province, Southwest Iran

α-Thalassemia (α-thal) is one of the most common inherited hemoglobin (Hb) disorders in the world. In addition to large deletions, over 50 different α-thal point mutations were detected around the world, thus, patients showed different phenotypes with regard to genotype. This study evaluated the genetic frequency of α-thal in Khuzestan Province, Southwest Iran, to help implement premarital and prenatal screening programs. The study was conducted on couples proposing to get married and parents who were referred to the genetic center of Shafa Hospital, Ahvaz, Iran, for prenatal diagnosis (PND) in 2012. Genomic DNA was purified by the salting-out method and tested using multiplex gap-polymerase chain reaction (gap-PCR), amplification refractory mutation system-PCR (ARMS-PCR), reverse hybridization test strips and DNA sequencing. Overall, 11 mutations were found on the α-globin genes. Based on gene frequency, the most common mutant allele was –α3.7 (rightward) (71.3%) followed by the two gene deletion – –MED (9.7%). Other common mutations were αcodon 19α (GCG>GC–, α2) (8.4%), the polyadenylation (polyA1) site αpolyA1α (AATAAA>AATAAG) (2.8%), and α–5 ntα (–TGAGG) (2.0%). In addition, an extremely rare mutation at αcodon 21α [Hb Fontainebleau, HBA2: c.64G > C (or HBA1)] was also found. The results of this study are critical for correct diagnosis of α-thal carriers, premarriage counseling and PND. This study suggests that the distribution of mutations on the α-globin genes differs among the ethnic groups in Khuzestan Province as well as in other provinces.

Analysis of α1 and α2 globin genes among patients with hemoglobin Adana in Malaysia.

Hemoglobin (Hb) Adana [HBA2: c179G>A (or HBA1); p.Gly60Asp] is a non-deletional α-thalassemia variant found in Malaysia. An improvement in the molecular techniques in recent years has made identification of Hb Adana much easier. For this study, a total of 26 Hb Adana α-thalassemia intermedia and 10 Hb Adana trait blood samples were collected from patients. Common deletional and non-deletional α-thalassemia genotypes were determined using multiplex gap polymerase chain reaction (PCR) and multiplex ARMS PCR techniques. Identification of the Hb Adana location on the α-globin gene was carried out using genomic sequencing and the location of the mutation was confirmed via restriction fragment length polymorphism-PCR. Among the 36 samples, 24 (66.7%) had the -α(3.7)/α(Cd59)α mutation, while the -α(3.7)/α(Cd59)α mutation accounted for 2 samples (5.6%) and the remaining 10 (27.8%) samples were α/α(Cd59)α. All 36 samples were found to have the Hb Adana mutation on the α2-globin gene. The position of the α-globin gene mutation found in our cases was similar to that reported in Indonesia (16%) but not to that in Turkey (0.6%). Our results showed that the Hb Adana mutation was preferentially present in the α2-globin genes in Malays compared to the other ethnicities in Malaysia. Thus, the Malays might have similar ancestry based on the similarities in the Hb Adana position.

A Fetus with Hb Bart’s Disease Due to Maternal Uniparental Disomy for Chromosome 16

We here report an unusual case of Hb Bart’s (γ4) disease. Thalassemia screening of a couple showed that the wife was an α0-thalassemia (α0-thal) carrier and her husband’s mean corpuscular volume (MCV) was normal. Chorionic villus sampling (CVS) was performed at 13 weeks’ gestation for positive Down syndrome screening and chromosomal study of the cultured CVS showed a normal karyotype. Ultrasound examination at 22 weeks’ gestation showed fetal cardiomegaly and raised middle cerebral artery peak systolic velocity. Cordocentesis confirmed fetal anemia and showed Hb Bart’s disease. Multiplex gap-polymerase chain reaction (gap-PCR) for α-thal deletions on DNA extracted from the CVS showed the presence of a homozygous α0-thal − −SEA (Southeast Asian) deletion. The husband was found to be a carrier of the α+-thal −α3.7 (rightward) deletion. Non paternity was excluded by fluorescent PCR using short tandem repeat (STR) markers on chromosomes 13, 18 and 21. A de novo terminal deletion of chromosome 16 was excluded by array comparative genomic hybridization (aCGH). Detection of uniparental disomy (UPD), using STR markers on chromosome 16 showed maternal uniparental isodisomy from 16pter to 16p13.2, and uniparental heterodisomy from 16p13.13 to 16qter.

The Value of Red Blood Cells (Rbc) Indices and Osmotic Fragility Test as Screening Tests in Malay Pregnant Women with Alpha Thalassaemia

Red blood cell (RBC) parameters obtained from hematology analyser has been very useful as the first line screening for thalassaemia. The changes are prominent in most type of β-thalassaemia but milder in α-thalassaemia. RBC parameters could have been normalized especially during pregnancy and in such situation screening these patients would require a different protocol. Blood samples from two hundred (200) Malay pregnant women attended obstetric clinic at Hospital Universiti Sains Malaysia (HUSM) were collected to screen for double α-gene deletion (-SEA, and –THAI), and the two single α-globin gene deletion (–α3.7 and -α4.2). Standard hematological analyses including red blood cell count and indices, and hemoglobin quantitation were performed on the blood samples. Of these, sixteen were excluded as they had HbA2 levels more than 4% and were diagnosed as HbE or β-thalassaemia trait. Then, multiplex GAP polymerase chain reaction (PCR) analyses of α-globin gene were performed on the remaining 184 blood samples. Total of 17 from 184 subjects confirmed to have α-thalassaemia (-α3.7/αα and --SEA/ αα genotype). The RBC indices were compared between those with α-thalassaemia and normal pregnant women and they were significantly different. -α3.7 kb single gene deletion (8.1%) was the commonest type followed by double gene South East Asia (--SEA) deletion (1.1%). We conclude that mean corpuscular volume (MCV) and mean corpuscular hemoglobin (MCH) with the cut off value of less than 86.3fl and 27.4 pg respectively are two useful RBC indices which can be used for screening of α-thalassaemia in pregnant women.

Variable Presentation of HB H Disease Due to Homozygosity for the Rare Polyadenylation Signal A TIndian (AATAAA>AATA– –) Mutation in Four Indian Families

The aim of this study was to identify the molecular defects leading to the variable clinical and hematological presentation of four patients with Hb H disease. Investigations included a complete blood count, high performance liquid chromatography (HPLC) analyses, cellulose acetate electrophoresis (pH 8.9), heat stability test, α genotyping by multiplex gap polymerase chain reaction (gap-PCR) to screen for the eight common α-globin gene deletions and DNA sequencing to detect the other deletional and nondeletional α-globin gene mutations. Two patients aged 15 and 5.5 years had a mild clinical presentation. The first patient aged 3 years had a severe presentation requiring regular transfusions. This patient also had an enlarged spleen and had to undergo splenectomy. The third patient, aged 5 years, also had severe anemia, had been transfused once and had a spleen of 4.5 cms. The hemoglobin (Hb) levels in the four patients ranged from 4.2 to 8.2 g/dL and they all had reticulocytosis (10.0 to 31.0%). Cellulose acetate electrophoresis at pH 8.9 showed a fast moving band that ranged from 18.0 to 25.9%. All the four patients were homozygous for the polyadenylation signal A (polyA) TIndian (AATAAA>AATA–) mutation. This mutation has been seen in Eastern India but not from Maharashtra and Uttar Pradesh where our patients originated.

A Single-Tube Multiplex Gap-Polymerase Chain Reaction for the Detection of Eight β-Globin Gene Cluster Deletions Common in Southeast Asia

Up to now, more than 200 different β-thalassemia (β-thal) mutations have been characterized. The majority are point mutations causing expression defects. Only approximately 10.0% of the defects are caused by large deletions involving the β-globin gene cluster causing β0-thal, (δβ)0-thal, Gγ(Aγδβ)0-thal and other conditions with or without persistence of fetal hemoglobin (Hb). For the prevention of severe forms of β-thal intermedia and β-thal major, it is important to identify carriers of point mutations as well as carriers of deletions.β-Thalassemia and related disorders are most commonly present among populations from all Mediterranean countries as well as Southeast Asia, India, Africa, Central America and the Middle East. Twelve relatively frequently occurring deletion types have been described involving the β-globin gene cluster. These include the 105 bp β0-thal deletion, the 619 bp deletion, the 3.5 kb deletion, the Southeast Asian (SEA) deletion, the Filipino deletion, Hb Lepore, the Thai (δβ)0-thal, the Siriraj J Gγ(Aγδβ)0-thal, the Chinese Gγ(Aγδβ)0-thal, the Asian Indian deletion-inversion Gγ(Aγδβ)0-thal as well as the (hereditary persistence of fetal hemoglobin) HPFH-6 and HPFH-7 deletions.To improve the rapid detection of the eight common β-globin cluster deletions in Southeast Asian countries, a simple molecular technique based on a single-tube multiplex gap-polymerase chain reaction (PCR) has been developed in this study. This technique provides a fast, simple and cost effective diagnostic test for deletion types of β-thal that can be applied in every molecular diagnostic laboratory having standard PCR equipment.

The Spectrum of α- And β-Thalassemia Mutations in Yunnan Province of Southwestern China

The aim of this study was to investigate the spectrum of thalassemia mutations in Yunnan Province, Southwestern China. We detected 450 thalassemia patients and carriers by multiplex gap polymerase chain reaction (gap-PCR), PCR reverse dot-blot hybridization and direct sequencing methods in 535 suspected patients. Four types of α-thalassemia (α-thal) mutations, – –SEA (59.2%), –α3.7 (rightward) (19.0%), Hb Constant Spring [Hb CS, α142, Term→Gln, TAA>CAA (α2), αCSα] (15.5%), and –α4.2 (leftward) (6.34%) were detected. Six types of β-thal mutations, the most prevalent being Hb E [β26(B8)Glu→Lys, GAG>AAG or codon 26 (G>A)] (30.5%), followed by codon 17 (A>T) (20.8%), codons 41/42 (−TCTT) (17.5%), IVS-II-654 (C>T) (17.2%), −28 (A>G) (6.95%), and codons 71/72 (+A) (2.42%) were also detected. Other rare mutations were codons 27/28 (+C), IVS-I-1 (G>T), Hb New York [β113(G15)Val→Glu, GTG>GAG], Hb D-Los Angeles [β121(GH4)Glu→Gln, GAA>CAA], codon 5 (–CT), Hb G-Taipei [β22(B4)Glu→Glu (GAA>GGA)], Hb J-Lome [β59(E3)Lys→Asn (AAG>AAC)], Hb J-Bangkok [β56(D7)Gly→Asp (GGC>GAC)], IVS-I-2 (T>C), and −31 (A>C). In this study, we provide a complete mutation spectrum of α- and β-thal mutations and a valuable strategy for accurate molecular diagnostic testing in Yunnan Province, People’s Republic of China (PRC).

Detection of α-globin gene deletion and duplication using quantitative multiplex PCR of short fluorescent fragments

The aim of this study was to establish a sensitive method that can detect the presence of not only the common but also the unusual or unknown α-globin gene deletions for screening of α-thalassemia. We used quantitative multiplex PCR of short fluorescent fragments (QMPSF) for the α-globin genes (HBA) to screen α-thalassemia deletions. We set up and validated HBA-QMPSF using 50 negative and 100 positive controls of deletional α-thalassemia. To evaluate its ability to detect the presence of the common and unusual or unknown α-globin gene deletions, 579 unrelated samples were simultaneously analyzed using this assay and multiplex Gap polymerase chain reaction (Gap-PCR). The inconsistent results were further confirmed by multiplex ligation-dependent probe amplification (MLPA). HBA-QMPSF was capable of detecting α-globin gene deletions with an acceptable variability as shown by mean values (SD) of allele dosage for the heterozygous deleted control obtained from intra- and inter-experimental replicates [0.63 (0.01) and 0.61 (0.03)]. In 572 out of the 579 unrelated subjects, HBA-QMPSF and multiplex Gap-PCR gave consistent results. In seven cases which were finally proved to be composed of one rare deletion--Thai/-α3.7, one novel deletion--SEA/-α2.8, four αααanti3.7/αα and one αααanti4.2/αα triplications, HBA-QMPSF showed deletion or duplication in the α-globin gene while multiplex Gap-PCR failed to give the correct diagnosis. HBA-QMPSF is able to detect the presence of the common and unusual or unknown α-thalassemia deletions and duplications. It can be used as an initial screening test for α-thalassemia caused by HBA gene copy number alteration.

Molecular Characterization of α-Thalassemia in the Dohuk Region of Iraq

The molecular basis of α-thalassemia (α-thal) has been addressed by several studies from the eastern Mediterranean region, but not from Iraq. To address this issue, we studied 51 individuals with unexplained hypochromia and/or microcytosis, as well as nine patients with documented Hb H disease from the Dohuk region in northern Iraq. We used multiplex gap-polymerase chain reaction (gap-PCR), reverse hybridization, and sequencing for this purpose. It was found that the most common genotypes in those with unexplained hypochromia and/or microcytosis were −α3.7/αα, followed by − −MED-I/αα, then −α3.7/−α 3.7, respectively, detected in 84.3% of the above individuals. Other genotypes identified sporadically were −α4.2/αα, αpoly A1α/αα (AATAAA>AATAAG), αAdanaα/αα [Hb Adana, codon 59 (Gly→Asp) or HBA1:c.179G>A], and αEvanstonα/αα [Hb Evanston, codon 14 (Trp→Arg) or HBA1:c.43 T>C]. Three cases (5.88%) remained uncharacterized even after sequencing. All nine Hb H cases carried the −α3.7/− −MED-I genotype. Such findings are rather different from those in other eastern Mediterranean populations, particularly with relevance to an Hb H molecular basis.