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PubMed2002

Flow cytometric DNA analysis on fine needle aspiration biopsies of liver lesions.

Flow cytometric DNA analysis on fine needle aspiration biopsies of liver lesions The DNA cell content of 39 fine needle aspiration biopsies (FNAs) from five benign liver lesions, nine hepatocellular carcinomas (HCCs), and 25 metastatic tumours was analysed in a prospective fashion by flow cytometry (FCM). All benign lesions were diploid. Aneuploidy was found in five (55.6%) HCCs and in nine (36%) metastatic tumours. DNA index (DI) differences were not significant. The S-phase fraction (SPF) was higher in the malignant tumours, both combined (P < 0.02) and separated primary and metastatic (P < 0.05). We could not demonstrate an association between diploidy and percentage of benign hepatocytes in the smears of malignant tumours. The serum alpha-fetoprotein (AFP) level did not correlate with ploidy, DI, or SPF in the HCCs. In conclusion, ploidy and DI do not discriminate between benign and malignant liver lesions, but the SPF is higher in malignant tumours. DNA analysis does not help to distinguish primary from metastatic liver tumours. The presence of benign hepatocytes in samples from malignant tumours does not seem to influence the analysis of ploidy by FCM.

Aneuploidy↗
PubMed1988

Restriction endonuclease DNA analysis of Leptospira interrogans serovars Icterohaemorrhagiae and Copenhageni.

Leptospira interrogans serovar icterohaemorrhagiae strains Ictero No. I and RGA and serovar copenhageni strains M20, Shiromizu and Shibaura were examined by restriction endonuclease DNA analysis. Fifteen endonucleases (AluI, BamHI, BglII, EcoRI, HaeIII, HhaI, HindIII, KpnI, PstI, SacI, SalI, SmaI, StyI, XbaI and XhoI) were used as the digesting enzymes. Strain Ictero No. I showed endonuclease cleavage patterns which differed from those of the other four strains only when it was digested with enzymes KpnI and HindIII. When digested with KpnI, an extra band of about 5.4 kb was clearly produced, and when digested with HindIII, an extra band of about 25 kb was produced. When the other 13 enzymes were used, no differences were found between the endonuclease cleavage patterns among the five strains. Moreover, strains RGA, M20, Shiromizu and Shibaura could not be distinguished by the restriction endonuclease DNA analysis using all 15 endonucleases. In addition, six newly isolated leptospires from patients with leptospirosis and from Rattus norvegicus were compared with the Ictero No. I and M20 strains, by restriction endonuclease DNA analysis using enzymes KpnI and HindIII. Three leptospires belonging to serovar icterohaemorrhagiae showed the same endonuclease cleavage patterns as the M20 strain. The other three strains, which belong to serovar copenhageni, showed almost the same endonuclease cleavage patterns as the M20 strain; only the Kai ima 702 strain produced an extra band which was not identical to the Ictero No. I-specific extra band when digested with HindIII. The leptospiral restriction endonuclease DNA analysis has revealed taxonomic structures that are unrecognized by serology alone.

Animals↗
PubMed1987

Flow cytometric DNA analysis of renal-cell carcinoma. A study of fine needle aspiration biopsies in comparison with multiple surgical samples.

The flow cytometric (FCM) DNA analysis of fine needle aspiration (FNA) biopsy material was compared with the DNA analysis of multiple surgical biopsy material from 44 renal-cell carcinomas. Twenty tumors were heterogeneous with respect to their DNA content. Eleven of the 17 tumors that had both diploid and aneuploid tumor cell clones in the surgical specimens gave a diploid DNA content in the aspiration biopsies; the other 6 cases showed aneuploidy in the aspirate. The fine needle aspirates from 18 homogeneously diploid tumors and 9 tumors with an aneuploid DNA content in all eight surgical samples revealed DNA indices similar to those found in the surgical samples. These findings show that aneuploid clones of renal-cell carcinoma can remain undetected by the use of FNA biopsy as a method for obtaining samples for FCM DNA analysis.

Biopsy↗
PubMed1986

Accuracy and reliability of flow cytometric DNA analysis using a simple, one-step ethidium bromide staining protocol.

Sources of variation and error were investigated for a simple flow cytometric analysis of DNA content of detergent-isolated nuclei stained with ethidium bromide. Using the ploidy classes of mouse liver nuclei, deviations from linearity were assessed for three different instruments. In more extreme settings, the maximum deviations for a FACS instrument were up to 6 to 9%, but in general deviations were around 1% or lower for all instruments. As biological DNA standards, human peripheral lymphocytes and trout erythrocytes appeared to be suitable and easy to store frozen. The erythrocytes had dye-binding characteristics similar to those of human lymphocytes and a 20% lower fluorescence, thus being well suited as an internal standard, as was demonstrated in tumor ploidy analyses performed with varied tissue concentration. Staining homogeneity was improved when staining time was extended to 24 h, at which time male and female lymphocytes were completely separated with an average difference in DNA content of 1.9%. A small difference in fluorescence between mitogen-stimulated and unstimulated lymphocytes was reduced to less than 1% after 24 h of staining. In general, the manipulations of the conditions for the analysis resulted in maximum variations of around 1%, indicating the robustness and reliability of the technique.

Animals↗
PubMed1992

Flow cytometric DNA analysis of excised breast lesions: use of fresh tissue needle aspirates obtained under guidance with mammography of the specimen.

Eighty consecutive biopsy specimens were studied to determine whether DNA analysis could be performed on fine-needle aspirates of excised clinically occult breast lesions obtained under guidance with mammography of the specimen before fixation to offer the advantages of fresh-tissue analysis. With use of single aspirates, cytologic analysis was possible in 50 cases (62%); DNA analysis was possible in 75 cases (94%). These methods combined offered no statistically significant increase in sensitivity for detection of malignancy compared with cytologic analysis alone. Forty-one percent of the analyzable invasive carcinomas showed aneuploidy. Aneuploidy and high S phase fractions of the invasive carcinomas showed no substantial correlation with patient age, nodal status, and size or appearance of the mammographic lesion. Aneuploidy was also seen in zero of four analyzable lesions showing ductal carcinoma in situ, two of 13 showing atypical hyperplasia (15%), and one of the 28 remaining benign lesions (4%). The authors conclude that this mammographic intervention is an effective means of obtaining fresh tissue samples of clinically occult lesions for DNA analysis.

Adult↗
PubMed1989

Cytologic and flow cytometric DNA analysis of multinucleated tumor cells and derived microcells.

Microcell production by means of Colcemid-induced micronucleation and subsequent enucleation with the density gradient technique was adjusted for use with the murine T-lymphoma line ESb-M. Modification of the standard protocol for a cell type on which no experiments had previously been performed required careful monitoring of the multiple steps in the procedure in order to optimize the final microcell yield. Traditional microscopic verification may sometimes be ambiguous, due to the lack of a clear cutoff point between small whole cells and cell fragments; in these conditions, the level of variability increases, thus impairing quantitative estimations. Flow cytometric (FCM) analysis of DNA content and size of donor cells and microcells was therefore applied in parallel to provide additional quantitative information. The FCM results supplemented the microscopic data in assessing which fraction recovered from the gradient has the lowest percentage of contaminant whole cells; however, FCM analysis may provide more statistically significant data due to the large size of the sample examined. Moreover, FCM is of prospective use in providing the basis for subsequent sorting of either pure microcells or specific subpopulations of defined DNA content and size.

Animals↗
PubMed1990

[Strategies in prenatal diagnosis of cystic fibrosis after the introduction of DNA analysis. Initial experience].

The authors describe their experience with the prenatal genetic diagnosis of cystic fibrosis (CF), using DNA analysis in the first trimester of pregnancy in three families with a 25% risk of CF. The authors examined polymorphisms of probes J3.11, met D, met H, KM-19 and XV-2c. All families were fully informative when one or two probes were used. In two families the development of unaffected children--carriers of the gene for CF was proved. In one of these foetuses in the 17th and 21st week false pathological values of microvilillous enzymes were assessed. With regard to this possibility the authors do not recommend to supplement the DNA analysis in the first trimester by biochemical examination of amniotic fluid. The results were confirmed by delivery of unaffected children. In one family DNA analysis revealed the development of an unaffected homozygote, the pregnancy was, however, terminated by a miscarriage. In women with an increased risk of abortion the authors recommend therefore to make the molecular genetic examination during the second trimester from amniotic fluid cells.

Chorionic Villi Sampling↗
PubMed1989

[A significance of dual parameter flow cytometric DNA analysis using the anti-keratin antibody].

Flow cytometric DNA analysis using the anti-cytokeratin antibody was carried out in order to estimate more reliable measurement in single cell suspension obtained from solid tumors. It was difficult to detect a DNA aneuploidy with DI of 2.0 by one parameter analysis of DNA. Whereas it could be detected easily by using dual parameter analysis of cytokeratin and DNA. And also, the pattern of DNA multiploidy could be selected for cytokeratin positive cell population by gate analysis.

Antibodies↗
PubMed1988

Cytophotometric DNA analysis of esophageal dysplasia and carcinoma induced in rats by N-methyl-N-amylnitrosamine.

A series of esophageal lesions, mild, moderate and severe dysplasia, carcinoma in situ (CIS), early and advanced squamous cell carcinoma were induced in rats with N-methyl-N-amylnitrosamine (MAN). To evaluate the biological nature of each lesion, the ploidy level was estimated by microspectrophotometrical measurement of cell nuclear DNA content. DNA distribution patterns were classified into types I, II, III and IV, according to the degree of dispersion and the peak modal value on the DNA histogram. The incidences of type III of high ploidy in early cancer, CIS and severe dysplasia were 3/11 (27.3%), 5/13 (33.3%) and 4/16 (25%), respectively. On the other hand, in moderate and mild dysplasia, 15/16 (93.8%) and 20/21 (95.2%) were low ploidy (types I and II), respectively. The mean DNA content of advanced and early cancer, CIS and severe dysplasia were 3.88c, 3.34c, 3.24c and 3.13c, respectively, while those of moderate and mild dysplasia were near diploid, showing 2.67c and 2.51c, respectively. These findings indicate that the biological nature of severe dysplasia may be considered as serious a lesion as cancer, in terms of DNA analysis. Cytophotometric DNA analysis aids the evaluation of various degrees of dysplasia and carcinoma of the esophagus.

Animals↗
PubMed1992

DNA-analysis of patients with autosomal dominant polycystic kidney disease.

Indirect DNA analysis was performed on 12 families totalling 80 people. The analysis used five genetic markers flanking the gene: 3'HVR, pGGG, 218 EP6, 24-1, 26-6. In 11 of the families (92%), a linkage with the PKD1 gene in chromosome 16 was established. In one family, the disease did not segregate with the polymorphic markers of PKD1-locus, thus excluding any possibility that a mutation in this locus was the cause of the autosomal dominant polycystic kidney disease (ADPKD). A correlation was discovered between the positive echographic diagnosis and the genotype in the PKD1-dependent patients with ADPKD. In 28.6 percent of the children studied, and in 12.5 percent of subjects under the age of 30, the echographic diagnosis was corrected through DNA analysis.

Adolescent↗
PubMed1995

Granulosa cell tumor of ovary: a clinicopathologic and flow cytometric DNA analysis.

Flow cytometric DNA ploidy and S-phase fraction (SPF) analysis was performed on 18 granulosa cell tumors of the ovary. Clinical and pathologic data from patients followed for an average of 10 years were compared to flow cytometry ploidy to determine its prognostic usefulness. Eleven (62%) tumors were diploid and seven (38%) were aneuploid. Aneuploidy was significantly associated with high stage, vascular or capsular invasion, and nuclear atypia but not with SPF or necrosis. Of the patients on whom follow-up was available, only 1 of 10 (10%) with euploid tumors died of disease, while 4 of 5 (80%) with aneuploid tumors died of their disease; this, however, did not reach a significant statistical correlation. SPF was not correlated with any clinical or histologic parameter. Aneuploidy in granulosa cell tumors is associated with other adverse histopathologic parameters and an apparent trend toward aggressive behavior.

Adult↗
PubMed2003

DNA analysis of neonatal human remains wrapped and kept in a vinyl bag for 15 years.

DNA analysis of a newborn baby wrapped and kept in a vinyl bag for 15 years was performed. DNA isolated from the femur and humerus was used to determine the sex and kinship between the infant and the putative parents. Amplification of mtDNA, ABO, HLA, CST3, CST5, VWA, D12S66, D21S11, CSF1PO, TPOX, THO1 and 10Y polymorphisms and the amelogenin gene was carried out. Several mtDNA types were obtained, suggesting that the sample was contaminated by exogenous DNAs. One of the DNA samples obtained from the femur showed an identical mtDNA sequence to that of the mother except for one site, and this pattern was also found in another DNA sample. None of our laboratory personnel had that type, so we thought it was possible that this sample contained the target DNA. However, maternity was denied by the CST3 polymorphism. Finally, we concluded that the sample had been contaminated with exogenous DNA before we started to examine the body. Although it is difficult to determine the sources of this contamination, PCR amplification from highly degraded DNA is very sensitive to such contamination, and we must be even more careful in DNA analysis of such samples than in that of not so severely degraded specimens.

DNA↗
PubMed2005

Electrochemical biosensors for DNA analysis.

Over the past few years, progress in electrochemical biosensors for DNA analysis is outstanding. This article briefly reviewed the principals of such biosensors, followed by a selection of topics that are of particular current interest. Selectivity and sensitivity are the two major challenges in DNA analysis. The former can be accomplished using peptide nucleic acids as probes, or relying on the DNA-mediated electron transfer. Special emphasis has been given to the efforts for high sensitivity, involving combination with polymerase chain reaction techniques, enzyme-labeled methods, direct label-free detection and nano-based techniques.

Biosensing Techniques↗
PubMed1991

Direct diagnosis by DNA analysis of the fragile X syndrome of mental retardation.

BACKGROUND: The fragile X syndrome, the most common form of inherited mental retardation, is caused by mutations that increase the size of a specific DNA fragment of the X chromosome (in Xq27.3). Affected persons have both a full mutation and abnormal DNA methylation. Persons with a smaller increase in the size of this DNA fragment (a premutation) have little or no risk of retardation but are at high risk of having affected children or grandchildren. The passage from premutation to full-mutation status occurs only with transmission from the mother. We have devised a method of identifying carriers of these mutations by direct DNA analysis. METHOD: We studied 511 persons from 63 families with the fragile X syndrome. Mutations and abnormal methylation were detected by Southern blotting with a probe adjacent to the mutation target. Analysis of EcoRI and EagI digests of DNA distinguished clearly in a single test between the normal genotype, the premutation, and the full mutation. RESULTS: DNA analysis unambiguously established the genetic status at the fragile X locus for all samples tested. This method was much more powerful and reliable than cytogenetic testing or segregation studies with closely linked polymorphic markers. The frequency of mental retardation in persons with premutations was similar to that in the general population, whereas all 103 males and 31 of 59 females with full mutations had mental retardation. About 15 percent of those with full mutations had some cells carrying only the premutation. All the mothers of affected children were carriers of either a premutation or a full mutation. CONCLUSIONS: Direct diagnosis by DNA analysis is now an efficient and reliable primary test for the diagnosis of the fragile X syndrome after birth, as well as for prenatal diagnosis and genetic counseling.

Blotting, Southern↗
PubMed2004

Control region sequences for East Asian individuals in the Scientific Working Group on DNA Analysis Methods forensic mtDNA data set.

The Scientific Working Group on DNA Analysis Methods (SWGDAM) mitochondrial DNA (mtDNA) population data set is used to infer the relative rarity of mtDNA profiles obtained from evidence samples and of profiles used to identify missing persons. In this study, the East Asian haplogroup patterns in the SWGDAM data sets were analyzed in a phylogenetic context to determine relevant single nucleotide polymorphisms (SNPs) and to describe haplogroup distributions for Asians (n = 753; with a breakdown of individuals from China n = 356, Korea n = 182, Japan n = 163, and Thailand n = 52). We focus on the patterns observed in the SWGDAM Chinese data set and refer to interesting differences in the smaller subgroup data sets for the other East Asian populations (Japanese, Korean, and Thai). A total of 218 SNPs were observed in the data set, including 37 observed positions not previously reported. In the largest of the East Asian SWGDAM data sets (Chinese), these SNPs ranged from having 1 to 29 changes in the phylogenetic tree, with site 16519 being the most variable. On average there were 4.5 changes for a character on the tree. The most variable sites (with 14 or more changes each listed from fastest to slowest) observed were 16519 (L = 29), 16311 (L = 27), 152 (L = 24), 146 (L = 21), 16172 (L = 17), 16189 (L = 17), 195 (L = 16), 16362 (L = 15), 16093 (L = 14), 16129 (L = 14) and 150 (L = 14). These rapidly changing sites are consistent with other published analyses. Only 28 SNPs are needed to identify all clusters containing 1% (n = 7) or more individuals in the East Asian data set. All 36 haplogroups previously observed in East Asian populations were also seen in the SWGDAM data sets and include: A, B, B4, B4a, B4b, B5a, B5b, C, D, D4, D4a, D4b, D5, D5a, F, F1, F1a, F1b, F1c, F2a, G2, G2a, M, M7a1, M7b, M7b1, M7b2, M7c, M8a, M9, M10, N9a, R, R9a, Y, and Z. Haplogroups A, B4a, D4, and F1a were the most commonly observed clusters in the Chinese data set (the largest of the data sets) with each of these occurring in more than 6% of the samples in the data set. The next most common haplogroups in the Chinese data set include the clusters C, M7b1, and N9a with each observed at frequencies greater than or equal to 4%. European Caucasian, and African haplogroups were rarely observed within the East Asian data sets. The various analyses revealed that the data set was similar to published East Asian data sets such as those from Han Chinese.

Asian People↗
PubMed1997

Neonatal screening for cystic fibrosis in the Trent region (UK): two-stage immunoreactive trypsin screening compared with a three-stage protocol with DNA analysis as an intermediate step.

OBJECTIVES: To assess neonatal screening for cystic fibrosis using immunoreactive trypsin, either alone or in conjunction with DNA analysis for the delta F508 mutation. A novel three-stage screening protocol was compared with the previously introduced two-stage immunoreactive trypsin-DNA protocol. DESIGN: (a) Collection of data from a 4 1/2 year period (phase 1) of two-stage immunoreactive trypsin screening. The initial dried blood samples were obtained at 6 days of age and repeat samples at 27 days of age from babies with results above the 99.5th centile. Babies with persistent hypertrypsinaemia were referred for a diagnostic sweat test. (b) Retrospective DNA analysis: patients with cystic fibrosis diagnosed in phase 1 were genotyped and most samples from babies with increased initial immunoreactive trypsin but normal results in the second sample were analysed for the delta F508 mutation. (c) Phase 2, a prospective study of a three-stage neonatal screening protocol, in which only babies heterozygous for the delta F508 cystic fibrosis mutation progressed to the second immunoreactive trypsin test. SETTING: The Trent neonatal screening programme. SUBJECTS: 437 859 babies born between August 1989 and March 1996. MAIN OUTCOME MEASURES: Proportions of unaffected babies requiring a second blood sample or a sweat test. Overall sensitivity for the detection of cystic fibrosis. RESULTS: The two-stage screen failed to identify six out of 94 cases of cystic fibrosis (without meconium ileus). The introduction of the DNA analysis step would have resulted in one additional case being missed. With the three-stage screen there was a 92% reduction in babies requiring a second blood sample and an 80% reduction in negative sweat tests, results close to the predictions of the retrospective study. CONCLUSIONS: The three-stage screening protocol is a marked improvement on the two-stage immunoreactive trypsin strategy and on the two-stage immunoreactive trypsin-DNA strategy recently introduced in some other screening programmes.

Cystic Fibrosis↗
PubMedDate not supplied

Flow cytometric DNA analysis of defined stages of rat seminiferous epithelial cycle during in vitro differentiation.

The stages of the rat seminiferous epithelial cycle have been isolated for flow cytometric analysis of DNA and for culture, using transillumination-assisted microdissection. Precise stages have been identified by phase contrast microscopy of live cell squashes from adjacent segments. Each stage of the cycle showed a characteristic flow cytometric pattern with haploid (1C), diploid (2C) and tetraploid (4C) peaks. Stages I to VIII of the cycle showed an additional hypofluorescent (0.25-0.70C) peak due to a reduced dye-binding capacity of maturation phase-spermatids at steps 15 through 19. The appearance of the hypofluorescent haploid peak coincided with the second nucleoprotein transition at step 15 of spermiogenesis and the homogeneous condensation of the chromatin seen in electron microscopy. As a concomitant of the formation of disulphide bonds during epididymal maturation, the fluorescence intensity decreased further to reach a relative value of 0.07C in the cauda epididymidis. The constant 1C peak was raised by round and elongating spermatids (steps 1-14), 2C by spermatogonia, secondary spermatocytes and Sertoli cells, and the 4C peak by primary spermatocytes and spermatogonia at G2 or M phase of the mitotic cycle. The proportion of each peak accurately reflected the relative proportion of cells in most stages of the cycle when compared with morphometric measurements of histologic preparations. DNA flow cytometry is a suitable method for quantitative evaluation of cultured seminiferous tubule segment DNA. Although the relative yield of the meiotic reductive divisions in vitro is comparable with that observed in vivo, steps 9 and 15 of spermiogenesis involving nucleoprotein transitions and spermiation itself did not occur under the present culture conditions.

Animals↗
PubMed1993

First-trimester prenatal diagnosis of osteogenesis imperfecta type II by DNA analysis and sonography.

Osteogenesis imperfecta type II was diagnosed prenatally by analysis of DNA obtained from chorionic villus sampling (CVS) performed at 12 weeks of gestation in a woman who previously had had an affected child. The father had been shown to be mosaic for a mutation in the gene (COL1A2) which encodes the alpha 2(I) chain of type I collagen. An affected fetus was predicted by detection of the mutation in amplified chorionic villus genomic DNA. Ultrasound examination at 13 weeks 4 days demonstrated femoral deformity and virtual absence of calvarial mineralization. In pregnancies at risk for osteogenesis imperfecta type II, sonographic evidence of skeletal abnormalities may be evident by 13 weeks' gestation.

Adult↗