Allele-specific PCR Amplification Research Articles

Determining the Self-incompatibility Alleles of Japanese Apple Cultivars

The S alleles of 15 Japanese apple cultivars were determined by using the allele-specific polymerase chain reaction amplification and restriction enzyme digestion system developed by Janssens et al. (1995). Both S alleles were identified in eight diploid cultivars, two S alleles in three triploid cultivars, and one S allele in the remaining four diploid cultivars. Two cultivars had S alleles different than those predicted by their parentage, and in one comparison of a cultivar with its sport, an identity problem was discovered. The technique helped to indicate the parent contributing the unreduced gamete in triploids.

PCR-based genotyping of MNSs blood group: subtyping of M allele to MG and MT.

PCR-based genotyping of MNSs blood group system was investigated in combination with restriction fragment length polymorphism (RFLP), single-stand conformation polymorphism (SSCP) and allele-specific PCR amplification (ASPA) techniques. M and N alleles are based on three nucleotide substitutions in exon 2 and one base change (G or T) in an intron of glycophorin A locus. The latter single base change was also found among M alleles analyzed in this study, so that M allele appeared to be subdivided into MG and MT. All three alleles, MG, MT and N were identified clearly by RFLP or SSCP analysis following a single amplification. S and s alleles are based on one nucleotide substitution in exon 3 of glycophorin B gene. Genotyping of Ss blood group system was also explored by PCR-SSCP or ASPA analysis, and problems in the methods were discussed.

Detection of maternal cells in human fetal blood during the third trimester of pregnancy using allele-specific PCR amplification.

Using a highly sensitive allele-specific PCR amplification method, we have previously shown that maternal cells could be detected in all 10 cord bloods tested. This raised the question of whether maternal cells are released into cord blood during the process of delivery or whether they are already present during pregnancy. We have now used the same PCR method to detect the presence of maternal cells in nine fetal blood samples collected at different gestational ages. Maternal cells were detected in eight samples obtained between 24 and 35 weeks of gestation. They were estimated to amount between 10(-4) and 10(-5) of nucleated fetal blood cells. In two cases mononuclear and polymorphonuclear cell fractions were separated by Ficoll gradient centrifugation and maternal cells were detected as comparable levels in both fractions. Maternal cells could not be detected in the one fetal blood sample obtained at 20 weeks of gestation, suggesting that maternal cells could appear at detectable levels in fetal blood during the third trimester of pregnancy. These results are discussed in terms of materno-fetal immune tolerance and of transmission of viruses (and more specifically of the human immunodeficiency virus) from mother to child.

Frequent occurrence of CYP2D6 gene duplication in Saudi Arabians

The polymorphic cytochrome P450 2D6 (CYP2D6) causing poor, extensive or ultrarapid metabolism of several clinically important drugs exhibits pronounced interethnic variation. Ultrarapid metabolism is caused by multiple copies of active CYP2D6 genes and recently 29% of an Ethiopian population has been shown to carry duplicated or multiduplicated CYP2D6 genes, whereas the corresponding frequency in other black, Oriental and European populations investigated is 1-2%. In order to characterize the distribution of alleles with multiple CYP2D6 copies in a neighbouring population and to characterize the CYP2D locus in general among Saudi Arabians, the CYP2D6 genotype of a Saudi Arabian population was examined using restriction fragment length polymorphism (RFLP) analysis and allele-specific polymerase chain reaction (PCR) amplification. Of 101 Saudi Arabians studied, 21 subjects had an EcoRI fragment indicative of CYP2D6 gene duplication. In contrast, only two individuals were heterozygous for a deletion of the whole gene (CYP2D6*5). The allele frequency of CYP2D6*4, the most common defective allele among Caucasians, was only 3.5% in the Saudi population. Two other alleles, CYP2D6*10 and *17, common in certain populations and which cause diminished enzyme activity, were found only at low allele frequencies of 3.0% each. These findings are in agreement with earlier Saudi Arabian phenotyping studies which reported a low frequency (1-2%) of poor metabolizers for CYP2D6 probe drugs. In conclusion, the Saudi Arabian population studied exhibited very few defective alleles and a large number of subjects carried duplicated CYP2D6 genes, implying a high conservation on functional CYP2D6 genes possibly due to dietary reasons and reveal the Saudi Arabians as an unique population in comparison with others examined.

Overlapping PCR for bidirectional PCR amplification of specific alleles: a rapid one-tube method for simultaneously differentiating homozygotes and heterozygotes.

Rapid detection of single-base changes is fundamental to molecular medicine. PASA (PCR Amplification of Specific Alleles) is a rapid method of genotyping single-base changes, but one reaction is required for each allele. Bidirectional PASA (Bi-PASA) was developed to distinguish between homozygotes and heterozygotes in one PCR reaction by utilizing novel primer design with appropriate cycling conditions. In Bi-PASA, one of the alleles is amplified by a PASA reaction in one direction while the second allele is amplified by a PASA reaction in the opposite direction. Two outer (P and Q) and two inner allele-specific (A and B) primers are required. In heterozygotes, three segments are amplified: a segment of size AQ resulting from one allele, another segment of size PB resulting from the second allele, and a combined segment of size PQ. In homozygotes, segment PQ and either segments AQ or PB amplify. The two inner primers (A and B) contain a relatively short complementary region and a 10-nucleotide G + C-rich 5' tail. The inner primers "switch" from low-efficiency to high-efficiency amplification when genomic DNA is replaced by previously amplified template DNA. In addition, the 5' tails prevent "megapriming". The parameters for optimizing Bi-PASA were investigated in detail for common mutations in the human factor V and catechol-O-methyltransferase genes. Guidelines for optimization of Bi-PASA also were developed and tested in a prospective study. Three additional Bi-PASA assays were optimized rapidly by utilizing these guidelines. In conclusion, Bi-PASA is a simple and rapid method for detecting the zygosity of known mutations in a single PCR reaction.

Polymorphisms of the TAP2 gene may influence antibody response to live measles vaccine virus

The transporter associated with antigen processing (TAP) gene products transport peptides from the cytosol to the endoplasmic reticulum for processing by the immune system. We hypothesized that polymorphisms within the TAP genes may influence measles vaccine antigen processing and hence antibody response. TAP genotypes were determined for subjects who were measles vaccine nonresponders ( n=32) and hyper-responders ( n=28). TAP1 and TAP2 alleles were determined by PCR amplification of specific alleles (PASA). Measles vaccine nonresponders were more likely to be homozygous at TAP2 position 665 than were hyper-responders (OR=5.0, P=0.016). Lastly, a trend was found in the overall distribution of all TAP2 genotype frequencies between hyper-responders and nonresponders ( P=0.08). No association was found between TAP1 polymorphisms and vaccine response. These data reveal an association between TAP2 genotype and measles vaccine antibody response which may explain one mechanism behind vaccine failure.

Validation of a Point Mutation of Acetylcholinesterase in Colorado Potato Beetle by Polymerase Chain Reaction Coupled to Enzyme Inhibition Assay

A serine to glycine point mutation of the acetylcholinesterase (AChE, EC 3.1.1.7) gene was identified previously in an azinphos-methyl-resistant (AZ-R) strain of the Colorado potato beetle,Leptinotarsa decemlineata(Say). To validate this mutation, the polymerase chain reaction (PCR) amplification of specific alleles (PASA) was coupled to a functional assay for AChE in individual insects. The remaining activities of AChE after inhibition by 50 μMazinphos-methyl-oxon was 22.3% ± 6.5 and 48.0% ± 3.9 (mean ± SD,n= 13) for the beetles from the azinphos-methyl-susceptible (SS) and AZ-R strains, respectively. This pattern of AChE inhibition established that AChE from the AZ-R beetles were significantly less sensitive to azinphos-methyl-oxon inhibition than that from the SS beetles. Using a competitive PASA technique to diagnose the azinphos-methyl-resistance allele of the AChE gene in these insects, the resistance allele was found in all AZ-R beetles but was never found in the SS beetles. These results agree well with the level of susceptibility of the AChE in individual insects and support the contension that the serine to glycine mutation is responsible for the reduced sensitivity of the AChE to inhibition by azinphos-methyl-oxon in the AZ-R strain of beetles. The utilization of the PASA technique for resistance monitoring in Colorado potato beetle is also discussed.

Genetic typing of human platelet antigen 1 (HPA-1) by oligonucleotide ligation assay in a specific and reliable semi-automated system.

Genotyping of platelet alloantigens with the possibility of using any type of cellular material as a source of DNA has become a preferred procedure, particularly in thrombocytopenic patients when platelet counts are too low for phenotyping. Recently human platelet antigen 1 (HPA-1) has been identified as an inherited risk factor for coronary thrombosis. The different detection methods currently used have disadvantages for large-scale DNA diagnosis, including the need for electrophoresis (allele-specific restriction enzyme analysis, amplification with sequence-specific primers) or the potential risk of reduced specificity (allele-specific oligonucleotide hybridization). In this report we describe the adaptation of an automated oligonucleotide ligation assay to genotype HPA-1 in polymerase chain reaction (PCR)-amplified DNA samples. HPA-1a and HPA-1b phenotypes corresponded to the results of the different genotyping assays. The genotypes determined with the ELISA-based PCR-oligonucleotide ligation assay were in 100% concordance with the results obtained by conventional allele-specific restriction enzyme site analysis and PCR amplification with sequence-specific primers. The automated oligonucleotide ligation assay provides a rapid, reliable, nonisotopic method to genotype human platelet antigens that can rapidly be applied to large population screening.

Muscle histopathology in diabetes mellitus associated with mitochondrial tRNALeu(UUR) mutation at position 3243

Diabetes mellitus associated with 3243 mitochondrial tRNALeu(UUR) mutation (DM-Mt3243) is a subtype of the mitochondrial multisystem syndromes, usually lacking myopathy. Muscle biopsies were obtained from 5 patients with diabetes and one patient with impaired glucose tolerance, all possessing the 3243 mutation without hallmarks of MELAS. The specimens were subjected to histochemical, biochemical, and genetic analysis. Ragged-red fibers were seen in 4 of the 6 patients (67%), and focal cytochrome c oxidase deficiency in 3 (50%). Strongly succinate dehydrogenase-reactive blood vessels was found in 5 patients (83%). The histochemical signs were present even when the mutant percentage was very low. The percentage of mutant DNA was almost always higher in muscles than in leukocytes. The combination of allele specific PCR amplification and PCR-RFLP method was useful to evaluate the mutant proportion. The mutant percentage in muscle was under 50% in 5 (83%) patients. Mitochondrial enzyme activity was deficient only in one patient. This study presents the detailed muscle histopathology in the DM-Mt3243 group. Abnormal histopathologic findings seemed similar to those noted in MELAS. However, mutant percentage in muscles was lower than that of MELAS, and respiratory chain enzyme activity was well preserved. © 1997 Elsevier Science B.V.

CYP2D6 polymorphism is not associated with essential tremor.

Recent reports have shown an association between cytochrome P450IID6 (CYP2D6) polymorphism and Parkinson's disease. We investigated the association between this polymorphism and the risk for developing essential tremor (ET). Leukocytic DNA from 91 unrelated ET patients and a control group of 258 unrelated healthy individuals was studied for the occurrence of eight different CYP2D6 allelic variants by using allele-specific PCR amplification Xbal and EcoRI-RFLP's analyses. The prevalence for these allelic variants in the ET and control groups were, respectively: CYP2D6*1 76.9 and 78.7%, CYP2D6*2 0.5 and 0.2%, CYP2D6*3 0 and 1%, CYP2D6*4 12.1 and 12.2%, CYP2D6*5 1.6 and 1.7%, CYP2D6*9 4.4 and 2.9%, CYP2D6*2x2 4.4 and 3.2%. The prevalence of subjects with absent CYP2D6 activity (those carrying two defect genes) was 1.1 and 3.1% in ET and control groups, respectively. Both groups studied were in Hardy-Weinberg equilibrium. These results indicate that mutations at the CYP2D6 gene do not seem to be a major factor in determining susceptibility to ET, and reinforces the view that ET and parkinsonism are distinct conditions.

Mannose-binding protein genetic polymorphisms in black patients with systemic lupus erythematosus.

To determine whether dysfunctional or deficient mannose-binding protein (MBP) variants are found with increased frequency in black patients with systemic lupus erythematosus (SLE) compared with controls. Allele-specific polymerase chain reaction amplification of 4 different polymorphic sites was performed on samples from 92 black SLE patients and 86 geographically matched black controls. Two structural polymorphisms of MBP, associated with low serum levels of MBP, were found with significantly increased frequency in the SLE patient population compared with controls. In contrast, a promoter haplotype associated with particularly high serum levels of MBP was negatively associated with SLE. Deficiencies of MBP predispose individuals to SLE.

Addition of a competitive primer can dramatically improve the specificity of PCR amplification of specific alleles.

Addition of a competitive primer can dramatically improve the specificity of PCR amplification of specific alleles.

Interferon-alpha 8b is the only variant of interferon-alpha 8 identified in a large human population.

Three variants of human interferon (IFN)-alpha 8a gene, that is, IFN-alpha 8b, and IFN-alpha 8c, have been reported previously. They differ from each other by changes in their coding region at nucleotide positions 359-360, 372, and 550. Human genomic DNA obtained from over 28,000 healthy blood donors and from 4 human cell lines was used in the polymerase chain reaction (PCR) designed for specific amplification of the IFN-alpha 8 gene fragments. The resulting PCR product was analyzed by (1) restriction endonuclease digestion, (2) DNA sequencing, and (3) allele-specific secondary PCR amplification. Only one sequence for IFN-alpha 8 was identified, and that was for IFN-alpha 8b. The sequences for IFN-alpha 8a and IFN-alpha 8c were not detected after PCR amplification either in the pooled leukocytes obtained from > 28,000 individuals or in cell lines tested. These data suggest that the naturally occurring variant or allele for IFN-alpha 8 in the population is IFN-alpha 8b. IFN-alpha 8a and IFN-alpha 8c variants were consistently below the level of detection of the assays and, if present at all in the population, are very rare.

Debrisoquin and S-mephenytoin hydroxylation phenotypes and CYP2D6 genotypes in an Estonian population.

The polymorphisms of debrisoquin (CYP2D6) and S-mephenytoin (CYP2C19) hydroxylation were studied in 210 unrelated healthy native Estonians by coadministration of mephenytoin and debrisoquin or dextromethorphan. Among the 210 volunteers 21 (10%) were poor metabolizers of debrisoquin/dextromethorphan and two (0.95%) were poor metabolizers of S-mephenytoin. By pooling these data with an earlier study on 156 Estonians, the prevalences of poor metabolizers of debrisoquin/dextromethorphan and poor metabolizers of S-mephenytoin were 7.6% and 2.2%, respectively. The CYP2D6 genotype of 151 subjects was analysed by allele-specific PCR amplification for the defect alleles CYP2D6A and CYP2D6B. All poor metabolizers of debrisoquin carried two defect CYP2D6-alleles. The phenotype (extensive or poor metabolizer) was in all subjects correctly predicted by the genotype. The frequencies of the defect alleles CYP2D6B and CYP2D6A among these 151 subjects (including 14 poor metabolizers-9.3%) were 21.5% and 2.3%, respectively. DNA from 6 subjects with very high CYP2D6 activity (debrisoquin MR < 0.1) was analysed by EcoRI RFLP to identify duplicated or amplified CYP2D6-genes. Two of the subjects were found to carry a duplicated CYP2D6L-gene. In conclusion, the distribution of genetically determined metabolic capacities of CYP2D6 and CYP2C19 in Estonian unrelated subjects did not differ significantly from that in other Caucasian populations. The CYP2D6 phenotype was predicted by PCR-based amplification for the CYP2D6A and CYP2D6B-alleles.

HLA-DRB1, DQA1, DQB1 DNA polymorphism in the Bulgarian population.

We describe for the first time the use of PCR based techniques to analyze the MHC class II polymorphism of the Bulgarian population. The present study provides the HLA-DRB, DQB1 allele frequencies in 116 Bulgarian individuals and DQA1 alleles frequencies in 100 subjects. DNA from these individuals was typed for DRB and DQB1 typed by the PCR-Allele Specific Amplification (PCR-ASA) method and DQA1 by PCR followed by hybridization using Sequence Specific Oligonucleotides (PCR-SSO). Allele and haplotype frequencies and linkage disequilibria are computed by the standard methods used for the XIth International Histocompatibility Workshop. The highest frequencies are 0.159, 0.109 and 0.085 for DRB1*1101, DRB1*1601 and DRB1*1301 respectively. Among the eight DQA1 alleles detected, DQA1*0501 (0.344) is found to be much more frequent than the two most frequent alleles DQA1*0102 (0.225) and DQA1*0101 (0.151). Twelve DQB1 alleles are found and three of them, DQB1*0301 (0.280), DQB1*0502 (0.153) and DQB1*0201 (0.133) showed the highest frequencies. The haplotype DRB1*1101-DQA1*0501-DQB1*0301 (0.079) predominate clearly, followed by DRB1*1601-DQA1*0102-DDQB1*0502 (0.055) and DRB1*0101-DQA1*0101-DQB1*0501. These results indicate that the Bulgarian population is characterized by features representative of the European anthropological type with a substantial contribution from the Southern Belt of Europe.

Simple and Rapid Detection of Factor V Leiden by Allele-specific PCR Amplification

Resistance to activated protein C is the most common hereditary cause for thrombosis and significantly linked to factor V Leiden. In this study, primers were designed to identify the factor V mutation by allele-specific PCR amplification. 126 patients with thromboembolic events were analysed using this technique, PCR-RFLP and direct sequencing. The concordance between these techniques was 100%. In 27 patients a heterozygous factor VGln506 mutation was detected, whereas one patient with recurrent thromboembolism was homozygous for the point mutation. Due to its time- and cost-saving features allele-specific amplification should be considered for screening of factor VGln506.

Activation of K-ras in aflatoxin B1-induced lung tumors from AC3F1 (A/J x C3H/HeJ) mice.

In addition to being a potent hepatocarcinogen, aflatoxin B1 (AFB1) is a pulmonary carcinogen in experimental animals and epidemiological studies have shown an association between AFB1 exposure and lung cancer in humans. Since point mutations at codons 12, 13 and 61 of the K-ras protooncogene are often implicated in chemically induced mouse lung tumors and in human lung adenocarcinomas, we undertook an investigation of the role of K-ras activation in AFB1-induced pulmonary carcinogenesis. Female AC3F1 (A/J x C3H/HeJ) mice were treated with AFB1 (150 mg/kg i.p., divided into 24 doses over 8 weeks), and 6-14 months after the completion of dosing mice were killed and pulmonary adenomas and carcinomas removed. Of the 76 AFB1-induced lung tumors analyzed by single strand conformation polymorphism (SSCP) and direct sequencing, 75 possessed K-ras codon 12 mutations (46 GTT, 14 GAT, 13 TGT and 2 TTT; normal, GGT) and one had a GGC-->CGC mutation in codon 13. The observation that K-ras mutations occurred only at G:C base pairs is in agreement with N7-guanine being the primary site of AFB1-DNA adduct formation and with guanine residues being targets for AFB1-induced oxidative DNA damage via formation of 8-hydroxydeoxyguanosine (8-OHdG). The AFB1-specific nature of the observed K-ras mutation spectrum and the fact that 100% of the tumor samples examined contained K-ras mutations is consistent with K-ras activation being an early, critical event in AFB1-induced pulmonary carcinogenesis in AC3F1 mice. The parental origin of the observed K-ras mutations was determined by allele-specific PCR amplification of AFB1-induced lung tumor DNA followed by SSCP analysis. In the vast majority of tumors (73/76), the mutated K-ras allele was derived from the lung tumor susceptible A/J parent. This finding supports the existence of a link between K-ras and differences in mouse lung tumor susceptibility.

Utility of a “Swish and Spit” Technique for the Collection of Buccal Cells for TAP Haplotype Determination

To demonstrate the utility of a "swish and spit" technique as a nucleated cell source for transporter associated with antigen processing (TAP) haplotype determination by molecular methods in large-scale clinical trials. Twenty normal volunteers were recruited for this prospective feasibility study. From each subject, buccal or blood cells (or both) were collected for use in TAP haplotype assignment by molecular methods and subjected to various storage conditions. As an alternative to use of lymphocytes obtained by venipuncture, we developed a swish and spit technique for collecting buccal cells for assigning TAP haplotype. For this technique, the subject vigorously swishes isotonic saline in the mouth and expectorates it into a collection container. DNA is extracted from the buccal cells by proteinase K digestion, phenol-chloroform extraction, and ethanol precipitation. In addition, we compared DNA extracted from mouthwash specimens stored under various conditions to which a specimen might be exposed if mailed. DNA extracted from buccal cells obtained by the swish and spit technique provided excellent templates for the polymerase chain reaction (PCR), and subject acceptance of this method was universal. In all cases, assigning TAP haplotype by PCR amplification of specific alleles with use of buccal or blood-derived specimens was successful. The integrity of the specimens was unaffected by storage at -20 degrees C, 4 degrees C, 25 degrees C, or 37 degrees C, and we were able to use the DNA from cells stored under any of these conditions for TAP haplotying. We conclude that DNA from buccal cells collected by the swish and spit technique for TAP haplotype assignment is an excellent substitute for DNA obtained from nucleated blood cells, and the technique is useful for large-scale clinical studies that require DNA from subjects geographically distant from the research site.

A molecular method for S-allele identification in apple based on allele-specific PCR

cDNA sequences corresponding to two self-incompatibility alleles (S-alleles) of the apple cv 'Golden Delicious' have previously been described, and now we report the identification of three additional S-allele cDNAs of apple, one of which was isolated from a pistil cDNA library of cv 'Idared' and two of which were obtained by reverse transcription-PCR (RT-PCR) on pistil RNA of cv 'Queen's Cox'. A comparison of the deduced amino acid sequences of these five S-allele cDNAs revealed an average homology of 69%. Based on the nucleotide sequences of these S-allele cDNAs, we developed a molecular technique for the diagnostic identification of the five different S-alleles in apple cultivars. The method used consists of allele-specific PCR amplification of genomic DNA followed by digestion of the amplification product with an allele-specific restriction endonuclease. Analysis of a number of apple cultivars with known S-phenotype consistently showed coincidence of phenotypic and direct molecular data of the S-allele constitution of the cultivars. It is concluded that the S-allele identification approach reported here provides a rapid and useful method to determine the S-genotype of apple cultivars.

Nonradioactive multiplex PCR screening strategy for the simultaneous detection of multiple low-density lipoprotein receptor gene mutations.

We have developed a rapid, nonradioactive screening test enabling the simultaneous analysis of three low-density lipoprotein receptor (LDLR) gene mutations (D154N, D206E, and V408M), which together account for familial hypercholesterolemia (FH) in approximately 90% of the South African Afrikaner population. The assay is designed so that FH patients, negative for these founder-related mutations (found in descendants of European settlers), subsequently can be screened for unknown mutations in the mutation-rich exon 4 of the LDLR gene. Our screening assay consists of two steps: (1) multiplex allele-specific PCR amplification of exons 4 and 9, and (2) simultaneous analysis of single- and double-strand conformational polymorphisms in exon 4 by vertical electrophoresis on low cross-linked polyacrylamide gels. The simplicity, specificity, and versatility of the multiplex assay makes it an ideal system for routine screening of FH mutations in large population samples.