Diagnosis of genetic disease by primer-specified restriction map modification, with application to cystic fibrosis and retinitis pigmentosa

A simple PCR-based genotyping method for M105I mutation of alpha-SNAP enhances the study of early pathological changes in hyh phenotype

alpha-SNAP is an essential component of the protein machinery responsible for membrane fusion events in different cell types. The hyh (hydrocephalus with hop gait) mouse carries a missense mutation in Napa gene that results in a point mutation (M105I) in alpha-SNAP protein. Homozygous animals for the mutant allele have been identified by the clinical and/or neuropathological phenotype, or by direct sequencing of PCR products. The aims of the present study were (i) to develop a high-throughput technique to genotype hyh mice, (ii) to correlate genotype-phenotype, and (iii) to analyze the earliest pathological changes of hyh mutant mice. As no restriction sites are affected by the hyh mutation, we resolved this problem by creating a BspHI restriction site with a modified (mismatch) polymerase chain reaction (PCR) primer in wild-type allele. This artificially created restriction site (ACRS)-PCR technique is a simple, rapid and reliable method to genotype hyh mice in a day-work procedure. Biochemical and histological analysis of genotyped hyh embryos at different developmental stages allowed us to identify and characterize the earliest brain pathological changes of the hyh phenotype, including the first signs of neuroepithelial disruption and neuronal ectopia. In addition, genotype-phenotype analysis of 327 animals confirmed that (i) hyh is a single-gene autosomal recessive disorder, and (ii) the disorder has 100% penetrance (i.e., the mutation was only present in affected mice). The genotyping method described here enhances the potentiality of hyh mouse as a unique in vivo model to study the role of membrane trafficking in different developmental and physiological processes.

Rapid and sensitive detection of Lophophora williamsii by loop-mediated isothermal amplification

We have developed a convenient method for the detection of Lophophora williamsii using loop-mediated isothermal amplification (LAMP). We designed six species-specific primers for L. williamsii, including two loop primers. This L. williamsii-specific primer set was used for LAMP of total DNA extracted from L. williamsii and from L. diffusa. Real-time monitoring of LAMP was achieved by measuring turbidity due to the formation of magnesium pyrophosphate. Amplification occurred in samples mixed with total DNA from L. williamsii, but not in those mixed with total DNA from L. diffusa. We could also visually observe L. williamsii by adding fluorescent detection reagent to the reaction tube and exposing it to UV light. This new method amplified L. williamsii selectively and is expected to be applicable to the detection of peyote.

Transgenic mice carrying the H258N mutation in the gene encoding the beta-subunit of phosphodiesterase-6 (PDE6B) provide a model for human congenital stationary night blindness

Mutations in the beta-subunit of cGMP-phosphodiesterase (PDE6beta) can lead to either progressive retinal disease, such as human retinitis pigmentosa (RP), or stationary disease, such as congenital stationary night blindness (CSNB). Individuals with CSNB in the Rambusch pedigree were found to carry the H258N allele of PDE6B (MIM# 180072); a similar mutation was not found in RP patients. This report describes an individual carrying the H258N allele, who presented with generalized retinal dysfunction affecting the rod system and a locus of dysfunction at the rod-bipolar interface. Also described are preclinical studies in which transgenic mice with the H258N allele were generated to study the pathophysiological mechanisms of CSNB. While Pde6b(rd1)/Pde6b(rd1) mice have severe photoreceptor degeneration, as in human RP, the H258N transgene rescued these cells. The cGMP-PDE6 activity of dark-adapted H258N mice showed an approximate three-fold increase in the rate of retinal cGMP hydrolysis: from 130.1 nmol x min(-1) x nmol(-1) rhodopsin in wild-type controls to 319.2 nmol x min(-1) x nmol(-1) rhodopsin in mutants, consistent with the hypothesis that inhibition of the PDE6beta activity by the regulatory PDE6gamma subunit is blocked by this mutation. In the albino (B6CBA x FVB) F2 hybrid background, electroretinograms (ERG) from H258N mice were similar to those obtained from affected Rambusch family members, as well as humans with the most common form of CSNB (X-linked), demonstrating a selective loss of the b-wave with relatively normal a-waves. When the H258N allele was introduced into the DBA background, there was no evidence of selective reduction in b-wave amplitudes; rather a- and b-wave amplitudes were both reduced. Thus, factors other than the PDE6B mutation itself could contribute to the variance of an electrophysiological response. Therefore, caution is advisable when interpreting physiological phenotypes associated with the same allele on different genetic backgrounds. Nevertheless, such animals should be of considerable value in further studies of the molecular pathology of CSNB.

A Study of Plant DNA Polymorphism Experiments for Students

Advances in molecular biology are being made in the fields of science, medicine, and pharmacy. The majority of students graduating from pharmaceutical university departments will be required to have knowledge of molecular biology techniques. Although it is not difficult to perform DNA experiments in a laboratory, they involve a series of operations. Therefore it is difficult to include such experiments in the curriculum for students at our university because of safety concerns and the experimental equipment and time required. This paper introduces a convenient experiment on plant DNA polymorphism using a polymerase chain reaction-restriction fragment-length polymorphism (PCR-RFLP) method that we developed. This experiment enables each student to handle DNA safely. Total DNA is extracted from a piece of leaf derived from Aconitum carmichaeli or Aquilegia flabellate, the nuclear 5.8S rRNA region is amplified by PCR, and the PCR product is digested by restriction enzymes. Different polymorphisms in the plants can be visualized on electrophoregrams. The total time required for the experiments is 2 days (about 4 h per day). In the field of pharmacognosy, authentication of herbal medicine using genetic analysis is increasingly important. Plant DNA polymorphisms required the same knowledge and techniques as genetic analysis and are part of the course content in medicinal plant science. The PCR-RFLP experiment proposed here is a suitable method to acquire molecular biological knowledge and techniques.

Application of single-nucleotide polymorphism analysis of the trnK gene to the identification of Curcuma plants

We previously found that Curcuma plants and drugs derived from Curcuma longa, C. phaeocaulis, C. zedoaria, and C. aromatica could be identified by the nucleotide differences at two sites and the existence of a 4-base indel on trnK gene. In this paper, based on species-specific nucleotide sequences, the application of a new method, single-nucleotide polymorphism (SNP) analysis was investigated to identify Curcuma plants more conveniently. First, three types of reverse primer were synthesized in different lengths, 34 mer, 26 mer, and 30 mer, to anneal the template DNAs from each species at sites immediately upstream from substitution positions 177 and 645, and at the site including the 4-base insertion from 728 to 731, respectively. After single-base extension reaction of these primers using fluorescent-labeled ddNTPs and PCR products of the trnK gene region as template, the resulting products were detected using an ABI PRISM 310 Genetic Analyzer. The electrophoretogram showed three or two peaks at different positions depending on the 27 mer, 31 mer, and 35 mer product lengths. Each peak was derived from the incorporated fluorescent-labeled ddNMPs complementary to template nucleotides at positions 645, 724, and 177, respectively. C. phaeocaulis showed three peaks of ddCMP, ddAMP, and ddAMP. The other three species showed two peaks derived from 27 mer and 35 mer products: peaks of ddCMP and ddAMP in C. longa, those of ddCMP and ddTMP in C. zedoaria, and those of ddTMP and ddAMP in C. aromatica. Thus SNP analysis to identify four Curcuma plants was newly developed.

dCAPS, a simple technique for the genetic analysis of single nucleotide polymorphisms: experimental applications in Arabidopsis thaliana genetics

PCR-based detection of single nucleotide polymorphisms is a powerful tool for the plant geneticist. Cleaved amplified polymorphic sequence analysis is the most widely used approach for the detection of single nucleotide polymorphisms. However, this technique is limited to mutations which create or disrupt a restriction enzyme recognition site. This paper presents a modification of this technique where mismatches in a PCR primer are used to create a polymorphism based on the target mutation. This technique is useful for following known mutations in segregating populations and genetic mapping of isolated DNAs used for positional based cloning of new genes. In addition, a computer program has been developed that facilitates the design of these PCR primers.

Genetic typing of the mouse and rat nude mutations by PCR and restriction enzyme analysis

A genetic typing method for the mouse and rat nude mutations by PCR and restriction fragment length polymorphism (RFLP) analysis was developed. Since restriction sites useful for RFLP analysis do not exist in the mouse nu and rat rnu mutations, artificial restriction sites were introduced by PCR with modified primers. Three genotypes in the mouse (nu/nu, nu/+ and +/+) or rat (rnu/rnu, rnu/+ and +/+) are rapidly differentiated with the PCR-RFLP assay. In addition, congenic nude strains can be efficiently established by using this assay. Finally, genetic mapping of the rnu locus was performed with microsatellite markers. The locus order on rat chromosome 10 was D10Mgh14-(2.0cM)-D10Mit2-(1.4cM)-rnu-(0.7cM++ +)-D10Mgh6-(2.7cM)-D10Mit8.

Allele walking: a new and highly accurate approach to HLA-DRB1 typing. Application to DRB1*04 alleles

We have developed a typing method, which can be used even in small laboratories, to produce a highly accurate and reliable allele assignment in any homozygous or heterozygous situation. We have called the method allele walking (AW) and it consists of sequential rounds of PCR-RFLP. After digestion, electrophoresis separates alleles positive for the mutation from the negative alleles; the cleaved fragment is then recovered from the gel and analyzed for mutations at another codon. In this way, AW is able to positively ascertain which mutations are in the same chromosome (cis-linkage) and assigns alleles independently from each other. Artificial sites are created in the PCR step in order to positively detect substitutions not naturally recognized by any of the existing or convenient enzymes. We report the application of AW for typing the 22 DRB1*04 alleles. The first PCR-RFLP round groups DRB1*04 alleles. Subsequently, the mutations at codons 86, 74, 71, 57 and 37 can be analyzed for the unambiguous assignment of the majority of the alleles. Additional polymorphisms at different codons can be assayed to resolve any undetermined alleles. The viability of all the restriction sites used as well as the feasibility of AW were successfully tested.

Allele-specific restriction analysis of human platelet antigen system 4

BACKGROUND

Diagnosis, and occasionally treatment, of disorders involving platelet-specific alloimmunization, including neonatal alloimmune thrombocytopenia and posttransfusion purpura, requires platelet allotyping. Allele-specific restriction analyses for convenient genotyping are available for the major human platelet antigen (HPA) systems except HPA-4.

STUDY DESIGN AND METHODS

An allele-specific restriction analysis for HPA-4 was developed by designing a polymerase chain reaction primer containing a single-base substitution (A for T) at glycoprotein IIIa cDNA position 529. The resulting mismatch did not interfere with DNA amplification. Digestion of the polymerase chain reaction product with BsmI allowed differentiation of HPA-4a and HPA-4b alleles.

RESULTS

A 126-bp polymerase chain reaction product was amplified with the novel primer. BsmI endonuclease cleaved product encoding HPA-4a into 104- and 22-bp fragments and left DNA encoding HPA-4b intact.

CONCLUSION

This rapid allele-specific restriction analysis for genotyping the HPA-4 system complements similar methods for other platelet alloantigenic determinants.

Detection of germline mutations in the von Hippel-Lindau disease gene by the primer specified restriction map modification method

Von Hippel-Lindau disease (VHL) is an inherited disorder characterised by a predisposition to develop tumours in the eyes, central nervous system, kidneys, and adrenal glands. Recently the VHL gene was cloned and shown to be mutated in 75% of US and Canadian VHL families. To develop simple, rapid methods for the detection of mutations found in large numbers of affected people, we designed based on the primer specified restriction site modification method. These tests have proved useful in identifying asymptomatic mutated VHL gene carriers who have the nt 505 T to C mutation or the nt 686 T to C mutation. Together with an MspI digestion test which can detect a mutation hot spot in codon 238, polymerase chain reaction/restriction endonuclease based tests can now detect VHL mutations in more than 50% of VHL type 2 families.

Multiplex genotype determination at a DNA sequence polymorphism cluster in the human immunoglobulin heavy-chain region

We have developed a method for multilocus genotype determination. The method involves using restriction fragment length polymorphisms (RFLPs) for allele discrimination. If a polymorphism is not an RFLP, it is converted into an RFLP during the polymerase chain reaction (PCR). After amplification and restriction enzyme digestion, samples are analyzed by sequential gel loading during electrophoresis. The efficiency of this method was demonstrated by determining the genotypes of 108 semen samples at seven DNA sequence polymorphic sites identified in the human immunoglobulin heavy-chain variable region. It was shown that more than 1000 PCR products could be easily analyzed per day per investigator. To show the reliability of this method, some of the typing results were confirmed by DNA sequence analysis. By computer simulation, most (98%) polymorphisms were shown to be natural or convertible (by changing 1 bp close to or next to each polymorphic site) RFLPs for the commercially available 4-base cutters.

Structure and expression of the CYP21 (P450c21, steroid 21-hydroxylase) gene with respect to its deficiency

Steroid 21-hydroxylase (P450c21) deficiency is the major cause of a common genetic disease, congenital adrenal hyperplasia, with the symptoms of virilization due to steroid imbalance. We have devised a fast diagnostic method to detect common mutations in the c21B gene by a two-step gene amplification procedure coupled to restriction digestion. This procedure does not require isotopes and is suitable for routine use in a hospital setting. In addition, we have developed a procedure for the production of active P450c21 in E. coli. We tested many different vector and bacterial strain combinations to find out the best condition for P450c21 expression. The bacteria harboring the P450c21 expression plasmid were grown in a rich media supplemented with trace metals, heme biosynthesis precursor delta-levulinic acid, and induced with IPTG at 20 degrees C for 48 h. We found that low growth temperature and long induction time were important for abundant synthesis of P450c21 in E. coli.

Discrimination between metachromatic leukodystrophy and pseudo-deficiency of arylsulfatase A by restriction digest of amplified gene fragments

Mutations causing metachromatic leukodystrophy and pseudo-deficiency were detected in the arylsulfatase A gene by methods based on different wild-type and mutant restriction sites. After polymerase chain reaction amplification of fragments of the arylsulfatase A gene and digestion by the appropriate endonuclease, the mixtures were separated by polyacrylamide gel electrophoresis and visualized by ethidium bromide staining. The common splice mutation in intron 2 (459 + 1G-->A) causing, in homozygosity, late-infantile metachromatic leukodystrophy and the common missense mutation in exon 8 (P426L) causing, in homozygosity, adult or juvenile metachromatic leukodystrophy were found to abolish Bst NI and Aci I sites, respectively. The polyadenylation pseudo-deficiency mutation (1619A-->G) was found to create a Mae III restriction site. The N-glycosylation pseudo-deficiency mutation (N350S) does not produce or destroy any known restriction site, and in this case, introduction of a single nucleotide mismatch in one of the primers enabled the authors to create a Bfa I site in the mutant allele.

Diagnosis of mutations by the PCR double RFLP method (PCR-dRFLP)

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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.

Current methods of mutation detection

Mutation detection is important in all areas of biology. Detection of unknown mutations can involve sequencing of kilobases of DNA, often in many patients. This has lead to the development of methods to screen DNA for mutations as well as methods to detect previously described mutations. This review discusses current methods used for such purposes with special emphasis on genetic diseases of humans. However, savings can be made by similar means in other areas of biology where repetitive or extensive sequencing for comparative purposes needs to be done. This review covers the methods used for detection of unknown mutations, namely the ribonuclease, denaturing gradient-gel electrophoresis, carbodiimide, chemical cleavage, single-strand conformation polymorphism, heteroduplex and sequencing methods. Once mutations have been defined they can be searched for repeatedly by methods referred to as diagnostic methods. Such methods include allele-specific oligonucleotide hybridization, allele-specific amplification, ligation, primer extension and the artificial introduction of restriction sites. We can now choose from a range of excellent methods, but the choice will usually depend on the background of the laboratory and/or the application in hand. Screening methods are evolving to more satisfactory forms, and the diagnostic methods can be automated to screen whole populations inexpensively.

A microtitre format point mutation assay: application to the detection of drug resistance in human immunodeficiency virus type-1 infected patients treated with zidovudine

An assay for the analysis of point mutations in DNA fragments amplified by the polymerase chain reaction is described. The method was applied to the analysis of mutations leading to single amino acid changes in the reverse transcriptase gene of human immunodeficiency virus type-1 that are associated with decreased sensitivity of the virus to the effects of the nucleoside analogue zidovudine. The assay uses a microtitre format allowing large numbers of clinical samples to be analysed, and is a quantitative assay giving information on the relative proportions of wild-type and mutant sequence at the point being analysed. The analysis of mutations in codons 67, 70, 215, and 219 of the RT gene in samples taken at various time points after the commencement of zidovudine therapy shows a high variability in the rate at which these mutations arise and in the proportions of wild-type and mutant sequences observed. The method we describe has wide application to the analysis of other point mutations in clinical or research studies.

Regulation of plasma membrane recycling by CFTR

The gene that encodes the cystic fibrosis transmembrane conductance regulator (CFTR) is defective in patients with cystic fibrosis. Although the protein product of the CFTR gene has been proposed to function as a chloride ion channel, certain aspects of its function remain unclear. The role of CFTR in the adenosine 3',5'-monophosphate (cAMP)-dependent regulation of plasma membrane recycling was examined. Adenosine 3',5'-monophosphate is known to regulate endocytosis and exocytosis in chloride-secreting epithelial cells that express CFTR. However, mutant epithelial cells derived from a patient with cystic fibrosis exhibited no cAMP-dependent regulation of endocytosis and exocytosis until they were transfected with complementary DNA encoding wild-type CFTR. Thus, CFTR is critical for cAMP-dependent regulation of membrane recycling in epithelial tissues, and this function of CFTR could explain in part the pleiotropic nature of cystic fibrosis.