Rapid prenatal diagnosis of sickle cell anemia by a new method of DNA analysis

In vitro PCR verification that lysozyme inhibits nucleic acid replication and transcription

Lysozyme can kill bacteria by its enzymatic activity or through a mechanism involving its cationic nature, which can facilitate electrostatic interactions with the viral capsid, the negatively charged parts of nucleic acids, and polymerase, so binding to nucleic acids may be another biological function of lysozyme. Here, PCR was used as a research tool to detect the effects of lysozyme on the replication and transcription of nucleic acids after treatment in different ways. We found that lysozyme and its hydrolysate can enter cells and inhibit PCR to varying degrees in vitro, and degraded lysozyme inhibited nucleic acid replication more effectively than intact lysozyme. The inhibition of lysozyme may be related to polymerase binding, and the sensitivity of different polymerases to lysozyme is inconsistent. Our findings provide a theoretical basis for further explaining the pharmacological effects of lysozyme, such as antibacterial, antiviral, anticancer, and immune regulatory activities, and directions for the development of new pharmacological effects of lysozyme and its metabolites.

PCR past, present and future

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

Successful pregnancy outcome after in vitro fertilisation following Pre-implantation Genetic Diagnosis/Polymerase Chain Reaction screening for single gene disorder (sickle cell anaemia) before embryo transfer: The clinical experience of an in vitro fertilisation clinic in Nigeria

A couple, both carriers of the sickle cell anaemia trait (Genotype HbAS) with an offspring already affected with the genetic disease underwent a Pre-implantation Genetic Diagnosis/Polymerase Chain Reaction screening of biopsied blastomeres. DNA analysis of single blastomeres was carried out to find out indicated a viable intra-uterine pregnancy with embryos which carried the sickle cell mutation, which resulted in a livebirth (HbAS). PGD/PCR in combination with IVF appears to be the most suitable treatment plan for patients who are at a higher risk of reproducing offspring affected with inheritable genetic diseases.

A One-Step Real-Time PCR Assay for Rapid Prenatal Diagnosis of Sickle Cell Disease and Detection of Maternal Contamination

INTRODUCTION

Mutations at the codon 6 of the beta-globin gene (hemoglobin [Hb] S and HbC) can be routinely identified by various methods and prenatal diagnosis has been available to affected families for several years. However, the presence of maternal cells in fetal samples constitutes a serious potential source of prenatal misdiagnosis and most methods currently used to detect maternal contamination are based on the analysis of highly polymorphic loci. In addition, these methods are labor intensive and time consuming and risk carry-over contamination.

METHOD

We describe here a one-step method for mutation detection that uses fluorescent hybridization probes with melting curve analysis for both simultaneously prenatal diagnosis of sickle cell disease and potential maternal contamination.

RESULTS

Retrospective and prospective prenatal diagnosis studies (conducted in 20 and 50 cases, respectively), using both the regular procedure and real-time PCR assay show perfect concordant results. We show in addition, that as little as 5% maternal contamination can be detected and that genotype determinations are unambiguous.

Enzymatic amplification of DNA by PCR: standard procedures and optimization

This unit describes a method for amplifying DNA enzymatically by the polymerase chain reaction (PCR), including procedures to quickly determine conditions for successful amplification of the sequence and primer sets of interest, and to optimize for specificity, sensitivity, and yield. Hot-start methods are described which can greatly improve specificity, sensitivity, and yield. This protocol suggests some relatively inexpensive methods to achieve hot start, and lists several commercial hot-start options which may be more convenient, but of course more expensive. The unit has recently been updated to include new information on reagents to enhance the reaction, better cycling parameters, and innovations in robotics and high-performance thermocyclers.

Enzymatic amplification of DNA by PCR: standard procedures and optimization

The polymerase chain reaction (PCR) is used to enzymatically amplify small quantities of specific DNA sequences. The reaction must optimized to specifically amplify the sequences and primers of interest; this includes titration of magnesium chloride and selection of enhancing agents, if appropriate, to minimize nonspecific primer target interactions and maximize the specificity, sensitivity, and yield.

Enzymatic amplification of DNA by PCR: standard procedures and optimization

This unit describes a method for amplifying DNA enzymatically by the polymerase chain reaction (PCR), including procedures to quickly determine conditions for successful amplification of the sequence and primer sets of interest, and to optimize for specificity, sensitivity, and yield. The first step of PCR simply entails mixing template DNA, two appropriate oligonucleotide primers, Taq or other thermostable DNA polymerases, deoxyribonucleoside triphosphates (dNTPs), and a buffer. Once assembled, the mixture is cycled many times (usually 30) through temperatures that permit denaturation, annealing, and synthesis to exponentially amplify a product of specific size and sequence. The PCR products are then displayed on an appropriate gel and examined for yield and specificity. Recommended optimization conditions are included.

Enzymatic amplification of DNA by PCR: standard procedures and optimization

This unit describes a method for amplifying DNA enzymatically by the polymerase chain reaction (PCR) and for optimizing this reaction for the sequence and primer set of interest. Important variables that can influence the outcome of PCR include the MgCl(2) concentration and the cycling temperatures. Additives that promote polymerase stability and processivity or increase hybridization stringency, and strategies that reduce nonspecific primer-template interactions, especially prior to the critical first cycle, can greatly improve sensitivity, specificity, and yield. This protocol is designed to optimize the reaction components and conditions in one or two stages. The first stage determines the optimal MgCl(2) concentration and screens several enhancing additives. To further improve specificity, sensitivity and yield, the second stage compares methods for optimizing initial specific hybridization to prevent polymerization of misprimed sequences prior to thermal cycling. For initial inhibition of polymerase activity, temperature (i.e., cooling reagents), physical separation ("hot start" method), and reversible antibody binding are compared.

Enzymatic amplification of DNA by PCR: standard procedures and optimization

This unit describes a method for amplifying DNA enzymatically by the polymerase chain reaction (PCR), including procedures to quickly determine conditions for successful amplification of the sequence and primer sets of interest, and to optimize for specificity, sensitivity, and yield. The first step of PCR simply entails mixing template DNA, two appropriate oligonucleotide primers, Taq or other thermostable DNA polymerases, deoxyribonucleoside triphosphates (dNTPs), and a buffer. Once assembled, the mixture is cycled many times (usually 30) through temperatures that permit denaturation, annealing, and synthesis to exponentially amplify a product of specific size and sequence. The PCR products are then displayed on an appropriate gel and examined for yield and specificity. Recommended optimization conditions are included.

Enzymatic amplification of DNA by PCR: standard procedures and optimization

This appendix describes a method for amplifying DNA enzymatically by the polymerase chain reaction (PCR), including procedures to quickly determine conditions for successful amplification of the sequence and primer sets of interest, and to optimize for specificity, sensitivity, and yield.

Sickle cell disease--pathophysiology, clinical and diagnostic implications

We review the current knowledge of the pathophysiology of sickle cell disease (SCD), the clinical complications and the state of the art in SCD diagnostics. Today, a flexible laboratory concept allows the fast and economic clarification of the patients' sickle cell hemoglobin (HbS) status, e.g. additional compound heterozygosities. In contrast to a well-investigated pathophysiology of the disease, factors influencing the severity of symptoms as well as some laboratory findings in SCD still lack a final explanation. In this review, we focus on red cell lysis resistance as an additional diagnostic tool in SCD. There is a need for further studies regarding lysis resistance in blood samples from patients with HbS.

Eugenics and genetic testing

Pressures to lower health-care costs remain an important stimulus to eugenic approaches. Prenatal diagnosis followed by abortion of affected fetuses has replaced sterilization as the major eugenic technique. Voluntary acceptance has replaced coercion, but subtle pressures undermine personal autonomy. The failure of the old eugenics to accurately predict who will have affected offspring virtually disappears when prenatal diagnosis is used to predict Mendelian disorders. However, when prenatal diagnosis is used to detect inherited susceptibilities to adult-onset, common, complex disorders, considerable uncertainty is inherent in the prediction. Intolerance and the resurgence of genetic determinism are current pressures for a eugenic approach. The increasing use of carrier screening (to identify those at risk of having affected offspring) and of prenatal diagnosis could itself generate intolerance for those who refuse the procedures. Genetic determinism deflects society from social action that would reduce the burden of disease far more than even the maximum use of eugenics.

Single-nucleotide polymorphism identification assays using a thermostable DNA polymerase and delayed extraction MALDI-TOF mass spectrometry

We report a simple method, the PinPoint assay, for detecting and identifying single-base variations (polymorphisms) at specific locations within DNA sequences. An oligonucleotide primer is annealed to the target DNA immediately upstream of the polymorphic site and is extended by a single base in the presence of all four dideoxynucleotide triphosphates and a thermostable DNA polymerase. The extension products are desalted, concentrated, and subjected to delayed-extraction MALDI-TOF mass spectrometry. The base at the polymorphic site is identified by the mass added onto the primer. Heterozygous targets produce two mass-resolved species that represent the addition of both bases complementary to those at the polymorphic site. The assay is suitable for double-stranded PCR products without purification or strand separation. More than one primer can be simultaneously extended and then mass-analyzed. The mass spectrometric method thus shows promise for high-volume diagnostic or genotyping applications.

DNA diagnosis for the practicing obstetrician

Laboratory advances in molecular genetics have resulted in numerous clinical applications for DNA analysis. Currently, because of cost, complexity, and resource limitations, DNA analysis is not used routinely for prenatal screening, but rather is targeted towards families at risk for an inherited condition. This article discusses the types of DNA analyses that are currently performed, the possible tissue sources of DNA for prenatal diagnosis, and the indications for DNA testing in obstetric practice. Internet addresses for the most up-to-date genetic information on a specific condition are given in this article.

Advances in the prenatal and molecular diagnosis of the hemoglobinopathies and thalassemias

Prenatal diagnosis is available for pregnancies at risk for virtually all inherited disorders of hemoglobin production. The field of reproductive genetics must confront many ethical, legal, and social concerns regarding its use, many of which derive from a woman's desire to bear children but legal right to abortion. The goal of more widespread utilization of prenatal diagnosis is sought in the context of questioning the ethical control to be exerted over the biological makeup of future generations. Its appropriate application would be facilitated greatly by the availability of reliable DNA markers of disease severity. Advances in fetal sampling and in detecting mutant globin genes have provided the safe, accurate methodology required for prenatal diagnosis. Chorionic villus sampling in the first trimester has become standard practice, but second trimester amniocentesis also is used for sampling fetal DNA. The use of preimplantation diagnosis and testing fetal cells from the maternal circulation will soon be practical. DNA-based detection of globin gene mutations has been facilitated greatly by the polymerase chain reaction revolution, and several reliable diagnostic methods are available. Polymerase chain reaction-based methods rely on restriction analysis, allele-specific hybridization or amplification, DNA sequence analysis, and new non-polymerase chain reaction methods for DNA amplification in vitro. These methods are available for detecting hemoglobinopathy, thalassemia, and thalassemic-hemoglobinopathy genes that affect alpha- or beta-globin loci.

Experience with 500 prenatal diagnoses of sickle cell diseases: the effect of gestational age on affected pregnancy outcome

Prenatal diagnosis of sickle cell diseases is obtained rapidly and precisely by polymerase chain reaction (PCR) with Ddel restriction analysis and dot-blotting with allele-specific oligonucleotides (ASO). Prenatal diagnosis of HgbSS and HgbSC was performed in 500 pregnancies, 196 by Southern blot and 304 by PCR. PCR drastically shortened the interval from sampling to reporting, allowing acceptance even of samples with unknown paternal phenotype, and resulted in an overall four-fold increase in diagnoses. In 108 pregnancies, the diagnosis was an affected fetus; 25 were HgbSC: 3 (12 per cent) were terminated; 83 were HgbSS: four ended in miscarriage; 40/79 (51 per cent) were terminated. The gestational age at the time of report to the mother appeared to be a major outcome determinant when the fetal diagnosis was HgbSS. The change-point in the maternal decision was found at 20 weeks of gestation. Before the 20th week, most mothers (64 per cent) chose termination; thereafter, the majority (72 per cent) chose continuation. The odds ratio of termination in earlier relative to later reporting was 4.7. In order to offer a choice to the mothers at risk of delivering a fetus affected by sickle cell disease, the diagnosis should be reported before the 20th week of gestation.

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.

Screening and prenatal diagnosis of the haemoglobinopathies

In this paper we have reviewed the social and technical aspects of carrier screening and prenatal diagnosis of the inherited haemoglobinopathies. The characteristics of programmes based on carrier screening and prenatal diagnosis ongoing in a number of at-risk Mediterranean populations have been described. The most relevant and common aspects of these programmes are the continuous educational campaign directed to the population at large, the voluntary basis and non-directive counselling. The target population has been most commonly couples before or after marriage. The vast majority of couples counselled accepted prenatal diagnosis. All programmes have encountered a high degree of success as indicated by the marked reduction in the birth rate of infants with thalassaemia major. No significant adverse effects have been reported. A programme with similar characteristics and for which the preliminary results are encouraging, is operating for sickle cell anaemia in the Cuban population. In a population with high frequency of hydrops fetalis, screening for deletion alpha-thalassaemia is recommended to prevent the negative effects on a pregnant woman of the presence of an hydropic fetus. Thalassaemia carrier screening is now carried out by automatic red cell indices and HbA2 determination. Definition of atypical cases may require iron studies, globin chain synthesis determination and/or alpha, beta- and delta-globin gene analysis. Identification of the carrier state is followed by definition of the mutation on enzymatically amplified DNA. Known mutations may be detected by restriction endonuclease analysis, non-denaturing polyacrylamide gel electrophoresis, allele-specific primers or allele-specific probes. The most promising procedures, which are also amenable to complete automation are reverse oligonucleotide hybridization and primer-specific amplification. Unknown mutations are defined by denaturing gradient gel electrophoresis, single-strand conformation polymorphism analysis, and chemical mismatch cleavage analysis followed by direct sequencing. The same methods on enzymatically amplified chorionic villus DNA are used for prenatal diagnosis. The potential pitfall resulting from maternal contamination can be avoided by careful dissection of the maternal decidua from the chorion and by the simultaneous amplification of a suitable polymorphism.

Polymerase chain reaction facilitates archival autopsy studies of sickle cell disease

Archival autopsy studies of sickle cell disease have often been hampered by inadequate documentation of the genotype. Although the polymerase chain reaction (PCR) has been applied to the prenatal diagnosis of sickle cell disease, its use has not been reported in archival studies of sickle cell disease. In this study, DNAs from formalin-fixed, paraffin-embedded archival tissues were amplified by PCR and analyzed by dot-blot hybridization using allele-specific oligonucleotides. These S and C genotypes for 9 of 10 archival specimens studied blindly were correctly identified by PCR. The tenth specimen consistently failed to amplify by PCR, yielding no result. These data demonstrate the utility of PCR for retrospective identification of the genotype of sickle cell disease. This application of PCR will significantly expand the number of autopsy cases suitable for retrospective studies of the morbidity and mortality of sickle cell disease.

Comparison of HPV detection in parallel biopsies and cervical scrapes by PCR

PCR was used to detect HPV DNA in cervical scrapes of 23 women with cervical cancer. Compared with PCR-assisted HPV DNA detection in parallel biopsies, the sensitivity was 81% and the specificity 100%. We conclude that cervical scrapes can be used for detection of HPV DNA in women with cervical cancer.

Laboratory methods for early detection of human immunodeficiency virus type 1 in newborns and infants

Cumulative data on serological testing of newborns and infants have shown that (i) maternal and newborn anti-HIV-1 IgG titers are high at delivery, which may explain the persistence of antibody in the infants of seropositive mothers; (ii) in some situations, serial HIV-1 antibody testing may identify infected infants; and (iii) detection of anti-HIV-1 IgA or IgM is specific for infection but the sensitivity of this assay may be compromised in certain situations, such as when infected infants are hypogammaglobulinemic or when the rise and fall of HIV-1-specific IgM synthesis following acute infection has been completed before delivery of the infant. Cumulative data on PCR, viral culture, and tests for antigen in newborns and infants have shown that (i) among all age groups, viral culture is probably the most specific test available for detection of HIV-1, as PCR and the p24 antigen test may (though rarely) give false-positive results; (ii) the sensitivity of these tests increases in the order of antigen, culture, and PCR, with relatively insensitive results in the first 3 months of life for all of these tests; (iii) the sensitivity of all of these tests improves and approximates 90 to 100% when infants over 6 months of age are tested; and (iv) data regarding the sensitivity, specificity, and usefulness of these virological assays in infants under 3 months of age are very scant and inconclusive.

DNA enzyme immunoassay: a rapid and convenient colorimetric method for diagnosis of cystic fibrosis

Genetic analysis of inherited diseases has been greatly facilitated by new approaches, involving genomic DNA amplification by the polymerase chain reaction (PCR), followed by hybridization with wild type-specific or mutation-specific oligonucleotide (MSO) probes. The main advantage of these methods is that they allow easy detection of point mutations starting from minimal amounts of biological materials. These techniques, however, require procedures which are not well suited to large-scale screening or use in routine laboratories. The development of dedicated kits to perform these tests efficiently in clinical laboratories is an important current issue. We developed a new non-radioisotopic assay to reveal specifically DNA-DNA hybrids between amplified DNA and MSO probes, and applied it to the detection of two mutations causing cystic fibrosis. The detection of hybrids is achieved by means of an anti double-stranded DNA antibody, in a format which is designed as a colorimetric assay resembling a common enzymatic immunoassay (EIA). The assay detects the hybridization event, independent of the nucleic acid sequences involved in the formation of the specific hybrids, and can be used with any combination of target DNA and probes. Therefore, this test represents a significant improvement for the clinical use of the polymerase chain reaction in the diagnosis of inherited diseases.

Recent advances in the polymerase chain reaction

The polymerase chain reaction (PCR) has dramatically altered how molecular studies are conducted as well as what questions can be asked. In addition to simplifying molecular tasks typically carried out with the use of recombinant DNA technology, PCR has allowed a spectrum of advances ranging from the identification of novel genes and pathogens to the quantitation of characterized nucleotide sequences. PCR can provide insights into the intricacies of single cells as well as the evolution of species. Some recent developments in instrumentation, methodology, and applications of the PCR are presented in this review.

Detection of human immunodeficiency virus type 1 by using the polymerase chain reaction and a time-resolved fluorescence-based hybridization assay

The polymerase chain reaction (PCR) has many potential applications in the field of nucleic acid diagnostics. In particular, it has been successfully applied to the detection of pathogens present in low copy numbers such as the human immunodeficiency virus type 1. Here we describe a time-resolved fluorescence-based hybridization assay which, combined with the PCR, offers an extremely sensitive method for the detection of nucleic acids. In this assay format, the PCR is run by standard procedures and the subsequent hybridization reaction is carried out in solution by using two oligonucleotide probes, one biotinylated and one labeled with europium (Eu3+). The sandwich hybrids are then collected onto a streptavidin-coated microtitration well, and the bound Eu3+ is measured in a time-resolved fluorometer. This assay is rapid, user friendly, and quantitative and lends itself to automation. The application of this assay to the detection of human immunodeficiency virus type 1 is described.

The polymerase chain reaction

In a short time the PCR techniques has revolutionized research technology in many areas of medicine. Because of the ease and rapidity of the technique it is quickly becoming a standard clinical test for many diseases. Clinical applications continue to emerge from research labs and should rapidly expand to facilitate rapid medical diagnosis.

Differentiation of pathogenic from nonpathogenic Entamoeba histolytica by restriction fragment analysis of a single gene amplified in vitro

We previously reported the identification of homologous cDNA clones derived from a pathogenic isolate and a nonpathogenic isolate of Entamoeba histolytica, which had been designated cEh-P1 and cEh-NP1, respectively. Sequence analysis of both clones had revealed 10% nucleic acid substitutions, which were dispersed over the entire sequence. This genetic difference had been found to be conserved between all four pathogenic and all five nonpathogenic laboratory strains of E. histolytica tested. On the basis of nucleic acid substitutions, we have now developed a sensitive assay to distinguish pathogenic from nonpathogenic forms of E. histolytica by using fresh clinical isolates. Comparing the sequence of cEh-P1 and cEh-NP1, we identified a 482-bp segment that contained identical 5' and 3' ends but differed in internal cleavage sites for restriction endonucleases. By using oligonucleotide primers corresponding to the 5' and 3' ends of this segment, the corresponding gene was amplified by the polymerase chain reaction. Endonuclease digestion of the amplified DNA yielded restriction fragments that are characteristic for pathogenic and nonpathogenic forms. This assay allows the detection and classification of fewer than 10 amoebae within a few hours. The differentiation of 48 isolates into pathogenic and nonpathogenic strains by using this method corresponded to the clinical status of the infected individuals and to the classification obtained by isoenzyme determination. The results further support the concept that pathogenic and nonpathogenic strains of E. histolytica constitute distinct subspecies.

Methodologies for in vitro nucleic acid amplification and their applications

The capability to detect the genetic elements (DNA or RNA) of a particular pathogen as a means of identifying the infectious agent has been the traditional function of nucleic acid hybridization assays. The low copy number of genetic material from several types of viral pathogens has fostered the development of in vitro nucleic acid amplification methods as a means to increase the copy number of the characteristic genetic elements of pathogenic agents. The polymerase chain reaction (PCR) and a transcription-based amplification system (TAS) are two amplification methods that have been developed to serve this function. Both methods have been employed to study both genetic and infectious disease problems. This review discusses the characteristics of these amplification methods and describes some of their applications, especially in the study of HIV-1.

The technique of polymerase chain reaction--a new diagnostic tool in microbiology and other scientific fields (review)

The polymerase chain reaction, a method of so far unknown sensitivity and specificity, is about to become an important diagnostic tool in microbiology. Practically even a single bacterium, virus particle, or parasite can be detected by it. Furthermore, this technique has been used with highly promising results in other scientific fields like genetics, forensic medicine and archeology. This article reviews technical aspects and variations of this new technique.

Rapid detection and sequencing of specific in vitro amplified DNA sequences using solid phase methods

We describe a rapid solid phase assay for detection and sequencing of DNA sequences based on selective introduction of biotin and isotope into the specific DNA fragment amplified by the polymerase chain reaction (PCR). A two-step PCR procedure is used to lower the background signal. The in vitro amplified material is immobilized on magnetic beads with covalently coupled streptavidin and the amount of bound label is measured. Samples identified as positive can be analysed by direct solid phase DNA sequencing. A strategy is also described to use general primers for detection, capturing and sequencing, which are not homologous to the specific sequence to be detected. The concept has been optimized using oligonucleotides specific for Staphylococci and Streptococci, respectively. Here, we show that the assay can be used for detection of Plasmodium falciparum in clinical samples.

Application of the polymerase chain reaction to the diagnosis of human genetic disease

In vitro DNA amplification by means of the polymerase chain reaction is currently revolutionizing human molecular genetics. Since its inception in 1985, a wide variety of different methods and their applications in the diagnosis of disease have been described. This review is intended to serve as a brief guide to current and emerging possibilities in this rapidly expanding field.

Rapid assessment of haemophilia A carrier state by non-invasive techniques using the polymerase chain reaction

The polymerase chain reaction (PCR) was used to amplify two polymorphic regions in the factor VIII gene. In vitro synthesis of DNA was achieved using samples obtained from buccal cells, urine, and hair follicles in addition to purified genomic and crude DNA samples prepared from whole blood. Female members of two kindreds affected with haemophilia A were assessed for carrier state using direct restriction fragment length polymorphism analysis of amplified gene products in the Bc1I and XbaI regions. It is concluded that this is a non-invasive, rapid, and inexpensive technique for carrier detection.

Amplification of a beta-haemoglobin sequence in individual human oocytes and polar bodies

A 680 base-pair sequence of the human beta-haemoglobin gene was reproducibly amplified in individual unfertilised human oocytes and in first polar bodies isolated from them. Specificity and sensitivity of amplification were achieved by two sequential reactions with two sets of primers, amplifying first a 725 base-pair sequence and secondly a 680 base-pair sequence from within the first amplified fragment. A restriction enzyme digest of the DNA amplified from a single oocyte with the endonuclease Dde I confirmed the identity of the amplified beta-haemoglobin fragment; this technique provides a diagnostic test for the genetic defect responsible for sickle cell anaemia. Analysis of the DNA from the first polar body may enable detection of such defects in unfertilised eggs from carrier women. Selection of eggs without the defect for fertilisation may therefore obviate the need for diagnostic procedures on embryos.

An evaluation of the polymerase chain reaction method for forensic applications

This paper describes the use of polymerase chain reaction (PCR) for amplifying small amounts of DNA obtained from samples of interest to the forensic scientist. A region of the HLA DQalpha (DQa) locus was amplified in DNA prepared from the following: hair roots, liquid blood, blood-stains, semen and vaginal swabs (semen free and semen contaminated). A population study was conducted using DNA from 78 unrelated individuals. The observed distribution of HLA DQa alleles varied from that reported for an American population but obeyed the Hardy-Weinberg equilibrium. Interpretation problems associated with the PCR technique are discussed.

Micromanipulation of embryos and germ cells: an approach to gene therapy?

Recent advances in mammalian gamete and embryo micromanipulation have stimulated the scientific and medical communities, and to some degree the public at large, to become aware that treatment of genetic disease by direct alteration of the genetic code may soon be possible. Because these micromanipulation techniques result in modification of the genotype at the earliest stages of development, such "gene therapy" affects not only the conceptus itself but also its germ cells. Thus such genetic modifications are heritable and can be transmitted indefinitely to succeeding generations of progeny. In the presentation, both narrow and broad definitions of gene therapy will be considered with respect to the techniques upon which they are based, their potential for treatment of genetic disease, and their current feasibility.

Molecular genetics and the future of pharmacogenetics

Recombinant DNA technology is a major innovation in medicine and is increasingly applied to study the mechanisms of inherited variations in drug response at the gene level. Three of these techniques are of particular importance to pharmacogenetics and for the study of the diversity of human genes. (1) Restriction analysis of genomic DNA, (2) enzymatic amplification of DNA by the polymerase chain reaction, and (3) the expression of cDNAs in cell culture. With these techniques large populations can be screened, normal and mutant DNA can be obtained from extremely small tissue samples, and functional expression of cDNAs allows the rapid search for potential new substrates of a polymorphic enzyme.

Hereditary amyloidosis: detection of variant prealbumin genes by restriction enzyme analysis of amplified genomic DNA sequences

The autosomal dominant prealbumin amyloidoses are late-onset disorders characterized by varying degrees of peripheral neuropathy, nephropathy and cardiomyopathy. To date, seven different single amino acid mutations in the plasma protein prealbumin (transthyretin) have been found to be associated with amyloidosis and each is the result of a single nucleotide change in the prealbumin gene. By virtue of the restriction endonuclease sites created by the point mutations which give rise to the protein variants, direct DNA tests using Southern analysis have already been developed for detection of the Met-30, Ile-33, Ala-60, Tyr-77 and Ser-84 prealbumin genes. As an alternative to Southern analysis, we have amplified discrete regions of the prealbumin gene using polymerase chain reaction (PCR) and used restriction enzyme analysis of the PCR products to detect the Met-30, Ala-60, Tyr-77 and Ser-84 prealbumin genes after agarose gel electrophoresis and staining with ethidium bromide. In comparison to Southern analysis these alternative tests yield results much more quickly and avoid the use and handling of radioactively labeled probes.

Prenatal detection of a gene for hereditary amyloidosis

Autosomal dominant amyloidosis of the Indiana/Swiss type (familial amyloidotic polyneuropathy type II) is a late-onset disorder characterized by carpal tunnel syndrome, peripheral neuropathy, vitreous opacities, and cardiomyopathy. The genetic basis of the disease is a variant of plasma prealbumin (transthyretin) which has a serine for isoleucine substitution at amino acid 84 of the 127 residue prealbumin molecule. Using the polymerase chain reaction (PCR), we amplified exon 3 of the prealbumin gene in DNA extracted from amniocytes of a fetus at-risk of carrying the serine-84 prealbumin gene. By allele-specific oligonucleotide analysis as well as restriction enzyme analysis of the amplification products it was determined that the fetus was a carrier of the serine-84 variant gene. This finding was confirmed at birth by Southern blot analysis using DNA obtained from cord blood. This is the first report of the prenatal detection of a gene for hereditary amyloidosis.

Polymerase chain reaction

The PCR, like recombinant DNA technology, has had an enormous impact in both basic and diagnostic aspects of molecular biology because it can produce large amounts of a specific DNA fragment from small amounts of a complex template. Recombinant DNA techniques create molecular clones by conferring on a specific sequence the ability to replicate by inserting it into a vector and introducing the vector into a host cell. PCR represents a form of "in vitro cloning" that can generate, as well as modify, DNA fragments of defined length and sequence in a simple automated reaction. In addition to its many applications in basic molecular biological research, PCR promises to play a critical role in the identification of medically important sequences as well as an important diagnostic one in their detection.

Characterization of rare human papillomavirus type 11 mRNAs coding for regulatory and structural proteins, using the polymerase chain reaction

Certain human papillomavirus (HPV) types cause warts, dysplasias, and carcinomas of the ano-genital and oral mucosa. Because of the inability to propagate HPVs in cultured cells, the paucity of viral mRNAs in human lesions, and the complexity of alternatively spliced transcripts derived from different promoters, it has not been possible to ascertain the exact structures of the majority of the mRNA species and the proteins encoded. We have adapted the recently developed polymerase chain reaction to amplify cDNAs of rare, type 11 HPV mRNAs isolated from a productively infected human foreskin xenograft in an athymic mouse. The oligonucleotide primers were designed to flank each of the mRNA splice sites previously mapped by electron microscopic analysis of heteroduplexes formed between cloned HPV-11 DNA and viral mRNAs isolated from genital warts. The splice junctions were determined by direct sequencing of the PCR-amplified cDNA products or after the cDNA was cloned into a plasmid vector. We provide the first direct evidence for the existence of rare mRNAs with the potential to encode regulatory proteins that have been hypothesized to exist for HPVs. Depending on the lengths of the upstream exons, the translation frame used and the possibility of internal reinitiation during translation, one pair of mRNAs with the same splice junction could encode the viral DNA copy number modulating protein E1-M, the enhancer repression protein E2-C, or both. A second pair of mRNAs, also with identical splice junctions, encode the enhancer-regulating protein E2; the longer of the two could also encode, in its 5' exon, either or both of the E6 and E7 proteins. Finally, we demonstrate that the doubly spliced late message for the major virion capsid protein L1 also contains the entire coding region for the early E1 E4 protein in the first two exons, with the initiation codon for the L1 protein located precisely at the splice acceptor of the third exon. The potential of this late mRNA to encode both the E1 E4 protein and the capsid protein could contribute to the preponderance of the E4 protein in the lesion.

Genetic diagnosis of the preimplantation embryo

Genetic diagnosis and therapy is well established in the antenatal period. The advancement of uterine and in vitro fertilization allow access to the early blastocyst. Simultaneously, laboratory techniques are being miniaturized to be sufficiently sensitive and specific for diagnosis with only a few cells. Thus genetic diagnosis and therapy may be extended from the antenatal patient to the antegravid patient. This article discusses the techniques of uterine lavage and in vitro fertilization as well as the diagnostic possibilities that this early embryonic period offers.

Bifunctional oligonucleotide probes synthesized using a novel CPG support are able to detect single base pair mutations

A novel multifunctional controlled pore glass, MF-CPG (Fig. 1), has been synthesized and used to incorporate 3' terminal primary aliphatic amines into synthetic oligonucleotides. MF-CPG consists of a unique succinic acid linking arm which possesses both a masked primary amine for label attachment and a dimethoxytrityl protected hydroxyl for nucleotide chain elongation. Using MF-CPG, we have devised a simple and convenient technique to attach non-radioactive labels to the 3' terminus of oligonucleotides. Bifunctional probes can then be constructed by 32P labeling the 5' terminus with T4 kinase and gamma 32P-ATP. Using such bifunctional oligonucleotide probes in conjunction with polymerase chain reaction (PCR) amplification, we were able to detect single base substitutions in a target segment of the human H-ras protooncogene employing either functionality. Our technique thus expands the potential applications for oligonucleotides as hybridization probes.

The polymerase chain reaction: an improved method for the analysis of nucleic acids

The polymerase chain reaction (PCR) is a method for the selective amplification of DNA or RNA segments of up to 2 kilobase-pairs (kb) or more in length. Synthetic oligonucleotides flanking sequences of interest are used in repeated cycles of enzymatic primer extension in opposite and overlapping directions. The essential steps in each cycle are thermal denaturation of double-stranded target molecules, primer annealing to both strands and enzymatic synthesis of DNA. The use of the heat-stable DNA polymerase from the archebacterium Thermus aquaticus (Taq polymerase) makes the reaction amenable to automation. Since both strands of a given DNA segment are used as templates, the number of target sequences increases exponentially. The reaction is simple, fast and extremely sensitive. The DNA or RNA content of a single cell is sufficient to detect a specific sequence. This method greatly facilitates the diagnosis of mutations or sequence polymorphisms of various types in human genetics, and the detection of pathogenic components and conditions in the context of clinical research and diagnostics; it is also useful in simplifying complex analytical or synthetic protocols in basic molecular biology. This article describes the principles of the reaction and discusses the applications in different areas of biomedical research.