Modified Proofreading PCR for Detection of Point Mutations, Insertions and Deletions Using a ddNTP-Blocked Primer

The development of simple, accurate, rapid and cost-effective technologies for mutation detection is crucial to the early diagnosis and prevention of numerous genetic diseases, pharmacogenetics, and drug resistance. Proofreading PCR (PR-PCR) was developed for mutation detection in 1998 but is rarely applied due to its low efficiency in allele discrimination. Here we developed a modified PR-PCR method using a ddNTP-blocked primer and a mixture of DNA polymerases with and without the 3'-5' proofreading function. The ddNTP-blocked primer exhibited the best blocking efficiency to avoid nonspecific primer extension while the mixture of a tiny amount of high-fidelity DNA polymerase with a routine amount of Taq DNA polymerase provided the best discrimination and amplification effects. The modified PR-PCR method is quite capable of detecting various mutation types, including point mutations and insertions/deletions (indels), and allows discrimination amplification when the mismatch is located within the last eight nucleotides from the 3'-end of the ddNTP-blocked primer. The modified PR-PCR has a sensitivity of 1-5 × 10² copies and a selectivity of 5 × 10^-5 mutant among 10⁷ copies of wild-type DNA. It showed a 100% accuracy rate in the detection of P72R germ-line mutation in the TP53 gene among 60 clinical blood samples, and a high potential to detect rifampin-resistant mutations at low frequency in Mycobacterium tuberculosis using an adaptor and a fusion-blocked primer. These results suggest that the modified PR-PCR technique is effective in detection of various mutations or polymorphisms as a simple, sensitive and promising approach.

"Finnish" mutations in LDL receptor gene: a rare cause of familial hypercholesterolemia in St. Petersburg and Petrozavodsk

The search for two mutations, FH-Helsinki and FH-North Karelia, in LDL receptor gene was carried out in patients with familial hypercholesterolemia from St. Petersburg (80 families) and Petrozavodsk (80 families) using allele-specific PCR and analysis of single-stranded DNA fragment conformation polymorphism (SSCP analysis) with subsequent sequencing. The FH-North Karelia mutation was found in one family in St. Petersburg and in one family in Petrozavodsk, while FH-Helsinki mutation was not detected in any of the samples. Hence, the two "Finnish" mutations together responsible for 2/3 familial hypercholesterolemia cases in Finland were extremely rare in the Russian regions neighboring Finland.

Phylogenetic and recombination analysis of the homing protein domain of grapevine fanleaf virus (GFLV) isolates associated with 'yellow mosaic' and 'infectious malformation' syndromes in grapevine

The RNA2 of seven grapevine fanleaf virus (GFLV) isolates from vines with yellow mosaic (YM) symptoms from different origin were sequenced. These sequences showed a high variability in the homing protein (2A(HP)) and, in five of them, a putative recombination with arabis mosaic virus (ArMV) was detected. To investigate recombination frequency, the partial sequences of the 2A(HP) of 28 additional GFLV isolates from nine different countries, showing either YM or infectious malformations (MF) symptoms, were obtained and compared with those of GFLV isolates from GenBank. The analysis confirmed the high level of sequence variability (up to 41 % at the nucleotide level) among isolates. In phylogenetic trees constructed using different approaches, the sequenced isolates always clustered in four conserved groups, three of which comprised YM strains (groups 1, 2 and 3), and one (group 4) the MF strains. Potential interspecific recombination sites between GFLV and ArMV were predicted in the 2A(HP) gene of several isolates, all of which were associated with YM symptoms.

Gel-based nonradioactive single-strand conformational polymorphism and mutation detection: limitations and solutions

Single-strand conformation polymorphism (SSCP) for screening mutations/single-nucleotide polymorphisms (SNPs) is a simple, cost-effective technique, saving an expensive exercise of sequencing each and every polymerase chain reaction product and assisting in choosing only the amplicons of interest with expected mutations. The principle of detection of small changes in DNA sequences is based on changes in single-strand DNA conformations. The changes in electrophoretic mobility that SSCP detects are sequence dependent. The limitations faced in SSCP range from routine polyacrylamide gel electrophoresis (PAGE) problems to the problems of resolving mutant DNA bands. Both these problems can be solved by controlling PAGE conditions and by varying physical and environmental conditions such as pH, temperature, voltage, gel type and percentage, addition of additives or denaturants, and others. Despite much upgrading of the technology for mutation detection, SSCP remains the method of choice to analyze mutations and SNPs in order to understand genomic variations, both spontaneous and induced, and the genetic basis of diseases.

Development of a sensitive deaminated single-strand conformation polymorphism (DSSCP)

The single-strand conformation polymorphism (SSCP), accompanied by sequencing, is a useful methods for identifying mutations in a DNA fragment. In this study, we have developed a modified SSCP with the aid of sodium bisulfite treatment. The corresponding PCR products for exon 3 of Hb gene were sequenced and samples with homozygote and heterozygote single nucleotide substitutions were identified. The PCR products were treated with sodium bisulfite, which deaminates all the cytosine residues. The reaction mixture was then analyzed on non-denaturing polyacrylamide gels. The modified method, which is called deaminated SSCP (DSSCP), was applied successfully in analysis of mutations in the beta-globin gene at positions relevant to codon 6. DSSCP is a very effective and reproducible method providing clear results that are easy to interpret without the involvement of radioactivity.

p53 alterations in sequential biopsies of Asian follicular lymphoma: a study of immunohistochemical staining pattern and gene mutations by PCR-SSCP in paraffin-embedded tissues

AIM

Tumour suppressor gene p53 is a common target in carcinogenesis, reported to be altered and functionally inactive in 70% of human cancers. Although p53 mutations are less commonly present in haematological malignancies when compared with other solid tumours, they have been reported in histological transformation of follicular lymphoma. We aimed to investigate the frequency of p53 gene alterations in paraffin-embedded tissue using commercially available PCR-SSCP, and to correlate the results with P53 protein expression by immunohistochemistry.

METHODS

Surgical samples from seven patients with a total of 17 sequential biopsies were retrieved for the study of p53 gene expression using immunohistochemical stain, and gene status by PCR-SSCP for exons 5-8. The tumours were graded according to the WHO classification criteria. P53 was distinctly over-expressed in five transformed higher grade biopsies, and all except one showed electrophoretic mobility shift in PCR-SSCP analysis. Sequencing analysis revealed single nucleotide substitutions in three of four of these high-grade transformed cases with band shift (75%), whereas some other studies reported a lower frequency of 25-30%, and mobility shift result was found to correlate with P53 expression. Lower grade tumours without P53 over-expression did not demonstrate band shift, and sequencing analysis did not reveal mutations.

CONCLUSIONS

We demonstrated the feasibility of adopting PCR-SSCP for screening of p53 mutations in archival tissue samples in this study, and there is a strong correlation of p53 gene over-expression and mutation events in high-grade transformed tumours.

Strain variation among Bordetella pertussis isolates from Québec and Alberta provinces of Canada from 1985 to 1994

Pulsed-field gel electrophoresis and gene typing were able to differentiate among 3,597 Bordetella pertussis isolates circulating in Alberta and Québec Provinces, Canada, from 1985 to 1994 and distinguish them from the strains used in vaccine production. This study provides a baseline for continued surveillance of prevalent and emerging strains of B. pertussis in Canada.

A high-throughput denaturing high-performance liquid chromatography method for the identification of variant alleles associated with dihydropyrimidine dehydrogenase deficiency

Dihydropyrimidine dehydrogenase (DPD) is the initial, rate-limiting enzyme in the catabolism of 5-fluorouracil (5-FU). A pharmacogenetic syndrome has been described in which DPD-deficient patients are at risk for toxicity following administration of 5-FU. To date, there are at least 21 previously described mutations and/or polymorphisms that have been associated with DPD deficiency. In this study we describe the development of a highly specific, sensitive, inexpensive, and robust denaturing HPLC (DHPLC) method for rapidly identifying sequence variations (mutations and/or polymorphisms) in the gene (DPYD) that codes for the DPD enzyme. DHPLC conditions were optimized at three temperatures for analysis of the 23 exons of the DPYD gene using 25 amplicons representing the entire coding sequence, including all intron/exon boundaries (splice sites). Resolution of all 25 amplicons at the optimized temperature can be performed in 4.2 h. All 21 previously described sequence variations (mutations and/or polymorphisms) were prepared using site-directed mutagenesis from the wild-type DPYD gene, confirmed by sequence analysis, and subsequently resolved by DHPLC using the optimized conditions. These analyses generated reference chromatogram patterns for all known sequence variations previously encountered in DPD-deficient patients. In order to examine the utility and sensitivity of this approach, samples from patients with known sequence variations in the DPYD gene were analyzed. This DHPLC technique resolved 100% of the known DPYD sequence variations and differentiated between homozygous and heterozygous genotypes. We conclude that this DHPLC method is a highly specific and sensitive technique for rapidly detecting known sequence variations in the DPYD gene. In addition, this approach can be used to identify currently unrecognized unknown sequence variations in the DPYD gene and should be useful in future pharmacogenetic studies examining DPD deficiency.

Increasing the sensitivity of single-strand conformation polymorphism analysis of the LDLR gene mutations in brazilian patients with familial hypercholesterolemia

Mutations in the low-density lipoprotein receptor (LDLR) gene cause familial hypercholesterolemia (FH), one of the most common single gene disorders. It is thought that FH affects approximately 1 of 500 individuals in most populations. Single-strand conformation polymorphism (SSCP) analysis is widely used to detect mutations in the LDLR gene. However, several factors such as temperature, pH, running time, gel composition and size of the DNA fragments can influence its sensitivity. We have optimized the electrophoretic conditions to screen mutations in the promoter region and exons 1-18 of the LDLR gene by varying temperature (5 degrees C, 8 degrees C, 12 degrees C and 15 degrees C), voltage (300 to 600 V), and running time (1 to 4 hours) in the semi-automated GenePhor system (Amersham Biosciences). The efficiency of the method was evaluated by using 30 positive controls (DNA samples with mutations and polymorphisms in the LDLR gene, previously characterized) and DNA samples from 90 Brazilian patients with FH. Our results show that the use of two temperatures (5 degrees C and 15 degrees C) in combination with other optimized conditions resulted in high mutation detection rate (97%), which was considered appropriate for routine screening. Therefore, this strategy could be useful for the diagnosis of genetic disorders, cancer, and for pharmacogenetic studies.

Non-Mendelian inheritance revealed in a genetic analysis of sexual progeny of Phytophthora cinnamomi with microsatellite markers

We report the development of four microsatellite loci into genetic markers for the diploid oomycete plant pathogen Phytophthora cinnamomi and that (AC)(n) and (AG)(n) microsatellites are significantly less frequent than in plant and mammal genomes. A minisatellite motif 14 bp long was also discovered. The four microsatellite loci were used to analyze sexual progeny from four separate crosses of P. cinnamomi. A large proportion of non-Mendelian inheritance was observed across all loci in all four crosses, including inheritance of more than two alleles at a locus and noninheritance of alleles from either parent at a locus. The aberrant inheritance is best explained by nondisjunction at meiosis in both the A1 parent and the A2 trisomic parents, resulting in aneuploid progeny. Two loci on the putative trisomic chromosome showed linkage and no loci were linked to mating type. One aneuploid offspring was shown to have lost alleles at two loci following subculture over 4 years, indicating that aneuploid progeny may not be mitotically stable.

A highly sensitive and nonradioactive mutation detection method based on vertical gradient temperature single-strand conformation polymorphism

The single-strand conformation polymorphism (SSCP) method is widely used for mutation detection. The sensitivity of the method depends on several factors, most importantly on the temperature at which electrophoresis of single-stranded DNA (ssDNA) takes place. The temperature has a profound effect on the folded conformation of ssDNA. The temperature factor is predominantly determined empirically in conventional SSCP, which can be very tedious especially when a large number of different DNA samples need to be screened. We have devised a novel SSCP method based on a vertical gradient temperature (VGT), which automatically subjects ssDNA to various temperatures in the same electrophoresis. The theory behind VGT-SSCP protocol is that when ssDNA is subjected to run in a wide range of gradient temperature, it will automatically acquire optimal resolution at an optimal temperature to distinguish between the wild type and the mutant type ssDNA. The sensitivity level of mutation detection of VGT-SSCP depends on whether the corresponding optimal secondary structure of a mutant DNA strand is within the preset gradient temperature range. In summary, the VGT-SSCP is a simple and robust nonradioactive method that is more sensitive than constant-temperature SSCP in detecting unknown mutations.

Conditions for single-strand conformation polymorphism (SSCP) analysis of BRCA1 gene using an automated electrophoresis unit

The single-strand conformation polymorphism procedure has been applied in routine testing for hereditary diseases and cancer. However, temperature, running time, gel composition, fragment length, etc. can influence its sensitivity. Mutation detection in the clinical setting depends on the development of automated technology, especially for large genes such as the breast cancer gene BRCA1. We analysed DNA samples with BRCA1 mutations in an automated system (GenePhor System; Amersham-Pharmacia Biotech, Uppsala, Sweden). The concentrations of DNA template and PCR primers, the effect of chilling after denaturation, and the temperature and time of the electrophoresis were investigated. All band-shifts were detected by electrophoresis at 5 degrees C for 2 h 15 min. Concentrations of DNA and samples used in the PCR did not affect the SSCP pattern, but chilling the PCR product in ice after denaturation was required. The type and position of mutation in the fragments did not influence the probability of a mobility shift, although SSCP analysis was more sensitive for fragments shorter than 350 bp. This automated SSCP method meets the requirements of fast turnaround and sensitivity and can be readily adapted to the screening of large genes such as BRCA1.

Human cytomegalovirus strains associated with congenital and perinatal infections

The genotypes of human cytomegalovirus (HCMV) isolates from pediatric patients differs from those of infected adults in Australia. Genotypes were determined by PCR amplification of glycoprotein B (gB) sequences, with subsequent analysis by restriction fragment length polymorphism, single-stranded conformation polymorphism, heteroduplex mobility analysis and direct DNA sequencing. Restriction fragment length polymorphism analysis of gB showed genotypes gB1 (39%) and gB3 (30%) were more prevalent in infected children and two new genotypes (gB6 and gB7) were found. Single-stranded conformation polymorphism was used to group isolates into 22 further subtypes and suggested longitudinal co-infection or viral mutation was occurring over time. Heteroduplex mobility analysis was found to be the most accurate and concise of the four methods used for genotyping HCMV isolates. DNA sequencing was used to confirm the results obtained from heteroduplex mobility analysis, and identified two isolates that were incorrectly genotyped by restriction fragment length polymorphism analysis. Heteroduplex mobility analysis efficiently genotyped all samples and allowed estimation of sequence variation between isolates. These data suggest certain gB genotypes are associated more commonly with childhood infections, and these differ from strains associated with invasive disease in HIV patients.

Single-strand conformation polymorphism analysis by capillary and microchip electrophoresis: a fast, simple method for detection of common mutations in BRCA1 and BRCA2

As a result of intensive studies on hereditary breast and ovarian cancers, two breast cancer susceptibility genes, BRCA1 and BRCA2, have been identified. In each gene, a small number of specific mutations have been found at relatively high frequency in certain ethnic populations. The mutations, 185delAG and 5382insC in BRCA1 and 6174delT in BRCA2, have been identified as common mutations in the Ashkenazi Jewish population, with a combined frequency of 2.0 to 2.5%. Women who have one of the above three common mutations are at a high risk of developing breast or ovarian cancer. Consequently, accurate and cost-effective detection of these three mutations may have important implications for risk assessment in susceptible women and men. In this report, we describe a fast and simple capillary electrophoresis (CE)-based method using a polymer network for screening the three common mutations in BRCA1 and BRCA2. Fluorescent dye-labeled primers (6-FAM-tagged) were used to amplify three DNA fragments of 258, 296, and 201 bp for detection of the 185delAG, 5382insC, and 6174delT mutations, respectively. After the PCR products were denatured, a single-strand conformation polymorphism (SSCP) profile could be obtained for each mutation in less than 10 min by CE in a polymer network. We demonstrate the potential provided by translating this assay to the microchip format where the SSCP analysis is complete in 120 s, representing only a fraction of the reduction in analysis time that can be achieved with microchip technology. The speed and simplicity of the SSCP methodology for detection of these mutations make it attractive for use in the clinical diagnostic laboratory.

A highly sensitive, fast, and economical technique for mutation analysis in hereditary breast and ovarian cancers

Mutation analysis of complex genes without hotspots for sequence variations, such as BRCA1, is time-consuming and expensive. Of all currently available methods, direct sequencing has the highest sensitivity, but also the highest costs. Other techniques, such as SSCP, DGGE, and PTT, are more economical but, depending on the experience of the investigator, have at best a sensitivity of 90%. We investigated in a prospective study the feasibility and accuracy of the DHPLC technique. We present the application of the DHPLC protocol for BRCA1 mutation detection on a HPLC device from Bio-Tek Kontron Instruments (Neufahrn, Germany). DNA from 46 women with hereditary breast and ovarian cancer undergoing genetic testing for BRCA1 mutations were tested. Of 1,518 amplicons analyzed by DHPLC, corresponding to 33 fragments spanning the entire BRCA1 gene, 626 were also directly sequenced. The comparison demonstrated that DHPLC detected all alterations found by direct sequencing. No false-positive signals were seen in cases of homozygous sequences. Further, no false-negative results were ever obtained in women with mutations or polymorphisms, or both. In cases of known genetic variations, the nature of the alterations could be predicted by DHPLC. We also compared different separation matrices. Up to about 500 injections, no significant differences in sensitivity could be observed between poly(styrene divinylbenzene) and end-capped silica based columns. However, after more than 500 injections, the resolution of hetero- from homoduplex deteriorated rapidly on silica columns.

A highly sensitive, fast, and economical technique for mutation analysis in hereditary breast and ovarian cancers

Mutation analysis of complex genes without hotspots for sequence variations, such as BRCA1, is time-consuming and expensive. Of all currently available methods, direct sequencing has the highest sensitivity, but also the highest costs. Other techniques, such as SSCP, DGGE, and PTT, are more economical but, depending on the experience of the investigator, have at best a sensitivity of 90%. We investigated in a prospective study the feasibility and accuracy of the DHPLC technique. We present the application of the DHPLC protocol for BRCA1 mutation detection on a HPLC device from Bio-Tek Kontron Instruments (Neufahrn, Germany). DNA from 46 women with hereditary breast and ovarian cancer undergoing genetic testing for BRCA1 mutations were tested. Of 1,518 amplicons analyzed by DHPLC, corresponding to 33 fragments spanning the entire BRCA1 gene, 626 were also directly sequenced. The comparison demonstrated that DHPLC detected all alterations found by direct sequencing. No false-positive signals were seen in cases of homozygous sequences. Further, no false-negative results were ever obtained in women with mutations or polymorphisms, or both. In cases of known genetic variations, the nature of the alterations could be predicted by DHPLC. We also compared different separation matrices. Up to about 500 injections, no significant differences in sensitivity could be observed between poly(styrene divinylbenzene) and end-capped silica based columns. However, after more than 500 injections, the resolution of hetero- from homoduplex deteriorated rapidly on silica columns.

Polymerase chain reaction-single strand conformation polymorphism or how to detect reliably and efficiently each sequence variation in many samples and many genes

A simple and fast method with high reliability is necessary for the identification of mutations, polymorphisms and sequence variants (MPSV) within many genes and many samples, e.g. to clarify the genetic background of individuals with multifactorial diseases. We evaluated polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) analysis to identify MPSV in several genes, which are thought to be involved in the pathogenesis of multifactorial autoimmune diseases like multiple sclerosis. The method is based on the property, that the electrophoretic mobility of single-stranded nucleic acids depends not only on its size but also on its sequence. The target sequence was amplified, digested into fragments ranging from 50-200 bp, heat-denatured and analyzed on native gels. The analysis of 55 PCR systems, including a total of 145 fragments demonstrates, that the detection rate of MPSV depends primarily on the fragment lengths. Appropriate dilutions of samples enhances the proportion of ssDNA compared to dsDNA. Changing the gel conditions, glycerol concentrations and/or the addition of urea may increase fragment resolution in some cases. In general, the detection of MPSV is neither influenced by their location within the fragment nor by the type of substitution, i.e. transitions or transversions. The standard PCR-SSCP system described here provides high reliability and detection rates and allows the efficient analysis of many samples and many genes.