Diagnosis of genetic disease using recombinant DNA

Opportunities and challenges associated with clinical diagnostic genome sequencing: a report of the Association for Molecular Pathology

This report of the Whole Genome Analysis group of the Association for Molecular Pathology illuminates the opportunities and challenges associated with clinical diagnostic genome sequencing. With the reality of clinical application of next-generation sequencing, technical aspects of molecular testing can be accomplished at greater speed and with higher volume, while much information is obtained. Although this testing is a next logical step for molecular pathology laboratories, the potential impact on the diagnostic process and clinical correlations is extraordinary and clinical interpretation will be challenging. We review the rapidly evolving technologies; provide application examples; discuss aspects of clinical utility, ethics, and consent; and address the analytic, postanalytic, and professional implications.

Direct endonuclease digestion and multi-analysis of restriction fragment length polymorphisms by microchip electrophoresis

A high-performance multi-analysis system for genotypic mutation by means of restriction fragment length polymorphisms (RFLP) involving endonuclease treatment of PCR-amplified DNA on a microchip and subsequent analysis by microchip electrophoresis for DNA sizing was developed. A Hitachi SV1210 system, with which 12 samples can be analyzed on a plastic chip with good accuracy as to DNA sizing between 25 and 300 bp, was employed for RFLP analysis. We performed RFLP analysis of the ABO genotypes of blood donors for whom the ABO type was known. Six blood samples were analyzed by PCR to amplify two different regions of the genomic DNA, each of the amplified DNAs containing a different nucleotide polymorphism. To analyze the genes at polymorphic sites 261 and 526, restriction endonucleases Kpn I and Ban I were employed, respectively. When an amplified DNA was digested with each endonuclease on a microchip for 20 min, sequential analysis revealed the presence or absence of the respective restriction site. This analysis was performed within 7 min using a 1/10 volume of a DNA sample in comparison with the conventional method, and the estimated DNA size differed from the predicted size by less than 10 bp. The results indicate the potential of microchip electrophoresis for RFLP with on-chip direct endonuclease digestion and sequential analysis, offering high resolution in a short time.

DNA fingerprints of dogs and cats

Human minisatellite probes consisting of tandem repeats of the 'core' sequence, a putative recombination signal in human DNA, cross-hybridize to multiple polymorphic fragments in dog and cat DNA to produce individual-specific DNA 'fingerprints'. Pedigree analysis shows that most of the DNA fragments detected in an individual are heterozygous, and that these fragments are derived from multiple dispersed autosomal loci. DNA fingerprints of cats and dogs should prove suitable for individual identification and for establishing family relationships. They are also suitable for rapid marker generation in large pedigrees and could be applied to linkage analysis in these animals.

Human gene mapping

It is now possible to map the human genome completely with a set of closely linked markers. Over 500 coding genes have been cloned and localized, as have approximately 2000 anonymous DNA fragments, most of which recognize two-allele polymorphisms that are caused by single base changes which alter the recognition site for a restriction enzyme (restriction fragment length polymorphisms). Most human chromosomes have been mapped, with markers in defined order placed approximately 10 map units apart. Chromosomes X and 21 are particularly well mapped, with over 200 probes ordered on X. The strategy during the next few years will encompass moving from a linkage map to a set of overlapping cosmid or phage clones, and finally to a complete sequence of regions of chromosomes and entire chromosomes. A complete sequence of the human genome should transform our understanding of development, the control of gene expression, and the parameters of genetic disease.

Strategies and applications of DNA level diagnosis in genetic diseases: past experiences and future directions

The development of technologies towards the detection of mutations represents one of the most important areas of molecular biology. It has played a pivotal role in the tremendous success of the elucidation of complex biological problems, including genetic diseases. Today, these proven and emerging technologies have become the basis of successful biological investigations. More importantly, they are expected to play a central role in medicine, particularly the diagnosis and prognosis of genetic diseases including genetic predispositions, the assessment of treatments including transplants and decisions on reproductive choices. In addition, these technologies hold the key to future breakthroughs. This review provides an up-to-date examination of the principles of genetic diseases, the theories behind current methods of genetic diagnosis and detection of mutations including strategies for modification and the development of future technologies as they impact on the practice of medicine and on society as a whole.

Diagnosis of human genetic disease using recombinant DNA. Fourth edition

Recombinant DNA methodology has greatly increased our knowledge of the molecular pathology of the human genome at the same time as providing the means of diagnosing inherited disease at the DNA level. Direct detection and analysis of a wide range of genetic lesions are now possible using cloned gene or oligonucleotide probes or by direct sequencing of the disease gene(s). In addition, the use of restriction fragment length polymorphisms (RFLPs) within and around these genes as indirect genetic markers has potentiated the tracking of disease alleles in affected pedigrees in cases where direct analysis is not yet feasible. RFLPs associated with linked anonymous DNA segments may also be used not only to diagnose hitherto undetectable disease states, but also for the chromosomal localization of the loci responsible. We present here an update to our previous list of reports describing the direct and indirect analysis/diagnosis of human inherited disease. This compilation is intended to serve as a guide to current molecular genetic approaches in diagnostic medicine.

Immunoenzymatic techniques applied to the specific detection of nucleic acids. A review

Numerous enzymatic and chemical methods are now available for the preparation of non-radioactive nucleic acid probes. Labels, such as enzymes, fluorophores, lumiphores can be attached to the nucleic acid probe either by covalent bonds (direct labelling) or by biospecific recognition after hybridization (indirect labelling). The principle of the latter method is based on the use of a hapten-labelled nucleic acid probe which is generally detected by an immunoenzymatic assay. Indirect labelling has several advantages: this procedure uses multienzyme complexes to increase the number of enzyme molecules associated with hybridization and hence provides an increase in detectability; moreover, haptens (biotin, dinitrophenol, acetylaminofluorene analogues, digoxigenin, brominated or sulphonylated pyrimidines) used to label nucleic acid probes are not sensitive to elevated temperatures (42-80 degrees C), extended incubation times (several hours), detergents and organic solvents currently required in hybridization techniques. The application of the immunoenzymatic and related techniques to nucleic acid probing is reviewed, focussing on the strategies of non-radioactive hybridization, hapten-labelling of nucleic acids and methods for the immunodetection of the hybrids.

Alkyl- and aryl-substituted salicyl phosphates as detection reagents in enzyme-amplified fluorescence DNA hybridization assays on solid support

Nine salicyl phosphate esters with hydrophobic substituents (5-phenyl, 5-(2,4-difluorophenyl), 5-tert-octyl, 5-cumyl, 5-(4-tert-butylphenyl, 5-(1-adamantyl), 5-(n-dodecyl), 5-(1,1-diphenylethyl, and 5-trityl) were synthesized and found to be good substrates for calf intestinal alkaline phosphatase. The enzymatic hydrolysis produced the corresponding salicylates, which were strongly fluorescent when excited by ultraviolet light around 300 nm with maximum emission at 420-435 nm. The salicylates were less soluble and/or more adhesive than the nonfluorescent salicyl phosphate substrates, resulting in localization of fluorescence signal, which is a requirement for membrane-based assays. The salicyl phosphates bearing 8-14 carbon substitutents were found to be suitable detection reagents for dot-blot DNA hybridization assays on nylon membrane using a biotinylated probe, allowing the detection of 125 pg of target pBR322 plasmid DNA using a simple apparatus consisting of a transilluminator, a camera. and a 455-nm cutoff optical filter.

Diagnosis of genetic disease using recombinant DNA. Third edition

Recombinant DNA methodology has greatly increased our knowledge of the molecular pathology of the human genome at the same time as providing the means to diagnose inherited disease at the DNA level. Direct detection and analysis of a range of genetic defects are now possible using cloned gene or oligonucleotide probes or by direct sequencing of the disease gene(s). In addition, the use of restriction fragment length polymorphisms (RFLPs) within and around these genes as indirect genetic markers has not potentiated the tracking of disease alleles in affected pedigrees in cases where direct analysis was not feasible. RFLPs associated with linked anonymous segments may also be used not only to diagnose hitherto undetectable disease states, but also for chromosomal localization of the loci responsible. We present here an updated list of reports describing both the direct and the indirect analysis/diagnosis of human inherited disease; it is intended to serve as a guide to current molecular genetic approaches in diagnostic medicine.

Forensics of birds of prey by DNA fingerprinting with 32P-labeled oligonucleotide probes

Paternity tests on confiscated families of eight species of birds of prey were carried out successfully by DNA fingerprinting with 32P-labeled oligonucleotide probes. Variations in the number of hybridized fragments, depending on the species of birds, are observed using the same probe, as well as differences of polymorphism by hybridizing the DNA samples with several oligonucleotide probes.

Diagnosis of genetic disease using recombinant DNA. Second edition

Recombinant DNA methodology has greatly increased our knowledge of the molecular pathology of the human genome at the same time as providing the means to diagnose inherited disease at the DNA level. Direct detection and analysis of a range of genetic defects are now possible using cloned gene or oligonucleotide probes or by direct sequencing of the disease gene(s). In addition, the use of restriction fragment length polymorphism (RFLPs) within and around these genes as indirect genetic markers has now potentiated the tracking of disease alleles in affected pedigrees in cases where direct analysis was not feasible. RFLPs associated with linked anonymous segments may also be used not only to diagnose hitherto undetectable disease states, but also for chromosomal localization of the loci responsible. We present here an up-to date list of reports describing both the direct and the indirect analysis/diagnosis of human inherited disease, which is intended to serve as a guide to current molecular genetic approaches in diagnostic medicine.

Dystrophin-related muscular dystrophies

The gene for the locus involved in Duchenne and Becker muscular dystrophies has been cloned and subject to intense analysis. The protein product of the locus is called dystrophin, and it has been shown to be associated with the muscle fiber membrane. The new knowledge of the molecular genetics of these disorders is being applied rapidly in clinical practice. Carrier detection and prenatal diagnosis have been revolutionized by the use of probes for the gene. These probes are also being employed to clarify cases where conventional clinical examination results in equivocal diagnoses. It is suggested that the disorders characterized by dystrophin abnormalities should be called dystrophin-related muscular dystrophies (DRMD). There are mouse and dog models for DRMD and these are being used to explore therapeutic strategies for treating DRMD patients.

Micro extraction of DNA from whole blood and amniocytes

We describe methods for extracting genomic DNA from a small amount of whole blood or cultured amniocytes. Nuclear DNA was extracted from whole blood spotted on blotting paper. Relatively large molecules of DNA with the average amount of 7-9 micrograms was extracted from 1 ml of blood spotted and stored for at most two years, being roughly 1/3 of that extracted directly from fresh whole blood. The estimated minimum amount of whole blood that gives a suitable autoradiogram of Southern hybridization was 0.3 ml. Another series of amounts of whole blood or an amniocyte suspension were molded in low-melting agarose into an 100 microliter gel block. The DNA extracted from a block that was made from at least 0.25 ml of whole blood, or from 1.25 x 10(5) amniocytes (equivalent to 1/8 of the number of confluent cells in a 25 cm2 culture flask) resulted in one suitable Southern analysis. Both methods described here are applicable to the diagnosis of newborns and/or fetuses at risk of a genetic disease and to the diagnosis of a patient from whom a large amount of blood material is difficult to obtain. These methods also make a long-way transportation of the materials possible.

The ligation amplification reaction (LAR)--amplification of specific DNA sequences using sequential rounds of template-dependent ligation

A novel DNA sequence detection method that utilizes the ligation of oligonucleotide pairs that are complementary to adjacent sites on appropriate DNA templates is described. The product is increased by either linear or exponential amplification using sequential rounds of template-dependent ligation. In the case of linear amplification, a single pair of oligonucleotides is ligated, the reaction is heated to dissociate the ligation product, and an additional round of ligation is performed. After n rounds there is a (1 + x) X n-fold amplification of product, where x is the efficiency of the ligation reaction. Exponential amplification utilizes two pairs of oligonucleotides, one complementary to the upper strand and one to the lower strand of a target sequence. The products of the ligation reaction serve as templates for subsequent rounds of ligation. In this case there is (1 + x)(n-1)-fold amplification of product after n rounds. A single base-pair mismatch between the annealed oligonucleotides and the template prevents ligation, thus allowing the distinction of single base-pair differences between DNA templates. At high template concentrations, the ligation reaction has an efficiency approaching 100%. In this report, we demonstrate the use of the ligation amplification reaction (LAR) to distinguish the normal from the sickle cell allele of the human beta-globin gene. We also report the use of LAR as a detection system for polymerase chain reaction-enriched DNA sequences.

Applications of molecular genetics to gastrointestinal and liver diseases. II. Clinical relevance

The use of DNA probes within or near disease genes is becoming increasingly important in clinical medicine. Probes are available for prenatal and carrier diagnosis for several of the more than 100 genetic diseases of the gastrointestinal tract and liver. These include familial adenomatous polyposis, haemochromatosis, cystic fibrosis, alpha 1-antitrypsin deficiency and the hereditary porphyrias. This review uses examples drawn from such diseases to show the relevance of these approaches to the clinician.

The use of DNA probes in preimplantation and prenatal diagnosis

DNA probes are now widely used for prenatal diagnosis, but the prospect of preimplantation diagnosis of genetic disorders requires the development of sensitive genetic tests that can be performed on small numbers of cells removed from a preimplantation-stage pre-embryo. The sensitivity of molecular tests can now be increased by specifically amplifying the target DNA with the polymerase chain reaction. In situ hybridisation with chromosome-specific DNA probes to repeated sequences also permits the detection of particular numerical chromosome aberrations or the distinction of male and female pre-embryos when only a few interphase nuclei are available. We have used in situ hybridisation to a Y chromosome-specific DNA probe to sex preimplantation-stage pre-embryos and to sex fetuses from samples of chorionic villus cells, amniotic fluid cells, and fetal blood. These two approaches (amplification of target DNA and in situ hybridisation) provide suitable tests for improving prenatal diagnosis particularly when few cells are available and they offer the possibility of tests suitable for preimplantation diagnosis.

A genetic linkage study of a family with Norrie's disease

A family having one member with Norrie's disease, X-linked retinal dysplasia associated with hearing loss and mental retardation, was studied using DNA markers. The DNA markers were used to try and confirm the diagnosis of Norrie's disease by detecting a deletion of the X chromosome. Linkage analysis using the polymorphic DNA markers was performed and this allowed more accurate determination of the carrier status of two sisters of the affected boy than by empiric risk calculation. The advantage of multiple polymorphic DNA markers for linkage analysis is illustrated.

The role of cloned genes in the prevention of genetic disease

The application of recombinant DNA technology to the study of human genetic disease promises to increase the scope for carrier detection and prenatal diagnosis. Here we summarize current experience with prenatal diagnosis of single-gene disorders by DNA analysis and highlight some of the technical and organizational problems that remain to be solved.

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.

Human aldolase A deficiency associated with a hemolytic anemia: thermolabile aldolase due to a single base mutation

Fructose-1,6-bisphosphate aldolase A (fructose-bisphosphate aldolase; EC 4.1.2.13) deficiency is an autosomal recessive disorder associated with hereditary hemolytic anemia. To clarify the molecular mechanism of the deficiency at the nucleotide level, we have cloned aldolase A cDNA from a patient's poly(A)+ RNA that was expressed in cultured lymphoblastoid cells. Nucleotide analysis of the patient's aldolase A cDNA showed a substitution of a single nucleotide (adenine to guanine) at position 386 in a coding region. As a result, the 128th amino acid, aspartic acid, was replaced with glycine (GAT to GGT). Furthermore, change of the second letter of the aspartic acid codon extinguished a F ok I restriction site (GGATG to GGGTG). Southern blot analysis of the genomic DNA showed the patient carried a homozygous mutation inherited from his parents. When compared with normal human aldolase A, the patient's enzyme from erythrocytes and from cultured lymphoblastoid cells was found to be highly thermolabile, suggesting that this mutation causes a functional defect of the enzyme. To further examine this possibility, the thermal stability of aldolase A of the patient and of a normal control, expressed in Escherichia coli using expression plasmids, was determined. The results of E. coli expression of the mutated aldolase A enzyme confirmed the thermolabile nature of the abnormal enzyme. The Asp-128 is conserved in aldolase A, B, and C of eukaryotes, including an insect, Drosophila, suggesting that the Asp-128 of the aldolase A protein is likely to be an amino acid residue with a crucial role in maintaining the correct spatial structure or in performing the catalytic function of the enzyme.

Improved methods for the detection of unique sequences in Southern blots of mammalian DNA by non-radioactive biotinylated DNA hybridization probes

Biotinylated DNA hybridization probes offers a stable, cheap and non-radioactive alternative to probes labelled with 32P. Insufficient sensitivity has, however, up till now, been prohibitive for the use of such probes in detecting unique sequences in Southern blots of human DNA. By optimizing the steps in the procedure we have improved the sensitivity enough for such use. We have showed (1) that long probes (greater than 500 nucleotides) perform unproportionally better than short probes; (2) that a simple affinity labelling with avidin alkaline phosphatase conjugate performs better than laborious immunochemical systems; (3) that use of 3% BSA as blocking agent at 37 degrees C and the presence of 0.5 mol/l NaCl together with 1% BSA during the affinity labelling nearly eliminate background staining; (4) that a dramatic gain in sensitivity is gained by affinity labelling at pH 9.0 instead of 7.5; (5) that biotin-labelling can be highly reproducibly performed on a preparative scale with cheap and easily synthesized bio-11-dUTP in a two step nick-translation and (6) that biotinylated probes and hybridization mixtures can be stored for months and reused. The study has resulted in the presentation of a fast procedure, which is generally applicable to routine DNA diagnostic work, also in parts of the world where it is difficult to get a regular supply of 32P.

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.

Bioassays. Patents and literature

Bioassays, including immunoassays, enzyme assays, and assays using enzyme electrodes, and nucleic acid hybridization probes have been the subject of considerable industrial and academic research. New bioassay methods have applications in the medical, chemical, pharmaceutical, and food products industries. Recent US patents and scientific literature on a variety of new bioassay methods are surveyed. A description of these patents and a list of references are given.

Diagnosis of genetic disease using recombinant DNA. Supplement

Recombinant DNA methodology has greatly increased our knowledge of the molecular pathology of the human genome at the same time as providing the means to diagnose inherited disease as the DNA level. We present here a list of recent reports of both direct and indirect analysis of human inherited disease which is intended to serve as a guide to current molecular genetic approaches to diagnostic medicine.

Molecular pathology of single gene disorders

Recent studies using recombinant DNA technology have led to an understanding of the basic molecular pathology of single gene disorders. Furthermore, methods are being developed for finding genes for conditions, whose underlying biochemistry is still not understood, or which may contribute to polygenic systems that underlie common diseases. As well as providing new approaches to carrier detection, prenatal diagnosis, and treatment of single gene disorders, these advances promise to provide important information about the pathophysiology of many common polygenic diseases.

The impact of DNA analysis on fetal diagnosis

There has been rapid progress in mapping disease-specific gene loci to particular chromosomal regions and in cloning the relevant genes or DNA sequences that can act as genetic markers. These advances will have an impact on fetal diagnosis of monogenic disorders for a number of reasons, the most important being the ability to use chorionic villus DNA taken in the first trimester to make a fetal diagnosis, no matter how tissue-specific the gene defect. Diagnosis based on analysis of the protein gene product requires a tissue that is expressing that gene. In a few disorders the mutation within the gene can be detected directly, but more often an approach, termed gene tracking, will be required to predict the genotype of the fetus. This requires blood samples from a few family members and the analysis must be carried out prior to the chorion sampling and ideally before the pregnancy. This initial family study is required to determine whether gene tracking is possible in that particular family. A number of potential problems, both technical and in clinical management, highlight the need for close collaboration between clinical geneticists, molecular geneticists and obstetricians.

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.

Regional localization and characterization of a DNA segment on the long arm of chromosome 21

A human genomic DNA fragment, pAM37 (HGM8; D21S22), was mapped to chromosome 21q2.1-q2.21 by in situ hybridization. This segment is therefore situated on the boundary of the "pathological region" of Down syndrome. A genomic restriction map encompassing 35 kb of chromosome 21 was derived and two restriction fragment length polymorphisms (RFLPs) were mapped and characterized. A homologous sequence was detected in the mouse genome but no homologous RNA was detected in a range of human tissues. This DNA segment will contribute to the linkage mapping of chromosome 21 and will facilitate delineation of the pathological region of Down syndrome.