Prenatal diagnosis of alpha-thalassemia by polymerase chain reaction and dual restriction enzyme analysis

PCR past, present and future

PCR has become one of the most valuable techniques currently used in bioscience, diagnostics and forensic science. Here we review the history of PCR development and the technologies that have evolved from the original PCR method. Currently, there are two main areas of PCR utilization in bioscience: high-throughput PCR systems and microfluidics-based PCR devices for point-of-care (POC) applications. We also discuss the commercialization of these techniques and conclude with a look into their modifications and use in innovative areas of biomedicine. For example, real-time reverse transcription PCR is the gold standard for SARS-CoV-2 diagnoses. It could also be used for POC applications, being a key component of the sample-to-answer system.

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.

The advantages of haplotype analysis of the promoter region of the human apolipoprotein E gene

Polymorphisms in the regulatory region of the human apolipoprotein E gene (gene, APOE; protein, apoE) have been implicated in Alzheimer's disease. Here we describe in detail the advantages of a simple method for haplotype analysis of this region (at -491 and -427 bases relative to the transcription start site of the gene). The promoter region of the APOE gene was amplified by polymerase chain reaction (PCR) and this fragment was then used as a template for PCR with "nested" primers to generate a 228-bp product incorporating both the -491 and the -427 loci. PCR products were then digested with DraI and AluI together and subjected to polyacrylamide gel electrophoresis. The distinct pattern of bands appearing on the gel was then used to ascribe [-491,-427] haplotypes to each subject, from which -491 and -427 genotypes were inferred. -491 and -427 genotypes were also confirmed by digestion with DraI alone or AluI alone. Haplotype analysis was successful in all 20 samples analyzed and was 100% consistent with genotyping. We suggest that this is a reliable, time-saving method that the will be useful in large-scale APOE promoter genotyping studies.

Electrospray tandem mass spectrometry in the rapid identification of alpha-chain haemoglobin variants

The potential use of electrospray tandem mass spectrometry in the rapid characterisation of haemoglobin variants found in the Swedish population has been assessed. Analysis times of the order of 5 -10 min were routinely achieved, and identification of variants using mass spectrometry as the sole analytical technique was possible. However, additional information, readily available from isoelectric focusing experiments, made identification simpler and more secure. In the present communication we report on the identification of the alpha-chain variants, Hb Russ, Hb Le Lamentin and Hb Q-Iran. The identifications were confirmed by the use of nucleotide sequencing techniques.

Diagnosis of thalassaemia by non-isotope detection of alpha/beta and zeta/alpha mRNA ratios

The alpha/beta and zeta/alpha messenger RNA (mRNA) ratios in the thalassaemia syndromes were investigated by polymerase chain reaction (PCR) with silver staining of the PCR products. In this study we used the PCR to amplify cDNA copies of circulating erythroid cell mRNA in order to measure the relative amounts of alpha-, beta- and zeta-globin contained within. Quantitation was performed by scanning the silver stain of specific globin cDNA bands. We found that there were significant differences of alpha/beta-mRNA and zeta/alpha-mRNA in patients with Hb H disease and alpha-thalassaemia-1 compared to normal subjects. There was a marked increase in the alpha/beta-mRNA ratio but not in the zeta/alpha-mRNA ratio in patients with beta-thalassaemia. In two beta-thalassaemia cases abnormal increases of zeta-globin bands were noted and they were confirmed through DNA analysis to be combined with alpha-thalassaemia-1. This method provides a simple, rapid and non-radioactive approach to detect thalassaemia syndromes, and can help to screen cases of beta-thalassaemia with alpha-thalassaemia-1.

Prenatal diagnosis of unusual hemoglobinopathies

While analyzing 280 hemoglobinopathy kindreds with prescribed molecular tests, 3 unusual mutations were observed that required additional characterization. In the first case, the hypervariable region flanking the alpha-globin genes generated an intermediate length 8.2 kb psi zeta-globin gene fragment on a Southeast Asian chromosome with two deleted alpha-globin genes. Rehybridization of the Southern blot with alpha-globin probe distinguished the mutation unambiguously. In the second case, restriction enzyme analysis of a PCR amplified black beta-globin gene detected a novel beta-83 point mutation adjacent to a promoter element. In the third case, which was uninformative with available allele specific oligonucleotides (ASOs), total genomic PCR amplification and sequencing identified a single basepair insertion in codon 36/37 of an Iranian beta-globin gene that shifted the reading frame and obliterated gene activity. Developing additional region-specific ASOs will further diminish the number of cases that must be characterized by genomic PCR sequencing.

Prenatal diagnosis of hemophilia involving grandpaternal mosaicism

Our Factor VIII and RFLP analyses identified previously unreported grandpaternal hemophilia A mosaicism in a male who transmitted the disease allele to 2 of 4 daughters and 2 of 4 grandsons. An uncommon flanking polymorphic DXS52 allele cosegregated with this grandpaternal mutant allele. This and other reports of mosaic hemophilia A carriers indicate that parental mosaicism can explain unusual segregation of low Factor VIII activities and DNA polymorphisms in about 1% of hemophilia A pedigrees.

Prenatal in situ hybridization test for deleted steroid sulfatase gene

X-linked ichthyosis results from steroid sulfatase (STS) deficiency; 90% of affected patients have a complete deletion of the entire 146 kb STS gene on the distal X chromosome short arm (Xp22.3). In these families prenatal diagnosis and carrier testing can be completed in 2 days by hybridizing simultaneously 2 different cosmid probes labeled with fluorescein or Texas red and counterstaining interphase nuclear DNA with DAPI. An STS gene probe labeled with Texas red hybridizes specifically to the steroid sulfatase gene on the X chromosome. A second flanking probe labeled with fluorescein hybridizes to both the normal Y chromosome and normal and STS deleted X chromosomes. In this fashion the interphase nuclei of normal males, affected males, normal females, and carrier females can be distinguished unambiguously. Because normal males and carrier females each show two yellow-green fluorescein spots and one Texas red STS spot, use of this test prenatally requires determining fetal sex independently with repetitive X and Y chromosome-specific probes. This procedure can be used with lymphocytes, direct and cultured chorionic villus cells, direct and cultured amniocytes, and fibroblasts. Similar methods are anticipated to be useful for rapid diagnostic assessment of other aneuploid gene disorders.

Mental retardation locus in Xp21 chromosome microdeletion

Xp21 microdeletion syndrome is associated with variable size Xp21 deletions that usually include the glycerol kinase locus. The clinical phenotypes we studied in this chromosome region include: Xpter - Aland Island eye disease (AIED) -adrenal hypoplasia (AH) -glycerol kinase (GKD) -Duchenne muscular dystrophy (DMD) -retinitis pigmentosa (RP) -ornithine transcarbamylase (OTC) -centromere. In a compilation of 18 individuals in 14 families with the AH, GKD, and DMD loci deleted, 17 were male and all were developmentally delayed. In contrast, we report mentally retarded female carriers in two Xp21 deletion syndrome families with DMD, GKD, and AH in affected males. In the first family with normal karyotypes, a submicroscopic deletion was associated with DMD in the retarded male and with retardation in carrier females. In the second family an X chromosome with a cytogenetically deleted Xp21 distal to the OTC and RP genes segregated in the affected male and retarded female carriers. DNA analysis at the DMD locus verified the cytogenetic findings. This report of mental retardation in otherwise asymptomatic female carriers of Xp21 deletion classifies one form of mental retardation in females.

DNA diagnosis for the detection of sickle hemoglobinopathies

At this time, the sole generally accepted use for DNA diagnosis in the hemoglobinopathies is for the prenatal detection of disease, which can be identified by these means early in the first trimester of pregnancy. By ascertaining genotype rather than phenotype, the confusion that results from diagnostic errors should be diminished. DNA diagnostics are the future of all genetic disease detection and this future will soon be upon us.

Prenatal diagnosis of Hb H disease due to compound heterozygosity for South-east Asian deletion and Hb constant spring by polymerase chain reaction

A pregnant woman has two children affected by moderately severe Hb H disease due to compound heterozygosity of South-east Asian deletion and Constant Spring mutation. In her third pregnancy, transabdominal chorionic villus sampling was performed at the tenth gestational week to obtain fetal DNA. The polymerase chain reaction was used for detection of both the South-east Asian deletion and the Constant Spring mutation. Hb H disease was diagnosed in the fetus. After genetic counselling, the couple elected to have the pregnancy terminated.

Carrier detection and prenatal diagnosis of alpha-thalassemia of Southeast Asian deletion by polymerase chain reaction

Alpha-thalassemia of Southeast Asian deletion (-- SEA/) is very common in Southeast Asia. Homozygosity of this genotype is the major cause of Hb Bart's hydrops fetalis in Taiwan. With polymerase chain reaction using three oligonucleotide primers bridging the common deletion breakpoint, a DNA fragment of 194 basepairs (bp) was amplified in chromosomes with the -- SEA determinant and a DNA fragment of 287 bp was amplified in chromosomes without this deletion. In our pilot study including 8 normal subjects, 20 obligate carriers, and 11 homozygotes of the deletion, all the genotypes were determined and then confirmed by Southern blotting and DNA hybridization with phi zeta globin gene probe. For prenatal diagnosis, 55 at-risk pregnancies were collected. Chorionic villus sampling was done in 51 cases and early amniocentesis was done in 4 cases. Fourteen cases (25.5%) were diagnosed as normal, 25 (45.5%) as heterozygotes, and 16 (29%) as homozygotes of -- SEA. All of the diagnoses were also confirmed as aforementioned. With polymerase chain reaction, the determination of the -- SEA deletion is straightforward and is much quicker and easier than with conventional Southern blotting and DNA hybridization. In areas with a high prevalence of -- SEA deletion, this method provides a rapid tool for carrier detection and prenatal diagnosis.