Allele-specific enzymatic amplification of beta-globin genomic DNA for diagnosis of sickle cell anemia

A sensitive, quantitative assay for measurement of allele-specific transcripts differing by a single nucleotide

We have found that the single nucleotide primer extension assay, a PCR-based assay currently used qualitatively to measure allelic differences in DNA, can be used quantitatively to measure allele-specific transcripts differing by only a single nucleotide. We show that total RNA containing the Pgk-1a transcript can be specifically detected even in a 1000-fold excess of RNA containing the Pgk-1b transcript.

Rapid HLA-DRB1 genotyping by nested PCR amplification

State of the art genotyping of HLA class II alleles with group-specific DNA amplification by the polymerase chain reaction (PCR) (1) and subsequent probing with sequence-specific oligonucleotides (2-4) is not suitable for typing cadaveric organ donors since the typing procedure takes far more than one working day. We designed specific oligonucleotide primer sets for nested PCR amplification which allowed typing for all serological HLA-DR specificities (DR1-DRw18) solely by the detection of amplified DNA in the reaction mixtures after agarose gel electrophoresis. Exon 2 of the DRB genes and a DRw52-group-specific part of DRB1 exon 2 was amplified directly from cell lysates without prior DNA extraction. The amplified DNA was subjected to a second round of amplification, which employed a set of 18 nested allele- or group-specific primer pairs. All alleles which have at least a single mismatched base at the terminal 3'-nucleotide of one primer were completely refractory to amplification. This assay is easy to perform and takes less than one working day to complete. Thus, this method may prove to be suitable for DNA typing of organ donors for prospective HLA-DR matching in renal transplantation.

Molecular genetic approaches to the analysis and diagnosis of human inherited disease: an overview

The advent of recombinant DNA technology has contributed enormously to our understanding of human genome pathology. In this review, current approaches to the analysis and diagnosis of human genetic disease are presented and their contribution to diagnostic medicine assessed. At the level of the gene, the nonrandom nature of human gene mutation is described and the role of the local DNA sequence environment explored.

From molecular variant to disease: initial steps in evaluating the association of transthyretin M119 with disease

Traditionally, clinical research has sought to determine the molecular basis of clinical signs and symptoms. Increasingly, the traditional process will be reversed, as many structural protein variants are elucidated as a result of powerful PCR-based methods. Herein we describe a variant of transthyretin (TTR) found by direct genomic sequencing and illustrate the utility of PASA (PCR amplification of specific alleles) in the initial characterization of such variants. TTR is an intriguing protein of unknown function, but deposition of mutant TTR produces familial amyloidotic polyneuropathy (FAP). We identify a carrier of a variant TTR in which threonine119 is changed to methionine (T119----M). T119 is invariant in five mammalian species, suggesting that this residue is important for normal protein function. To determine the frequency of the M119 variant, individuals of northern- and western-European descent were rapidly screened by generating a PASA assay for the sequence change. Four additional individuals were found to be heterozygous for the mutation, for a total of five M119 alleles in 1,666 genes (1/333). Clinical records, initial clinical interviews, and family history of these patients hint at a high frequency of early-onset venous insufficiency and perhaps mild renal dysfunction. Haplotype analysis on the heterozygotes could be performed, despite the absence of samples from relatives, by performing "double PASA." The haplotype data suggest that the M119 variant derives from a common ancestor. The putative functional deficiency caused by TTR M119 should be most marked in the homozygotes, who can be calculated to occur in 1/100,000 conceptions. If viable, these individuals may provide important clues about the physiological role of TTR. Although the nature (if any) of disease caused by TTR M119 remains to be defined, the genetic and clinical data indicate that this mutation does not cause FAP. Future family studies can determine whether the heterozygous state for TTR M119 cosegregates with a disease or trait.

Detection and discrimination of Mycoplasma pneumoniae and Mycoplasma genitalium by the in vitro DNA amplification

By using the primers designed on the bases of the sequences of the 16S rRNA genes of Mycoplasma pneumoniae and Mycoplasma genitalium, respectively, specific and sensitive in vitro DNA amplification assay system for the detection and discrimination of these two mycoplasmas was established. The detection limit of the assay was 100 cells for M. pneumoniae and 1,000 cells for M. genitalium. Neither other human mycoplasmas nor oral bacteria existing in human saliva showed any cross-reactions with these primers.

Trapped-oligonucleotide nucleotide incorporation (TONI) assay, a simple method for screening point mutations

We present a simple screening method for detecting a known point mutation, using only one 5'-biotinylated oligonucleotide primer, with its 3' end adjacent to the mutation site. In parallel reactions, an amplified DNA template encompassing the biotinylated oligonucleotide and mutation site undergoes 40 step-cycles of single nucleotide incorporation using Taq thermostable DNA polymerase and only one radioactive [alpha-32P]dNTP, specified by either the normal or mutant sequence. The oligonucleotides, now radioactively labelled at the 3' end according to the template sequence, are then trapped by streptavidin-coated magnetic beads, and the percent of radiolabel incorporated is determined directly by the Cerenkov method in a scintillation counter. The trapped-oligonucleotide nucleotide incorporation (TONI) assay has been used for the screening of a mitochondrial polymorphism, and has also been shown to distinguish the genotypes of hemoglobin A/C, A/A, A/S, and S/S. It is reproducible over at least a 100-fold range of radioisotope and a 10-fold range of oligonucleotide primer. This method is particularly useful for diagnosing mutations which do not produce alterations detectable by restriction enzyme analysis, since optimization of conditions is rarely necessary. In addition, it requires only a single oligonucleotide, and no electrophoretic separation of the allele-specific products. It thus represents an improved and simplified modification of the existing allele-specific primer extension methods (Kuppuswamy et al., Proc Natl Acad Sci USA 88:1143-1147, 1991; Sokolov, Nucl Acids Res 18:3671, 1989; Syvanen et al., Genomics 8:684-692, 1990).

A modified approach to identification of the sickle cell anemia mutation by means of allele-specific polymerase chain reaction

The allele-specific PCR approach has been modified by introducing a second mismatch at the 3'-penultimate link of the primer and used to identify the sickle cell anemia mutation (A-->T transversion in the sixth codon of the human beta-globin gene causing Glu-->Val substitution in the protein), thus obviating the problem of an interpretationally ambiguous 3'-terminal mismatch including T residue.

Genotyping and haplotyping of polymorphisms directly from genomic DNA via coupled amplification and sequencing (CAS)

Coupled amplification and sequencing (CAS) allows a segment of DNA to be sequenced directly from genomic DNA. An initial PCR amplification stage selects and amplifies the target. During a subsequent stage both strands of the target segment are sequenced simultaneously and amplified further. We show that CAS can readily identify variant base pairs. Genotyping of a population for known sequence variation can be achieved simply and directly from genomic DNA of each organism by performing CAS only for the variant bases. The procedure supercedes development and optimization of alternative typing assays based on oligonucleotide hybridization or ligation. In addition, we show that competitive oligonucleotide priming with allelic primers can be readily performed in concert with the second stage of CAS. The combination of techniques allows sequencing of a single chromosome from a heterozygous genomic sample and direct haplotyping of the polymorphism at the priming site with any others encompassed within the amplified segment.

The molecular characterization of an A:T to G:C transition in the Hbb-b1 gene of the murine homologue of hemoglobin Rainier

An N-ethyl-N-nitrosourea (ENU)-induced mutation in the Hbb-b1 gene of the mouse hemoglobin-beta complex (Hbb) has been shown to result in a high-oxygen affinity hemoglobin, homologous with hemoglobin Rainier in man (Peters, J., et al., Genetics 110:709, 1985). Substitution of beta 145 tyrosine by cysteine had occurred in both human and mouse forms, probably as the result of a point mutation. Provided that sufficient sequence information is available, point mutations can be directly and rapidly analyzed by allele-specific amplification (ASA), as this technique is sensitive enough to detect single nucleotide differences. We report the use of ASA to detect and characterize the mutation in the murine beta-globin gene, Hbb-b1d-m1, and find that the codon for beta 145 tyrosine (TAC) has been replaced by the codon for cysteine (TGC). Therefore, ENU induced an A:T----G:C transition.

Characterization of seven novel mutations of the c-erbA beta gene in unrelated kindreds with generalized thyroid hormone resistance. Evidence for two "hot spot" regions of the ligand binding domain

Genetic analysis in our laboratory of families with generalized thyroid hormone resistance (GTHR) has demonstrated tight linkage with a locus, c-erbA beta, encoding a nuclear T3 receptor. Three point mutations and two deletions in this locus have previously been reported in affected individuals in unrelated families as potential molecular bases for this disorder. In the present study, we have used direct sequencing of polymerase chain reaction-amplified exons of the c-erbA beta gene to rapidly identify novel point mutations from seven previously uncharacterized kindreds with GTHR. Six single base substitutions and one single base insertion were identified and found to be clustered in two regions of exons 9 and 10 in the ligand binding domain of the receptor: in the distal ligand-binding subdomain L2 and across the juncture of the taui and dimerization subdomains. Reduction of T3-binding affinity in each of four mutations tested as well as segregation of all mutations to clinically affected individuals strongly supports the hypothesis that these changes are the cause of GTHR in these kindreds. In view of the diversity of clinical phenotypes manifested, the distinct topographic clustering of the mutations provides an invaluable genetic tool for the molecular dissection of thyroid receptor function.

The polymerase chain reaction and its potential role in clinical diagnostics and research

In-vitro amplification of deoxyribonucleic acid molecules by means of the polymerase chain reaction (PCR) must be regarded as the most important advance in the life sciences to take place during the last decade. Originally applied to the identification of mutations in well-known and fully sequenced human genes, its applications have now been extended to a wide variety of biological and medical disciplines, accompanied by significant technical improvements and sophisticated variations of the basic principle. Specialized molecular genetics laboratories were the first to employ this new method, and they still are in the process of extending its potential. Due to its unique properties, applications of PCR quickly spread to other areas of research, and numerous clinical studies have already employed PCR. The field is currently still expanding rapidly.

Mutation detection

The detection and characterization of mutations in genes has become a major area of interest in many areas of biology. Such variation may account for speciation, tumour formation, drug resistance, as well as the more obvious nature of inherited disease.

Analysis of the gene sequences of the insulin receptor and the insulin-sensitive glucose transporter (GLUT-4) in patients with common-type non-insulin-dependent diabetes mellitus

Insulin resistance is a common feature of non-insulin-dependent diabetes mellitus (NIDDM) and "diabetes susceptibility genes" may be involved in this abnormality. Two potential candidate genes are the insulin receptor (IR) and the insulin-sensitive glucose transporter (GLUT-4). To elucidate whether structural defects in the IR and/or GLUT-4 could be a primary cause of insulin resistance in NIDDM, we have sequenced the entire coding region of the GLUT-4 gene from DNA of six NIDDM patients. Since binding properties of the IRs from NIDDM subjects are normal, we also analyzed the sequence of exons 16-22 (encoding the entire cytoplasmic domain of the IR) of the IR gene from the same six patients. When compared with the normal IR sequence, no difference was found in the predicted amino acid sequence of the IR cytoplasmic domain derived from the NIDDM patients. Sequence analysis of the GLUT-4 gene revealed that one patient was heterozygous for a mutation in which isoleucine (ATC) was substituted for valine (GTC) at position 383. Consequently, the GLUT-4 sequence at position 383 was determined in 24 additional NIDDM patients and 30 nondiabetic controls and all showed only the normal sequence. From these studies, we conclude that the insulin resistance seen in the great majority of subjects with the common form of NIDDM is not due to genetic variation in the coding sequence of the IR beta subunit, nor to any single mutation in the GLUT-4 gene. Possibly, a subpopulation of NIDDM patients exists displaying variation in the GLUT-4 gene.

Modified PCR-RFLP method for HLA-DPB1 and -DQA1 genotyping

We previously developed a new technique for HLA class II genotyping by digestion of polymerase chain reaction-amplified genes with restriction endonucleases (PCR-RFLP method). This PCR-RFLP method is an efficient and convenient typing technique for class II alleles. However, small fragments or bands located close to each other on polyacrylamide gels sometimes prevent precise analysis of the RFLP bands. Furthermore, the restriction enzymes we have reported in the previous papers are not sufficient to identify the genotypes of all heterozygous individuals. Here, we report an improved PCR-RFLP method using some informative restriction enzymes which have either a single cleavage site or, alternatively, no cleavage site in the amplified DNA region, depending on the HLA alleles, making reading of RFLP band patterns much easier. Each second exon of the HLA-DQA1 or -DPB1 gene was selectively amplified from genomic DNAs of 70 HLA-homozygous B-cell lines and 100 healthy Japanese by PCR. Amplified DNAs were digested with restriction endonucleases and then subjected to electrophoresis assaying simply for cutting, or no cutting, of the DNA. ApaLI, HphI, BsaJI, FokI, MboII and Mn1I can discriminate eight alleles of the DQA1 gene. Similarly 19 alleles of the DPB1 gene can be discriminated with Bsp1286I, FokI, DdeI, BsaJI, BssHII, Cfr13I, RsaI, EcoNI, and AvaII enzymes. This modified PCR-RFLP method can be successfully applied to heterozygotes. Thus, the method is technically simpler and more practical for routine HLA typing work than our previous PCR-RFLP method.

Identification of mutations in two families with sporadic hemophilia A

Direct sequencing of segments of the factor VIII gene in 30 hemophiliacs with sporadic disease (32+ kb of sequence in total) revealed two missense transitions: glutamate 1704 to lysine (E1704----K) in a patient with severe hemophilia A and proline 2300 to serine (P2300----S) in a patient with mild hemophilia. Both transitions are likely to be causative mutations because the amino acids affected were evolutionarily conserved. Haplotype and sequence analysis of the mother and grandparents of patient HA12 (E1704----K) indicate that the mutation arose in the grandfather who was 27 years old when his daughter was conceived. The origin of mutation in patient HA39 (P2300----S) could not be determined. As mutations that cause mild disease can be found in seemingly unrelated families, 96 unrelated hemophiliacs were screened rapidly for the P2300----S mutation with polymerase chain reaction (PCR) amplification of specific alleles (PASA). None of these patients had the mutation. PASA was also used to conveniently assess a polymorphic site in intron 7. The polymorphism is estimated to be informative in 13% of Korean females and in 23% of Western European females.

DNA polymerase fidelity and the polymerase chain reaction

High-fidelity DNA synthesis conditions are those that exploit the inherent ability of polymerases to discriminate against errors. This review has described several experimental approaches for controlling the fidelity of enzymatic DNA amplification. One of the most important parameters to consider is the choice of which polymerase to use in PCR. As demonstrated by the data in Tables 2 and 3, high-fidelity DNA amplification will be best achieved by using a polymerase with an active 3'-->5' proofreading exonuclease activity (Fig. 1E). For those enzymes that are proofreading-deficient, the in vitro reaction conditions can significantly influence the polymerase error rates. To maximize fidelity at the dNTP insertion step (Fig. 1A,B), any type of deoxynucleoside triphosphate pool imbalance should be avoided. Similarly, stabilization of errors by polymerase extension from mispaired or misaligned primer-termini (Fig. 1D) can be minimized by reactions using short synthesis times, low dNTP concentrations, and low enzyme concentrations. Additional improvements in fidelity can be made by further manipulating the reaction conditions. To perform high-fidelity PCR with Taq polymerase, reactions should contain a low MgCl2 concentration, not in large excess over the total concentration of dNTP substrates, and be buffered to approximately pH 6 (70 degrees C) using Bis-Tris Propane or PIPES (Table 2). These buffers have a pKa between pH 6 and pH 7 and a small temperature coefficient (delta pKa/degree C), allowing the pH to be maintained stably throughout the PCR cycle. For amplifications in which fidelity is the critical issue, one should avoid the concept that conditions generating more DNA product are the better conditions.(ABSTRACT TRUNCATED AT 250 WORDS)

Direct haplotype determination by double ARMS: specificity, sensitivity and genetic applications

We have developed a novel double Amplification Refractory Mutation System (double ARMS) using a highly polymorphic region 5' to the human delta-globin gene as a model system. The double ARMS approach involves using two allele-specific ARMS primers simultaneously during DNA amplification by the polymerase chain reaction (PCR). The resulting system is highly sensitive and more specific than single ARMS. In addition, this approach enables the elucidation of the relationship of polymorphic sites on the same chromosome and thus allows the direct determination of haplotypes. We have also demonstrated that this system can be used in conjunction with inverse PCR, the resulting double ARMS inverse PCR (DARMSI-PCR) may allow haplotype determination on polymorphic sites which are separated further apart than the length limit imposed by PCR. The double ARMS approach has numerous other applications in molecular biology including HLA typing, virology, forensic pathology and the investigation of the phenomenon of chimerism following bone marrow transplantation.

T296----M, a common mutation causing mild hemophilia B in the Amish and others: founder effect, variability in factor IX activity assays, and rapid carrier detection

By direct genomic sequencing, we have delineated the causative mutation in 64 families of European decent with hemophilia B. Six (9%) had a C----T transition at base 31008, which substitutes methionine for threonine 296 (T296----M) in the catalytic domain of factor IX. Five of the patients had the same haplotype (frequency of 16% in the northern European population). These individuals are of Amish/German descent and they are likely to share a common ancestor. The sixth patient had a different haplotype, which indicates that his mutation had an independent origin. The data highlight the importance of clinical criteria for the classification of hemophilia B. All six patients had clinically mild disease and their factor IX coagulant activities were in the range of 3%-6% when tested simultaneously in one laboratory, yet the factor IX activities provided with patient records varied 40-fold. Due to the high frequency of this mutation, we have utilized the technique of polymerase chain reaction amplification of specific alleles (PASA) to perform rapid and inexpensive carrier diagnoses in the families with this mutation. This is of particular importance for the Amish since the mutation should account for much of, if not all, the mild hemophilia B that is commonly found in this population.

delta-Aminolevulinate dehydratase deficient porphyria: identification of the molecular lesions in a severely affected homozygote

delta-Aminolevulinate dehydratase deficient porphyria, a recently recognized inborn error of heme biosynthesis, results from the markedly deficient activity of the heme biosynthetic enzyme, delta-aminolevulinate dehydratase (ALA-D). The four homozygotes described to date with this disorder have remarkably distinct phenotypes, ranging from a severely affected infant with failure to thrive to an essentially asymptomatic 68-year-old male. To investigate the molecular nature of the lesions causing the severe infantile-onset form, total RNA was isolated from cultured lymphoblasts of the affected homozygote, RNA was reverse-transcribed to cDNA, and the 990-bp ALA-D-coding region was amplified by the PCR. Heterozygosity for an RsaI RFLP within the ALA-dehydratase-coding region permitted identification of the paternal and maternal mutant alleles prior to sequencing. The maternal mutation (designated G133R), a G-to-A transition of nucleotide 397, predicted a glycine-to-arginine substitution at residue 133 at the carboxyl end of the highly conserved zinc-binding site in the enzyme subunit. The G133R mutation created a PstI site and permitted the confirmation and rapid detection of this lesion in amplified genomic DNA from maternal relatives. The paternal mutation, a G-to-A transition of nucleotide 823, predicted a valine-to-methionine substitution of residue 275 (designated V275M). This mutation was confirmed in genomic DNA from family members by the competitive PCR technique. Both missense mutations, which occurred at CpG dinucleotides, resulted in the synthesis of enzyme subunits such that the activity of the homooctameric enzyme was markedly reduced, thereby causing the severe infantile-onset phenotype in the affected homozygote.

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.

Rapid diagnosis of familial defective apolipoprotein B-100

A method is described for the rapid, economic and non-radioactive examination of DNA samples from hypercholesterolaemic patients for familial defective apolipoprotein B-100, using a modified polymerase chain reaction (PCR) protocol and restriction enzyme isoform genotyping. Because of the high prevalence of familial defective apolipoprotein B-100, which is estimated to be one in 500 in most screened general populations, interest is focussed on a simple method for detection of this point mutation. In our protocol a diagnostic restriction site is created by PCR, using a specifically designed partly mismatched primer. In the case of familial defective apolipoprotein B-100 the amplified DNA segment contains an additional ScaI site, whereas DNA amplified from the normal allele is resistant to ScaI digestion. A rapid differentiation between the two alleles is achieved by agarose gel electrophoresis of the ScaI-digested PCR product.

Correction of a human beta S-globin gene by gene targeting

As a step toward using gene targeting for gene therapy, we have corrected a human beta S-globin gene to the normal beta A allele by homologous recombination in the mouse-human hybrid cell line BSM. BSM is derived from a mouse erythroleukemia cell line and carries a single human chromosome 11 with the beta S-globin allele. A beta A-globin targeting construct containing a unique oligomer and a neomycin-resistance gene was electroporated into the BSM cells, which were then placed under G418 selection. Then 126 resulting pools containing a total of approximately 29,000 G418-resistant clones were screened by PCR for the presence of a targeted recombinant: 3 positive pools were identified. A targeted clone was isolated by replating one of the positive pools into smaller pools and rescreening by PCR, followed by dilution cloning. Southern blot analysis demonstrated that the isolated clone had been targeted as planned. The correction of the beta S allele to beta A was confirmed both by allele-specific PCR and by allele-specific antibodies. Expression studies comparing the uninduced and induced RNA levels in unmodified BSM cells and in the targeted clone showed no significant alteration in the ability of the targeted clone to undergo induction, despite the potentially disrupting presence of a transcriptionally active neomycin gene 5' to the human beta A-globin gene. Thus gene targeting can correct a beta S allele to beta A, and the use of a selectable helper gene need not significantly interfere with the induction of the corrected gene.

EcoRI-RFLP of the Apo B gene: a study in a sample group from south Italy

EcoRI restriction analysis at codon 4154 of the Apo B gene was performed in a sample of 90 subjects from southern Italy (sample S), using total blood cell DNA amplified by PCR. A group of 46 subjects from northern Italy (sample N) was also investigated for comparison. Southern Italians showed an incidence of the R2 allele (absence of the cutting site) twice as high as that found in northern Italians (48 v. 21%). By ASPCR the mutation which abolishes the restriction site was confirmed as being G----A at the first base of the 4154 codon of the Apo B gene (Glu----Lys) in both S and N samples. By studying the variability of cholesterolaemia among different EcoRI genotypes in the S sample, it was estimated that the average effect of the R2 allele is to lower serum cholesterol by 8.5 mg/dl.

HLA-DRB1*01 subtyping by allele-specific PCR amplification: a sensitive, specific and rapid technique

The two DR1-associated cellular specificities Dw1 and Dw20, as well as DR'Br' (Dw'BON'), cannot be unequivocally assigned by serological typing or restriction fragment length polymorphism (RFLP) analysis. We have developed and compared two polymerase chain reaction-based (PCR) typing methods for distinguishing these DRB1 alleles; allele-specific amplification of DRB1*01 alleles followed by an agarose gel electrophoresis detection step and group-specific DRB1*01 amplification followed by hybridization with sequence-specific oligonucleotide probes. The two typing strategies gave completely concordant results in the 33 DRB1*01-positive and the 46 DRB1*01-negative individuals and cell lines studied. No false-negative or false-positive typing results were obtained. All possible heterozygous combinations of the DRB1*0101-0103 alleles could be distinguished by both typing methods. DRB1*01 subtyping by allele-specific PCR amplification was performed in less than 3 hours, including PCR amplification, detection and interpretation steps. The technique will be a valuable complement to DR typing by serology and RFLP analysis. Allele-specific DRB1 amplifications or group-specific amplifications followed by directed allele-specific amplifications of DRB1 alleles, typing based on the absence or presence of amplified products, may well prove to be the technical innovation that will firmly establish PCR-based DR typing in routine clinical tissue typing.

Maternal phenylketonuria syndrome in cousins caused by mild, unrecognized phenylketonuria in their mothers homozygous for the phenylalanine hydroxylase Arg-261-Gln mutation

Intrauterine growth retardation, microcephaly, and developmental delay in two first cousins lead to the recognition of phenylketonuria (PKU) in their mothers, 24- and 23 year-old sisters with blood phenylalanine concentrations of approx. 1.2 mmol/l who had never been treated and had no overt mental retardation. Both mothers were shown to be homozygous for a point mutation leading to an Arg-to-Gln substitution at codon 261 of the phenylalanine hydroxylase gene, a mutation which has been recently identified and tentatively associated with a mild variant of PKU. Our observation suggests that homozygosity for the Arg-261-Gln mutation can indeed result in "mild" PKU with little or perhaps no mental retardation, but also indicates that in such women, who may go unrecognized if not screened for, blood phenylalanine is elevated enough to cause the maternal PKU syndrome in their offspring.

The effect of temperature and oligonucleotide primer length on the specificity and efficiency of amplification by the polymerase chain reaction

The polymerase chain reaction (PCR) is most effectively performed using a thermostable DNA polymerase such as that isolated from Thermus aquaticus. Since temperature and oligonucleotide length are known to control the specificity of oligonucleotide hybridization, we have investigated the effect of oligonucleotide length, base composition, and the annealing temperature on the specificity and efficiency of amplification by the PCR. Generally, the specificity of PCR is controlled by the length of the oligonucleotide and/or the temperature of annealing of the primer to the template. An empirical relationship between oligonucleotide length and ability to support amplification was determined. This relationship allows for the design of specific oligonucleotide primers. A model is proposed which helps explain the observed dependence of PCR on annealing temperature and length of the primer.

Single nucleotide primer extension to detect genetic diseases: experimental application to hemophilia B (factor IX) and cystic fibrosis genes

In this report, we describe an approach to detect the presence of abnormal alleles in those genetic diseases in which frequency of occurrence of the same mutation is high (e.g., cystic fibrosis and sickle cell disease), and in others in which multiple mutations cause the disease and the sequence variation in an affected member of a given family is known (e.g., hemophilia B). Initially, from each subject, the DNA fragment containing the putative mutation site is amplified by the polymerase chain reaction. For each fragment two reaction mixtures are then prepared. Each contains the amplified fragment, a primer (18-mer or longer) whose sequence is identical to the coding sequence of the normal gene immediately flanking the 5' end of the mutation site, and either an alpha-32P-labeled nucleotide corresponding to the normal coding sequence at the mutation site or an alpha-32P-labeled nucleotide corresponding to the mutant sequence. Single nucleotide primer extensions are then carried out and analyzed by denaturing polyacrylamide gel electrophoresis and autoradiography. As predicted by the Watson-Crick base-pair rule, in the wild type only the normal base, in an affected member only the mutant base, and in carriers both the normal and the mutant base are incorporated into the primer. Thus, an essential feature of the present methodology is that the base immediately 3' to the template-bound primer is one of those altered in the mutant, since in this way an extension of the primer by a single base will give an extended molecule characteristic of either the mutant or the wild type. The method is rapid and should be useful in carrier detection and prenatal diagnosis of every genetic disease with a known sequence variation.

An assay for the rapid detection of the arylsulfatase A pseudodeficiency allele facilitates diagnosis and genetic counseling for metachromatic leukodystrophy

Metachromatic leukodystrophy (MLD) is a lysosomal storage disorder caused by the deficiency of arylsulfatase A (ASA). A substantial ASA deficiency has also been described in clinically healthy persons, a condition for which the term pseudodeficiency was introduced. The discrimination of both kinds of deficiencies based on ASA activity determination is difficult and unreliable. This creates a serious problem in the genetic counseling and diagnosis of MLD. The mutations characteristic for the pseudodeficiency (PD) allele have recently been identified. A non-radioactive assay based on the polymerase chain reaction is described, which allows the rapid detection of the ASA pd allele. The assay utilizes pairs of primers that allow either the amplification of the ASA PD allele or of other ASA alleles, since their 3' residues match either the ASA PD allele or other ASA alleles.

Allele-specific amplification of genomic DNA for detection of deletion mutations: identification of a French-Canadian Tay-Sachs mutation

A rapid and efficient method for the detection of a 7.6-kb deletion in the beta-hexosaminidase A alpha-subunit gene, a mutant allele causing Tay-Sachs disease in French Canadians, is described. The protocol involves PCR (polymerase chain reaction) amplification of target sequences on normal and mutant chromosomes. Three amplification primers, a single 5' primer complementary to normal and mutant DNA templates and two 3' primers specific for normal and mutant DNA templates are required. The primers direct amplification of two unique fragments (normal and mutant) that are easily separated by gel electrophoresis. Allele-specific oligonucleotide hybridization using normal and mutant probes to genomic DNA samples from normal, heterozygous and homozygous individuals confirms these results and is consistent with results of genotypic classification of individuals using Southern analysis. The method is applicable to detection of deletion mutations in cases where some deletion-flanking sequence is known.

Rapid detection of the hemoglobin C mutation by allele-specific polymerase chain reaction

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Automated DNA diagnostics using an ELISA-based oligonucleotide ligation assay

DNA diagnostics, the detection of specific DNA sequences, will play an increasingly important role in medicine as the molecular basis of human disease is defined. Here, we demonstrate an automated, nonisotopic strategy for DNA diagnostics using amplification of target DNA segments by the polymerase chain reaction (PCR) and the discrimination of allelic sequence variants by a colorimetric oligonucleotide ligation assay (OLA). We have applied the automated PCR/OLA procedure to diagnosis of common genetic diseases, such as sickle cell anemia and cystic fibrosis (delta F508 mutation), and to genetic linkage mapping of gene segments in the human T-cell receptor beta-chain locus. The automated PCR/OLA strategy provides a rapid system for diagnosis of genetic, malignant, and infectious diseases as well as a powerful approach to genetic linkage mapping of chromosomes and forensic DNA typing.

The polymerase chain reaction: miracle or mirage? A critical review of its uses and limitations in diagnosis and research

Since publication of the polymerase chain reaction (PCR) technique in 1985 (Saiki et al. Science 1985; 230: 1350-1354), there has been an explosion of reports on its use in medicine and science. We critically review its use both as a diagnostic technique and as a research tool, and show the pathologist how to evaluate PCR data and how to avoid the pitfalls of overinterpretation. We discuss the value of PCR in the characterization of genetic defects, prenatal diagnosis, carrier testing, HLA typing, detecting micro-organisms, identifying activated oncogenes, and in the characterization of leukaemias and lymphomas, and summarize the main applications in biomedical research.

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.

Direct electrophoretic detection of the allelic state of single DNA molecules in human sperm by using the polymerase chain reaction

We have developed a procedure that allows the detection of polymerase chain reaction (PCR) products derived from a single target DNA molecule in a human sperm without using radioactive probes. With this method, three genetic loci present in a single sperm can be amplified simultaneously. The amplification procedure is specific as well as efficient and permits detection of the PCR product by ethidium bromide staining after polyacrylamide gel electrophoresis. When allele-specific PCR primers that differ in length are used, the size of the PCR products of different alleles also vary in length, allowing the allelic state at each locus to be determined electrophoretically. Studies on individual sperm by using this procedure should facilitate the measurement of genetic recombination in humans over small physical distances. The ability to directly analyze the allelic state of PCR products from one cell rapidly and simply will also be useful for the prenatal diagnosis of genetic disease, especially in the analysis of single blastomeres taken from in vitro fertilized eggs prior to implantation.

Clinical applications of the polymerase chain reaction

The polymerase chain reaction (PCR) is a technique that allows a million-fold, or greater, amplification of defined regions of DNA or RNA. It is potentially capable of detecting a single copy of a gene, present only once in 105 eukaryotic cells. This remarkable level of sensitivity has allowed the development of many diagnostic assays for human pathogens and disease states. These include: the detection of viral, bacterial and protozoal agents; diagnosis and genetic analysis of inherited diseases such as β-thalassaemia, sickle cell disease, haemophilia, Tay-Sachs disease and many others; diagnosis and analysis of neoplastic disorders such as, chronic myelogenous leukaemia (CML), acute lymphocytic lymphoma (ALL), follicular lymphomas and various other cancers, including the detection of activated oncogenes; prenatal and pre-implantation diagnosis; and the development of genetic risk prediction.

The PCR can greatly simplify diagnostic processes that were previously difficult to perform, particularly where the initial amounts of biological material were very limited. In other cases, PCR provides the only method available for detection and diagnosis. However, although simple in theory, the PCR technique remains, for routine clinical diagnostic purposes, currently in the domain of the specialist laboratory. This is because of its sensitivity to nucleic acid contamination from other sources that can cause misleading results. Procedures and precautions are being developed to minimize this problem and there is little doubt that, in many instances, the PCR will be the diagnostic method of choice within the next few years.

Mutational analysis of human NRAS genes in malignant melanoma: rapid methods for oligonucleotide hybridization and manual and automated direct sequencing of products generated by the polymerase chain reaction

Three methods to detect single base mutations in codon 61 of the human NRAS gene from human melanoma DNA are described and compared: oligonucleotide hybridization analysis and direct manual and automated sequence analysis. Point mutations are detected by oligonucleotide hybridization and direct manual and direct automated sequence analysis of in vitro amplified genomic DNA. Heterozygosity for mutant alleles is reliably detected by oligonucleotide hybridization and by direct manual, but not by direct automated, sequence analysis. Generating single-stranded DNA via "asymmetric polymerase chain reaction (PCR)" and utilizing alpha 35S-dATP as radiolabel for manual sequencing and fluorescent-dye labeled primers for automated sequencing (Applied Biosystems, Inc.), we can obtain sequence information from either strand. The use of several of these methodologies to detect single base changes in the human NRAS gene is illustrated. In addition, the use of these and other related techniques to define the involvement of RAS oncogenes in human melanomas more precisely is reviewed.

A specific base transition occurs on replicating hepatitis delta virus RNA

Three independent lines of evidence showed that when an infectious clone of hepatitis delta virus of known sequence was used to initiate genome replication, up to 41% of the genomes were specifically mutated in the amber termination codon (UAG to UGG) for the open reading frame of the delta antigen, thereby increasing the length of the predicted protein from 195 to 214 amino acids. This change was detected only on molecules that participated in RNA-directed RNA synthesis.

Effects of primer-template mismatches on the polymerase chain reaction: human immunodeficiency virus type 1 model studies

We investigated the effects of various primer-template mismatches on DNA amplification of an HIV-1 gag region by the polymerase chain reaction (PCR). Single internal mismatches had no significant effect on PCR product yield while those at the 3'-terminal base had varied effects. A:G, G:A, and C:C mismatches reduced overall PCR product yield about 100-fold, A:A mismatches about 20-fold. All other 3'-terminal mismatches were efficiently amplified, although the G:G mismatches appeared to be more sensitive to sequence context and dNTP concentrations than other mismatches. It should be noted that mismatches of T with either G, C, or T had a minimal effect on PCR product yield. Double mismatches within the last four bases of a primer-template duplex where one of the mismatches is at the 3' terminal nucleotide, in general, reduced PCR product yield dramatically. The presence of a mismatched T at the 3'-terminus, however, allowed significant amplification even when coupled with an adjacent mismatch. Furthermore, even two mismatched Ts at the 3'-terminus allowed efficient amplification.

Quantitation of mRNA by the polymerase chain reaction

A method for the quantitation of specific mRNA species by the polymerase chain reaction (PCR) has been developed by using a synthetic RNA as an internal standard. The specific target mRNA and the internal standard are coamplified in one reaction in which the same primers are used. The amount of mRNA is then quantitated by extrapolating against the standard curve generated with the internal standard. The synthetic internal standard RNA consists of a linear array of the sequences of upstream primers of multiple target genes followed by the complementary sequences to their downstream primers in the same order. This quantitative PCR method provides a rapid and reliable way to quantify the amount of a specific mRNA in a sample of less than 0.1 ng of total RNA. In addition, the same internal standard RNA is used, with appropriate primer pairs, to quantitate multiple different mRNA species.

A novel method for detecting point mutations or polymorphisms and its application to population screening for carriers of phenylketonuria

We describe a method termed PCR (polymerase chain reaction) amplification of specific alleles (PASA), a generally applicable technique for detection of point mutations or polymorphisms. The ease and technical simplicity of PASA will make genetic analyses more accessible to the general medical community. In addition, PASA shows promise for population screening because the technique is rapid, highly reproducible, inexpensive, nonisotopic, and amenable to automation. PASA is a modification of PCR that depends on the synthesis of a PCR oligonucleotide primer that precisely matches with one of the alleles but mismatches with the other. When the mismatch occurs near the 3' end of the PCR primer, amplification is inefficient. Therefore, preferential amplification of the perfectly matched allele is obtained. We demonstrate the applicability of PASA by performing carrier detection in the family of a patient with phenylketonuria (PKU) and by screening a population of unrelated subjects for the presence of the two mutations most commonly associated with PKU. Multiple persons were screened simultaneously for the mutant alleles because a mutation could be detected in the presence of at least a 40-fold excess of the normal allele. The two PKU mutations could be detected concurrently by using a mixture of only three PCR primers, an indication that simultaneous screening of multiple mutations can be done even if three or more mutations are closely clustered. In addition to the detection of mutations, PASA can be used to detect polymorphic alleles rapidly and to distinguish pseudogenes or repetitive sequences that differ by as little as one base.