DNA polymorphism and molecular pathology of the human globin gene clusters

Hemoglobin F production in heterocellular hereditary persistence of fetal hemoglobin and its linkage to the beta globin gene complex

Some types of nondeletional heterocellular hereditary persistence of fetal hemoglobin (HPFH) appear to be caused by mutations in the beta globin gene cluster near the gamma globin genes, while in other cases the condition is associated with a gene or genes outside the beta globin gene complex. We have used DNA probes for chromosome 11 markers to localize the HPFH determinant in a large Australian kindred with nondeletional heterocellular HPFH. In 13 of the 58 family members studied the Hb F levels are increased to between 1.8% and 7.9%, the Hb F being composed predominantly of A gamma chains. All family members were typed for restriction fragment length polymorphisms detected by probes from the beta globin gene complex, and the nearby genetic markers D11S12, INS, and HRAS. Linkage analysis showed HPFH is closely linked to the beta globin gene cluster (confidence limits of theta, 0.0-0.19), D11S12 (theta, 0.0-0.23) and the insulin gene (theta, 0.0-0.11). These data and the gamma chain composition are consistent with HPFH in this family being caused by a mutation within the beta globin gene cluster.

DNA polymorphisms of the apolipoprotein genes--their use in the investigation of the genetic component of hyperlipidaemia and atherosclerosis

DNA probes for all eight of the major apolipoprotein genes are now available. The chromosomal location, the basic structure and in many cases the nucleotide sequences of the normal genes are known. Common DNA polymorphisms of all of the genes have been detected. These have been been used in a number of ways to investigate rare inherited defects of the apolipoprotein genes, to study the potential involvement of different variants of the genes in the development of hyperlipidaemia in patients, and to investigate the contribution of common variation in these genes in the determination of serum lipid levels in the normal population.

The prevention and avoidance of genetic disease: summing up

The preceding papers have dealt with major advances in understanding and detecting the mutational basis of human disease. If these advances are to be of practical benefit, systems of effective, efficient and acceptable delivery of the technology to the relevant population groups will need to be planned. In these delivery systems, the key figure is likely to be the clinical geneticist, still a somewhat shadowy figure, difficult to define: a doctor among scientists, and a scientist among doctors. The clinical geneticist, among other duties, acts as a user-friendly interface between the public (including the medical profession) and the conceptually quite difficult fields of modern genetics. Few people in this age of transition to computer literacy will underestimate the importance of a user-friendly interface, without which even the most powerful analytical machines are underused, error prone, or even incomprehensible.

A novel beta thalassemia gene with a single base mutation in the conserved polypyrimidine sequence at the 3' end of IVS 2

An adult Algerian patient with homozygous beta thalassemia was found to have a unique beta thalassemia gene. Cloning and sequencing revealed that the only abnormality present in this beta gene is a transversion in the polypyrimidine stretch at the 3' end of the large intervening sequence (IVS 2) six bases 5' to the consensus AG dinucleotide sequence (CCGCCCACAG instead of CCTCCCACAG). In addition, digestion of the cloned fragment by the enzyme Mnl I demonstrates the disappearance of a restriction site as expected. This is the first example of a defect in the consensus sequence at the 3' end of an IVS leading to a thalassemia phenotype presumably due to decreased splicing.

An erythroid specific nuclear factor binding to the proximal CACCC box of the beta-globin gene promoter

We have used the gel retardation and DNAase I assays to investigate the binding of nuclear proteins to the human beta-globin promoter. Upon incubation with beta-globin promoter fragments containing the duplicated CACCC boxes, nuclear proteins from human erythroid cells generate complexes yielding four retarded bands in acrylamide gels; the three slowest bands are common to both erythroid and non erythroid cells. The fast band is present only in K562 erythroleukemic cells induced to differentiation and hemoglobin accumulation and in fetal and adult erythroblasts, but absent in uninduced K562 cells. Binding occurs on a short DNA region including the proximal CACCC box, and is not significantly competed by excess gamma-globin fragments containing the CACCC box; the CACCC box appears to be essential for this binding, as shown by the failure of a fragment containing a natural beta-thalassemic mutation (-87, C----G) to bind significantly to nuclear factors. These data suggest that the erythroid specific CACCC binding factor might play a role in the developmental activation of beta-globin transcription.

DNA polymorphism and the study of disease associations

Recombinant DNA approaches to disease analysis may be as applicable to studies of disease association as they are to the analysis and diagnosis of single-gene defects. Population and/or family association analyses, using restriction fragment length polymorphisms around candidate genes as markers, have been employed to study conditions such as atherosclerosis and disease with an HLA-association. Progress made to date in disease-association studies using recombinant DNA methodology is reviewed, the rationale behind such studies is examined and associated problems and pitfalls discussed.

The CpG dinucleotide and human genetic disease

Reports of single base-pair mutations within gene coding regions causing human genetic disease were collated. Thirty-five per cent of mutations were found to have occurred within CpG dinucleotides. Over 90% of these mutations were C----T or G----A transitions, which thus occur within coding regions at a frequency 42-fold higher than that predicted from random mutations. These findings are consistent with methylation-induced deamination of 5-methyl cytosine and suggest that methylation of DNA within coding regions may contribute significantly to the incidence of human genetic disease.

The use of recombinant DNA techniques for the diagnosis of familial hypercholesterolaemia

In the UK, about 5% of patients with familial hypercholesterolaemia have a detectable deletion or rearrangement of part of the LDL-receptor gene. This results in the detection of shorter or abnormal sized fragments of the LDL-receptor gene in a Southern blot hybridization. This can be used to follow the inheritance of the defective gene, and for diagnosis in the families of these individuals. In the families of the rest of the patients, diagnosis may be possible using linked restriction fragment length polymorphisms (RFLPs) detected with the LDL-receptor probe. There are now ten common RFLPs of the LDL-receptor gene, with variable sites in the 3' half of the gene. Over 80% of patients are heterozygous for at least one of these RFLPs, and therefore potentially informative for DNA diagnosis. For a foetus at risk of homozygous familial hypercholesterolaemia, antenatal diagnosis may also be possible using these methods. However, family studies require samples to be available from affected or unaffected relatives of the patient, and this limits the applicability of the tests. For some mutations, the base pair change causing the defect in the LDL-receptor itself creates or destroys a site for a restriction enzyme. Such 'mutation-specific' RFLPs could be used for population screening, but so far have only been reported for the familial hypercholesterolaemia mutation that is common in Lebanon. In the future it may be possible to develop mutation-specific oligonucleotide probes for the diagnosis of familial hypercholesterolaemia. These would be appropriate for population screening or screening patients with hyperlipidaemia. This information may be useful if different mutations require different therapeutic strategies.

Molecular genetic approaches to the analysis of human ophthalmic disease

In this review of the recent literature, the contribution that the new techniques of molecular genetics has made in the analysis and diagnosis of human ophthalmic conditions is presented and discussed. Among the disorders reviewed are X-linked retinitis pigmentosa, Norrie's disease, gyrate atrophy and retinoblastoma, and there are also sections on crystallins and visual pigments.

Apolipoprotein CII (apo CII) gene expression defect in an individual with familial apo CII deficiency

We have examined the expression of the apolipoprotein CII (apo CII) gene in an individual with familial apo CII (apo CII) deficiency. Total RNA was prepared from this patient's liver tissue and analysed in Slot Blot and Northern Blot experiments using a cloned apo CII cDNA as a probe. In this patient, there is at least a four-fold decrease in the level of apo CII mRNA, when compared to liver tissue from a control individual. The residual apo CII mRNA detected in this patient is of normal length. These results suggest that the failure to detect apo CII protein in this patient's serum is not due to a failure to transcribe or process apo CII mRNA, but probably to a defect in the translation of the apo CII message. This defect results in partial degradation of the apo CII message leading to the much reduced levels which we have observed.

Beta-thalassaemia in Campania: DNA polymorphism analysis in beta A and beta thal chromosomes and its usefulness in prenatal diagnosis

In order to evaluate the feasibility of first trimester prenatal diagnosis of beta-thalassaemia by restriction fragment length polymorphism (RFLP) in Campania, one of the most affected regions in Southern Italy, DNA polymorphism analysis was performed on 40 unrelated patients, affected with homozygous beta-thalassaemia, and on their parents. Frequency of the presence of the Hinc II epsilon, Hind III G gamma and A gamma, Hinc II psi beta and 3' psi beta, Ava II psi beta, Ava II beta and Bam HI 3' beta sites have been determined in the beta A and beta thal chromosome samples. In 31 families (over 75%), RFLPs enabled tracing the beta-thalassaemia mutations in both father and mother (100% diagnosis). In the remaining nine families, RFLPs enabled tracing only one of the two mutations (50% diagnosis) because the other parent was found to be homozygous in all the analysed polymorphic sites. Restriction haplotypes, assembled on the basis of linkage analysis, were most heterogeneous, hence a wide heterogeneity of mutations is expected.

Disorders of haemoglobin in China

A large scale survey of haemoglobinopathies and thalassaemia has been carried out in China, involving 900,000 people in 28 provinces. It has resulted in the finding of many new variants and some interesting cases of thalassaemia, and in a study on the chemical structure of abnormal haemoglobins and DNA analysis of thalassaemia. We report here data on haemoglobin disorders in the Chinese, mainly the characterisation of the geographical distribution of haemoglobin variants, the analysis of globin genes of alpha, beta, gamma, or delta beta thalassaemia, and the progress in prenatal diagnosis of alpha and beta thalassaemia conducted in the authors' laboratory.

DNA analysis for antenatal diagnosis of thalassaemia and haemophilia

Two years' experience with DNA analysis for the antenatal diagnosis of thalassaemia and haemophilia is described. The advantages of DNA testing, including a first-trimester diagnosis and greater availability, must be considered in relation to the problems that are associated with this procedure. In particular, the risk of recombination in DNA polymorphism studies should be understood and explained fully to the patient.

DNA polymorphisms in human population studies: a review

The use of restriction endonucleases and DNA probes to expand the range of informative polymorphisms should be of immense value in the study of human populations. To date, this approach has been only minimally used, but results are available for markers in the major histocompatibility complex and the globin gene clusters. In addition, isolated studies using other probes have been published. The ease of the techniques involved, the rate at which new DNA polymorphisms are being found and the range of information provided should ensure that use of this approach expands rapidly.

A benign form of thalassaemia intermedia may be determined by the interaction of triplicated alpha locus and heterozygous beta-thalassaemia

In this paper we report that the combination of a triplicated alpha globin locus with heterozygous beta-thalassaemia produces a clinical phenotype of thalassaemia intermedia in five Italian subjects from four unrelated families, while in two other cases the phenotype was thalassaemia minor. The haematological findings of the five patients were uniform, producing a benign form of thalassaemia intermedia, transfusion independent, with a long life expectancy. The pattern of inheritance of the two genetic determinants and the more pronounced beta/alpha globin chain imbalance, demonstrates that the genetic combination is indeed the cause of the phenotype. The pattern of restriction enzyme site polymorphisms suggests the presence of the beta IVS I 110 G----A mutation at least in three of these cases.

Unequal crossing-over between two alu-repetitive DNA sequences in the low-density-lipoprotein-receptor gene. A possible mechanism for the defect in a patient with familial hypercholesterolaemia

We have previously identified a patient with familial hypercholesterolaemia (FH), where the defect appears to be caused by a deletion in the 3' region of the low-density lipoprotein (LDL)-receptor gene. We have now isolated the LDL-receptor gene from the patient and have studied the defect at the DNA level. Restriction mapping and sequence analysis demonstrate that a 4-kb DNA deletion has occurred between two alu-repetitive sequences that are in the same orientation, one in intron 12 and the other in intron 14. This deletion eliminates exons 13 and 14, and changes the reading frame of the resulting spliced mRNA such that a stop codon is created in the following exon. Immuno- and ligand-blot analysis using cultured fibroblasts from this patient revealed the normal gene product, but failed to detect any smaller receptor protein. This implies that the truncated receptor protein that is synthesised is rapidly degraded. We suggest that in this patient the deletion is caused by an unequal crossing-over event that occurred between two homologous chromosomes at meiosis.

Characteristics of beta A chromosome haplotypes in Japanese

DNA polymorphism patterns linked to the beta A-globin gene were analyzed in healthy Japanese using four different restriction endonucleases. The chromosomes with the beta A-globin gene were mapped through an evaluation of the presence of seven different restriction sites (HincII 5' to epsilon; HindIII in G gamma and A gamma; HincII in, and 3' to, psi beta 1; AvaII in beta; Bam-HI 3' to beta). Among 36 chromosomes analyzed, 20 chromosomes had a haplotype of [+-----+]. Among 55 individuals examined, 7 possessed a homozygous haplotype of [+-----+]. All Japanese with the A gamma T-globin gene had a subhaplotype of [-++-+] 5' to the delta-globin gene. Their major haplotypes were [-++-+-+] and [-++-++-]. It was expected that the presence of the A gamma T-globin gene in Japanese may be deduced from subhaplotypes 5' to the delta-globin gene.

Nucleotide sequence of the beta-globin genes in gorilla and macaque: the origin of nucleotide polymorphisms in human

Part of the beta-globin genes of Macaca cynomolgus and Gorilla gorilla has been cloned and sequenced. Ten putatively neutral nucleotide polymorphisms have been described at the beta-globin locus in humans. They are associated in seven combinations, which define seven different haplotypes of the beta-globin gene: four major frameworks--1, 2, 3, and 3--and three minor frameworks, which we term KI1, KA1, and OR1. The nucleotide sequences of these frameworks are compared with those of homologous sequences in chimpanzee, colobus, macaque, and gorilla. This comparison provides strong evidence that framework 2 was the earliest framework in the human lineage. From framework 2, a rooted parsimonious tree for the six other frameworks is constructed. This phylogenetic tree is discussed in terms of the evolution of nucleotide polymorphisms as well as in terms of genetic affinities between human populations. For each position at which there is base difference in comparing human, gorilla, and chimpanzee beta-globin genes, the phyletic lineage where the corresponding substitution occurred has been identified using the maximum parsimony procedure. The data provide evidence that polymorphisms may represent a significant component of differences between closely related species. If so, nucleotide polymorphisms may strongly bias estimates of small evolutionary distances.

Nucleotide sequence of the delta-beta-globin intergenic segment in the macaque: structure and evolutionary rates in higher primates

A 5600-base-pair (bp) fragment including the beta-globin gene and about 4000 bp of its 5' flanking sequence was cloned from the DNA of Macaca cynomolgus (an Old World monkey), and the 5' flanking region was sequenced. Comparison with human, chimpanzee, mouse, rabbit, and Xenopus orthologous sequences reveals a tandemly repeated sequence called RS4 at the same position (about 500 bp 5' from the transcription start of the adult beta-globin gene) in all six species. We suggest that a tandemly repeated sequence has been maintained by functional constraints since the divergence between amphibians and reptiles. Excluding tandemly repeated sequences as well as about 400 nucleotides upstream from the cap site, the average base substitution frequencies among human, chimpanzee, and macaque intergenic sequences were calculated. They appear to be strongly correlated with the delta T50 values measured between the corresponding nuclear DNAs. They are also similar to base substitution frequencies calculated by Chang and Slightom (1984) at the pseudo-eta-globin locus. Thus, exclusion of sequences involved in specific modes of variation might allow the use of intergenic sequences for the accurate calculation of genetic distances. Using a time scale based on the dating of the Atlantic split, we estimate the base substitution rate of primate noncoding DNA to be 1.0 X 10(-9) substitution/site/year.

Variable number of tandem repeat (VNTR) markers for human gene mapping

A large collection of good genetic markers is needed to map the genes that cause human genetic diseases. Although nearly 400 polymorphic DNA markers for human chromosomes have been described, the majority have only two alleles and are thus uninformative for analysis of genetic linkage in many families. A few known marker systems, however, detect loci that respond to restriction enzyme cleavage by producing a fragment that can have many different lengths. This polymorphism is due to variation in the number of tandem repeats of a short DNA sequence. Because most individuals will be heterozygous at such loci, these markers will provide linkage information in almost all families. Ten oligomeric sequences derived from the tandem repeat regions of the myoglobin gene, the zeta-globin pseudogene, the insulin gene, and the X-gene region of hepatitis B virus, were used to develop a series of single-copy probes. These probes revealed new, highly polymorphic genetic loci whose allele sizes reflected variation in the number of tandem repeats.

Association of thalassaemia intermedia with a beta-globin gene haplotype

We have identified 14 Asian patients with homozygous beta zero thalassaemia who had a mild clinical disorder related to an augmented production of haemoglobin F. None of their parents had an elevated level of Hb F. Restriction fragment length polymorphism analysis of the beta-globin cluster of these patients and a control group of Asian thalassaemia major patients showed that 6/14 of the thalassaemia intermedia patients were homozygous for a particular 5' beta-globin haplotype (-+-++), in contrast to 1/42 of the thalassaemia major patients. Furthermore, the -+-++ beta haplotype is also associated with amelioration of disease severity in beta thalassaemia in an Italian population. This beta haplotype is linked to a DNA sequence variation 5' (at position -158) to the G gamma globin gene which can be detected by the presence (+) of an Xmn I restriction enzyme site. The possible role of the Xmn I-gamma polymorphism in relation to this variant HPFH is discussed. We conclude that much of the observed clinical variability of beta thalassaemia can now be explained by the inheritance of beta thalassaemia chromosomes with different propensities for fetal haemoglobin production.

DNA polymorphic patterns and haplotype arrangements of the apo A-1, apo C-III, apo A-IV gene cluster in different ethnic groups

The allelic frequency of five different restriction fragment length polymorphisms (RFLPs) in the A-1, C-III, A-IV gene region has been determined in Caucasians, Negroes, Indian Asians, and Japanese. The polymorphic sites are with Taq-1 at the 5' end of the A-1 gene, with Msp-1 in the third intron of the A-1 gene, with Pst-1 in the intergenic sequence between the A-1 and C-III genes, with Sst-1 in the 3' non-coding region of the C-III gene, and with Pvu-II in the third intron of the C-III gene. The alleles identified by three of the RFLPs showed large differences in frequency amongst the races, especially between Caucasians and non-Caucasians. Alleles of the Msp-1 polymorphism and Sst-1 polymorphism, which were rare in Caucasians (frequencies 0.03 and 0.01), were more common in Japanese (frequencies 0.37 and 0.35), Indian Asians (frequencies 0.37 and 0.26), and Negroes (frequencies 0.31 and 0.31). In contrast with a Pvu-II polymorphism one allele was rare in Japanese and in Indian Asians (frequency 0.01) but more common in Caucasians (frequency 0.11). Linkage disequilibrium was evident between some of the alleles and a total of seven haplotypes were identified among the different races.

Alpha-thalassemia haplotypes in the Algerian population

DNA mapping was performed in seven unrelated Hb H patients and nine carriers for alpha-thalassemia trait originating from Algeria. This study has allowed us to identify four alpha-thalassemia haplotypes: the (-alpha 3.7) haplotype, which is the most frequent (18 of 23 alpha-thalassemic chromosomes), the (-(alpha)20.5) haplotype, a (--) haplotype, and an (alpha alpha)T haplotype. Our results also show that the (-alpha 3.7) haplotypes encountered in the Algerian population are heterogeneous and differ by the site of the unequal crossover responsible for the 3.7-kb deletion and the size of the interzeta fragment. In addition, during this survey we observed that normal chromosomes bearing a polymorphic BglII site are associated with different interzeta fragments.

DNA polymorphism patterns in the beta-globin gene cluster in the Japanese population

Restriction site polymorphisms in the beta-globin gene cluster on chromosome #11 were analyzed in healthy Japanese. The beta A chromosomes were mapped by scoring the presence (+) or the absence (-) of seven different restriction sites (Hinc II site 5' to the epsilon-globin gene; Hind III sites in the G gamma- and A gamma-globin genes; Hinc II sites in and 3' to the psi beta 1-globin gene; Ava II site in the beta-globin gene; Bam HI site 3' to the beta-globin gene). No chromosomes with [- +] for two Hind III sites in the G gamma- and A gamma-globin genes, or those with [+ -] for two Hinc II sites in and 3' to the psi beta 1-globin gene, were observed. It was observed that homozygosity for the presence of the Hinc II site 5' to the epsilon-globin gene (+/+) always accompanied the homozygosity for the absence of the Hinc II sites in and 3' to the psi beta 1-globin gene (--/--). Almost all A gamma T chromosomes possessed a subhaplotype [- + + - +] 5' to the beta-globin gene. More than half of the beta A chromosomes observed in the Japanese showed haplotype VII, which may be characteristic for Asians. It was deduced that frameworks 1, 2, and 3 of the beta-globin gene in the Japanese comprised 16%, 18%, and 66%, respectively.

Oligonucleotide screening of beta thalassemia mutations in the south east of France

France is a non-endemic region for beta thalassemia. In this country, the sporadic cases of Cooley's disease encountered affect almost constantly subjects of Mediterranean origin. In this report, we have screened, using oligonucleotide probes, the distribution of the main beta thalassemia mutations present in the population of South-eastern France whose origins lie in the mixing of several Mediterranean ethnic groups. Among 105 beta thalassemia chromosomes, we have observed a limited number of alleles, since, by using oligonucleotide probes for six mutations, we have characterized the molecular defect in 90% of the chromosomes. The four main mutations were found in more than 85% of the chromosomes and the others in about 5%. The distribution of the beta thalassemia mutations within the various ethnic groups was determined.

Exclusion of autosomal dominant dystonia gene from large regions of chromosomes 11p, 13q, and 21q by multi-point linkage analysis

Multi-point linkage analyses of autosomal dominant form of torsion dystonia with linkage groups on chromosomes 11p, 13q, 21q are reported. Analyses are based on family data from a single, large, non-Jewish pedigree. Large portions of chromosomes 11p and 13q, and virtually the entire long arm of chromosome 21 are excluded from linkage with dystonia. Practical aspects of designing multi-point analyses are discussed.

A new strategy for mapping the human genome

Recent advances in agarose gel electrophoresis of large DNA fragments raise the possibility of an entirely new approach to mapping mammalian genomes. In this article is discussed the potential of this technology for tackling problems such as construction of linkage maps, identifying chromosome translocation breakpoints, and moving from linked markers to genes causing diseases such as the muscular dystrophies and Huntington's chorea.

Beta thalassemia due to a novel mutation in IVS 1 sequence donor site consensus sequence creating a restriction site

During a systematic screening of Algerian thalassemics by determining the DNA polymorphism haplotypes in the beta globin gene cluster, a novel haplotype was identified. The DNA of a homozygous individual was cloned and sequenced. The mutation, a G----A change, at position 5 of the small intervening sequence, probably interferes with normal splicing events, and, moreover, creates a new Eco RV restriction site that provides a useful diagnostic tool for detecting this condition.

The evolution of the alpha- and beta-globin gene clusters in human populations

DNA analysis of the alpha- and beta-globin gene clusters has revealed substantial variability between individuals and populations. As well as restriction enzyme site and length polymorphisms, variation in gene copy number and type is observed. Because of this extensive polymorphism DNA analysis offers a highly informative method of studying genetic affinities between human populations. Haplotypes, consisting of a set of restriction enzyme polymorphisms distributed along the cluster, have been developed for both loci. Analysis of the molecular basis of numerous beta-thalassaemia alleles has revealed, in general, different sets of mutations in different populations, indicating that these postdate the racial divergence. Recent microepidemiological studies on the distribution of alpha-thalassaemia support the hypothesis that this condition, like the beta s-mutation, has been selected because it confers protection against malaria. Population-specific DNA polymorphisms at these and other loci promise to be of considerable value to genetic anthropology.

The isolation of genomic recombinants for the human apolipoprotein B gene and the mapping of three common DNA polymorphisms of the gene--a useful marker for human chromosome 2

We have used four independently isolated cDNA probes for human apolipoprotein B (apo B), to isolate overlapping genomic recombinants for the 3' portion of the apo B gene. The cDNA clones and a unique fragment from the genomic recombinant have been used to identify the human apo B gene in DNA from a series of rodent X human somatic cell hybrids. Our results provide evidence for the assignment of this gene to the short arm of human chromosome 2 (p23-pter). We have used the cDNA probes to identify three common DNA polymorphisms. The first, detected with the restriction enzyme XbaI and our probe pAB4, has a rare allele frequency of 0.48. The other two polymorphisms are detected with the probe pAB3. The enzyme MspI detects at least three alleles, with frequencies of 0.67, 0.16 and 0.15, while that detected with the enzyme EcoRI has a rare allele frequency of 0.12. The relative position of these polymorphisms has been mapped using the genomic recombinants. Investigation of a small number of haplotypes indicates that there is linkage equilibrium between the polymorphisms, which have a total polymorphism information content (PIC) value of more than 0.8. These polymorphisms will provide useful markers for genetic studies on chromosome 2 and for the analysis of the involvement of variants of the apo B gene in the development of hyperlipidaemia.

Analysis of the human alpha-globin gene cluster reveals a highly informative genetic locus

Extensive molecular studies have characterized 15 dimorphic and 2 multiallelic genetic markers within the human alpha-globin gene cluster. Analysis of these markers in 9 populations has shown that the alpha-globin locus is remarkably polymorphic and is therefore an ideal marker on chromosome 16 for the construction of a human genetic linkage map. The combined analysis of 9 polymorphic markers has established alpha-globin haplotypes that provide the means to study the molecular genetics and common mutants of this cluster. The novel association of a conventional restriction fragment length polymorphism haplotype and linked, hypervariable regions of DNA should allow a comparison of the rate of change of such markers.

A silent deletion in the beta-globin gene cluster

A survey of the gamma-globin gene region of over 1000 normal individuals revealed a novel 2.5 kb deletion which removes the 5' end of the A gamma-globin gene. Unusually, this deletion in the beta-globin gene cluster is not associated with increased fetal haemoglobin production. Sequence analysis of the deletion endpoints revealed no significant homology at the breakpoint and failed to support a role for a proposed recombination hotspot in IVS-2 in the generation of this illegitimate recombination event. The existence of small "silent" deletions in the beta-globin gene cluster emphasizes the importance of deletion size in altering expression of the fetal globin genes.

There are two gene sequences for human apolipoprotein CI (apo CI) on chromosome 19, one of which is 4 kb from the gene for apo E

A cDNA probe corresponding to the mRNA sequence for apolipoprotein E (apo E) was used to screen two independently-constructed human genomic libraries. Two recombinants (lambda E-2, and lambda E2-1), isolated using the apo E cDNA probe, also contain part or all of the apo CI gene. Hybridisation studies using both apo E and apo CI cDNA probes show that these two genes are in the same orientation and separated by 4 kb.

Diagnosis of genetic disease using recombinant DNA

Recombinant DNA technology promises to make an important contribution to the analysis and diagnosis of inherited human disease. Direct detection and analysis of various genetic defects at the DNA level are now possible using cloned gene or oligonucleotide probes. In addition, the use of restriction fragment length polymorphisms associated with linked DNA segments should permit not only the diagnosis of hitherto undetectable disease states but also the chromosomal localization of the loci responsible. The eventual isolation of disease loci should lead to a better understanding of the molecular basis of inherited disease.

Estimation of linkage disequilibrium from conditional haplotype data: application to beta-globin gene cluster in American blacks

Simple estimators of gene frequencies and linkage disequilibria are proposed when haplotype data are available from four parental chromosomes of a child (or fetus) for whom genetic counseling is sought for a disease condition. The method is illustrated with restriction site polymorphisms associated with sickle-cell anemia (Hb-beta S) gene as surveyed in genetic counseling data from American blacks. The method suggested here is shown to be useful in testing for the significance of interactions of site-specific variations of any order in the chromosomal region assayed.

DNA-polymorphic patterns linked to the beta-globin genes in German families affected with hemoglobinopathies and thalassemias: a comparison to other ethnic groups

DNA haplotype constellations of the beta-globin gene cluster have been analyzed in German families with hemoglobinopathies (Hb Freiburg, Hb Köln, Hb Presbyterian) and beta-thalassemias. The polymorphic patterns obtained were compared to those found in families from Greece, Italy, and Turkey affected by beta-thalassemia syndromes. With the combined analysis of seven restriction site polymorphisms a DNA-diagnostic prediction for additional offspring could be made with an overall frequency of 75% in the four ethnic groups.

Hemophilia A. Detection of molecular defects and of carriers by DNA analysis

To understand the molecular basis of hemophilia A and to provide heterozygote detection and prenatal diagnosis by DNA analysis, we used cloned factor VIII:C DNA fragments to study 10 affected families. In four of these families, inhibitors of factor VIII:C had developed in affected persons. In one such family a deletion of approximately 80 kb within the factor VIII:C gene was identified. Carriers of the deletion were identified through detection of an abnormal DNA fragment located at the deletion end points. In another family a single nucleotide change in the coding region of the factor VIII:C gene produced a nonsense codon leading to premature termination of factor VIII:C synthesis. Carrier detection was performed in eight female members of this four-generation family. In a third family a small change in the size of a restriction-endonuclease fragment correlated with the presence of the mutant gene, and in the other seven families the molecular defect has not yet been identified. In addition, we used two common polymorphic sites in the factor VIII:C gene to differentiate the normal from the defective gene in four of six obligate female carriers from families with patients in whom inhibitors did not develop. Carrier detection was possible in other members of these families. These data suggest that DNA analysis of the factor VIII:C gene provides an accurate method of carrier detection and, potentially, of prenatal diagnosis in at least 50 per cent of the pedigrees affected by hemophilia A.

A common DNA polymorphism of the low-density lipoprotein (LDL) receptor gene and its use in diagnosis

A cloned gene probe coding for the low-density lipoprotein (LDL) receptor was used to detect a restriction fragment length polymorphism with the enzyme Pvu II. The frequency of the rare allele is approximately 0.2 both in normal controls and individuals with familial hypercholesterolaemia (FH). About 30% of individuals are heterozygous for the polymorphism, and are potentially informative for family studies and for early diagnosis of FH. This polymorphism was used to follow the inheritance of the LDL receptor gene in two families with FH. In these families, the polymorphism co-segregates with the disease unambiguously, and therefore can be used for early diagnosis.