Application of endonuclease mapping to the analysis and prenatal diagnosis of thalassemias caused by globin-gene deletion

Genomic Diagnosis for Pediatric Disorders: Revolution and Evolution

Powerful, recent advances in technologies to analyze the genome have had a profound impact on the practice of medical genetics, both in the laboratory and in the clinic. Increasing utilization of genome-wide testing such as chromosomal microarray analysis and exome sequencing have lead a shift toward a "genotype-first" approach. Numerous techniques are now available to diagnose a particular syndrome or phenotype, and while traditional techniques remain efficient tools in certain situations, higher-throughput technologies have become the de facto laboratory tool for diagnosis of most conditions. However, selecting the right assay or technology is challenging, and the wrong choice may lead to prolonged time to diagnosis, or even a missed diagnosis. In this review, we will discuss current core technologies for the diagnosis of classic genetic disorders to shed light on the benefits and disadvantages of these strategies, including diagnostic efficiency, variant interpretation, and secondary findings. Finally, we review upcoming technologies posed to impart further changes in the field of genetic diagnostics as we move toward "genome-first" practice.

The unsolved rare genetic disease atlas? An analysis of the unexplained phenotypic descriptions in OMIM®

For years, the genetics community has estimated the number of individual rare genetic diseases to be approximately 6,000-8,000. A commonly quoted derivation of this estimate is based on the simple addition of the number of phenotypic entries with and without confirmed molecular etiologies in the Online Mendelian Inheritance in Man (OMIM®). Here, we examine the validity of this estimation by mining the phenotypic entries in OMIM that are of likely or suspected Mendelian inheritance without a molecular cause (MIM number prefix "%" or "null"). Of the 3,204 unsolved phenotypic entries in OMIM, only two-thirds (2,034 entries) represented rare diseases. Of these, 8% were considered "well-established" based on their description in commonly used reference textbooks. We hypothesize based on the large proportion of entries that represent single families reported prior to 2011, that a number of the unsolved entries represent pathogenic variants in known genes. The novel gene discovery potential of these entries is therefore likely lower than originally thought. Given that the majority of the ~300 new disease-gene associations curated each year by OMIM were never associated with a "%" or "null" sign, the true scope of the rare disease atlas is likely much larger than previously anticipated.

Traditional Prenatal Diagnosis: Past to Present

In the nearly 60 years since prenatal diagnosis for genetic disease was first offered, the field of prenatal diagnosis has progressed far past rudimentary uterine puncture to provide fetal material to assess gender and interpret risk. Concurrent with the improvements in invasive fetal sampling came technological advances in cytogenetics and molecular biology that widened both the scope of genetic disorders that could be diagnosed and also the resolution at which the human genome could be interrogated. Nowadays, routine blood work available to all pregnant women can determine the risk for common chromosome abnormalities; chorionic villus sampling (CVS) and amniocentesis can be used to diagnose nearly all conditions with a known genetic cause; and the genome and/or exome of a fetus with multiple anomalies can be sequenced in an attempt to determine the underlying etiology. This chapter will discuss some of the major advances in prenatal sampling and prenatal diagnostic laboratory techniques that have occurred over the past six decades.

Diagnostic exome sequencing to elucidate the genetic basis of likely recessive disorders in consanguineous families

Rare, atypical, and undiagnosed autosomal-recessive disorders frequently occur in the offspring of consanguineous couples. Current routine diagnostic genetic tests fail to establish a diagnosis in many cases. We employed exome sequencing to identify the underlying molecular defects in patients with unresolved but putatively autosomal-recessive disorders in consanguineous families and postulated that the pathogenic variants would reside within homozygous regions. Fifty consanguineous families participated in the study, with a wide spectrum of clinical phenotypes suggestive of autosomal-recessive inheritance, but with no definitive molecular diagnosis. DNA samples from the patient(s), unaffected sibling(s), and the parents were genotyped with a 720K SNP array. Exome sequencing and array CGH (comparative genomic hybridization) were then performed on one affected individual per family. High-confidence pathogenic variants were found in homozygosity in known disease-causing genes in 18 families (36%) (one by array CGH and 17 by exome sequencing), accounting for the clinical phenotype in whole or in part. In the remainder of the families, no causative variant in a known pathogenic gene was identified. Our study shows that exome sequencing, in addition to being a powerful diagnostic tool, promises to rapidly expand our knowledge of rare genetic Mendelian disorders and can be used to establish more detailed causative links between mutant genotypes and clinical phenotypes.

Human genetics and genomics a decade after the release of the draft sequence of the human genome

Substantial progress has been made in human genetics and genomics research over the past ten years since the publication of the draft sequence of the human genome in 2001. Findings emanating directly from the Human Genome Project, together with those from follow-on studies, have had an enormous impact on our understanding of the architecture and function of the human genome. Major developments have been made in cataloguing genetic variation, the International HapMap Project, and with respect to advances in genotyping technologies. These developments are vital for the emergence of genome-wide association studies in the investigation of complex diseases and traits. In parallel, the advent of high-throughput sequencing technologies has ushered in the 'personal genome sequencing' era for both normal and cancer genomes, and made possible large-scale genome sequencing studies such as the 1000 Genomes Project and the International Cancer Genome Consortium. The high-throughput sequencing and sequence-capture technologies are also providing new opportunities to study Mendelian disorders through exome sequencing and whole-genome sequencing. This paper reviews these major developments in human genetics and genomics over the past decade.

Thalassemia: an overview of 50 years of clinical research

The thalassemias are attributable to the defective production of the α- and β-globin polypeptides of hemoglobin. Significant discoveries have illuminated the pathophysiology and enhanced the prevention and treatment of the thalassemias, and this article reviews many of the advances that have occurred in the past 50 years. However, the application of new approaches to the treatment of these disorders has been slow, particularly in the developing world where the diseases are common, but there is definite progress. This article emphasizes how the increasing knowledge of cellular and molecular biology are facilitating the development of more effective therapies for these patients.

Mutations in the promoter region of the aldolase B gene that cause hereditary fructose intolerance

Hereditary fructose intolerance (HFI) is a potentially fatal inherited metabolic disease caused by a deficiency of aldolase B activity in the liver and kidney. Over 40 disease-causing mutations are known in the protein-coding region of ALDOB. Mutations upstream of the protein-coding portion of ALDOB are reported here for the first time. DNA sequence analysis of 61 HFI patients revealed single base mutations in the promoter, intronic enhancer, and the first exon, which is entirely untranslated. One mutation, g.-132G>A, is located within the promoter at an evolutionarily conserved nucleotide within a transcription factor-binding site. A second mutation, IVS1+1G>C, is at the donor splice site of the first exon. In vitro electrophoretic mobility shift assays show a decrease in nuclear extract-protein binding at the g.-132G>A mutant site. The promoter mutation results in decreased transcription using luciferase reporter plasmids. Analysis of cDNA from cells transfected with plasmids harboring the IVS1+1G>C mutation results in aberrant splicing leading to complete retention of the first intron (~5 kb). The IVS1+1G>C splicing mutation results in loss of luciferase activity from a reporter plasmid. These novel mutations in ALDOB represent 2% of alleles in American HFI patients, with IVS1+1G>C representing a significantly higher allele frequency (6%) among HFI patients of Hispanic and African-American ethnicity.

A life-long quest to understand and treat genetic blood disorders

This year's Lasker-Koshland Special Achievement Award in Medical Science is conferred on Sir David Weatherall for his 50 years of dedication to biomedical research, his groundbreaking discoveries about genetic blood diseases, and his life-long passion for bringing improved medical care to the developing world.

Genes, mutations, and human inherited disease at the dawn of the age of personalized genomics

The number of reported germline mutations in human nuclear genes, either underlying or associated with inherited disease, has now exceeded 100,000 in more than 3,700 different genes. The availability of these data has both revolutionized the study of the morbid anatomy of the human genome and facilitated "personalized genomics." With approximately 300 new "inherited disease genes" (and approximately 10,000 new mutations) being identified annually, it is pertinent to ask how many "inherited disease genes" there are in the human genome, how many mutations reside within them, and where such lesions are likely to be located? To address these questions, it is necessary not only to reconsider how we define human genes but also to explore notions of gene "essentiality" and "dispensability."Answers to these questions are now emerging from recent novel insights into genome structure and function and through complete genome sequence information derived from multiple individual human genomes. However, a change in focus toward screening functional genomic elements as opposed to genes sensu stricto will be required if we are to capitalize fully on recent technical and conceptual advances and identify new types of disease-associated mutation within noncoding regions remote from the genes whose function they disrupt.

Increased prevalence of mutant null alleles that cause hereditary fructose intolerance in the American population

Mutations in the aldolase B gene (ALDOB) impairing enzyme activity toward fructose-1-phosphate cleavage cause hereditary fructose intolerance (HFI). Diagnosis of the disease is possible by identifying known mutant ALDOB alleles in suspected patients; however, the frequencies of mutant alleles can differ by population. Here, 153 American HFI patients with 268 independent alleles were analyzed to identify the prevalence of seven known HFI-causing alleles (A149P, A174D, N334K, Delta4E4, R59Op, A337V, and L256P) in this population. Allele-specific oligonucleotide hybridization analysis was performed on polymerase chain reaction (PCR)-amplified genomic DNA from these patients. In the American population, the missense mutations A149P and A174D are the two most common alleles, with frequencies of 44% and 9%, respectively. In addition, the nonsense mutations Delta4E4 and R59Op are the next most common alleles, with each having a frequency of 4%. Together, the frequencies of all seven alleles make up 65% of HFI-causing alleles in this population. Worldwide, these same alleles make up 82% of HFI-causing mutations. This difference indicates that screening for common HFI alleles is more difficult in the American population. Nevertheless, a genetic screen for diagnosing HFI in America can be improved by including all seven alleles studied here. Lastly, identification of HFI patients presenting with classic symptoms and who have homozygous null genotypes indicates that aldolase B is not required for proper development or metabolic maintenance.

Alpha-thalassaemia

Alpha-thalassaemia is one of the most common human genetic disorders. Couples in which both partners carry alpha(0)-thalassaemia traits have a 25% risk of having a fetus affected by homozygous alpha-thalassaemia or haemoglobin Bart's disease, with severe fetal anaemia in utero, hydrops fetalis, stillbirth or early neonatal death, as well as causing various maternal morbidities. This disorder is common in southeast Asia and southern China, and the expanding populations of southeast Asian immigrants in the US, Canada, UK and Europe mean that this disorder is no longer rare in these countries.

Thalassemia: The Continued Challenge

This overview describes the history of transfusion therapy and consequent iron overload in thalassemia. It emphasizes the importance of measurement of hepatic iron and reviews the history of chelation therapy. It briefly describes the discoveries of the genetic basis of thalassemia and the application of that knowledge in prenatal diagnosis. The review goes on to emphasize pharmaceutical efforts to induce fetal hemoglobin synthesis in thalassemic red cells and ends with a discussion of oral iron chelators, stem cell transplant, and the status of gene therapy.

The detection of large deletions or duplications in genomic DNA

While methods for the detection of point mutations and small insertions or deletions in genomic DNA are well established, the detection of larger (>100 bp) genomic duplications or deletions can be more difficult. Most mutation scanning methods use PCR as a first step, but the subsequent analyses are usually qualitative rather than quantitative. Gene dosage methods based on PCR need to be quantitative (i.e., they should report molar quantities of starting material) or semi-quantitative (i.e., they should report gene dosage relative to an internal standard). Without some sort of quantitation, heterozygous deletions and duplications may be overlooked and therefore be under-ascertained. Gene dosage methods provide the additional benefit of reporting allele drop-out in the PCR. This could impact on SNP surveys, where large-scale genotyping may miss null alleles. Here we review recent developments in techniques for the detection of this type of mutation and compare their relative strengths and weaknesses. We emphasize that comprehensive mutation analysis should include scanning for large insertions and deletions and duplications.

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.

Molecular analysis of common aldolase B alleles for hereditary fructose intolerance in North Americans

The diagnosis of hereditary fructose intolerance (HFI) presents a difficult challenge that often involves procedures of high risk to the patient. A relatively noninvasive method that involves molecular analysis of common alleles would offer a decided advantage. The molecular defects in the aldolase B gene were studied in 31 HFI subjects (23 pedigrees, 47 apparently independent alleles) from the United States and Canada. We screened for the three most common European alleles by direct hybridization of allele-specific oligodeoxyribonucleotides (ASOs) to portions of the aldolase B gene that were amplified by PCR. Fifty-five percent of mutant North American alleles were A149P (ala149----pro), the most common mutation in the European population. The other two alleles, A174D (ala174----asp) and N334K (asn334----lys), represent 11 and 2% of North American alleles, respectively. Nine patients, representing 32% of independent alleles studied, had an HFI allele that was not of this common missense class. This North American allele distribution is significantly different from that in Europe, where 13% of HFI alleles are not of this type. Preliminary screening of amplified DNA with this set of ASOs indicated that 80% of symptomatic HFI patients can be identified in the American population by this simple genetic test.

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Beta-thalassemia in Turkey

A review is presented of the various beta-thalassemia alleles observed in nearly 191 patients with beta-thalassemia major and their 182 heterozygous relatives. Determination was by gene amplification and dot-blot hybridization with synthetic probes, specific for 27 different mutations. Eighteen mutations have been observed; six of these account for nearly 83% of all thalassemia abnormalities. A new mutation, i.e. a G----C mutation at the acceptor splice site of IVS-I, was found in one teenager who was homozygous for this disease. The high consanguinity among the families was considered the main reason for the high number of patients with a homozygosity for the IVS-I-110 (G----A) mutation. Combinations of different mutations were present in many patients; some were mildly affected because of the specific mutation present on one chromosome. Combinations of classical beta-thalassemia and an abnormal hemoglobin mainly concerned Hb S. Hbs Knossos and Lepore were rare occurrences. A comparison of hematological data for adults with heterozygosities for some of the common alleles confirmed the low Hb A2 values in IVS-I-6 (T----C) heterozygotes and the high Hb F values for codon 8 (-AA), IVS-II-1 (G----A), and IVS-I-1 (G----A) heterozygotes.

Prenatal diagnosis of inherited hemoglobinopathies

This paper reviews the methodology available to make prenatal diagnosis of inherited hemoglobinopathies by DNA analysis and the strategy to be used for the large scale application of this procedure to high-risk populations. The most straightforward approach for prenatal diagnosis is nowadays based on the analysis of DNA enzymatically amplified by the polymerase chain reaction (PCR). The mutations, produced by gross structural rearrangement of the DNA and those affecting a restriction recognition site, are directly detected by visualization following ethidium bromide staining of the electrophoretic pattern resulting from enzymatic digestion of amplified DNA. The remaining ones are detected by dot blot analysis with allelic specific oligonucleotide probes. Because in each population a limited number of specific beta-thalassemia mutations are prevalent, prenatal diagnosis by DNA analysis may be carried out by a population-specific strategy based on the amplification of those regions of the beta-globin genes containing the mutations most frequently occurring in each population followed by dot blot analysis with allelic specific oligonucleotide probes. This approach has the great advantage of being very simple, because radioactive probes are not necessary, very rapid, the results being obtained within 24 hours from sampling and very sensitive, only a limited amount of DNA in the order of 50 ng being necessary.

Prenatal diagnosis of homozygous alpha 0-thalassaemia by direct DNA analysis of chorionic villi in Singapore

First-trimester prenatal diagnosis by DNA analysis was carried out for seven pregnancies at risk for homozygous alpha 0-thalassaemia. Transabdominal placental biopsy was carried out at 10-12 weeks' gestation. The presence of alpha-globin genes in the fetal DNA was determined by restriction endonuclease mapping and hybridization with cloned alpha-globin probe. Homozygous alpha 0-thalassaemia was detected in two fetuses and the pregnancies were interrupted. Alpha 0-thalassaemia in both cases was confirmed by electrophoresis of the umbilical cord blood where only haemoglobin Bart's was detected. The remaining five fetuses were diagnosed as normal or as possessing alpha-thalassaemia-1 trait and the pregnancies are being carried to term. The use of DNA analysis in prenatal diagnosis of fetuses at risk for homozygous alpha 0-thalassaemia enables detection of the haemoglobinopathy at 10 weeks' gestation.

Norrie disease: linkage analysis using a 4.2-kb RFLP detected by a human ornithine aminotransferase cDNA probe

Previous study has shown that the usual DNA marker for Norrie disease, the L1.28 probe which identifies the DXS7 locus, can recombine with the disease locus. In this study, we used a human ornithine aminotransferase (OAT) cDNA which detects OAT-related DNA sequences mapped to the same region on the X chromosome as that of the L1.28 probe to investigate the family with Norrie disease who exhibited the recombinational event. When genomic DNA from this family was digested with the PvuII restriction endonuclease, we found a restriction fragment length polymorphism (RFLP) of 4.2 kb in size. This fragment was absent in the affected males and cosegregated with the disease locus; we calculated a lod score of 0.602, at theta = 0.00. No deletion could be detected by chromosomal analysis or on Southern blots with other enzymes. These results suggest that one of the OAT-related sequences on the X chromosome may be in close proximity to the Norrie disease locus and represent the first report which indicates that the OAT cDNA may be useful for the identification of carrier status and/or prenatal diagnosis.

Thalassemia: molecular pathology and management

Recent advances in molecular biology have allowed us to develop an almost complete picture of the molecular pathology of the thalassemia syndromes. The different classes of mutations that are responsible for the thalassemia syndromes will be discussed along with the special insights they have provided into the controls of eukaryotic gene expression. While management of these disorders has not kept pace with our understanding of their cause, there have been notable advances in treatment. Perhaps even more exciting is what the future holds, as the continued march of molecular biology is melded with novel approaches to the definitive treatment of thalassemias.

The spectrum of beta-thalassaemia mutations in Sicily

To characterize beta-thalassaemia genes among the Sicilian population we have previously determined the DNA haplotypes in the beta-globin gene cluster of 99 beta-thal chromosomes. We found seven haplotypes, although 95 of 99 beta-thal chromosomes contained framework 1 and framework 3 beta genes. We have now determined the mutation in all 99 of these beta-thal genes by the use of oligonucleotide hybridization. PCR-amplification and direct genomic sequencing, and direct restriction analysis. Our results indicate that (1) the beta (0)-39 mutation is most frequent (35%); (2) beta(0)-39, IVS-1 nt 110 and IVS-1 nt 6 mutations account for 90% of beta-thal genes: (3) the IVS-1 nt 6 mutation is more frequent in thalassaemia intermedia (77%) than in Cooley's disease (34%): (4) the association between haplotypes and specific mutations is imperfect, but mutation spread has occurred within haplotypes containing the same beta-gene framework: (5) the beta(0)-39 and the IVS-1 nt 6 mutations, with a mutation spread to two major haplotypes, may be older than the IVS-1 nt 110 mutation: (6) these data make possible first-trimester prenatal diagnosis in many families (85%) in Sicily using only three pairs of oligonucleotides. In addition, a new mutation, a frameshift at codon 76 due to loss of a C residue, was found in a single beta-thal chromosome.

Genotypic analysis using a Y-chromosome-specific probe following bone marrow transplantation

To monitor successful engraftment after bone marrow transplantation, we performed Southern hybridization analysis or dot blot analysis of DNA in a set of sex-mismatched cases using a Y-chromosome-specific DNA probe (pHY10). This method was extremely sensitive and rapid for checking which cells contain the Y-chromosome. Using this probe, analysis of cells from peripheral blood and bone marrow after transplantation demonstrated the usefulness of confirming engraftment of donor cells and of detecting mixed lymphohematopoietic chimerism.

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.

Huntington's disease: two families with differing clinical features show linkage to the G8 probe

To test the hypothesis that interfamily variability in Huntington's Disease (HD) is due to mutation at different loci, linkage analysis was undertaken in two large HD kindreds that differed in ethnicity, age-at-onset, and neurologic and psychiatric features. Both families showed linkage of the HD locus to the G8 probe. Several recombinants were documented in each family, and the best estimate of the recombination fraction for the two families was 6 percent with a 95 percent confidence interval of 0 to 12 percent. Although the data support the existence of a single HD locus, use of the G8 probe for presymptomatic testing in these kindreds would have resulted in a 12 percent error rate in genotype assignment at the HD locus.

Alpha thalassaemia in British people

Although alpha thalassaemia is rare in north Europeans, it has been identified in British people with no known foreign ancestry. Twelve such patients were studied, of whom eight shared a distinctive molecular defect, which was clearly different from defects seen in subjects of Mediterranean or South East Asian origin. A rare but specific form of alpha thalassaemia is therefore present in the British population. In addition, two patients from families of mixed racial origin were encountered who had a moderately severe form of thalassaemia (HbH disease) due to the inheritance of one form of alpha thalassaemia from the British parent and another type from the foreign parent. This shows the importance of careful genetic counselling of British patients with haematological findings of thalassaemia.

Alpha-globin gene organisation and prenatal diagnosis of alpha-thalassaemia in Chinese

DNA samples from 60 Chinese patients with haemoglobin H disease were analysed by restricted endonuclease mapping to determine the patterns of alpha-globin gene organisation and the distribution of these patterns in China. Restriction endonuclease analysis and rapid micro-DNA hybridisation on nitrocellulose membranes were also used to analyse DNA from amniotic fluid cells or from chorionic villi in 7 pregnancies at risk of haemoglobin Barts hydrops fetalis, in 1 at risk of haemoglobin H disease, and 1 at risk of both disorders.

Prenatal diagnosis of beta-thalassaemia with the synthetic-oligomer technique

103 couples attending the antenatal clinic in Sardinia were screened for the beta o-39 (nonsense) mutation, which codes for beta-thalassaemia, with the oligonucleotide method. In 94 couples both members had the beta o-39 mutant and thus were eligible for antenatal testing with this method. These pregnancies were monitored with amniocentesis (61) or trophoblast biopsy (33). Prenatal diagnosis in those monitored with amniocentesis was carried out with DNA analysis of uncultivated amniocytes (19) or cultivated cells (38). In 4 pregnancies results were unsatisfactory, and prenatal diagnosis was repeated with fetal-blood analysis. Trophoblast biopsy was unsuccessful in 1 pregnancy and gave a misdiagnosis in another because of maternal contamination. In the latter case the genotype of the fetus was established with amniocyte DNA analysis and globin-chain-synthesis studies.

Origin of cell populations after bone marrow transplantation. Analysis using DNA sequence polymorphisms

After successful bone marrow transplantation, patient hematopoietic and lymphoid cells are replaced by cells derived from the donor marrow. To document and characterize successful engraftment, host and donor cells must be distinguished from each other. We have used DNA sequence polymorphism analysis to determine reliably the host or donor origin of posttransplant cell populations. Using a selected panel of six cloned DNA probes and associated sequence polymorphisms, at least one marker capable of distinguishing between a patient and his sibling donor can be detected in over 95% of cases. Posttransplant patient peripheral leukocytes were examined by DNA restriction enzyme digestion and blot hybridization analysis. We have studied 18 patients at times varying from 13 to 1,365 d after marrow transplantation. Mixed lymphohematopoietic chimerism was detected in 3 patients, with full engraftment documented in 15. One patient with severe combined immunodeficiency syndrome was demonstrated to have T cells of purely donor origin, with granulocytes and B cells remaining of host origin. Posttransplant leukemic relapse was studied in one patient and shown to be of host origin. DNA analysis was of particular clinical value in three cases where failure of engraftment or graft loss was suspected. In two of the three cases, full engraftment was demonstrated and in the third mixed lymphohematopoietic chimerism was detected. DNA sequence polymorphism analysis provides a powerful tool for the documentation of engraftment after bone marrow transplantation, for the evaluation of posttransplant lymphoma or leukemic relapse, and for the comprehensive study of mixed hematopoietic and lymphoid chimeric states.

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)

Prenatal diagnosis of thalassemia and of the hemoglobinopathies; a review

Prenatal diagnosis of thalassemia and of the hemoglobinopathies is now accepted as an effective measure to reduce the impact of these diseases in populations where they occur in high frequencies. The procedure has been carried out on more than 5,000 cases over the past decade. Evaluation of the results shows a significant decrease of the yearly number of affected newborns and reflects a considerable gain in economic and medical resources. Methodology has improved over the years so as to make the procedure safer, faster, and less expensive. Among recent advances, gene mapping on trophoblast DNA (as early as the 9th week of pregnancy) represents a major step which will gradually replace conventional procedures (performed during the 18-20th week of pregnancy) in concerned laboratories.

A new DNA polymorphism for prenatal diagnosis of beta-thalassaemia in Mediterranean populations

The prevalence of a new polymorphism for the restriction enzyme Ava II in the psi beta-gene of the beta-globin gene cluster was determined in Mediterranean families with at least one beta-thalassaemia homozygote. The polymorphic site was absent in 54/115 beta-thalassaemic chromosomes but only in 4/120 normal chromosomes. The difference in frequencies of this polymorphism between normal and thalassaemic chromosomes greatly increases the feasibility of prenatal diagnosis of beta-thalassaemia by DNA analysis in this population.

A screening protocol for a prenatal population at risk for inherited hemoglobin disorders: results of its application to a group of Southeast Asians and blacks

Several inherited hemoglobin disorders are present among certain racial subgroups of the United States population, particularly among blacks and Southeast Asians. Many of these disorders are unfamiliar to the obstetrician-gynecologist but may have important implications for care in pregnancy, including genetic counseling and prenatal diagnosis. A simple, effective screening tool was devised for detection of thalassemias and hemoglobinopathies in a prenatal clinic population. Use of the tool resulted in diagnosis of a hemoglobin disorder in 20% of a group of black patients; diagnoses included alpha-thalassemia trait, beta-thalassemia trait, hemoglobin C trait, hemoglobin S/C disease, hemoglobin S trait, sickle cell anemia, and hemoglobin Lepore. In a group of Southeast Asian patients, 39% had a hemoglobin disorder, including alpha-thalassemia trait, beta-thalassemia trait, hemoglobin E disease, and hemoglobin H disease. Implications for care are discussed.