Diagnostic single strand conformational polymorphism, (SSCP): a simplified non-radioisotopic method as applied to a Tay-Sachs B1 variant

Determination of mutated genes in the presence of wild-type DNA by using molecular beacons as probe

Low-abundance mutations in the presence of wild-type DNA can be determined using molecular beacon (MB) as probe. A MB is generally used as DNA probe because it can distinguish single-base mismatched target DNA from fully matched target DNA. However, the probe can not determine low-abundance mutations in the presence of wild-type DNA. In this study, this limitation is addressed by enhancing the stability of unpaired base-containing dsDNA with a hydrogen-bonding ligand, which was added after hybridization of the MB to the target DNA. The ligand formed hydrogen bonds with unpaired bases and stabilized the unpaired base-containing dsDNA if target DNA is mutated one. As a result, more MBs were opened by the mutant genes in the presence of the ligand and a further increase in the fluorescence intensity was obtained. By contrast, fluorescence intensity did not change if target DNA is wild-type one. Consequent increase in the fluorescence intensity of the MB was regarded as a signal derived from mutant genes. The proposed method was applied in synthetic template systems to determine point mutation in DNA obtained from PCR analysis. The method also allows rapid and simple discrimination of a signal if it is originated in the presence of mutant gene or alternatively by a lower concentration of wild gene.

A simple and precise diagnostic method for spinal muscular atrophy using a quantitative SNP analysis system

A simple and precise diagnostic method for spinal muscular atrophy (SMA) using high-resolution CE-based single-strand conformation polymorphism (CE-SSCP) was developed in this study. SMA is a common genetic disorder caused by an abnormality in the relative copy numbers of SMN1 and its centromeric copy SMN2, which differ only in two nucleotides, namely at exons 7 and 8. Therefore, the precise discrimination of the differences in sequence as well as their relative quantities is crucial for the diagnosis of SMA. Multiplex ligation-dependent probe amplification and sequence-sensitive DNA separation using hydroxyethyl cellulose and hydroxypropyl cellulose blended polymer matrix are currently the available methods used in the diagnosis of SMA. However, these methods are limited by their extended hybridization step and low resolution. In this study, the simultaneous discrimination of SMN exons 7 and 8 was successfully demonstrated using high-resolution CE-SSCP. Unlike the previously reported alternative method, single base differing amplicons were baseline-separated because of its extraordinary resolution, thus providing accurate and precise quantification of each paralog.

EMS mutagenesis in mature seed-derived rice calli as a new method for rapidly obtaining TILLING mutant populations

BACKGROUND

TILLING (Targeting Induced Local Lesions IN Genomes) is a reverse genetic method that combines chemical mutagenesis with high-throughput genome-wide screening for point mutation detection in genes of interest. However, this mutation discovery approach faces a particular problem which is how to obtain a mutant population with a sufficiently high mutation density. Furthermore, plant mutagenesis protocols require two successive generations (M1, M2) for mutation fixation to occur before the analysis of the genotype can begin.

RESULTS

Here, we describe a new TILLING approach for rice based on ethyl methanesulfonate (EMS) mutagenesis of mature seed-derived calli and direct screening of in vitro regenerated plants. A high mutagenesis rate was obtained (i.e. one mutation in every 451 Kb) when plants were screened for two senescence-related genes. Screening was carried out in 2400 individuals from a mutant population of 6912. Seven sense change mutations out of 15 point mutations were identified.

CONCLUSIONS

This new strategy represents a significant advantage in terms of time-savings (i.e. more than eight months), greenhouse space and work during the generation of mutant plant populations. Furthermore, this effective chemical mutagenesis protocol ensures high mutagenesis rates thereby saving in waste removal costs and the total amount of mutagen needed thanks to the mutagenesis volume reduction.

Association of HLA-DRB alleles and pulmonary tuberculosis in North Chinese patients

Human leukocyte antigen (HLA) plays a central role in the regulation of the immune response. HLA class II molecules are essential for T cell-mediated adaptive immunity and present peptide antigens to CD4(+) T cells. Because of its important role in the immune response and its high degree of polymorphism, the HLA system is associated with many diseases. We examined the polymorphisms of HLA-DRB alleles and the sequences of the HLA-DRB promoter region in 97 unrelated patients with pulmonary tuberculosis and in 62 unrelated normal controls of the Han nationality from North China, using PCR with sequence-specific primers and PCR direct sequencing. We found that the frequency of HLA-DRB1*15 was significantly higher in the pulmonary tuberculosis group than in the healthy control group. The P value was 0.001, and the odds ratio was 3.793. The pulmonary tuberculosis group had the same HLA-DRB1 promoter region sequences as the control group. We concluded that the HLA-DRB1*15 allele is associated with pulmonary tuberculosis in the Han nationality from North China. The HLA-DRB1 promoter region sequences had no association with the development of pulmonary tuberculosis.

Analysis of HLA-A, HLA-B and HLA-DRB1 alleles in Chinese patients with lung cancer

The primary function of the human leukocyte antigen (HLA) system is to regulate the immune response. Because of its important role in the immune response and its high degree of polymorphism, the HLA system is associated with many diseases. We examined the polymorphisms of HLA-A, B and DRB1 alleles in 100 unrelated patients with lung carcinoma and in 438 unrelated normal controls of Han nationality from North China, using sequence-based typing and PCR with sequence-specific primers. We found that the frequencies of HLA-A*0201, A*2601, B*1518, B*3802, DRB1*0401, DRB1*0402, and DRB1*1201 were higher in the lung carcinoma group than in the normal control group. The P values were 0.035, 0.040, 0.001, 0.017, 0.014, 0.004, and 0.019, respectively, and the odds ratio values were 1.052, 3.513, 4.047, 3.054, 4.237, 19.397, and 2.128, respectively. The frequency of HLA-DRB1*1302 was lower in the lung carcinoma group than in the normal control group (P = 0.046, odds ratio = 0.168). We concluded that patients with lung cancer and healthy controls of Han nationality from North China differ in the frequencies of various HLA alleles.

PCR-SSCP: a method for the molecular analysis of genetic diseases

Single strand conformation polymorphism (SSCP) is a reproducible, rapid and quite simple method for the detection of deletions/insertions/rearrangements in polymerase chain reaction amplified DNA. All the details for the use of PCR-SSCP are presented in the direction of genetic diseases (beta-thalassaemia, cystic fibrosis), optimum gel conditions, sensitivity and the latest modifications of the method, which are applied in most laboratories. This non-radioactive PCR-SSCP method can be reliably used to identify mutations in patients (beta-globin, CFTR), provided suitable controls are available. Moreover, it is widely used for mutation identification in carriers (beta-thalassaemia, cystic fibrosis), making it particularly useful in population screening.

Familial gene analysis for Wilson disease from north-west Indian patients

BACKGROUND

A number of polymerase chain reaction (PCR) based techniques like single-strand conformational polymorphism (SSCP), amplification refractory mutation system (ARMS)-PCR, semi-nested PCR and dinucleotide-repeat marker analysis have been used in the diagnosis of asymptomatic Wilson disease (WD) patients and the carrier status of WD families. In the present study, we explore the utility of mutation analysis in combination with restriction fragment length polymorphism (RFLP) in the genetic diagnosis of WD.

AIM

The study was planned to provide a molecular diagnostic tool for the diagnosis of asymptomatic WD patients as well as assessment of the carrier status of WD families.

SUBJECTS AND METHODS

Four WD families were analyzed in which parents and siblings showed no clinical manifestations or biochemical abnormalities. The parents of the WD patients were not consanguineous and had no family history of WD. Mutations in ATP7B were characterized using SSCP and DNA sequencing. Further, RFLP was developed for the analysis of characterized mutations in ATP7B from the WD patients, their parents and siblings.

RESULTS

Three mutations, Q1256R, A1003T and I1102T, were characterized in WD patients, using SSCP and DNA sequencing. These mutations created/deleted restriction sites for AccII, Bsh1236I and EcoRI restriction enzymes respectively. Despite having no clinical manifestations nor any significant alteration in biochemical investigations, eight carriers and one asymptomatic WD patient were diagnosed in 13 members of the patients families by restriction digestion analysis.

CONCLUSION

The report demonstrates that mutation analysis in combination with RFLP is useful for diagnosis of asymptomatic WD patients as well as for the elucidation of the carrier status of the patients' family members. It is noteworthy that this combinational methodology provides a positive diagnosis in siblings/parents where biochemical parameters are ambiguous.

Molecular and immunohistochemical analysis of the prognostic value of cell-cycle regulators in urothelial neoplasms of the bladder

OBJECTIVE

To evaluate the prognostic and predictive value of molecular and immunohistochemical markers related to cell-cycle control in terms of recurrence, progression, and survival in urothelial neoplasms of the bladder (UNB).

PATIENTS AND METHODS

Clinical and pathological findings of 84 patients with UNB were assessed. Homozygous deletion (HD) and promoter methylation of p14ARF, p15INK4B, p16INK4A, loss of heterozygosity of the locus 9p21, p53 mutations, and immunohistochemical expression of p53, p16, p14, p21, p27, pRb, Ki67, MDM2, and cyclin D1 proteins were evaluated in relation to overall survival (OS), recurrence-free survival (RFS), and progression-free survival (PFS).

RESULTS

In the univariate analysis, RFS was shorter in cases with p14ARF (p=0.006), p15INK4B (p=0.003), p16INK4A (p=0.03) HD, low p14 immunoreactivity index (IRI) (p=0.01) and high Ki67 IRI (p=0.04); HD of the 9p21 locus genes and p14 IRI remained as independent prognostic factors for early UNB recurrence (p=0.006) whereas tumour stage (p=0.00001) and cyclin D1 IRI (p=0.049) were related to worse PFS in the multivariate analysis. In the univariate analysis, IRI for Ki67 (p=0.002), cyclin D1 (p=0.06), p53 (p=0.00008), p16 (p=0.02), p27 (p=0.0005) MDM2 (p=0.01) and p53 mutations (p=0.03) were related to poor OS, and only the Ki67 IRI retained their independent value in the multivariate analysis.

CONCLUSION

9p21 HD and p14 IRI constitute independent predictive factors for UNB recurrence and cyclin D1 IRI and tumour stage for progression. In addition, Ki67 IRI and tumour stage are independent prognostic factors for overall survival in UNB.

Haplotype characterization of transcribed ovine major histocompatibility complex (MHC) class I genes

The ovine major histocompatibility complex (MHC) remains poorly characterized compared with those of other livestock species. Molecular genetic analysis of the bovine MHC has revealed considerable haplotype and allelic diversity that earlier serological analysis had not detected. To develop cellular and molecular tools to support development of vaccines against intracellular pathogens of sheep, we have undertaken a molecular genetic analysis of four distinct ovine MHC haplotypes carried by two heterozygous Blackface rams. We have identified 12 novel class I transcripts and used a class I sequence-specific genotyping system to assign each of these transcripts to individual haplotypes. Using a combination of phylogenetic analysis, haplotype and transcript expression data, we identified at least four distinct polymorphic class I MHC loci, three of which appear together in a number of combinations in individual haplotypes. The haplotypes were further characterized at the highly polymorphic Ovar-DRB1 locus, allowing selection of the progeny of the two founder rams for the establishment of an MHC-defined resource population.

Novel mutations in the P-protein (glycine decarboxylase) gene in patients with glycine encephalopathy (non-ketotic hyperglycinemia)

Eight novel mutations were found in the P-protein (glycine decarboxylase) gene (GLDC) of the glycine cleavage system (EC 2.1.1.10) by screening five exons of the gene in patients with glycine encephalopathy (NKH). The mutations identified were of eight single base changes: a one-base deletion 1054del A, a splice site mutation IVS18-2A-->G and six amino acid substitutions A283P, A313P, P329T, R410K, P700A, and G762R.

Mutational analysis of Portuguese families with multiple endocrine neoplasia type 1 reveals large germline deletions

OBJECTIVE

To determine the spectrum of MEN1 mutations in Portuguese kindreds, and identify mutation-carriers.

PATIENTS, DESIGN AND RESULTS

Six unrelated MEN1 families were studied for MEN1 gene mutations by single-strand conformational polymorphism (SSCP) and DNA sequence analysis of the coding region and exon-intron boundaries of the MEN1 gene. These methods identified 4 different heterozygous mutations in four families: two mutations are novel (mt 1539 delG and mt 655 ims 11 bp) and two have been previously observed (mt 735 del 46p and mt 1656 del C) all resulting in a premature stop codon. In the remaining two families, in whom no mutations or abnormal MEN1 transcripts were detected, segregation studies of the 5' intragenic marker D11S4946 and codon 418 polymorphism in exon 9 revealed two large germline deletions of the MEN1 gene. Southern blot and tumour loss of heterozygosity analysis confirmed and refined the limits of these deletions, which spanned the MEN1 gene at least from: exon 7 to the 3' untranslated region, in one family, and the 5' polymorphic site D11S4946 to exon 9 (obliterating the initiation codon), in the other family. Twenty-six mutant-gene carriers were identified, 6 of which were asymptomatic.

CONCLUSIONS

These results emphasize the importance of the detection of MEN1 germline deletions in patients who do not have mutations of the coding region. Important clues indicating the presence of such deletions may be obtained by segregation studies using the intragenic polymorphisms D11S4946 and at codon 418. The detection of these mutations will help in the genetic counselling of clinical management of the MEN1 families in Portugal.

Molecular characterization of the CCR 5 gene in seronegative individuals exposed to human immunodeficiency virus (HIV)

BACKGROUND

Both clinical and laboratory evidence in exposed seronegative (ESN) individuals to human HIV-1 has suggested the existence of mechanisms of natural resistance to the infection. A 32 base-pair deletion in the gene that codes for the CCR5, which is the main coreceptor for HIV-1, confers a high degree of resistance to HIV-1 infection. However, the genotype Delta32/Delta32 is present only in 2-4% of Caucasoid ESN individuals suggesting the existence of other mechanisms of protection. Mutations different from Delta32 have also been proposed as playing a role in resistance/susceptibility to this infection.

OBJECTIVE

To screen for different mutations along the entire coding region of the ccr5 gene that can potentially explain the persistent seronegativity in a group of ESN individuals.

STUDY DESIGN

Of a total of 86 individuals analyzed for Delta32 mutation by the PCR technique, 36 scored HIV seropositive (SP) and 50 were ESN. The entire group of ESN individuals was screened for other mutations in the ccr5 gene by single strand conformational polymorphism (SSCP) and DNA sequencing.

RESULTS

The frequency of the mutant allele Delta32 was 4% (4/100) for ESN individuals and 4.2% (3/72) for SP individuals. The homozygous mutant genotype (Delta32/Delta32) was found in only 2% (1/50) of ESN individuals, but in no SP individuals. The heterozygous genotype was found in 8.3% (3/36) of SP individuals and in 4% (2/50) of ESN individuals. The differences in the allelic and genotypic frequencies among the groups were not statistically significant. A comparison between the observed and the expected genotypic frequencies showed that they were significantly different for the ESN group, suggesting a protective, yet indirect effect of the mutant genotype.

CONCLUSIONS

The screening of the entire coding region of the ccr5 gene in all ESN did not revealed no other mutations that could account for resistance to HIV-1 infection. Although the CCR5 molecule is the most important coreceptor for HIV-1, mutations in this gene do not account for most of the cases of natural resistance to this virus that have so far been reported.

Population structure, history and gene flow in a group of closely related land snails: genetic variation in Partula from the Society Islands of the Pacific

Previous studies of Partula land snails from the Society Islands, French Polynesia, have shown that populations within species are highly differentiated in terms of their morphology, behaviour, ecology and molecular genetic variation. Despite this level of variability, differences between species are sometimes small, possibly reflecting the fact that reproductive isolation is not always complete and there exists the opportunity for genetic exchange between taxa through hybridization. The present study uses sequence data from a mitochondrial gene to further investigate genetic variation in Society Island Partula. Most populations are found in this study to be highly differentiated, but within individual species there seems to be no simple relationship either between genetic distance and geographical proximity, or between variation in mitochondria and that in allozymes or morphological characteristics. Among species there appears to be no simple correlation between degrees of reproductive isolation and genetic relatedness according to mitochondrial DNA. The results suggest that past events as well as ongoing drift and selection may have been important in affecting patterns of variation. Similarities among species at specific localities suggest that there must have been some genetic exchange in the past, although this may not necessarily reflect ongoing rates of hybridization. The discrepancy between results for different markers probably reflects the differential effects of drift and selection on mitochondrial and nuclear genes.

Matrix effect on the analysis of oligonucleotides by using a mass spectrometer with a sonic spray ionization source

Matrix or impurities remaining in a DNA sample solution after various sample treatment procedures may influence a subsequent DNA analysis. In this work, several matrices were investigated concerning their effects on the analysis of oligonucleotide by using an ion-trap mass spectrometer equipped with a sonic spray ionization source. Inorganic salts of sodium chloride and magnesium chloride depressed the signal intensity by about 50% when the content of the salts was about 10 microM. dNTPs and Taq showed more severe depression on the oligonucleotide. However, Tris, or (hydroxymethyl)aminomethane, intensified the signal intensity, if its content was within an appropriate range. When the content of Tris was about 500 microM, the signal intensity was enhanced by factors of 3 and 5 for the 6-mer and the 20-mer oligonucleotides, respectively. With the existence of Tris, matrix effects from the inorganic salts, dNTPs and Taq were reduced.

Simple method for determining biovar and serovar types of Ureaplasma urealyticum clinical isolates using PCR-single-strand conformation polymorphism analysis

Ureaplasma urealyticum has been associated with urethritis in men, obstetric problems in women, and respiratory distress syndrome in preterm infants. U. urealyticum can be divided into two biovars comprising 14 serovars. Partial sequences of genes encoding the multiple-banded antigens of the cell surface are known. Using a commercially available precast DNA mutation detection gel system, we have developed a simple and reproducible PCR-single-strand conformation polymorphism analysis method for differentiating the biovars of this species that reveals five patterns among the 14 serovars and enables clinical isolates to be typed directly from broth cultures.

Crocidolite induces cell transformation and p53 gene mutation in BALB/c-3T3 cells

Cell transformation is one of the most common assays used to study morphological changes in the multistep process of carcinogenesis. The present study was initiated to investigate the ability of crocidolite to induce cell transformation in BALB/c-3T3 cells and to analyze the relationship between p53 mutations and crocidolite-induced cell transformation, if any. Cell transformation was carried out according to standard procedures. Exponentially growing cells were exposed to different concentrations (0.2-20 microg/cm(2)) of crocidolite fibers for 72 h. Foci obtained from cell transformation were analyzed for their ability to grow in soft agar (anchorage-independence) and p53 alterations. The results of this study demonstrate that there was an increase in transformation frequency (TF) with an increase in concentration of crocidolite. Also, focal cells were able to grow on soft agar, indicating anchorage-independence. cDNA was prepared from RNA isolated from Type 3 foci and subjected to mutational analysis. Eleven exons of the p53 gene from eight transformed cell lines were analyzed for alterations using polymerase chain reaction single-strand conformation polymorphism (PCR-SSCP). Alterations were found in seven of eight cell lines, two of them were in exons 4-6, and five in exons 9-11. The alterations were randomly scattered among the crocidolite dose groups. These results suggest that crocidolite induces mutations predominantly in exons 9-11 of the p53 gene in a nondose-dependent manner.

Genetic variation in a Pacific Island land snail: population history versus current drift and selection

Previous studies of Partula land snails from the Society Islands, French Polynesia, have shown that there can be striking differences in shell shape, colour and banding pattern between nearby populations, even in the absence of any obvious geographical barriers to the movement of snails, or environmental gradients. Elsewhere, there may be relative uniformity over large distances. Analysis of a mitochondrial gene from Partula taeniata (Mörch) shows a similar pattern. The relative frequencies of two mitochondrial haplotypes change abruptly over small distances, seemingly independent of the environment. Although the transition roughly coincides with clines in the frequencies of some morphological characteristics, it appears to be unrelated to others. It is likely that many of the differences accumulated while populations were isolated from one another, through the effects of random genetic drift and selection. Isolation of populations may have occurred as a result of demographic changes, or during the process of colonization if occasional long-distance migrants establish populations ahead of the main invading front. Current genetic drift, even without restrictions to gene flow, may contribute to genetic patchiness on a small scale, although it is likely that conspicuous characteristics such as shell colours and banding patterns are also influenced by selection.

Application of single-strand conformation polymorphism to the study of bovine viral diarrhea virus isolates

Single-strand conformation polymorphism (SSCP) analysis of polymerase chain reaction (PCR) products is a genetic screening technique for rapid detection of nucleotide substitutions in PCR-amplified genomic DNA or cDNA. It is based on the observation that partially formamide-denatured double-stranded DNA migrates as 2 single-stranded DNA molecules when electrophoresed in nondenaturing polyacrylamide gels. The mobility depends on the 3-dimensional conformation of the strand under the conditions used. It is possible to discriminate between DNA strands differing in only 1 nucleotide. The method was applied to the analysis of Bovine Viral Diarrhea Virus (BVDV) isolates. Reference and Argentinian strains were assessed for variations in their 5' untranslated region (5'-UTR). The PCR products of the 5'-UTR ends were formamide denatured and compared by SSCP analysis in nondenaturing 15% polyacrylamide and 15% polyacrilamide-5% glycerol gels. The reference strains SD-1, Singer, and Oregon C24V had differences in electrophoretic patterns. Despite the high conservation among the 5'-UTR of pestiviruses, the method allowed discrimination among all 9 Argentinian isolates. The 5'-UTR of a fetal kidney-derived isolate (1R93) was PCR amplified and cloned in a plasmid vector; the SSCP analysis of 30 PCR products obtained by direct amplification over randomly selected clones produced 5 different banding patterns, indicating the existence of viral quasispecies. The results show that SSCP may be used to identify and differentiate among BVDV isolates.

The effects of p53 status and human papillomavirus infection on the clinical outcome of patients with stage IIIB cervical carcinoma treated with radiation therapy alone

BACKGROUND

It has been suggested that the p53 tumor suppressor gene regulates the radiosensitivity in human malignancies after irradiation; however, in cervical carcinoma, the role of the p53 gene is still unclear because of inactivation of functional p53 by infection with human papillomavirus (HPV). The objective of this study was to clarify the effects of p53 status and HPV infection on the clinical outcome of patients with cervical carcinoma after undergoing radiation therapy.

METHODS

Fifty-two patients with International Federation of Gynecology and Obstetrics Stage IIIB squamous cell carcinoma of the cervix who received radiation therapy alone were reviewed. The combination of external beam irradiation therapy and three sessions of intracavity brachytherapy irradiation was performed for all patients. Genomic DNA extracted from paraffin embedded tissues was examined for HPV types 16, 18 and 33 by the polymerase chain reaction (PCR) method and for p53 status by PCR-single-strand conformation polymorphism (PCR-SSCP) technique. The effects of HPV infection, p53 status, and other parameters on clinical outcome were investigated by univariate analysis.

RESULTS

HPV-DNA was detected in 40 patients (76.9%), and 14 patients (26.9%) had mutations of the p53 gene in the study. There was a significant correlation between the existence of HPV and p53 status (P < 0.001). Mutations of the p53 gene were detected in 6 of 12 patients (50%) who had local recurrent tumors, whereas p53 were wild type in 32 of 40 patients (80%) who achieved local control. The p53 mutation had a significant correlations with local tumor recurrence. Furthermore, p53 status caused statistical significant differences in the curves of the recurrence free survival rate and local control rate as determined by the log rank test (P = 0.02 and P = 0.03, respectively). Conversely, no obvious correlation with any clinical outcome for patients with cervical carcinoma was found concerning HPV infection.

CONCLUSIONS

It is possible that the p53 gene may be used as a predictive factor in radiation therapy for patients with Stage IIIB squamous cell carcinoma of the cervix.

MS for identification of single nucleotide polymorphisms and MS/MS for discrimination of isomeric PCR products

ESI (electrospray ionization) MS and tandem mass spectrometry (MS/MS) were used for the analysis of single nucleotide polymorphisms (SNPs) and more complex genetic variations. Double-stranded (ds) PCR products were studied. PCR products of the proline [5'-x(G17)-x(C38)x-3'] and arginine variants [(5'-x(Gl7)-x(G38)x-3'] of the p53 gene are distinguished by an SNP (cytosine or guanine) and were discriminated using both quadrupole and quadrupole ion trap MS analysis. A 69 bp arginine mutant PCR product [5'-x(C17)-x(G38)x-3'] with a negating switch has the same mass as the proline variant but was readily distinguishable on ion trap MS/MS analysis; fragments containing the mutation site, but not the polymorphism, were identified. The 69 bp PCR products were restriction-enzyme-digested, to create 43 bp fragments. ESI quadrupole ion trap MS/MS analysis of the 43 bp product-ion spectra readily demonstrated both polymorphism and negating switch sites. MS and MS/MS are powerful and complementary techniques for analysis of DNA. MS can readily distinguish SNPs but MS/MS is required to differentiate isomeric PCR products (same nucleotide composition but different sequence).

High-throughput single-strand conformation polymorphism analysis by automated capillary electrophoresis: robust multiplex analysis and pattern-based identification of allelic variants

Genetic diagnosis of an inherited disease or cancer often involves analysis for unknown point mutations in several genes; therefore, rapid and automated techniques that can process a large number of samples are needed. We describe a method for high-throughput single-strand conformation polymorphism (SSCP) analysis using automated capillary electrophoresis. The operating temperature of a commercially available capillary electrophoresis instrument (ABI PRISM 310) was expanded by installation of a cheap in-house designed cooling system, thereby allowing us to perform automated SSCP analysis at 14-45 degrees C. We have used the method for detection of point mutations associated with the inherited cardiac disorders long QT syndrome (LQTS) and hypertrophic cardiomyopathy (HCM). The sensitivity of the method was 100% when 34 different point mutations were analyzed, including two previously unpublished LQTS-associated mutations (F157C in KVLQT1 and G572R in HERG), as well as eight novel normal variants in HERG and MYH7. The analyzed polymerase chain reaction (PCR) fragments ranged in size from 166 to 1,223 bp. Seventeen different sequence contexts were analyzed. Three different electrophoresis temperatures were used to obtain 100% sensitivity. Two mutants could not be detected at temperatures greater than 20 degrees C. The method has a high resolution and good reproducibility and is very robust, making multiplex SSCP analysis and pattern-based identification of known allelic variants as single nucleotide polymorphisms (SNPs) possible. These possibilities, combined with automation and short analysis time, make the method suitable for high-throughput tasks, such as genetic screening.

Regional evolution of venom-gland phospholipase A2 isoenzymes of Trimeresurus flavoviridis snakes in the southwestern islands of Japan

Conventional chromatographic analysis showed that phospholipase A(2) (PLA(2)) isoenzymes of the venom of Trimeresurus flavoviridis (Habu snake) of Okinawa island are profoundly different in composition from those of T. flavoviridis of Amami-Oshima and Tokunoshima islands. The most striking feature was that myotoxic [Lys(49)]PLA(2) isoenzymes, called BPI and BPII, which are expressed abundantly in the venoms of Amami-Oshima and Tokunoshima T. flavoviridis, are missing from the venom of Okinawa T. flavoviridis. Northern blot analysis of Okinawa T. flavoviridis venom-gland mRNA species showed the absence of BPI and BPII mRNA species. Analysis by single-stranded conformational polymorphism-PCR of venom-gland mRNA species of T. flavoviridis from three islands, with reference to five DNA species each encoding different PLA(2) isoenzymes from Tokunoshima T. flavoviridis venom gland, also suggested that BPI and BPII mRNA species are not expressed in Okinawa T. flavoviridis venom gland. In contrast, genomic Southern blot analysis with a variety of probes showed that only the bands corresponding to the upstream and downstream regions of the genes for BPI and/or BPII can be detected in Okinawa T. flavoviridis. These results suggested that the genes for BPI and BPII in Okinawa T. flavoviridis genome had been inactivated to form pseudogenes. Differently from Amami-Oshima and Tokunoshima T. flavovirdis genomic DNAs, PCR amplification of the segments of BPI and BPII genes between the 5' moiety of second exon and the middle portion of second intron failed for Okinawa T. flavoviridis genomic DNAs. In sequence analysis of the two segments involving polymorphism between BPI and BPII genes, which are located in first exon and third exon, respectively, only one base was detected at the polymorphic positions for pseudogene in Okinawa T. flavoviridis genome. Based on these facts, it became evident for pseudogene that the upstream region of BPI gene down to the 5' moiety of second exon and the downstream region of BPII gene starting from the middle portion of second intron are in a linked form with a possible insertion. Such observations suggest that venom-gland genes for PLA(2) isoenzymes in T. flavoviridis snakes isolated for one to two million years have evolved independently. Their evolution is regional and seems, from several lines of consideration and observation, to be adaptive to the environment.

Effect of a dCTP:dTTP pool imbalance on DNA replication fidelity in Friend murine erythroleukemia cells

Nucleotide pool imbalances have been reported to affect the fidelity of DNA replication and repair in prokaryotic and eukaryotic cells. We have reported previously that the mutagen-hypersensitive thymidine kinase (TK)-deficient Friend erythroleukemia (FEL) cells (subclones 707BUF and 707BUE), have a more than sixfold increase in the dCTP:dTTP pool ratio when compared to that of wild-type, TK-positive (TK(+)) clone 707 cells. In this study we present the results of an investigation of the effect of the dCTP:dTTP pool imbalance on the accuracy of DNA replication within 707BUF cells. We examined the spontaneous mutation spectra occurring at the adenine phosphoribosyltransferase (aprt) locus within clone 707 (TK(+)) and 707BUF (TK(-)) FEL cells. Mutations recovered at the aprt locus in FEL cells comprised: base substitutions (43:73), frameshifts (14:13.5), and deletions (43:13.5) [clone 707 (TK(+)):707BUF (TK(-)), respectively, expressed as percentages]. A comparison of the mutation spectra obtained for the two cell lines did not reveal any significant increase in misincorporation of dCTP, the nucleotide in excess, in 707BUF (TK(-)) cells, during DNA replication synthesis. These data suggest that the dCTP:dTTP pool imbalance does not alter the fidelity of DNA replication synthesis in 707BUF (TK(-)) FEL cells. Rather, the predominance of GC --> AT transitions (53%) in the 707BUF (TK(-)) spectrum may reflect a reduced efficiency of repair by uracil DNA glycosylase of uracil residues within these cells.

Single nucleotide polymorphisms of the N-formyl peptide receptor in localized juvenile periodontitis

BACKGROUND

Neutrophils from patients with localized juvenile periodontitis (LJP) exhibit decreased binding and responsiveness to various chemotactic agents, including N-formyl-1-methionyl-1-leucyl-1-phenylalanine (FMLP). This altered reaction of neutrophils is thought to account in part for the increased susceptibility of LJP patients to infections by periodontal organisms. Receptors for FMLP are involved in the activation and the subsequent response to certain chemotactic stimuli.

METHODS

In order to determine if this decreased response is due to a genetic variation in the receptor, we directly compared DNA encoding the FMLP receptor from controls matched for gender and race and LJP patients by single-strand conformation polymorphism analysis (SSCP).

RESULTS

Using this technique, we observed a characteristic SSCP pattern in 29 out of 30 patient samples in the FMLP receptor DNA. This pattern differed from those obtained from the 20 control subjects as well as 31 patients with adult periodontitis. DNA sequencing of 30 patients indicated single nucleotide polymorphisms (SNPs) in the FMLP receptor DNA from the LJP patients when compared to 20 controls (P = 0.0005). Two single nucleotide base alterations were consistently seen: either a thymine to cytosine substitution at base 329 in 17 LJP patients or a cytosine to guanine substitution at base 378 in 5 LJP patients. A combination of both alterations were seen in 7 LJP patients. Both alterations resulted in amino acid changes in the second intracellular loop of the receptor, specifically phenylalanine to serine at residue 110 and cysteine to tryptophan at residue 126. This region of the FMLP receptor has recently been shown to play a role in ligand binding and G-protein activation.

CONCLUSIONS

This study suggests that a molecular alteration in the second intracellular loop of the FMLP receptor molecules in LP patients may play a role in the decreased chemotactic activity reported for some LJP patients.

Selection of conserved TCR VDJ rearrangements in chronic psoriatic plaques indicates a common antigen in psoriasis vulgaris

Psoriasis vulgaris is a common HLA-associated inflammatory skin disease. Although its etiology is still unknown, it is thought to involve T cell-mediated inflammatory mechanisms. In examining the lesional psoriatic TCR beta chain (TCRB) usage in a pair of identical twins concordant for psoriasis, we observed repetitive TCR VDJ rearrangements which indicated antigen-specific oligoclonal T cell expansion. Several of these TCRB rearrangements were identical or highly homologous in the amino acid composition of the complementarity determining region 3 (CDR3), suggesting that T cells with these TCR might be important for disease manifestation. This conclusion was strengthened by TCR analysis of other psoriasis patients. Several repetitive lesional TCRB rearrangements were found that were similar to the conserved CDR3 seen in the twins. Since TCR antigen specificity is largely determined by the beta chain CDR3, selection of T cells with conserved TCRB CDR3 motifs could indicate the presence of a common antigen as a major target of the lesional psoriatic immune response.

High incidence of synchronous cancer of the oral cavity and the upper gastrointestinal tract

A high incidence of synchronous esophageal or gastric carcinoma in preoperative patients with carcinoma of the oral cavity was reported. Esophageal carcinoma was found in seven out of 56 patients (12.5%) and gastric cancer in five patients (8.9%) by videoendoscopy aided with lugol staining in the esophagus and indigocarmine solution in the stomach, although all patients were completely asymptomatic for these lesions. All patients were male, regular drinkers and heavy smokers. The depth of invasion of such tumors was limited to either mucosa or submucosa. Those esophageal and gastric lesions beside the primary oral cancers were positive for p53 protein by immunohistochemistry. Careful preoperative evaluation of not only the esophagus but also the stomach should be a routine procedure in patients with carcinoma of the oral cavity.

Mucinous carcinoma of the colon in a 16-year-old Turkish boy with Bloom syndrome: cytogenetic, histopathologic, TP53 gene and protein expression studies

A 17-year-old Turkish boy with Bloom syndrome (BS) developed mucinous carcinoma of the transverse colon. He was followed from 2 to 17 years of age. Increased sister chromatid exchanges (SCE) were observed, and he was diagnosed with BS at the age of 7. Sun-sensitive skin lesions were examined by skin biopsy, and histopathological studies of these lesions were done. During the follow-up period, an intraabdominal mass at the transverse colon was found, and mucinous carcinoma of colon was diagnosed at the age of 16. We examined TP53 protein expression from paraffin-embedded colon tissue of the patient with an immunohistochemical method. Polymerase chain reaction products of exons 4-9 of the TP53 gene were examined by SSCP. No evidence of overexpression of TP53 protein or mutations of the TP53 gene was observed. The patient in this report is the first case with a mucinous carcinoma of colon diagnosed at an early age in the Bloom Syndrome Registry. Based on our results, carcinoma of the colon in BS patient may occur earlier than 35 years of age and the TP53 gene may not be directly related to carcinoma in Bloom syndrome.

Recent enhancements in SSCP

High sensitivity, robustness and scalability are the three criteria which influence whether techniques for rapid mutation detection will be used in the future. PCR-SSCP, one of the most popular methods for detecting mutation, especially in the field of medical genetics, is being improved (1) to efficiently detect mutations in long stretches of PCR products; (2) to simplify data interpretation by removing PCR artifacts and (3) to minimize human involvement in the process of mutation detection by a simple post-PCR fluorescence labeling followed by separation using automated DNA sequencers.

Detection of point mutations by non-isotopic single strand conformation polymorphism

We have developed a procedure for nonradioactive single strand conformation polymorphism analysis and applied it to the detection of point mutations in the human tumor suppressor gene p53. The protocol does not require any particular facilities or equipment, such as radioactive handling, large gel units for sequencing, or a semiautomated electrophoresis system. This technique consists of amplification of DNA fragments by PCR with specific oligonucleotide primers, denaturation, and electrophoresis on small neutral polyacrylamide gels, followed by silver staining. The sensitivity of this procedure is comparable to other described techniques and the method is easy to perform and applicable to a variety of tissue specimens.

Association between an R338L mutation in the thyroid hormone receptor-beta gene and thyrotoxic features in two unrelated kindreds with resistance to thyroid hormone

Resistance to thyroid hormone (RTH) is a rare syndrome characterized by reduced sensitivity to thyroid hormone due to thyroid hormone receptor-beta (TRbeta) gene mutations or deletion. RTH has been classified on the basis of clinical features into generalized (GRTH) and pituitary (PRTH) resistance. There is, however, overlap of clinical and biochemical findings in patients with the two forms of resistance, and similar TRbeta gene mutations have been identified in both. The 2 subtypes of RTH, therefore, are considered to be different manifestations of a single genetic entity. We report a mutation of the TRbeta gene, an arginine to leucine substitution at codon 338 (R338L), in 2 unrelated RTH kindreds of northern Italian ancestry. The same mutation was already reported in a single unrelated kindred affected by PRTH. Five individuals, 3 in the first and 2 in the second family, were clinically evaluated and followed for 3-11 years. During the long-term follow-up, the patients manifested symptoms and signs of hyperthyroidism including palpitations, fine tremors, heat intolerance, increased sweating, increased deep tendon reflexes, moist and warm skin, cardiac rhythm abnormalities, reduced body weight, and reduced bone mineral density. The clinical features of these kindreds are consistent with a predominant PRTH phenotype.

No evidence for overexpression of the p53 protein and mutations in exons 4-9 of the p53 gene in a large family with adenomatous polyposis

OBJECTIVE

Familial adenomatous polyposis coli (FAP) is an autosomal dominant disease characterized by an early onset of numerous adenomatous polyps of the colon and a high risk of colon carcinoma. The role of the p53 gene in the multistage process of FAP is as yet poorly defined. In the present study, a large family with evidence of polyposis and colon cancer was screened for the mutations of the p53 gene and protein overexpression.

METHODS

We examined p53 protein expression from individuals with immunohistochemical techniques using monoclonal antibody PAb1801. Polymerase chain reaction products of exons 4-9 of the p53 were examined from individuals by single strand, conformational polymorphism analysis.

RESULTS

We could find no evidence of overexpression and mutations of the p53 in any lesion including adenomas and carcinomas.

CONCLUSION

We found that p53 gene alterations do not contribute to the genesis of adenoma or carcinoma of FAP patients for this large family examined.

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

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

Assessment of the interphotoreceptor matrix proteoglycan-1 (IMPG1) gene localised to 6q13-q15 in autosomal dominant Stargardt-like disease (ADSTGD), progressive bifocal chorioretinal atrophy (PBCRA), and North Carolina macular dystrophy (MCDR1)

We have recently characterised the genomic organisation of a novel interphotoreceptor matrix proteoglycan, IMPG1, and have mapped the gene locus to chromosome 6q13-q15 by fluorescence in situ hybridisation. As the interphotoreceptor matrix (IPM) is thought to play a critical role in retinal adhesion and the maintenance of photoreceptor cells, it is conceivable that a defect in one of the IPM components may cause degenerative lesions in retinal structures and thus may be associated with human retinopathies. By genetic linkage analysis, several retinal dystrophies including one form of autosomal dominant Stargardt-like macular dystrophy (STGD3), progressive bifocal chorioretinal atrophy (PBCRA), and North Carolina macular dystrophy (MCDR1) have previously been localised to a region on proximal 6q that overlaps the IMPG1 locus. We have therefore assessed the entire coding region of IMPG1 by exon amplification and subsequent single stranded conformational analysis in patients from 6q linked multigeneration families diagnosed with PBCRA and MCDR1, as well as a single patient from an autosomal dominant STGD pedigree unlinked to either of the two known STGD2 and STGD3 loci on chromosomes 13q and 6q, respectively. No disease associated mutations were identified. In addition, using an intragenic polymorphism, IMPG1 was excluded by genetic recombination from both the PBCRA and the MCDR1 loci. However, as the autosomal dominant Stargardt-like macular dystrophies are genetically heterogeneous, other forms of this disorder, in particular STGD3 previously linked to 6q, may be caused by mutations in IMPG1.

Polymerase chain reaction-single-strand conformational polymorphism analysis of antigen receptor rearrangements in monitoring therapeutic effect in childhood ALL

The rearrangement of the immunoglobulin heavy chain (IgH) genes can be used as a marker of cell lineage and clonality. The polymerase chain reaction (PCR) technique using consensus primers for the IgH gene was used for remission and minimal residual disease (MRD) analysis in the follow-up of childhood acute lymphoblastic leukemia (ALL) of B-cell lineage. Single-strand conformational polymorphism (SSCP) was used to distinguish the specific clonal amplicons from the background. The Authors found that, in a series of 22 patients followed-up for 5.3 to 11.1 years, the PCR-SSCP technique could detect at least one rearrangement at initial diagnosis in 21 (95%). All patients who remained in continuous complete remission were PCR-SSCP negative at remission controls. Ten of the 22 patients had one or more bone marrow relapses. The PCR-SSCP method demonstrated MRD in three of them. In 6 of the 7 (86%) of patients with disease recurrence from whom samples were taken within 6 months before a clinically overt relapse, PCR-SSCP became positive. The Authors conclude that PCR-SSCP of a rearrangement marker might have a role as a convenient technique for monitoring emerging relapse. It may also detect unrelated clones or ongoing secondary recombination events during progression. However, PCR-SSCP is not sensitive enough to detect MRD in all patients in whom disease will later recur.

Do molecular markers predict survival in non-small-cell lung cancer?

Patients with non-small-cell lung cancer (NSCLC) survive for variable lengths of time, even when adjustment is made for pathological stage. Numerous reports suggest that biological markers predict survival in patients undergoing surgery for NSCLC with curative intent, but many of these claims are unconfirmed or conflicting. We postulated that the use of multiple putative markers might provide greater power in predicting survival. We studied 101 consecutive patients with NSCLC who underwent exploratory thoracotomy and who were followed for at least 2 yr. We assessed mutations in the p53 tumor suppressor gene (exons 5-8) and the K-ras oncogene (codons 12 and 13) by polymerase chain reaction amplification and single strand conformation polymorphism of the product. We identified 19 K-ras mutations (all adenocarcinomas except for two) and 40 p53 mutations among the 101 cases. We also evaluated p53 protein, bcl-2 protein, c-erbB-1 protein, c-erbB-2 protein, and MIA-15-5 antigen by standard immunocytochemical techniques, and we found that all of these antigens were variably expressed. As expected, we found a strong inverse association between surgical tumor stage and survival. Of the molecular markers studied, only MIA-15-5 antigen expression correlated strongly with survival by univariate analysis (p = 0.001) and it remained a significant predictor by multivariate analysis (p = 0.01). However, in this study, overexpression of MIA-15-5 antigen predicted an improved survival, whereas the original report showed a worse prognosis (N. Engl. J. Med. 1992;327:14). We conclude the multiple cell markers are not clinically useful in predicting survival among patients undergoing surgery for NSCLC. Differences between our results and prior reports may be due to chance, to true population differences, or to other factors.

Point mutations of the human parathyroid calcium receptor gene are not responsible for non-suppressible renal hyperparathyroidism

The calcium-dependent secretion of parathyroid hormone (PTH) is mediated through an extracellular G protein-coupled calcium receptor (CaR). Inactivating point mutations of this receptor have been found in familial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism. These diseases feature a decreased calcium sensitivity of the parathyroid glands, resulting in a rightward shift of the Ca2(+)-PTH relationship. Severe non-suppressible renal hyperparathyroidism (rHPT) is often characterized by similar setpoint shifts to the right. Thus, point mutations of the CaR gene could contribute to non-suppressible rHPT. We examined genomic DNA of hyperplastic or mainly nodular tissues of 39 parathyroids from 25 rHPT-patients with resistance to calcitriol therapy. Amplification of the six exons of the CaR gene was followed by single-strand conformation polymorphism (SSCP) analysis. DNA sequencing was performed where band shifts were observed. No point mutations in the coding sequence of the CaR gene were detected using the PCR-SSCP strategy. Point mutations in the coding regions of the CaR gene probably play no role in the evolution of renal HPT and are not responsible for the calcitriol resistance of PTH secretion.

Two new polymorphisms in the arylsulfatase A gene and their haplotype associations with normal, metachromatic leukodystrophy and pseudodeficiency alleles

Linkage disequilibrium exists between metachromatic leukodystrophy (MLD) and pseudodeficiency mutations and selected polymorphisms within the arylsulfatase A gene. We have identified 2 new polymorphic NlaIII sites, NlaIII1 and NlaIII2, in the gene that, when used in combination with the known BsrI and BamHI polymorphisms, extends the haplotype associations of the pseudodeficiency and the most common infantile onset MLD alleles. Fixed haplotypes have also been established for 3 other recurring MLD mutations, ala212val, pro426leu, and thr274met. The NlaIII2 site is relatively rare and was found only in association with the pseudodeficiency variant carrying the glycosylation site mutation alone.

High resolution single strand conformation polymorphism analysis using formamide and ethidium bromide staining

Single strand conformation polymorphism (SSCP) analysis using ethidium bromide can be improved by adding formamide as the denaturant. This gives higher resolution than previous SSCP methods; it had 100% sensitivity in the discrimination of 14 PCR samples from two different genes, even for a long fragment close to the upper limit of 250 base pairs. This modified procedure is a rapid, simple, safe, and yet highly sensitive method for detecting structural differences in DNA fragments.

Single-strand conformation polymorphism analysis with high throughput modifications, and its use in mutation detection in familial hypercholesterolemia

The identification of the specific mutation causing an inherited disease in a patient is the framework for the development of a rationale for therapy and of DNA-based tests for screening relatives. We present here a review of the single-strand conformational polymorphism (SSCP) method, which allows DNA fragments that have been amplified with specific primers and PCR to be scanned rapidly for any sequence variation. The general principles of the method are described, as are the major factors that must be considered in developing an optimal SSCP strategy, namely the length of the PCR fragment and the temperature of the gel run. Options for sample denaturing gel characteristics and detection of DNA fragments are discussed. In addition, several modifications are presented that have been developed for high-throughput mutational analysis. The application of these techniques to screen for mutations in the LDL receptor gene in patients with familial hypercholesterolemia are described.

Single-strand conformation polymorphism analysis of RT-PCR products of UK isolates of barley yellow mosaic virus

Single-strand conformation polymorphism (SSCP) analysis of the bipartite genomes of several UK isolates of barley yellow mosaic virus (Ba YMV) was done using fragments of cDNA amplified by RT-PCR. Isolates differed in their SSCP patterns in several regions, but in no case was the pattern able to distinguish between common and resistance-breaking strains. In regions where the nucleotide sequences of UK isolates had been determined, there was no simple relationship between numbers of nucleotide differences and SSCP patterns: differences of only 2 or 3 nucleotides (nt) gave different SSCP patterns, whereas differences of as many as 29 nt did not. Although SSCP analysis has some potential as a rapid and sensitive tool for distinguishing virus isolates, differences detected do not necessarily relate to biological properties and the results are highly dependent on gel conditions.

Single-strand conformation polymorphism analysis of PCR-amplified ribosomal DNA internal transcribed spacers to differentiate species of Aspergillus section Flavi

A novel genetic approach for classifying the species of Aspergillus Section Flavi is described here. This approach consists of PCR amplification of the 5.8S ribosomal DNA-intervening internal transcribed spacer regions (ITS I-5.8S-ITS II) with universal primers and of analysis of the PCR product by the principle of single-strand conformation polymorphism (SSCP). The approximately 570- to 590-bp PCR products were denatured and subjected to electrophoresis on a polyacrylamide gel supplemented with 20% formamide. The SSCP patterns of these species became more distinct by the addition of formamide to the gel and by visualization with ethidium bromide staining. A little interspecific length polymorphism among amplified ribosomal DNAs was enhanced to be detected by PCR-SSCP analysis. This analysis was capable of classifying 67 of the 68 Aspergillus Section Flavi strains tested into the following four groups, regardless of origin: A. flavus/A. oryzae, A. parasiticus/A. sojae, A. tamarii, and A. nomius. The results of restriction fragment length polymorphism analysis with PCR products of the ITS regions were consistent with those of PCR-SSCP analysis, except for A. nomius, which was not clearly differentiated from A. parasiticus/A. sojae. Nonradiolabelled PCR-SSCP analysis is inexpensive and practical to perform without special apparatus or skill and should assist in fungal morphological identification.

Conditions for single strand conformation polymorphism (SSCP)analysis with broad applicability: a study on the effects of acrylamide, buffer and glycerol concentrations in SSCP analysis of exons of the p53 gene)

We examined the influence of electrophoretic conditions on the detectability of small sequence alterations in DNA fragments by single strand conformation polymorphism (SSCP) analysis. Three acrylamide concentrations, 7.5, 14 and 20%, were selected, and all three gel types were prepared with four different Tris/borate/EDTA buffer concentrations. In addition, all these twelve gels were prepared both with and without 10% glycerol. All electrophoretic runs were performed at ambient temperature of 20-24 degrees C. The resulting 24 different electrophoretic conditions were used for the SSCP analysis of DNA fragments of exons 5, 7 and 8 of the human p53 gene; the results were evaluated primarily in relation to detectability of mutants. Six out of the 24 conditions permitted the detection of all mutants. For practical reasons, 14% acrylamide, 44.5 mmol/1 Tris, 44.5 mmol/1 boric acid, 1 mmol/1 EDTA, pH 8.0, with and without addition of glycerol was chosen as the most suitable. These "selected conditions" were applied in the SSCP analysis of an arbitrarily chosen set of mutant DNA fragments with single base exchanges,and all but one of seven mutants were detected in the gel system containing glycerol. Our results indicate that the set of "selected conditions" is of broad applicability, permitting the detection of even small sequence differences like single base exchanges with high reliability. It should prove especially useful in screening for unknown mutations.

Molecular analysis of a series of alleles in humans with reduced activity at the triosephosphate isomerase locus

Individuals with 50% of expected triosephosphate isomerase (TPI) enzyme activity have been previously identified in families during the screening of approximately 2,000 newborn children for quantitative variation in activity of 12 erythrocyte enzymes. The frequency of the trait was 9/1,713 individuals in the Caucasian population and 7/168 individuals among the African-American population studied. Genetic transmission of the trait was confirmed in all families. The frequency of the presumptive deficiency allele(s) at the TPI locus was greater than expected, given the reported incidence of clinical TPI deficiency. We report the molecular characterization of the variant alleles from seven African-American and three Caucasian individuals in this group of unrelated individuals. Three amino acid substitutions--a Gly-->Ala substitution at residue 72, a Val-->Met at residue 154, and a previously described Glu-->Asp substitution at residue 104--were identified in the Caucasian individuals. The substitutions occur at residues that are not directly involved in the active site but are highly conserved through evolutionary time, suggesting important roles for these residues in maintenance of subunit structure and conformation. The variant allele in the seven African-American individuals had nucleotide changes at positions -8 and -5 (5' of) from the transcription-initiation site. In three of these individuals, an additional T-->G substitution was detected in a TATA box-like sequence located 24 nucleotides 5' of the transcription-initiation site and on the same chromosome as the -5/-8 substitutions. Thus, molecular alterations at the TPI locus were detected in 10 unrelated individuals in whom segregation of a phenotype of reduced TPI activity previously had been identified.

Fluorescence-based mutation detection. Single-strand conformation polymorphism analysis (F-SSCP)

Conventional SSCP analysis of DNA amplified by polymerase chain reaction (PCR-SSCP) is one of the simplest and most reliable tools for identifying point mutations, and small insertions or deletions. The sensitivity of the technique is increased by using the Applied Biosystems (ABI) semiautomated DNA sequencer equipped with GENESCAN 672 software for F-SSCP. The four-dye ABI system permits a red dye-labeled internal lane standard to be run in the same lanes as the DNA being examined, leaving three dye colors for labeling DNA of interest. The internal lane standard is used to normalize gels or correct for minor differences in apparent electrophoretic mobility between lanes. Correction for these lane-dependent differences in migration and the capability to stack data from two different lanes on the computer screen makes it possible to detect sequence variants that produce very small mobility shifts. Coelectrophoresis of control and unknown DNA in the same lane, using different dye labels for each, is also helpful for detecting sequence variants that produce small mobility changes. Multiplexing multiple F-SSCP targets in the same lane increases sample throughput.

Combined PCR-heteroduplex and PCR-SSCP analysis for matching of HLA-A, -B and -C allotypes in marrow transplantation

We describe a method for rapid matching of HLA-A, -B and -C allotypes using simultaneous polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) and heteroduplex analysis. Electrophoresis is performed at ambient temperature without requirements for buffer cooling. SSCP and heteroduplexes are revealed as discrete spatially separated band clusters. Using HLA-A, -B and -C locus-specific PCR primers, matching for alleles at these loci can be performed in 5 h. We tested 17 serologically matched patient-unrelated donor pairs and found considerable microheterogeneity at the DNA level. We propose that this technology has several advantages over conventional low-resolution typing methods and represents a potentially valuable screening method in unrelated donor selection.

HLA-DQB1 and DQA1 matching by ambient temperature PCR-SSCP

We have developed a polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) protocol for rapid matching of DQA1 and DQB1 alleles. Electrophoresis can be performed at ambient temperature within the range 18-28 degrees C without continuous gel cooling. The method has been tested on 27 patient-potential bone marrow donor pairs for DQB1 and 31 pairs for DQA1. Bone marrow pairs were chosen to represent a broad range of common alleles based upon previous restriction fragment length polymorphism (RFLP) analysis type assignments. Samples were re-typed by PCR with sequence-specific primers (PCR-SSP) and the results compared to matching by PCR-SSCP analysis. There was a 100% correlation between PCR-SSP and PCR-SSCP analysis for DQB1, and a 97% correlation for DQA1 matching.

Molecular identification of bacteria by fluorescence-based PCR-single-strand conformation polymorphism analysis of the 16S rRNA gene

PCR-single-strand conformation polymorphism (PCR-SSCP) analysis is a rapid and convenient technique for the detection of mutations and allelic variants. We have adapted this technique for the identification of bacteria by PCR with fluorescein-labeled primers chosen from the conserved regions of the 16S rRNA gene flanking a variable region. The PCR product was denatured, separated on a nondenaturing gel, and detected by an automated DNA sequencer. The mobility of the single-stranded DNA is sequence dependent and allows the identification of a broad panel of bacteria. A single nucleotide difference in the amplified region was sufficient to obtain different PCR-SSCP patterns. The simultaneous amplification of multiple polymorphic regions by multiplex PCR with subsequent multiplex SSCP increased the discriminatory power of PCR-SSCP. A broad range of gram-negative and gram-positive bacteria were tested by PCR-SSCP, including, e.g., Escherichia coli, Enterobacter spp., Klebsiella spp., Haemophilus spp., Neisseria spp., Staphylococcus spp, Streptococcus spp., Enterococcus spp., and Bacillus spp. In total, a panel of 178 strains of bacteria representing 51 species in 21 genera was examined. Although a limited number of strains from each species were tested, the strains tested gave species-specific patterns, with only one exception: Shigella species were indistinguishable from E. coli. PCR is a sensitive technique; as few as 10 CFU of E. coli was sufficient to produce PCR-SSCP patterns suitable for identification. The whole fluorescence PCR-SSCP procedure takes approximately 8 h for the detection and identification of low numbers of bacteria.2+ fluorescence PCR-SSCP seems to be a promising method for the differentiation of a broad range of pathogens found in usually sterile clinical sites, such as blood and cerebrospinal fluid.