Prenatal diagnosis of alpha- and beta-thalassemias: experience in Hong Kong

The incidence of alpha-thalassemia trait (alpha-thal-1 and alpha-thal-2) among Southern Chinese in Hong Kong is about 3%. From June 1983 to September 1987, prenatal diagnosis for homozygous alpha-thal-1 was performed in 88 pregnancies at risk, using direct DNA analysis of amniotic fluid cells or chorionic villi. Twenty-one homozygous alpha-thal-1 fetuses were aborted and confirmed as Hb Bart's hydrops fetalis, and two were "Hb H" hydrops fetalis. Of 47 pregnancies delivered, 26 were alpha-thal-1 heterozygotes, 10 normal, eight alpha-thal-1/normal. Twenty-one pregnancies, diagnosed as alpha-thal-1/normal, await delivery. Based on a 6% incidence of beta-thalassemia minor among pregnant women in Hong Kong, the number of pregnancies at risk for beta-thalassemia major should be 288 per annum. However, since February 1984, only 25 diagnoses were performed. Comprehensive screening and education programs need to be implemented. The majority of beta-thalassemia defects in Southern Chinese are point mutations, single nucleotide insertions or minor deletions, not detectable by standard gene mapping techniques. With linkage analysis of the defective gene to polymorphic restriction sites, a definitive diagnosis can be obtained in 50% of the families, while in the remaining there is a 50% exclusion rate. We routinely use the Hind III-3' beta, Bam HI-3' beta, Ava II-beta, and Hinc II-psi beta sites for linkage analysis. For first pregnancies, the marked linkage disequilibrium of the Bam HI polymorphism can be applied in 29% of the cases. In nonconclusive cases, fetal blood beta/gamma globin chain synthetic ratio was used.(ABSTRACT TRUNCATED AT 250 WORDS)     

Prenatal diagnosis of sickle cell anemia by restriction and endonuclease analysis: HindIII polymorphisms in gamma-globin genes extend test applicability.

Polymorphism for a Hpa I restriction endonuclease site associated with about 60% of beta S genes in American Blacks allows exact prenatal diagnosis of sickle cell anemia by amniocentesis in 36% of couples at risk. In three families in whom exact diagnosis by Hpa I sites was impossible, we found analysis for the presence of polymorphic HindIII sites in the G gamma and A gamma intervening sequences would allow an exact prenatal diagnosis of sickle cell status in all three. In one of these families, the presence of an A gamma HindIII site in amniocyte DNA confirmed the diagnosis (sickle cell trait) made by synthetic studies using fetal erythrocytes obtained at fetoscopy. Studies of other Black families and individuals provide evidence for linkage disequilibrium in the G gamma-A gamma-delta-beta gene complex involving the four sites, G gamma HindIII, A gamma HindIII, beta S, and Hpa I, which span 33 kilobases (kb). Ten of 14 chromosomes bearing a beta S gene in a 7.6-kb Hpa I fragment contained a G gamma but not an A gamma HindIII site, whereas 16 of 16 chromosomes bearing a beta S gene in a 13-kb Hpa I fragment lacked both the G gamma and A gamma HindIII sites. Two-thirds of beta A-bearing chromosomes lacked both G gamma and A gamma sites, whereas one-third contained either the G gamma or both G gamma and A gamma sites. These data demonstrate that combined analysis of both Hpa I and HindIII polymorphisms and verification of their linkage phase should increase the fraction of couples for whom amniocentesis can provide an exact diagnosis of sickle cell status from 36% to greater than 80%.     

Prenatal diagnosis of polymorphic ventricular tachycardia using 64-channel magnetocardiography

We describe polymorphic ventricular tachycardia (VT) diagnosed using fetal magnetocardiography (FMCG). The fetus of a 33-year-old Japanese female at 24 weeks of pregnancy was diagnosed as bradycardia (60 beats/min) by fetal cardiotocography (CTG). Ultrasound findings indicated a diagnosis of an atrioventricular (AV) block involving extrasystole, but FMCG revealed a polymorphic VT followed by ventricular asystole. Standard ECG immediately after cesarean section at 37 weeks of pregnancy confirmed long QT syndrome followed by nonsustained polymorphic VT and an advanced AV block with wide QRS. Echocardiography demonstrated moderate left ventricular dysfunction in the neonate requiring implantation with a permanent pacemaker.     

A nosocomial outbreak of Branhamella catarrhalis confirmed by restriction endonuclease analysis

An outbreak of respiratory illness due to Branhamella catarrhalis occurred in the intermediate care unit of a Veterans Administration hospital and involved patients and staff members. Four patients had pneumonia and four had bronchitis. Infected patients were placed in a cohort separated from noninfected patients and were treated. Pharyngeal culture was used to survey prevalence in staff and all other patients on the unit; three of 18 staff members and two of 19 asymptomatic patients were positive for B. catarrhalis. A case-control study showed that respiratory therapy, steroid use, and location within the unit were significant risk factors for B. catarrhalis infection or colonization. Strains from five patients and two staff members had identical bacterial restriction endonuclease digestion patterns with three different enzymes; these patterns were distinct from those of control strains. This study is the first to document an outbreak of B. catarrhalis infection confirmed with a typing system and thus establishes B. catarrhalis as a nosocomial pathogen.     

Carrier detection for hemophilia B: evaluation of multiple polymorphic sites

DNA analysis was performed in families with hemophilia B. Restriction fragment length polymorphisms (RFLPs) produced by endonucleases Taql, Xmnl, and Ddel were studied by two factor IX genomic probes, F9(VIII) and F9(XIII). Fifty-seven subjects from ten families were investigated; of them, 31 were carriers (11 obligate and 20 potential). Of the potential carriers, ten displayed laboratory features allowing for a phenotypic diagnosis of heterozygosity. Segregation analysis of the markers was informative in 19/20 potential carriers, which belong to nine of the ten studied families. Among the potential carriers, Taql allowed the carriership assessment in 15 (78.9%), Xmnl in 15 (94.7%), and Ddel in two (10.4%). Diagnosis was not possible in one family since a homozygosity in the key individuals with all the employed enzymes (Taql, Xmnl, Ddel, + BamHI) was found. Hemophilia B syndrome in two families likely results from a new mutation. In one family, a first-trimester prenatal diagnosis was performed. The use of RFLP analysis allowed us to improve genetic counseling as compared with the phenotypic evaluation by clotting factor assays. Indeed, evaluation of RFLP increased by 26% the carriership assessment of the potential carriers of the hemophilia B trait.     

Prenatal diagnosis by amniocentesis and chorionic villus biopsy of mtDNA mutation 8993T>G

Summary The mtDNA mutation 8993T > G is associated with neurogenic muscle weakness, ataxia and retinitis pigmentosa (NARP) and Leigh syndrome. There are few reported cases of prenatal testing for mtDNA disorders. Specifically for 8993T > G, there are six cases in which prenatal diagnosis has been reported. We describe prenatal diagnosis in a 36-year-old G3P1 woman with 33% heteroplasmy in white blood cells. She had a previous child who died from Leigh disease (92% heteroplasmy). She underwent prenatal testing by both CVS and amniocentesis of the 8993T > G heteroplasmy levels. This is the first reported case in which both procedures were used. Heteroplasmy was similar in both tissues (58.6% CVS and 55% amniocentesis), in support of the theory that this testing is reliable and may be considered in prenatal cases where this mutation is known in the mother. To date, her child is 20 months old and developing normally. Heteroplasmy determination in the child was refused. Although the infant is developmentally normal, consistent with the observation that levels of heteroplasmy below 60% are compatible with a mild phenotype, this conclusion must be tempered by the limited period of observation and the fact that patients with the NARP phenotype often present later than 20 months of age. Electronic Supplementary Material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Online citation: JIMD Short Report #051 (2007) Online     

Prenatal diagnosis of hemoglobinopathies by DNA analysis

Restriction site polymorphisms are normal inherited variations in DNA that can be readily detected by restriction endonuclease analysis. Currently, 17 such polymorphisms are recognized within a 60 kb (kilobase) stretch of DNA which includes the beta-globin gene complex. Because of their proximity to the beta-globin gene, often these restriction site polymorphisms can be used to predict inheritance of beta-globin variants that produce disease. For example, restriction site polymorphisms can be used for prenatal diagnosis for the large majority of couples at risk of having a child with beta-thalassemia. When each member of such a couple is heterozygous at one or more of these 17 sites, family studies are usually successful in determining which forms of the polymorphism are co-inherited with the beta-thalassemia genes in that particular family. Subsequently, study of fetal DNA isolated from amniocytes obtained by midtrimester amniocentesis or from chorionic villi obtained by first trimester chorion biopsy will reveal which DNA polymorphisms that fetus has inherited. By deductive reasoning one can then predict which beta-globin genes it has co-inherited. Because of the general nature of these polymorphisms, which are related to the beta-globin gene and its variants only because of their proximity on chromosome 11, they are potentially useful in the prenatal diagnosis of any beta-chain hemoglobinopathy. Some hemoglobinopathies (including alpha-thalassemia, sickle cell anemia, and some cases of beta-thalassemia) can be detected directly by DNA analysis. In these cases in utero diagnosis does not need to rely on restriction site polymorphisms, which require preliminary family studies and are not applicable in all at risk pregnancies. Recently, genetic probes, which are necessary for detecting restriction site polymorphisms, have been isolated for sequences of several genes whose protein products are important in blood coagulation. These include probes for all three genes whose polypeptide products combine to form the fibrinogen molecule as well as probes for the prothrombin, Factor IX, Factor VIII, and antithrombin III genes. Defects in these genes are expected to be the causes of afibrinogenemia, prothrombin deficiency, hemophilia B, hemophilia A, and antithrombin III deficiency, respectively. From experience with other genes, it is expected that restriction site polymorphisms within and/or flanking these genes will be found.(ABSTRACT TRUNCATED AT 400 WORDS)     

Nonrandom association of polymorphic restriction sites in the β-globin gene cluster

By using probes for ε-, Ψβ₁-, and β-globin genes, we found four additional polymorphic restriction sites that have frequencies >0.1 in persons of Mediterranean area origin, Asian Indians, and American Blacks. Three of these (HincII sites) and the two previously described polymorphic HindIII sites [one in intervening sequence (IVS) II of each γ-globin gene] are distributed over 32 kilobases (kb) of DNA located 5′ to the δ-globin gene. This region of DNA comprises two-thirds of the β-globin gene cluster. Since each of these five polymorphic sites can be present (+) or absent (-), in theory there exist 32 possible combinations of sites (haplotypes). However, in Italians, Greeks, Indians, and Turks, 3 of the 32 haplotypes, (+----), (-+-++), and (-++-+), account for 92% of 89 β^A chromosomes examined. The observed frequencies for these haplotypes are 0.64, 0.15, and 0.13 in the populations studied, in contrast to expected frequencies (based on the observed gene frequencies at each of the five sites) of 0.20, 0.006, and 0.005, respectively. In American Blacks, a fourth haplotype, (----+), which is rare in non-Black populations, has a frequency of 0.37 in contrast to its expected frequency of 0.05. These results suggest a nonrandom association of DNA sequences over 32 kb 5′ to the δ-globin gene in all populations studied. Two other polymorphic sites 3′ to the δ gene (the newly discovered Ava II site in IVS II of the β-globin gene and the BamHI site 3′ to it) are nonrandomly associated with each other but randomly distributed with respect to the above haplotypes. This suggests that randomization of sequences has occurred within 12 kb of DNA between these two nonrandomly associated sequence clusters. Nonrandom association of polymorphic restriction sites has practical consequences in that it limits the usefulness of these additional HincII sites for prenatal diagnosis of hemoglobinopathies by linkage analysis. These sites provide little additional information for detection of β-thalassemia, while the polymorphic Ava II site, which lies outside the nonrandomly associated sequences 5′ to the δ gene, improves the test applicability from 52% to 70% of couples at risk.     

Polymorphism in mitochondrial DNA of humans as revealed by restriction endonuclease analysis.

Mitochondrial DNA samples from each of 21 humans of diverse racial and geographic origin were digested with each of 18 restriction endonucleases. The sizes of the resulting DNA fragments were compared after gel electrophoresis. No differences among the samples were detected in digest with 7 of the enzymes. Analysis of digests with the remaining enzymes showed one or more differences. Each of the 21 samples could be characterized individually on the basis of these digests. All between-sample differences could be explained by single base substitutions. No evidence for sequence rearrangements (inversions, transpositions) was obtained. Fourteen of the site alterations were shared by two or more samples; six of these were shared between races. The data indicate that individuals differ from a postulated ancestral mtDNA sequence at 0.18% of their base pairs. On the basis of an estimated rate for base substitution of 1% per 10(6) years [Brown, W. M., George, M., Jr. & Wilson, A. C. (1979) Proc. Natl. Acad. Sci. USA 76, 1967-1971], Homo sapiens could have speciated or passed through a severe population constriction as recently as 180,000 years ago. The data suggest that group-specific patterns of cleavage exist. The high resolution and precision afforded by this method of analysis makes possible the investigation of many questions concerning human population genetics, evolution, and recent history.     

Prenatal diagnosis of Glanzmann thrombasthenia using the polymorphic markers BRCA1 and THRA1 on chromosome 17

Glanzmann thrombasthenia is an autosomal recessive bleeding disorder caused by mutations in the genes encoding platelet GPIIb or GPIIIa. Both genes map to chromosome 17q21 and polymorphisms within this chromosomal region have been identified. In the current study, prenatal diagnosis was performed for a family that already had one affected child, patient 1, who had a compound heterozygous mutation in GPIIb. At the time of prenatal diagnosis, the maternal GPIIb mutation had been identified but the paternal GPIIb mutation was unknown. By sequence analysis, the fetus was identified as a carrier of the mother's mutation. To determine the probability of the fetus inheriting the father's mutation, haplotype analysis of DNA samples from the fetus, mother, father and affected child were performed using polymorphic markers on chromosome 17q12-q21. These markers included polymorphisms within the thyroid hormone receptor α1 gene (THRA1), the breast cancer gene (BRCA1), GPIIb, GPIIIa, and an anonymous marker D17S579. Heterozygosity within the THRA1, BRCA1 and GPIIIa polymorphic markers predicted that the fetus carried the father's normal allele. Based on genetic linkage studies, no recombination was identified with any of the informative markers, and from the map distance between GPIIb and BRCA1 the accuracy of diagnosis was predicted to be >98%. The father's mutation was subsequently identified and direct sequence analysis of fetal DNA confirmed that the fetus did not inherit the fathers' mutant allele.     

Human fibrinogen polymorphic site analysis by restriction endonuclease digestion and allele-specific polymerase chain reaction amplification: identification of polymorphisms at positions A alpha 312 and B beta 448

In the fibrinogen molecule, a total of seven sites have been tentatively identified as polymorphic; however, disagreements about these sites have been observed among the various protein and DNA sequence data published. To allow examination of the potential polymorphic sites at the DNA level, human genomic DNA samples were prepared from 110 unrelated, healthy individuals. Either allele- specific polymerase chain reaction (ASPCR) amplification or PCR amplification followed by restriction endonuclease digestion was used to detect the presence of possible polymorphisms. Two polymorphic sites were confirmed, one at A alpha 312 (Thr/Ala) by RsaI restriction analysis, and a second at B beta 448 (Arg/Lys) by MnlI restriction analysis. Mendelian inheritance of both polymorphisms was demonstrated and allele frequencies were estimated as 0.76/0.24 and 0.85/0.15 for the A alpha 312 and B beta 448 sites, respectively. The sites at A alpha 47, A alpha 296, B beta 162, B beta 296, and gamma 88 showed no evidence of variation in any of our samples. The amino acid polymorphisms at A alpha 312 and B beta 448 reflect conservative residue changes with unknown effects on fibrinogen structure or function. An additional, previously unrecognized DNA sequence variant was detected in a single individual in the second intron of the A alpha chain using HinfI restriction analysis.     

Estimation of phylogenetic relationships from DNA restriction patterns and selection of endonuclease cleavage sites.

The distribution of cleavage sites and their related sequences have been analyzed for 54 restriction endonucleases in the genome of human mitochondrial DNA; in three papova viruses, BK, simian virus 40, and polyoma; and in three bacteriophages, phi X174, fd, and G4. The results show that the cleavage sites and related sequences for most of the restriction enzymes tested are distributed nonrandomly. These results (i) constitute prima facie evidence for the action of natural selection, either direct or indirect on the restriction sites, and (ii) suggest that estimates of phylogenetic relationship, based on a phenetic approach using restriction enzyme data, will be biased.     

Specificity of substrate recognition by the EcoRI restriction endonuclease.

The substrate specificity of the EcoRI restriction endonuclease can be varied in vitro by changing the pH and the ionic environment of the reaction. Phosphodiester bond cleavage occurs at a DNA hexanucleotide sequence d(N-G-A-A-T-T-C-N)/d(N-C-T-T-A-A-G-N) when the ionic strength is high, 100 mM Tris-HCl, 50 mM NaCl, 5 mM MgCl2, and the pH is approximately 7.3. Lowering the ionic strength to 25 mM Tris-HCl, 2 mM MgCl2, and adjusting the pH to 8.5 reduces the recognition specificity of the EcoRI endonuclease to the tetranucleotide sequence, d(N-A-A-T-T-N)/d(N-T-T-A-A-N). The enzymatic activity responsible for this substrate recognition is referred to as EcoRI. Cleavage of pVH51 plasmid DNA under EcoRI conditions results in a number of partial digest fragments, some of which disappear slowly over a prolonged digestion period. This suggests that different recognition sites are cleaved at different rates. Comparison of DNA fragment patterns of modified and unmodified pVH51 DNA indicates that the canonical EcoRI sequence is the most rapidly cleaved site under EcoRI conditions. DNA modified in vivo by the EcoRI methylase is not cleaved by the EcoRI endonuclease under standard conditions, but is cleaved under EcoRI conditions at sites other than the standard EcoRI substrate.     

Identification of beta variant hemoglobins by DNA restriction endonuclease mapping

An alternative method for identifying beta variant hemoglobins is described. Computer analysis of restriction sites was used to predict which beta variants could be detected by DNA mapping. 61 of 217 variants were shown to have changes in restriction fragment patterns which were useful markers for the abnormal hemoglobin. A further 25 could be identified by polyacrylamide electrophoresis. Implications of DNA analysis in diagnosis of variant hemoglobins are discussed.     

Half tetrad analysis in alfalfa using multiple restriction fragment length polymorphism markers.

A maximum likelihood approach of half tetrad analysis (HTA) based on multiple restriction fragment length polymorphism (RFLP) markers was developed. This procedure estimates the relative frequencies of 2n gametes produced by mechanisms genetically equivalent to first division restitution (FDR) or second division restitution and simultaneously locates the centromere within a linkage group of RFLP marker loci. The method was applied to the diploid alfalfa clone PG-F9 (2n = 2x = 16) previously selected because of its high frequency of 2n egg production. HTA was based on four RFLP loci for which PG-F9 was heterozygous with codominant alleles that were absent in the tetraploid tester. Models including three linked and one unlinked RFLP loci were developed and tested. Results of the HTA showed that PG-F9 produced 6% FDR and 94% second division restitution 2n eggs. Information from a marker locus belonging to one linkage group was used to more precisely locate the centromere on a different linkage group. HTA, together with previous cytological analysis, indicated that in PG-F9, FDR 2n eggs are likely produced by diplospory, a mechanism common among apomictic species. The occurrence of FDR 2n eggs in plant species and their importance for crop evolution and breeding is discussed together with the potential applicability of multilocus HTA in the study of reproductive mutants.     

Anatomy of herpes simplex virus DNA: strain differences and heterogeneity in the locations of restriction endonuclease cleavage sites.

Digestion of herpes simplex virus DNA by the HinIII or Eco RI restriction endonucleases yielded 11 to 15 fragments with molecular weights between 1 x 10(6) and 28 x10(6). The electrophoretic profiles obtained in 0.3% agarose gels with DNA fragments from none different strains of herpes simplex virus type 1 could be readily differentiated from the patterns exhibited by the corresponding fragments from four separate strains of type 2 virus; however, with each serotype, the laboratory strains differed significantly among themselves and also from isolates passaged a minimum number of times outside the human host. Digestion of all DNAs of herpes simples virus with either enzyme reproducibly generated two classes of fragments (major and minor) which differed in molar ocncentration. Moreover, although the molecular weight of an intact herpes simplex 1(F1) DNA molecule is approximately 98 x 10(6), the summed molecular weights of all major and minor HinIII fragments totalled 160 x 10(6), and the seven major fragments alone accounted for only 60 x 10(6). These unusual features indicate the existence of limited heterogeneity in the positions of cleavage sitet along individual molecules. We have eliminated the possibility that minor fragments arose from contamination with the defective DNA of high byoyant density which appears on serial undiluted passage of the virus. In fact, this latter type of DNA was resistant to cleavage by HinIII and gave large amounts of only two species of EcoRI fragments; suggesting that the defective molecules consist of many tandem repeats of a small segment of viral DNA. The heterogeneity in the viral DNA of normal density appears to be related to the structural organization of the molecules and does not necessarily imply differences in genetic content.