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PubMed1997

Diagnosis of sickle-cell disease by DNA analysis in Nigeria.

OBJECTIVE: To compare genotyping of leucocyte DNA by PCR and Dde I with the conventional genotyping of haemoglobin of the same subject. DESIGN: Comparative study. SUBJECTS: 25 adults, 16 males and nine females. MAIN OUTCOME MEASURES: Predictability. RESULTS: In all cases the results were comparable. CONCLUSIONS: The technology can be applied locally to prenatal diagnosis of sickle-cell disease by chorionic sampling and, therefore, improve the management of sickle-cell disease in Nigeria.

Adult↗

PubMed2003

Flow-cytometric DNA analysis in cutaneous fibrohistiocytic tumors.

BACKGROUND: Fibrohistiocytic tumors are rare skin tumors. There are many kinds of fibrohistiocytic tumors. It is often difficult to differentiate dermatofibrosarcoma protuberans (DFSP) and malignant fibrous histiocytoma (MFH) from dermatofibroma (DF) and other benign tumors. OBJECTIVE: In this study, the possible usefulness of DNA ploidy for the differentiation was studied. METHODS: Five MFH, 9 DFSP, 3 DF, 2 lipofibromas and 2 scars were studied for DNA ploidy using a flow cytometer. RESULTS: All the 7 benign tumors showed a diploid pattern. Of 14 malignant fibrohistiocytic tumors, 8 cases (57.1%) showed an aneuploid and 6 a diploid pattern. Two of 5 MFH (40.0%) and 6 of 9 DFSP (66.7%) showed an aneuploid pattern. These results showed that fibrohistiocytic tumors with an aneuploid pattern are malignant, though those with a diploid pattern may be benign or malignant. CONCLUSION: Analysis of DNA ploidy using flow cytometry was concluded to be useful for the differentiation of malignant fibrohistiocytic tumors from benign ones.

DNA↗

PubMed1993

Retrospective DNA analysis using fixed tissue specimens.

The recent explosion of scientific and technical knowledge in the field of molecular biology has allowed us to make important advances in our understanding of the molecular basis of many human diseases. This technology has now entered the clinical laboratory where identification of specific genetic sequences can aid in the precise diagnosis of hematologic and other malignancies, inherited diseases, specific infectious agents, and inherited predisposition to disease. In addition, it can be applied to prenatal diagnosis, paternity testing, identification of minimal residual disease following treatment, and assessment of drug sensitivity or resistance. In many cases in diagnostic pathology, the need for molecular analysis often is not realized until after a critical tissue specimen has been fixed, embedded, and examined microscopically. Thus, there is a clear need for development of techniques that would allow the retrospective study of archival tissues that have been fixed and embedded in paraffin. This review examines in depth those factors which influence the quality of the DNA available from fixed embedded tissues and discusses the usefulness of polymerase chain reaction amplification in obtaining sufficient diagnostically useful DNA from archival specimens. It is hoped that this review will aid the diagnostic pathologist interested in the application of molecular techniques in the retrospective study of fixed embedded tissues.

DNA↗

PubMed1997

DNA analysis of human cholesteatomas.

HYPOTHESIS: The hypothesis tested in this article is that if cholesteatomas are a low-grade squamous cell neoplasm, then evidence of genetic instability, in the form of abnormal or aneuploid amounts of DNA, should be evident. BACKGROUND: Cholesteatoma is a destructive lesion of the middle ear and/or mastoid process that produces complications by erosion of the temporal bone. The clinical hallmarks of cholesteatomas, namely invasion, migration, uncoordinated proliferation, altered differentiation, aggressiveness, and recidivism, are traits typically associated with the neoplastic cell. However, there is little evidence to support or refute the speculation that cholesteatomas are a low-grade squamous cell neoplasm. the existence of defects in the genetic complement of the major cellular constituents comprising a cholesteatoma, fibroblasts and keratinocytes, would support the speculation that cholesteatomas are a neoplasm, since cancers commonly manifest quantitative and qualitative alterations in the normal euploid complement of genetic information, resulting in a cell that has an abnormal or aneuploid amount of DNA. METHODS: DNA content (ploidy) within cholesteatoma tissues was measured by flow cytometry and image analysis. RESULTS: The DNA content of 11 human cholesteatomas and nine postauricular skin specimens was analyzed using flow cytometry, while the DNA content of 10 cholesteatoma specimens was analyzed using image analysis. Interpretable data was obtained from 10 cholesteatoma specimens and six postauricular skin specimens. One cholesteatoma specimen demonstrated an abnormal aneuploid DNA content, whereas the remaining nine cholesteatomas and the six postauricular skin specimens demonstrated a normal euploid DNA content. CONCLUSIONS: We conclude that, due to the lack of overt genetic instability, as evidenced by the presence of a normal euploid DNA content, cholesteatomas are not low-grade neoplasms.

Adult↗

PubMed1992

Image cytometric DNA analysis in human breast cancer analysis may add prognostic information in diploid cases with low S-phase fraction by flow cytometry.

Measurements of DNA ploidy can be performed either with image cytometry (ICM) or flow cytometry (FCM); both methods provide independent prognostic information in primary breast cancer. The aim of the present investigation was to compare the two methods and to relate the findings to prognosis (median follow-up 42 months). Concordance in ploidy status (diploid, tetraploid, aneuploid) was obtained in 76% of the samples (168/222). When the fraction of S-phase cells (SPF) from FCM analysis was also taken into consideration, four different groups of samples were obtained (Flow I-IV), which were considered to correspond to the Auer classification (Auer I-IV) of DNA histograms obtained from image cytometry. Complete concordance between the two techniques now was 70% (155/222). Samples classified as Flow I (diploid or near-diploid with low SPF) and Auer I had a distant metastasis rate of 3/60 (5%), as compared to 62/154 (40%) for all other combinations of the Flow and Auer classifications taken together. Thus, the only findings of prognostic importance were that some samples were Flow I but not Auer I, or vice versa. These two groups represent 17 (7.7%) and 14 (6.3%), respectively, of the total number of samples, and had frequencies of distant metastasis similar to those of the other high-risk groups, namely, 7/17 and 5/14, respectively. In a multivariate analysis, flow cytometric S-phase value was a stronger prognostic factor than either the Flow and Auer classification. We conclude that when routine FCM DNA analysis is used, diploid or near-diploid samples with a low S-phase value should be reanalyzed with ICM.

Breast Neoplasms↗

PubMed1993

[DNA analysis in stomach cancer--correlation of aneuploidy with tumor site].

The DNA status and the proliferative activity was determined in 37 gastric carcinomas applying computerized image analysis. Aneuploidy was found in 51.4% (n = 19) of the tumors. Comparing diploid and aneuploid lesions the latter ones had statistically significant increased DNA amount, DNA index and proliferative rate (7.4 pg, 1.03 and 16.4% versus 12.8 pg, 1.78 and 30.7%; p < 0.05). Aneuploidy occurred more frequently in tumors at proximal sites (p < 0.05), but was not associated with histological type, differentiation and tumor stage. The prognostic impact of DNA aneuploidy remains controversial, since tumor aggressiveness per se is not directly related to aneuploidy.

Adult↗

PubMed2001

Mitochondrial DNA analysis of the presumptive remains of Jesse James.

We report here the results of mtDNA analysis of remains exhumed in July, 1995 from Mt. Olivet Cemetery in Kearney, Nebraska, that are thought to be those of Jesse James. The remains were poorly preserved, presumably due to wet and slightly acidic soil conditions, and insufficient DNA for analysis was obtained from two bone samples. However, two of four teeth, and two hairs recovered in 1978 from the original burial site on the James Farm, did yield reproducible mtDNA sequences. These mtDNA sequences from the teeth and hairs were all identical, suggesting that they came from the same individual; furthermore, this mtDNA sequence was identical to mtDNA sequences determined from blood samples from two maternal relatives of Jesse James. Therefore, either the remains are indeed those of Jesse James, or they are from an unrelated individual who, by chance, happens to have the same mtDNA sequence. To assess the probability that an unrelated individual would have the same sequence, we searched the forensic mtDNA database, and found that this sequence does not appear among the 2426 mtDNA sequences therein. Hence, the mtDNA analysis supports the identification of the exhumed remains from Mt. Olivet Cemetery as those of Jesse James.

Crime↗

PubMed1998

[The recent progress and future prospects of diagnostic DNA testing--experience in DNA analysis of serum enzymes].

Rapid progress in the molecular technology has stimulated attempts to establish DNA diagnosis of human diseases. However, advances in technology have led to improvements at the research level but not in routine laboratory work because only few laboratory tests are covered by medical insurance; the methodologies cannot be easily applied to routine work; and the equipment and reagents are relatively expensive. This paper provides an overview of recent progress in DNA diagnosis and my experience in the DNA diagnostic field. I started working in the DNA diagnostic field in January 1988 with research on mutation analysis of lactate dehydrogenase subunit deficiency. I worked in Dr. Steven Li's laboratory at the National Institutes of Health in North Carolina and discussed with him about screening the patient's genomic library instead of using PCR because PCR was not adequate for mutation analysis. We successfully completed the mutation analysis and I returned to Japan. Thereafter, PCR has been increasingly improved and is now applicable to mutation analysis. Currently, amplification is essential for many DNA diagnostic technologies. The Human Genome Project has progressed and will be finished around 2002. In this process, DNA diagnosis will play an important role in the clinical laboratory. Common diseases, such as atherosclerosis, diabetes mellitus, hypertension and so on, have also been analyzed and the responsible genes will have been identified. Each laboratory should have a specialty and characteristic, and should be ready to help and assist each other via a network. Network communication is clearly needed by laboratories in the future.

Arteriosclerosis↗

PubMed1993

[Effect of neoadjuvant chemotherapy (CDDP.UFT therapy) upon cell DNA analysis by flow cytometry in gastric carcinoma].

Neoadjuvant chemotherapy with CDDP and UFT was performed on far advanced gastric carcinoma cases whose curative resection was impossible. These trials were carried out on 10 patients who had Borrmann 4 type carcinoma. PR was found in 6 cases, for an efficacy rate of 60% (6/10). The DNA content in gastric carcinoma was determined before and after treatment by flow cytometry. The relationship between the change of DNA ploidy pattern and effects of chemotherapy was investigated. Aneuploidy was found in 6 of 10 patients (60.0%). DNA ploidy patterns showed no correlation with effectiveness. In aneuploid cases, the group of responders showed seemingly the change of ploidy pattern, from aneuploid to diploid. In non-responders the percentage of aneuploid cells increased. In diploid cases, an accumulation of S-phase fraction was observed in the group of responders. These results suggested that DNA ploidy analysis may provide additional diagnostic criteria for better assessment of chemotherapeutic effects.

Adult↗

PubMed2001

Maximization of injection volumes for DNA analysis in capillary electrophoresis.

We report concentration and separation of DNA in the presence of electroosmotic flow (EOF) using poly(ethylene oxide) (PEO) solution. DNA fragments migrating against EOF stacked between the sample zone and PEO solution. To maximize the injection volume, several factors, such as concentrations of Tris-borate (TB) buffer and PEO solution, capillary size, and matrix, were carefully evaluated. The use of 25 mM TB buffers, pH 10.0, containing suitable amounts (less than 10 mM) of salts, such as sodium chloride, sodium phosphate, and sodium acetate, to prepare DNA is essential for the concentration of large-volume samples. In the presence of salts, the peaks also became sharper and the fluorescence intensity of DNA complexes increased. Using 2.5% PEO and a 150 microm capillary filled with 400 mM TB buffer, pH 10.0, up to 5 microL DNA samples (phiX 174 RF DNA-HaeIII digest or the mixture of pBR 322/HaeIII, pBR 328/Bg/I, and pBR 328/HinfI digests) have been analyzed, resulting in more than 400-fold improvements in the sensitivity compared to that by conventional injections (ca. 36 nL). Moreover, this method allows the analysis of 3.5 microL PCR products amplified after 17 cycles without any sample pretreatment.

Buffers↗

PubMed2003

Identification of Candida spp. by randomly amplified polymorphic DNA analysis and differentiation between Candida albicans and Candida dubliniensis by direct PCR methods.

Because Candida species have innately highly variable antifungal susceptibilities, the availability of a fast and reliable species identification test is very important so that suitable and effective therapeutic measures may be taken. Using three oligonucleotide primers, we established a randomly amplified polymorphic DNA (RAPD) analysis method that enabled direct identification of the most common opportunistic pathogenic Candida species. RAPD analysis revealed a characteristic molecular fingerprint for each Candida species. Differences between the profiles for Candida albicans and C. dubliniensis were evident. RAPD analysis is a relatively easy, reproducible, and reliable technique that can be useful in providing genetic fingerprints for the identification of strains. In addition, a collection of different C. albicans strains was identified by a specific PCR based on multiple secreted aspartic proteinase (SAP) genes and the dipeptidyl aminopeptidase (DAP2) gene. Our findings demonstrate that PCR based upon the SAP and DAP2 sequences is a simple, rapid, clear, and direct technique for the identification and differentiation of C. albicans and C. dubliniensis.

Candida↗

PubMed2002

Quantitative Epstein-Barr virus DNA analysis and detection of gene promoter hypermethylation in nasopharyngeal (NP) brushing samples from patients with NP carcinoma.

PURPOSE: Nasopharyngeal carcinoma (NPC) is highly prevalent in southern China and characterized by a strong association with EBV. We aimed to detect EBV DNA and cancer-related gene promoter hypermethylation in nasopharyngeal (NP) brushing samples and provide a novel noninvasive approach for NPC detection. EXPERIMENTAL DESIGN: Twenty-eight NPC cases and 26 noncancerous subjects were prospectively recruited. NP brushing samples were subjected to quantitative real-time PCR analysis of EBV DNA and methylation-specific PCR analysis of the DAP-kinase, RASSF1A, and p16 genes. RESULTS: EBV DNA quantity in NP brushing samples from NPC patients (median, 8.94 copies/actin) was significantly higher than that of controls (median, 0 copies/actin; P < 0.0001). Twenty-seven of 28 NPC patients had detectable EBV DNA in NP brushes, whereas 25 of 26 controls had undetectable or very low levels of EBV DNA. Elevated EBV DNA level in brushing samples as a tumor marker had a sensitivity of 96.4% and a specificity of 96.2% for NPC detection. Moreover, T(1) disease had a significantly lower EBV DNA level as compared with locally more advanced disease (P = 0.037). In brushing samples of NPC patients, the frequencies of DAP-kinase, RASSF1A, and p16 promoter hypermethylation were 50.0%, 39.3%, and 46.4%, respectively. Seventy-eight percent of cases showed methylation of at least one gene. No aberrant hypermethylation was detected in control samples. CONCLUSIONS: Our study demonstrated the feasibility of detecting multiple molecular tumor markers in NP brushing samples with a high sensitivity and specificity for NPC detection. It offers a powerful yet noninvasive approach for the diagnosis of NPC in high-risk populations.

Adult↗

PubMed1993

Flow cytometric DNA analysis of adenocarcinomas of the vermiform appendix. Brief report.

The DNA ploidy status and S-phase fraction of eight adenocarcinomas of the vermiform appendix diagnosed in Iceland during 1974-1990 were analyzed by flow cytometry. Four cases were classified as Dukes' stage B2 and four cases as Dukes' stage D. Seven tumors were diploid and one was aneuploid. The DNA aneuploid tumor was the only one which metastasized outside the abdominal cavity. The S-phase fraction in general was low. The results of this study do not indicate any significant correlation between ploidy status and clinical behavior.

Adenocarcinoma↗

PubMedDate not supplied

Molecular phylogeny of Philippine freshwater sardines based on mitochondrial DNA analysis.

The commercially important Sardinella species (family Clupeidae or herrings) usually thrive in marine environments. An exception is Sardinella tawilis of Taal Lake, Batangas, Philippines, the only known freshwater sardine. This species is believed to have immigrated from Balayan Bay to the lake when it was formed in the course of volcanic eruptions some 240 years ago. To determine the relationship of S. tawilis to the marine species S. albella, S. fimbriata, and S. longiceps from the Balayan Bay we sequenced 358 bp of the cytochrome b gene and the mitochondrial control region. The cytochrome b gene was highly conserved and contained little phylogenetic information. The control region sequences, however, demonstrated two highly diversified main haplotypes grouping S. tawilis with S. albella, as shown by maximum parsimony and neighbor-joining analysis. The haplotypes are characterized by the presence of an 81 bp indel and up to eight 35 bp tandem repeat elements. The repeat copy number varied within individuals of S. tawilis and S. albella, thus showing heteroplasmy in these two species only. The analysis of two subpopulations of S. tawilis revealed restricted substitutions that may indicate the beginning of genetic differentiation of the two subpopulations.

Animals↗

PubMed2004

Random amplified polymorphic DNA analysis of kinship within host-associated populations of the symbiotic water mite Unionicola foili (Acari: Unionicolidae).

Kinship relations within populations of unionicolid water mites are not well known, owing to their complex life cycles and the fact that interactions between active and resting stages for some species are transitory. A number of species of unionicolid water mites are, however, obligate symbionts of freshwater mussels and spend most of their life cycle in association with these hosts. Among these species of mites, parents and offspring are more likely to co-occur and thus provide opportunities to address questions related to the structure of the mating system. The present study employs random amplified polymorphic DNA (RAPD) analysis to address kinship within populations of Unionicola foili living in symbiotic association with the host mussel Utterbackia imbecillis. DNA was amplified from adult mites and a representative number of eggs or larvae (n = 20-30) that were removed from mussels collected on three separate occasions (July, November, and March) over a 12-month period. Parsimony analyses of the molecular data for adults and progeny collected from mussels during July, November, and March revealed distinct groupings, that for the most part, corresponded to mites collected from each of the sampling periods. Many of the genetic markers obtained for male and female U. foili were not evident among the larvae or eggs, suggesting that adults obtained from a host mussel at the time of collection were not the parents of a majority of the progeny. However, female mites and eggs collected from mussels during March and November shared more markers than did females and progeny examined during July. Furthermore, many offspring in the July sampling period were found to have one or more parents absent from the sampled population. Overall, RAPD profiling appears to have limited usage in determining kinship within populations of U. foili, due to its recruitment patterns, and the relatively large number of adults and progeny per mussel. It may, however, prove to be a useful method for assessing genetic relatedness among unionicolid mussel-mites that have substantially lower population densities.

Animals↗

PubMed2003

DNA analysis by fluorescence quenching detection.

The analysis of human genetic variations such as single nucleotide polymorphisms (SNPs) has great applications in genome-wide association studies of complex genetic traits. We have developed an SNP genotyping method based on the primer extension assay with fluorescence quenching as the detection. The template-directed dye-terminator incorporation with fluorescence quenching detection (FQ-TDI) assay is based on the observation that the intensity of fluorescent dye R110- and R6G-labeled acycloterminators is universally quenched once they are incorporated onto a DNA oligonucleotide primer. By comparing the rate of fluorescence quenching of the two allelic dyes in real time, we have extended this method for allele frequency estimation of SNPs in pooled DNA samples. The kinetic FQ-TDI assay is highly accurate and reproducible both in genotyping and in allele frequency estimation. Allele frequencies estimated by the kinetic FQ-TDI assay correlated well with known allele frequencies, with an r(2) value of 0.993. Applying this strategy to large-scale studies will greatly reduce the time and cost for genotyping hundreds and thousands of SNP markers between affected and control populations.

Alleles↗

PubMed1996

Application of random amplified polymorphic DNA analysis to differentiate strains of Salmonella enteritidis.

A random amplified polymorphic DNA (RAPD) fingerprinting method has been developed to differentiate Salmonella enteritidis isolates. A total of 65 arbitrary primers were screened with S. enteritidis isolates of different phage types. This allowed selection of a panel of primers capable of detecting DNA polymorphisms among S. enteritidis isolates. This panel was used to examine a panel of 29 isolates of S. enteritidis which had been previously characterized by other subtyping methods, including phage typing (PT) (n = 7), ribotyping (RT) (n = 13), and pulsed-field gel electrophoresis (PFGE). Applied collectively, these three methods resolved the collection into 20 different subtypes. However, by the RAPD fingerprinting method alone, 14 RAPD subtypes were revealed. Eight isolates of S. enteritidis phage type 8 that failed to be discriminated by other typing methods (PT, RT, and PFGE) were resolved into three different subtypes by RAPD analysis. In contrast, isolates that were derived from the same sources were not differentiated by any of the subtyping methods employed, including PT, RT, PFGE, and RAPD analysis. This RAPD approach to S. enteritidis subtyping provided more discriminatory power than did any of several other subtyping methods applied individually. Once the challenging step of primer identification was accomplished, determinations of the appropriate concentrations of arbitrary primer, DNA template, and MG2+ ion were also necessary for optimal discriminatory power. The bacterial DNA used in this RAPD protocol was obtained by boiling the bacterial sample. This simple procedure yielded DNA that produced fingerprint patterns as consistent as those obtained from phenol-chloroform-extracted DNA. Clearly, when appropriately constituted primer sets are identified and employed, RAPD analysis provides a simple, rapid, and powerful subtyping method for S. enteritidis.

Bacterial Typing Techniques↗

PubMed2000

Existence of two geographically-linked clonal lineages in the bacterial fish pathogen Photobacterium damselae subsp. piscicida evidenced by random amplified polymorphic DNA analysis.

In this work, we applied the random amplified polymorphic DNA (RAPD) technique to evaluate the genetic diversity in Photobacterium damselae subsp. piscicida (formerly Pasteurella piscicida), an important pathogen for different marine fish. Regardless of the oligonucleotide primer employed, the 29 isolates of Ph. damselae subsp. piscicida tested were separated into two groups, the RAPD-PCR analysis differentiated the European strains from the Japanese strains. The similarity between both groups estimated on the basis of the Dice coefficient was 75-80%. These results show that European and Japanese isolates of Ph. damselae subsp. piscicida, regardless of their host fish species, belong to two different clonal lineages. Our findings also indicate that RAPD profiling constitutes a useful tool for epidemiological studies of this fish pathogen.

Animals↗